diff --git a/docs/implementations/aggregator.rst b/docs/implementations/aggregator.rst new file mode 100644 index 000000000..09aeac3f1 --- /dev/null +++ b/docs/implementations/aggregator.rst @@ -0,0 +1,16 @@ +Aggregator Implementation +================== + +.. warning :: + + Highly incomplete! + +This wraps any number of other implementations, multiplexing queries and aggregating results, treating +as if it were a single unified endpoints + +Code +---- + +.. currentmodule:: oaklib.implementations.aggregator.aggregator_implementation + +.. autoclass:: AggregatorImplementation diff --git a/docs/implementations/bioportal.rst b/docs/implementations/bioportal.rst index 80a58bb91..b31f6b58e 100644 --- a/docs/implementations/bioportal.rst +++ b/docs/implementations/bioportal.rst @@ -16,4 +16,3 @@ Code .. currentmodule:: oaklib.implementations.bioportal.bioportal_implementation .. autoclass:: BioportalImplementation - :members: create diff --git a/docs/implementations/index.rst b/docs/implementations/index.rst index 65f280174..fade8d9a0 100644 --- a/docs/implementations/index.rst +++ b/docs/implementations/index.rst @@ -22,6 +22,7 @@ The most mature implementations are: obofiles sqldb robot + funowl skos ols bioportal @@ -30,4 +31,6 @@ The most mature implementations are: ontobee ols bioportal + kgx + aggregator diff --git a/docs/implementations/obofiles.rst b/docs/implementations/obofiles.rst index f2721c47a..6d5ae5d2c 100644 --- a/docs/implementations/obofiles.rst +++ b/docs/implementations/obofiles.rst @@ -15,4 +15,3 @@ Code .. currentmodule:: oaklib.implementations.pronto.pronto_implementation .. autoclass:: ProntoImplementation - :members: create diff --git a/docs/implementations/ols.rst b/docs/implementations/ols.rst index a7e446f99..f9dc34824 100644 --- a/docs/implementations/ols.rst +++ b/docs/implementations/ols.rst @@ -3,9 +3,9 @@ Ontology Lookup Service (OLS) Endpoint .. warning :: - not yet implemented! + very partially implemented! -When implemented this will also provide implementation of the mapping interface via OxO +Also provides interface to OxO Code ---- @@ -13,4 +13,3 @@ Code .. currentmodule:: oaklib.implementations.ols.ols_implementation .. autoclass:: OlsImplementation - :members: create diff --git a/docs/implementations/ontobee.rst b/docs/implementations/ontobee.rst index 1581d4d32..eef394856 100644 --- a/docs/implementations/ontobee.rst +++ b/docs/implementations/ontobee.rst @@ -14,4 +14,3 @@ Code .. currentmodule:: oaklib.implementations.ontobee.ontobee_implementation .. autoclass:: OntobeeImplementation - :members: create diff --git a/docs/implementations/owlery.rst b/docs/implementations/owlery.rst index 9a5cab114..0f605b3c0 100644 --- a/docs/implementations/owlery.rst +++ b/docs/implementations/owlery.rst @@ -11,4 +11,3 @@ Code .. currentmodule:: oaklib.implementations.owlery.owlery_implementation .. autoclass:: OwleryImplementation - :members: create diff --git a/docs/implementations/sparql.rst b/docs/implementations/sparql.rst index b880ab738..1b00c365e 100644 --- a/docs/implementations/sparql.rst +++ b/docs/implementations/sparql.rst @@ -5,4 +5,4 @@ Sparql Endpoint .. currentmodule:: oaklib.implementations.sparql.sparql_implementation .. autoclass:: SparqlImplementation - :members: create + diff --git a/docs/implementations/ubergraph.rst b/docs/implementations/ubergraph.rst index 22c75f708..df9b9d676 100644 --- a/docs/implementations/ubergraph.rst +++ b/docs/implementations/ubergraph.rst @@ -21,7 +21,6 @@ Code .. currentmodule:: oaklib.implementations.ubergraph.ubergraph_implementation .. autoclass:: UbergraphImplementation - :members: create .. autoclass:: RelationGraphEnum diff --git a/docs/index.rst b/docs/index.rst index 79c250b2b..70b1f26d1 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -11,10 +11,12 @@ Ontology Access Kit (OAK) Documentation :caption: Contents: introduction + intro/index architecture interfaces/index implementations/index cli + selectors datamodels/index utilities notebooks diff --git a/docs/interfaces/mapping-provider.rst b/docs/interfaces/mapping-provider.rst new file mode 100644 index 000000000..2a52e28b3 --- /dev/null +++ b/docs/interfaces/mapping-provider.rst @@ -0,0 +1,7 @@ +Mapping Provider +============== + +.. currentmodule:: oaklib.interfaces.mapping_provider_interface + +.. autoclass:: MappingProviderInterface + :members: diff --git a/docs/selectors.rst b/docs/selectors.rst new file mode 100644 index 000000000..f6cbe4bde --- /dev/null +++ b/docs/selectors.rst @@ -0,0 +1,121 @@ +.. _selectors: + +Ontology Implementation Selectors +================= + +In the command line interface and in Python code, *descriptors* can be used as a shorthand way to refer to either a local or remote ontology, plus +a method for parsing/querying it. The OntologyResource that is returned can be used +to instantiate an implementation. The descriptors can also be used in the :ref:`cli` + +Syntax +----- + +A descriptor is EITHER: + + - prefixed with a *scheme* OR + - is a *path (in which case the scheme is inferred) + +Examples +----- + +Examples of scheme-less descriptors, implicit implementation: + +- :code:`tests/input/go-nucleus.obo` - local obo format file loaded with pronto +- :code:`tests/input/go-nucleus.json` - local obojson format file loaded with pronto +- :code:`tests/input/go-nucleus.owl` - local OWL rdf/xml format file (loaded with pronto at the moment may change) +- :code:`tests/input/go-nucleus.db` - local sqlite3 db loaded with SqlImplementation +- :code:`http://purl.obolibrary.org/obo/pato.obo` - NOT IMPLEMENTED; download locally for now +- :code:`http://purl.obolibrary.org/obo/pato.owl` - NOT IMPLEMENTED; download locally for now + +Examples of explicit schemes: + +- :code:`pronto:tests/input/go-nucleus.obo` - local obo format file loaded with pronto +- :code:`pronto:tests/input/go-nucleus.json` - local obojson format file loaded with pronto +- :code:`pronto:tests/input/go-nucleus.owl` - local OWL rdf/xml format file (loaded with pronto at the moment may change) +- :code:`pronto:tests/input/go-nucleus.db` - local sqlite3 db loaded with SqlImplementation +- :code:`prontolib:pato.obo` - remote obo format file loaded from OBO Library with pronto +- :code:`prontolib:pato.owl` - remote owl format file loaded from OBO Library with pronto +- :code:`bioportal:` all of bioportal +- :code:`bioportal:pato` pato in bioportal (NOT IMPLEMENTED) +- :code:`ontobee:` all of ontobee +- :code:`ontobee:pato` pato in ontobee (NOT IMPLEMENTED) +- :code:`ols:` all of OLS +- :code:`ols:pato` pato in OLS (NOT IMPLEMENTED) +- :code:`ubergraph:` all of OLS +- :code:`ubergraph:pato` pato in ubergraph (NOT IMPLEMENTED) + +See :ref:`cli` for more examples + +Schemes +------- + +pronto +^^^^ + +Implementation: :ref:`ProntoImplementation` + +The slug is a path to a file on disk. Must be in obo or owl or json + +prontolib +^^^^ + +Implementation: :ref:`ProntoImplementation` + +The slug is the name of the resource on obo, e.g. pato.obo, cl.owl + +sqlite +^^^^ + +Implementation: :ref:`SqlImplementation` + +The slug is the path to the sqlite .db file on local disk + +obosqlite +^^^^ + +Implementation: :ref:`SqlImplementation` + +The slug is the name of the ontology, e.g 'hp', 'uberon' + +TODO: download from s3 + +ontobee +^^^^ + +Implementation: :ref:`OntobeeImplementation` + +Currently the slug is ignored + +ols +^^^^ + +Implementation: :ref:`OlsImplementation` + +Currently the slug is ignored + +bioportal +^^^^ + +Implementation: :ref:`BioportalImplementation` + +Currently the slug is ignored + +funowl +^^^^ + +Implementation: :ref:`OwlImplementation` + +NOT IMPLEMENTED YET + +owlery +^^^^ + +Implementation: :ref:`OwleryImplementation` + +NOT IMPLEMENTED YET + +Functions +---- + +.. automodule:: oaklib.selector + :members: diff --git a/docs/utilities.rst b/docs/utilities.rst index a4d1b12a8..a0a137fbe 100644 --- a/docs/utilities.rst +++ b/docs/utilities.rst @@ -6,10 +6,15 @@ Where possible, this library uses simple standalone python functions organized i Note: some of these may involve iterated calls on a remote backend, these are candidates for being turned into :ref:`interfaces`. +.. currentmodule:: oaklib + :toctree: src + + selector + .. currentmodule:: oaklib.utilities .. autosummary:: - :toctree: DIRNAME + :toctree: src obograph_utils graph.relationship_walker diff --git a/src/oaklib/__init__.py b/src/oaklib/__init__.py index cf3acff40..b6aa58a1f 100644 --- a/src/oaklib/__init__.py +++ b/src/oaklib/__init__.py @@ -9,3 +9,6 @@ """ __version__ = '0.1.0' + +from oaklib.interfaces import BasicOntologyInterface + diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index fa10e032b..a2912f938 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -22,11 +22,14 @@ from oaklib.implementations.sqldb.sql_implementation import SqlImplementation from oaklib.implementations.ubergraph.ubergraph_implementation import UbergraphImplementation from oaklib.interfaces import BasicOntologyInterface, OntologyInterface, ValidatorInterface, SubsetterInterface +from oaklib.interfaces.mapping_provider_interface import MappingProviderInterface from oaklib.interfaces.obograph_interface import OboGraphInterface from oaklib.interfaces.search_interface import SearchInterface from oaklib.interfaces.text_annotator_interface import TextAnnotatorInterface from oaklib.io.streaming_csv_writer import StreamingCsvWriter +from oaklib.io.streaming_yaml_writer import StreamingYamlWriter from oaklib.resource import OntologyResource +from oaklib.selector import get_resource_from_shorthand from oaklib.types import PRED_CURIE from oaklib.utilities.apikey_manager import set_apikey_value from oaklib.utilities.iterator_utils import chunk @@ -35,6 +38,7 @@ from oaklib.utilities.obograph_utils import draw_graph, graph_to_image, default_stylemap_path import sssom.writers as sssom_writers from oaklib.datamodels.vocabulary import IS_A, PART_OF, EQUIVALENT_CLASS +from oaklib.utilities.subsets.slimmer_utils import roll_up_to_named_subset @dataclass @@ -117,36 +121,11 @@ def main(verbose: int, quiet: bool, input: str): logging.basicConfig(level=logging.ERROR) resource = OntologyResource() resource.slug = input - impl_class: Type[OntologyInterface] - # TODO: move to a separate module + if input: - if ':' in input: - toks = input.split(':') - scheme = toks[0] - rest = ':'.join(toks[1:]) - if scheme == 'sqlite': - impl_class = SqlImplementation - resource.slug = f'sqlite:///{Path(rest).absolute()}' - elif scheme == 'ubergraph': - impl_class = UbergraphImplementation - resource = None - elif scheme == 'ontobee': - impl_class = OntobeeImplementation - resource = None - elif scheme == 'bioportal': - impl_class = BioportalImplementation - resource = None - elif scheme == 'obolibrary': - impl_class = ProntoImplementation - if resource.slug.endswith('.obo'): - resource.format = 'obo' - resource.local = False - resource.slug = resource.slug.replace('obolibrary:', '') - else: - raise ValueError(f'Scheme {scheme} not known') - else: - resource.local = True - impl_class = ProntoImplementation + impl_class: Type[OntologyInterface] + resource = get_resource_from_shorthand(input) + impl_class = resource.implementation_class logging.info(f'RESOURCE={resource}') settings.impl = impl_class(resource) @@ -268,10 +247,21 @@ def viz(terms, predicates, down, view, stylemap, configure, output_type: str, ou """ impl = settings.impl if isinstance(impl, OboGraphInterface): + terms_expanded = [] + for term in terms: + if term.startswith('in_subset='): + term = term.replace('in_subset=', '') + terms_expanded += list(impl.curies_by_subset(term)) + else: + terms_expanded.append(term) if stylemap is None: stylemap = default_stylemap_path() actual_predicates = _process_predicates_arg(predicates) - curies = list(impl.multiterm_search(terms)) + if isinstance(impl, SearchInterface): + curies = list(impl.multiterm_search(terms_expanded)) + else: + logging.warning(f'Search not implemented: using direct inputs') + curies = terms_expanded if down: graph = impl.subgraph(curies, predicates=actual_predicates) else: @@ -409,6 +399,63 @@ def terms(output: str): else: raise NotImplementedError(f'Cannot execute this using {impl} of type {type(impl)}') +@main.command() +@output_option +def mappings(output): + """ + List all SSSOM mappings in the ontology + """ + impl = settings.impl + writer = StreamingYamlWriter(output) + if isinstance(impl, MappingProviderInterface): + for mapping in impl.all_sssom_mappings(): + writer.emit(mapping) + else: + raise NotImplementedError(f'Cannot execute this using {impl} of type {type(impl)}') + +@main.command() +@output_option +def aliases(output): + """ + List all aliases in the ontology + """ + impl = settings.impl + writer = StreamingCsvWriter(output) + if isinstance(impl, BasicOntologyInterface): + for curie in impl.all_entity_curies(): + for pred, aliases in impl.alias_map_by_curie(curie).items(): + for alias in aliases: + writer.emit(dict(curie=curie, pred=pred, alias=alias)) + else: + raise NotImplementedError(f'Cannot execute this using {impl} of type {type(impl)}') + +@main.command() +@output_option +@click.argument('subsets', nargs=-1) +def subset_rollups(subsets: list, output): + """ + For each subset provide a mapping of each term in the ontology to a subset + """ + impl = settings.impl + #writer = StreamingCsvWriter(output) + if isinstance(impl, OboGraphInterface): + impl.enable_transitive_query_cache() + term_curies = list(impl.all_entity_curies()) + output.write("\t".join(['subset', 'term', 'subset_term'])) + if len(subsets) == 0: + subsets = list(impl.all_subset_curies()) + for subset in subsets: + logging.info(f'Subset={subset}') + m = roll_up_to_named_subset(impl, subset, term_curies, predicates=[IS_A, PART_OF]) + for term, mapped_to in m.items(): + for tgt in mapped_to: + output.write("\t".join([subset, term, tgt])) + output.write("\n") + #writer.emit(dict(subset=subset, term=term, subset_term=tgt)) + else: + raise NotImplementedError(f'Cannot execute this using {impl} of type {type(impl)}') + + @main.command() @output_option diff --git a/src/oaklib/implementations/aggregator/__init__.py b/src/oaklib/implementations/aggregator/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/src/oaklib/implementations/aggregator/aggregator_implementation.py b/src/oaklib/implementations/aggregator/aggregator_implementation.py new file mode 100644 index 000000000..77933a69c --- /dev/null +++ b/src/oaklib/implementations/aggregator/aggregator_implementation.py @@ -0,0 +1,75 @@ +import logging +from abc import ABC +from collections import defaultdict +from dataclasses import dataclass +from typing import List, Iterable, Type, Iterator, Union, Tuple, Callable, Optional, Any, Dict + +from oaklib.datamodels.obograph import Node +from oaklib.datamodels.validation_datamodel import ValidationConfiguration, ValidationResult +from oaklib.interfaces.basic_ontology_interface import BasicOntologyInterface, RELATIONSHIP_MAP, PRED_CURIE, ALIAS_MAP, \ + METADATA_MAP, PREFIX_MAP +from oaklib.interfaces.mapping_provider_interface import MappingProviderInterface +from oaklib.interfaces.obograph_interface import OboGraphInterface +from oaklib.interfaces.search_interface import SearchInterface, SearchConfiguration +from oaklib.interfaces.validator_interface import ValidatorInterface +from oaklib.interfaces.rdf_interface import RdfInterface +from oaklib.interfaces.relation_graph_interface import RelationGraphInterface +from oaklib.types import CURIE, SUBSET_CURIE + + + +@dataclass +class AggregatorImplementation(ValidatorInterface, RdfInterface, RelationGraphInterface, OboGraphInterface, SearchInterface, MappingProviderInterface): + """ + """ + implementations: List[BasicOntologyInterface] = None + + def _delegate_iterator(self, func: Callable) -> Iterable: + for i in self.implementations: + for v in func(i): + yield v + + def _delegate_simple_tuple_map(self, func: Callable, strict=False) -> Dict[Any, List[Any]]: + m = defaultdict(list) + for i in self.implementations: + for k, vs in func(i).items(): + m[k] += vs + return m + + + def _delegate_first(self, func: Callable, strict=False) -> Optional[Any]: + for i in self.implementations: + v = func(i) + if v is not None: + return v + if strict: + raise ValueError(f'No value for {func}') + + def validate(self, configuration: ValidationConfiguration = None) -> Iterable[ValidationResult]: + pass + + def all_entity_curies(self) -> Iterable[CURIE]: + return self._delegate_iterator(lambda i: i.all_entity_curies()) + + def get_simple_mappings_by_curie(self, curie: CURIE) -> Iterable[Tuple[PRED_CURIE, CURIE]]: + return self._delegate_iterator(lambda i: i.get_simple_mappings_by_curie(curie)) + + def get_label_by_curie(self, curie: CURIE) -> str: + return self._delegate_first(lambda i: i.get_label_by_curie(curie)) + + def alias_map_by_curie(self, curie: CURIE) -> ALIAS_MAP: + return self._delegate_simple_tuple_map(lambda i: i.alias_map_by_curie(curie)) + + def all_subset_curies(self) -> Iterable[SUBSET_CURIE]: + return self._delegate_iterator(lambda i: i.all_subset_curies()) + + def curies_by_subset(self, subset: SUBSET_CURIE) -> Iterable[CURIE]: + return self._delegate_iterator(lambda i: i.curies_by_subset(subset)) + + def node(self, curie: CURIE, strict=False) -> Node: + return self._delegate_first(lambda i: i.node(curie, strict=False), strict=strict) + + + + + diff --git a/src/oaklib/implementations/bioportal/bioportal_implementation.py b/src/oaklib/implementations/bioportal/bioportal_implementation.py index 0c1420171..3e0c5f258 100644 --- a/src/oaklib/implementations/bioportal/bioportal_implementation.py +++ b/src/oaklib/implementations/bioportal/bioportal_implementation.py @@ -11,6 +11,7 @@ from oaklib.interfaces.text_annotator_interface import TextAnnotatorInterface from oaklib.types import CURIE from oaklib.utilities.apikey_manager import get_apikey_value +from oaklib.utilities.rate_limiter import check_limit from sssom import Mapping from sssom.sssom_datamodel import MatchTypeEnum @@ -72,6 +73,7 @@ def annotate_text(self, text: str) -> Iterator[TextAnnotation]: 'text': text} if self.bioportal_api_key is None: self.load_bioportal_api_key() + check_limit() r = requests.get(REST_URL + '/annotator', headers=self._headers(), params=params) @@ -107,6 +109,7 @@ def json_to_results(self, json_list: List[Any], text: str) -> Iterator[TextAnnot def basic_search(self, search_term: str, config: SearchConfiguration = SearchConfiguration()) -> Iterable[CURIE]: if self.bioportal_api_key is None: self.load_bioportal_api_key() + check_limit() r = requests.get(REST_URL + '/search', headers=self._headers(), params={'q': search_term, 'include': ['prefLabel']}) @@ -124,6 +127,7 @@ def basic_search(self, search_term: str, config: SearchConfiguration = SearchCon next_page = obj['links']['nextPage'] #print(f'NEXT={next_page}') if next_page: + check_limit() r = requests.get(next_page, headers=self._headers()) obj = r.json() collection = obj['collection'] diff --git a/src/oaklib/implementations/ols/ols_implementation.py b/src/oaklib/implementations/ols/ols_implementation.py index b502f9e34..b69bb0e22 100644 --- a/src/oaklib/implementations/ols/ols_implementation.py +++ b/src/oaklib/implementations/ols/ols_implementation.py @@ -34,6 +34,9 @@ class OlsImplementation(TextAnnotatorInterface, SearchInterface, MappingProvider """ Implementation over OLS and OxO APIs + .. note:: + + """ ols_api_key: str = None label_cache: Dict[CURIE, str] = field(default_factory=lambda: {}) diff --git a/src/oaklib/implementations/pronto/pronto_implementation.py b/src/oaklib/implementations/pronto/pronto_implementation.py index d865af3a4..3a96c92b7 100644 --- a/src/oaklib/implementations/pronto/pronto_implementation.py +++ b/src/oaklib/implementations/pronto/pronto_implementation.py @@ -2,12 +2,14 @@ from abc import ABC from collections import defaultdict from dataclasses import dataclass -from typing import List, Iterable, Type +from typing import List, Iterable, Type, Iterator, Union import pronto +import sssom from deprecated import deprecated from oaklib.interfaces.basic_ontology_interface import BasicOntologyInterface, RELATIONSHIP_MAP, PRED_CURIE, ALIAS_MAP, \ METADATA_MAP, PREFIX_MAP +from oaklib.interfaces.mapping_provider_interface import MappingProviderInterface from oaklib.interfaces.obograph_interface import OboGraphInterface from oaklib.interfaces.search_interface import SearchInterface, SearchConfiguration from oaklib.interfaces.validator_interface import ValidatorInterface @@ -17,12 +19,13 @@ from oaklib.types import CURIE, SUBSET_CURIE from oaklib.datamodels import obograph from oaklib.datamodels.obograph import Edge, Graph -from oaklib.datamodels.vocabulary import LABEL_PREDICATE, IS_A, HAS_DBXREF, SCOPE_TO_SYNONYM_PRED_MAP +from oaklib.datamodels.vocabulary import LABEL_PREDICATE, IS_A, HAS_DBXREF, SCOPE_TO_SYNONYM_PRED_MAP, SKOS_CLOSE_MATCH from pronto import Ontology, LiteralPropertyValue, ResourcePropertyValue, Term +from sssom.sssom_datamodel import MatchTypeEnum @dataclass -class ProntoImplementation(ValidatorInterface, RdfInterface, RelationGraphInterface, OboGraphInterface, SearchInterface): +class ProntoImplementation(ValidatorInterface, RdfInterface, RelationGraphInterface, OboGraphInterface, SearchInterface, MappingProviderInterface): """ Pronto wraps local-file based ontologies in the following formats: @@ -139,7 +142,7 @@ def curies_by_subset(self, subset: SUBSET_CURIE) -> Iterable[CURIE]: if subset in t.subsets: yield t.id - def get_label_by_curie(self, curie: CURIE): + def get_label_by_curie(self, curie: CURIE) -> str: t = self._entity(curie) if t: return t.name @@ -227,6 +230,8 @@ def get_definition_by_curie(self, curie: CURIE) -> str: def alias_map_by_curie(self, curie: CURIE) -> ALIAS_MAP: t = self._entity(curie) + if t is None: + return {} m = defaultdict(list) m[LABEL_PREDICATE] = [t.name] for s in t.synonyms: @@ -278,11 +283,24 @@ def create_subontology(self, curies: List[CURIE]) -> "ProntoImplementation": # TODO - complete object return ProntoImplementation(wrapped_ontology=subontology) + # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + # Implements: MappingsInterface + # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + + def get_sssom_mappings_by_curie(self, curie: Union[str, CURIE]) -> Iterator[sssom.Mapping]: + t = self._entity(curie) + for x in t.xrefs: + yield sssom.Mapping(subject_id=curie, + predicate_id=SKOS_CLOSE_MATCH, + object_id=x.id, + match_type=MatchTypeEnum.Lexical) + + # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ # Implements: OboGraphInterface # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - def node(self, curie: CURIE) -> obograph.Node: + def node(self, curie: CURIE, strict=False) -> obograph.Node: t = self._entity(curie) if t is None: return obograph.Node(id=curie) diff --git a/src/oaklib/implementations/sqldb/sql_implementation.py b/src/oaklib/implementations/sqldb/sql_implementation.py index e0c16a704..0bd65ddb0 100644 --- a/src/oaklib/implementations/sqldb/sql_implementation.py +++ b/src/oaklib/implementations/sqldb/sql_implementation.py @@ -192,6 +192,7 @@ def ancestors(self, start_curies: Union[CURIE, List[CURIE]], predicates: List[PR q = q.filter(EntailedEdge.subject == start_curies) if predicates is not None: q = q.filter(EntailedEdge.predicate.in_(tuple(predicates))) + logging.debug(f'Ancestors query: {q}') for row in q: yield row.object diff --git a/src/oaklib/interfaces/mapping_provider_interface.py b/src/oaklib/interfaces/mapping_provider_interface.py index 70c55b81f..2de52d197 100644 --- a/src/oaklib/interfaces/mapping_provider_interface.py +++ b/src/oaklib/interfaces/mapping_provider_interface.py @@ -13,10 +13,23 @@ class MappingProviderInterface(BasicOntologyInterface, ABC): TODO: move code from mapping-walker """ - def all_mappings(self) -> Iterable[sssom.Mapping]: - raise NotImplementedError + def all_sssom_mappings(self) -> Iterable[sssom.Mapping]: + """ + All SSSOM mappings in the ontology + + :return: + """ + for curie in self.all_entity_curies(): + for m in self.get_sssom_mappings_by_curie(curie): + yield m def get_sssom_mappings_by_curie(self, curie: CURIE) -> Iterable[sssom.Mapping]: + """ + All SSSOM mappings about a curie + + :param curie: + :return: + """ raise NotImplementedError def get_transitive_mappings_by_curie(self, curie: CURIE) -> Iterable[sssom.Mapping]: diff --git a/src/oaklib/io/streaming_csv_writer.py b/src/oaklib/io/streaming_csv_writer.py index 847fb7877..09511b93b 100644 --- a/src/oaklib/io/streaming_csv_writer.py +++ b/src/oaklib/io/streaming_csv_writer.py @@ -1,11 +1,13 @@ import csv import sys from dataclasses import dataclass, field -from typing import Any +from typing import Any, Dict, Union from linkml_runtime import CurieNamespace from linkml_runtime.utils.enumerations import EnumDefinitionImpl from linkml_runtime.utils.yamlutils import YAMLRoot +from oaklib.io.streaming_writer import StreamingWriter + def _keyval(x: Any) -> str: if isinstance(x, CurieNamespace): @@ -17,16 +19,23 @@ def _keyval(x: Any) -> str: @dataclass -class StreamingCsvWriter: - file: Any = field(default_factory=lambda: sys.stdout) +class StreamingCsvWriter(StreamingWriter): + """ + A writer that streams CSV/TSV output + """ + header_emitted: bool = None delimiter: str = '\t' writer: csv.DictWriter = None - def emit(self, obj: YAMLRoot): + def emit(self, obj: Union[YAMLRoot, Dict]): + if isinstance(obj, dict): + obj_as_dict = obj + else: + obj_as_dict = vars(obj) if self.writer is None: - self.writer = csv.DictWriter(self.file, delimiter=self.delimiter, fieldnames=list(vars(obj))) + self.writer = csv.DictWriter(self.file, delimiter=self.delimiter, fieldnames=list(obj_as_dict)) self.writer.writeheader() - self.writer.writerow({k: _keyval(v) for k, v in vars(obj).items()}) + self.writer.writerow({k: _keyval(v) for k, v in obj_as_dict.items()}) diff --git a/src/oaklib/io/streaming_writer.py b/src/oaklib/io/streaming_writer.py new file mode 100644 index 000000000..e91ee1dc1 --- /dev/null +++ b/src/oaklib/io/streaming_writer.py @@ -0,0 +1,11 @@ +import sys +from dataclasses import dataclass, field +from typing import Any + + +@dataclass +class StreamingWriter: + """ + Base class for streaming writers + """ + file: Any = field(default_factory=lambda: sys.stdout) \ No newline at end of file diff --git a/src/oaklib/io/streaming_yaml_writer.py b/src/oaklib/io/streaming_yaml_writer.py new file mode 100644 index 000000000..a5c3dfec9 --- /dev/null +++ b/src/oaklib/io/streaming_yaml_writer.py @@ -0,0 +1,32 @@ +import csv +import sys +from dataclasses import dataclass, field +from typing import Any + +from linkml_runtime import CurieNamespace +from linkml_runtime.dumpers import yaml_dumper +from linkml_runtime.utils.enumerations import EnumDefinitionImpl +from linkml_runtime.utils.yamlutils import YAMLRoot +from oaklib.io.streaming_writer import StreamingWriter + + +def _keyval(x: Any) -> str: + if isinstance(x, CurieNamespace): + return str(x.curie()) + #if isinstance(x, EnumDefinitionImpl): + # if x.curie: + # return str(x.curie) + return str(x) + + +@dataclass +class StreamingYamlWriter(StreamingWriter): + """ + A writer that emits one document at a time in one stream + """ + + def emit(self, obj: YAMLRoot): + self.file.write(yaml_dumper.dumps(obj)) + self.file.write("\n---\n") + + diff --git a/src/oaklib/resource.py b/src/oaklib/resource.py index 84d5fcaae..f3d5c5de8 100644 --- a/src/oaklib/resource.py +++ b/src/oaklib/resource.py @@ -1,5 +1,7 @@ +import logging from dataclasses import dataclass from pathlib import Path +from typing import Type, Union @dataclass @@ -18,6 +20,7 @@ class OntologyResource: local: bool = False in_memory: bool = False data: str = None + implementation_class: Union[Type] = None @property def local_path(self) -> Path: diff --git a/src/oaklib/selector.py b/src/oaklib/selector.py new file mode 100644 index 000000000..404458ceb --- /dev/null +++ b/src/oaklib/selector.py @@ -0,0 +1,95 @@ +import logging +from dataclasses import dataclass +from pathlib import Path +from typing import Type, Union + +from oaklib.implementations.bioportal.bioportal_implementation import BioportalImplementation +from oaklib.implementations.ols.ols_implementation import OlsImplementation +from oaklib.implementations.ontobee.ontobee_implementation import OntobeeImplementation +from oaklib.implementations.pronto.pronto_implementation import ProntoImplementation +from oaklib.implementations.sqldb.sql_implementation import SqlImplementation +from oaklib.implementations.ubergraph import UbergraphImplementation +from oaklib.interfaces import OntologyInterface +from oaklib.resource import OntologyResource + + +def get_implementation_from_shorthand(descriptor: str, format: str = None) -> OntologyResource: + """ + See :ref:`get_resource_from_shorthand` + + Example: + + .. code :: python + + >>> oi = get_implementation_from_shorthand('my-ont.owl') + >>> for term in oi.all_entities(): + >>> ... + + :param descriptor: + :param format: + :return: + """ + +def get_resource_from_shorthand(descriptor: str, format: str = None) -> OntologyResource: + """ + Maps from a shorthand descriptor to an OntologyResource. + + + + + :param descriptor: + :param format: + :return: + """ + resource = OntologyResource() + resource.slug = descriptor + impl_class: Type[OntologyInterface] + if descriptor: + if ':' in descriptor: + toks = descriptor.split(':') + scheme = toks[0] + rest = ':'.join(toks[1:]) + if not rest: + rest= None + resource.slug = rest + if scheme == 'sqlite': + impl_class = SqlImplementation + resource.slug = f'sqlite:///{Path(rest).absolute()}' + elif scheme == 'ubergraph': + impl_class = UbergraphImplementation + if rest: + raise NotImplementedError(f'Ontologies within ubergraph not supported yet') + elif scheme == 'ontobee': + impl_class = OntobeeImplementation + elif scheme == 'bioportal': + impl_class = BioportalImplementation + elif scheme == 'ols': + impl_class = OlsImplementation + elif scheme == 'pronto': + impl_class = ProntoImplementation + if resource.slug.endswith('.obo'): + resource.format = 'obo' + resource.local = True + resource.slug = rest + elif scheme == 'obolibrary' or scheme == 'prontolib': + impl_class = ProntoImplementation + if resource.slug.endswith('.obo'): + resource.format = 'obo' + resource.local = False + resource.slug = rest + elif scheme == 'http' or scheme == 'https': + raise NotImplementedError(f'Web requests not implemented yet') + else: + raise ValueError(f'Scheme {scheme} not known') + else: + logging.info(f'No schema: assuming file path {descriptor}') + if descriptor.endswith('.db') or (format and format == 'sqlite'): + impl_class = SqlImplementation + resource.slug = f'sqlite:///{Path(descriptor).absolute()}' + else: + resource.local = True + impl_class = ProntoImplementation + else: + raise ValueError(f'No descriptor') + resource.implementation_class = impl_class + return resource diff --git a/src/oaklib/utilities/graph/relationship_walker.py b/src/oaklib/utilities/graph/relationship_walker.py index 12fcd68e5..8a4eff809 100644 --- a/src/oaklib/utilities/graph/relationship_walker.py +++ b/src/oaklib/utilities/graph/relationship_walker.py @@ -1,3 +1,9 @@ +""" +Utilities for traversing Ontology Graphs +==================== + + +""" from copy import copy from dataclasses import dataclass from typing import List, Union, Dict, Iterable, Tuple diff --git a/src/oaklib/utilities/lexical/lexical_indexer.py b/src/oaklib/utilities/lexical/lexical_indexer.py index 7129aac1b..8ec2cacd6 100644 --- a/src/oaklib/utilities/lexical/lexical_indexer.py +++ b/src/oaklib/utilities/lexical/lexical_indexer.py @@ -143,8 +143,8 @@ def create_mapping(term: str, r1: RelationshipToTerm, r2: RelationshipToTerm, predicate_id=pred, confidence=confidence, match_string=term, - subject_match_field=r1.predicate, - object_match_field=r2.predicate, + subject_match_field=[r1.predicate], + object_match_field=[r2.predicate], match_type=MatchTypeEnum.Lexical, mapping_tool='oaklib' ) diff --git a/src/oaklib/utilities/subsets/slimmer_utils.py b/src/oaklib/utilities/subsets/slimmer_utils.py index f39e09654..470855607 100644 --- a/src/oaklib/utilities/subsets/slimmer_utils.py +++ b/src/oaklib/utilities/subsets/slimmer_utils.py @@ -1,6 +1,13 @@ +""" +Utilities for working with ontology subsets (slims) +---- +""" + +import logging from typing import List, Dict from oaklib.interfaces import RelationGraphInterface +from oaklib.interfaces.obograph_interface import OboGraphInterface from oaklib.types import CURIE, PRED_CURIE def filter_redundant(oi: RelationGraphInterface, curies: List[CURIE], predicates: List[PRED_CURIE] = None) -> List[CURIE]: @@ -13,23 +20,34 @@ def is_redundant(oi: RelationGraphInterface, curie: CURIE, curies: List[CURIE], return True return False -def roll_up_to_named_subset(oi: RelationGraphInterface, subset: CURIE, curies: List[CURIE], +def roll_up_to_named_subset(oi: OboGraphInterface, subset: CURIE, curies: List[CURIE], predicates: List[PRED_CURIE] = None) -> Dict[CURIE, List[CURIE]]: + """ + Rolls up all specified curies to a named subset, e.g. goslim_generic + + :param oi: + :param subset: + :param curies: + :param predicates: + :return: + """ # see https://metacpan.org/dist/go-perl/view/scripts/map2slim terms_in_subset = set(oi.curies_by_subset(subset)) - print(f'SUBSET={list(terms_in_subset)}') - subset_ancs = {t: [a for a in oi.ancestors(t, predicates) if a != t] for t in terms_in_subset} + #print(f'SUBSET={list(terms_in_subset)}') + logging.info(f'Terms in {subset} = {len(terms_in_subset)}') + subset_anc_map = {t: [a for a in oi.ancestors(t, predicates) + if a != t and a in terms_in_subset] for t in terms_in_subset} m = {} for curie in curies: + logging.info(f' Mapping {curie}') ancs = list(oi.ancestors(curie, predicates=predicates)) - print(f'{curie} ANCS={list(ancs)}') + #print(f'{curie} ANCS={list(ancs)}') ancs_in_subset = terms_in_subset.intersection(ancs) - print(f' xx ANCS={list(ancs_in_subset)}') - nr_ancs_in_subset = filter_redundant(oi, ancs_in_subset, predicates) - #exclude = set() - #for a in ancs_in_subset: - # exclude.update(subset_ancs[a]) - # print(f'+{a} ==> EXC {exclude}') + #print(f' xx ANCS={list(ancs_in_subset)}') + redundant = set() + for a in ancs_in_subset: + redundant.update(subset_anc_map[a]) + nr_ancs_in_subset = [a for a in ancs_in_subset if a not in redundant] m[curie] = nr_ancs_in_subset return m diff --git a/tests/input/interneuron.obo b/tests/input/interneuron.obo new file mode 100644 index 000000000..89aa2e826 --- /dev/null +++ b/tests/input/interneuron.obo @@ -0,0 +1,17594 @@ +format-version: 1.2 +ontology: interneuron +subsetdef: added_for_HCA "Classes tagged with this subset property were added upon request from the Human Cell Atlas (HCA)." +subsetdef: cumbo "CUMBO" +subsetdef: cyclostome_subset "cyclostome structures" +subsetdef: defined_by_cytoarchitecture "brain region defined by cyto-architecture" +subsetdef: defined_by_ordinal_series "classes that are defined by relative position counting from first in a series of elements along an axis in an individual organism rather than by strict homology" +subsetdef: developmental_classification "developmental_classification" +subsetdef: dubious_grouping "Indicates that subclasses in AOs may be inappropriately linked" +subsetdef: early_development "A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes." +subsetdef: efo_slim "EFO slim" +subsetdef: emapa_ehdaa2 "derived from the union of EHDAA2 and EMAPA - still to be checked" +subsetdef: feed_aligned "subset of classes that have logical defs text defs and synonyms aligned with FEED" +subsetdef: functional_classification "functional_classification" +subsetdef: grouping_class "Subset consisting of classes creating for grouping purposes" +subsetdef: homology_grouping "A grouping class that depends on an assumption of homology between subclasses" +subsetdef: human_reference_atlas "" +subsetdef: inconsistent_with_fma "classes that have some inconsistency with FMA" +subsetdef: location_grouping "" +subsetdef: major_organ "somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads" +subsetdef: metazoa_core "core classes typically found across metazoa. one purpose is to create a rough set of terms that could be used to start a new metazoan AO. Note this subset is not yet fully fleshed out" +subsetdef: non_informative "abstract class brought in to group ontology classes but not informative" +subsetdef: organ_slim "organs, excluding individual muscles and skeletal elements" +subsetdef: pheno_slim "Phenotype slim" +subsetdef: phenotype_rcn "A subset specifically created for the 2012 Phenotype RCN meeting. Includes some human-specific terms that may eventually be removed when they are adequately represented with part of relationships in FMA" +subsetdef: uberon_slim "Uberon slim - subset that excludes obscure terms and deep compositional terms" +subsetdef: unverified_taxonomic_grouping "Indicates that the class encompasses classes from other AOs that have not been verified" +subsetdef: upper_level "abstract upper-level terms not directly useful for analysis" +subsetdef: vertebrate_core "core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO" +synonymtypedef: ABBREVIATION "abbreviation" +synonymtypedef: BRAIN_NAME_ABV "brain name abbreviations (drosophila)" +synonymtypedef: COMPARATIVE_PREFERRED "preferred term in the context of comparative anatomy" +synonymtypedef: DEPRECATED "A historic synonym, no longer encouraged" +synonymtypedef: DEVELOPMENTAL "developmental term" +synonymtypedef: DUBIOUS "dubious or contested synonym" +synonymtypedef: HOMOLOGY "a synonym made on the basis of a possibly homologous structure in another species" +synonymtypedef: HUMAN_PREFERRED "preferred term when talking about an instance of this class in Homo sapiens" +synonymtypedef: INCONSISTENT "indicates that a synonym is used in an inconsistent or confusing way, typically between species" +synonymtypedef: LATIN "latin term" +synonymtypedef: MISSPELLING "a mis-spelling that is in common use and thus recorded" +synonymtypedef: NON_AMNIOTE "synonym that is inappropriate for amniotes" +synonymtypedef: NON_MAMMAL "synonym that is inappropriate for mammals" +synonymtypedef: PENDING_REVIEW "expert consultation and attribution required" +synonymtypedef: PLURAL "plural term" +synonymtypedef: SENSU "taxonomic disambiguation" +synonymtypedef: SYSTEMATIC "a systematic synonym used as the base name for design patterns" + +[Term] +id: CL:0000000 +name: cell +def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] +subset: prefixes.ttl:upper_level +xref: CALOHA:TS-2035 +xref: FMA:68646 +xref: GO:0005623 +xref: KUPO:0000002 +xref: VHOG:0001533 +xref: WBbt:0004017 +xref: XAO:0003012 + +[Term] +id: CL:0000003 +name: native cell +def: "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment)." [CARO:mah] +subset: prefixes.ttl:upper_level +synonym: "cell in vivo" NARROW [] +xref: CARO:0000013 +is_a: CL:0000000 ! cell + +[Term] +id: CL:0000007 +name: early embryonic cell (metazoa) +def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] +is_a: CL:0002321 ! embryonic cell (metazoa) + +[Term] +id: CL:0000008 +name: migratory cranial neural crest cell +def: "Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination." [https://orcid.org/0000-0001-5208-3432, ZFA:0007091] +is_a: CL:0000333 ! migratory neural crest cell + +[Term] +id: CL:0000030 +name: glioblast +xref: FBbt:00005145 +is_a: CL:0000055 ! non-terminally differentiated cell + +[Term] +id: CL:0000031 +name: neuroblast (sensu Vertebrata) +def: "A cell that will develop into a neuron often after a migration phase." [GOC:NV, http://en.wikipedia.org/wiki/Neuroblast] +synonym: "neuroblast" EXACT [] +xref: BTO:0000930 +xref: FMA:70563 +is_a: CL:0000055 ! non-terminally differentiated cell +is_a: CL:0000548 ! animal cell + +[Term] +id: CL:0000034 +name: stem cell +def: "A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." [GOC:tfm, MESH:A11.872] +synonym: "animal stem cell" EXACT [] +xref: CALOHA:TS-2086 +xref: FMA:63368 +is_a: CL:0011115 ! precursor cell + +[Term] +id: CL:0000035 +name: single fate stem cell +def: "A stem cell that self-renews as well as give rise to a single mature cell type." [GOC:tfm] +synonym: "unipotent stem cell" EXACT [] +synonym: "unipotential stem cell" EXACT [] +xref: FMA:70569 +is_a: CL:0000723 ! somatic stem cell + +[Term] +id: CL:0000036 +name: epithelial fate stem cell +synonym: "epithelial stem cell" EXACT [] +is_a: CL:0000035 ! single fate stem cell + +[Term] +id: CL:0000037 +name: hematopoietic stem cell +def: "A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119." [GOC:add, GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Hematopoietic_stem_cell, PMID:19022770] +synonym: "blood forming stem cell" EXACT [] +synonym: "colony forming unit hematopoietic" RELATED [] +synonym: "hemopoietic stem cell" EXACT [] +synonym: "HSC" EXACT [] +xref: BTO:0000725 +xref: CALOHA:TS-0448 +xref: FMA:70337 +xref: FMA:86475 +xref: VHOG:0001485 +is_a: CL:0000723 ! somatic stem cell +is_a: CL:0008001 ! hematopoietic precursor cell +is_a: CL:0011026 ! progenitor cell + +[Term] +id: CL:0000038 +name: erythroid progenitor cell +def: "A progenitor cell committed to the erythroid lineage." [GOC:add, ISBN:0721601464] +synonym: "BFU-E" RELATED [] +synonym: "blast forming unit erythroid" RELATED [] +synonym: "burst forming unit erythroid" RELATED [] +synonym: "CFU-E" RELATED [] +synonym: "colony forming unit erythroid" RELATED [] +synonym: "erythroid stem cell" RELATED [] +xref: BTO:0004911 +is_a: CL:0000764 ! erythroid lineage cell +is_a: CL:0000839 ! myeloid lineage restricted progenitor cell + +[Term] +id: CL:0000039 +name: germ line cell +def: "A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring." [GOC:tfm, ISBN:0721662544] +subset: prefixes.ttl:upper_level +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0000048 +name: multi fate stem cell +def: "A stem cell that can give rise to multiple lineages of cells." [GOC:add] +synonym: "multi-fate stem cell" EXACT [] +synonym: "multifate stem cell" EXACT [] +synonym: "multipotent cell" EXACT [] +synonym: "multipotent stem cell" EXACT [] +xref: FMA:84789 +is_a: CL:0000034 ! stem cell +is_a: CL:0002371 ! somatic cell + +[Term] +id: CL:0000049 +name: common myeloid progenitor +def: "A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages." [GOC:add, ISBN:0878932437, MESH:D023461] +synonym: "CFU-GEMM" RELATED [ISBN:0878932437] +synonym: "CFU-S" RELATED [ISBN:0878932437] +synonym: "CMP" EXACT [ISBN:0878932437] +synonym: "colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte" RELATED [ISBN:0878932437] +synonym: "common myeloid precursor" EXACT [] +synonym: "multipotential myeloid stem cell" RELATED [ISBN:0878932437] +synonym: "myeloid stem cell" RELATED [ISBN:0878932437] +synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437] +xref: BTO:0004730 +is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell + +[Term] +id: CL:0000050 +name: megakaryocyte-erythroid progenitor cell +def: "A progenitor cell committed to the megakaryocyte and erythroid lineages." [GOC:add, GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Megakaryocyte-erythroid_progenitor_cell, MESH:D055015, PMID:16647566] +synonym: "CFU-EM" EXACT [] +synonym: "CFU-MegE" EXACT [] +synonym: "colony forming unit erythroid megakaryocyte" EXACT [] +synonym: "Meg/E progenitor" EXACT [] +synonym: "megakaryocyte/erythrocyte progenitor" EXACT [] +synonym: "megakaryocyte/erythroid progenitor cell" EXACT [] +synonym: "MEP" EXACT [] +is_a: CL:0000763 ! myeloid cell +is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell +is_a: CL:0011026 ! progenitor cell + +[Term] +id: CL:0000051 +name: common lymphoid progenitor +def: "A oligopotent progenitor cell committed to the lymphoid lineage." [GOC:add, GOC:dsd, GOC:tfm, PMID:10407577, PMID:16551251] +synonym: "CLP" EXACT [] +synonym: "committed lymphopoietic stem cell" RELATED [] +synonym: "common lymphocyte precursor" EXACT [] +synonym: "common lymphocyte progenitor" EXACT [] +synonym: "common lymphoid precursor" EXACT [] +synonym: "early lymphocyte progenitor" RELATED [] +synonym: "ELP" RELATED [] +synonym: "lymphoid stem cell" RELATED [] +synonym: "lymphopoietic stem cell" RELATED [] +is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell +is_a: CL:0011026 ! progenitor cell + +[Term] +id: CL:0000052 +name: totipotent stem cell +def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] +synonym: "totipotential stem cell" EXACT [] +xref: FMA:84790 +is_a: CL:0000723 ! somatic stem cell + +[Term] +id: CL:0000055 +name: non-terminally differentiated cell +def: "A precursor cell with a limited number of potential fates." [SANBI:mhl] +synonym: "blast cell" EXACT [] +xref: BTO:0000125 +xref: FMA:84782 +is_a: CL:0011115 ! precursor cell + +[Term] +id: CL:0000056 +name: myoblast +def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:A11.635, PMID:21849021] +xref: BTO:0000222 +xref: CALOHA:TS-0650 +xref: FBbt:00005083 +xref: FMA:70335 +xref: VHOG:0001529 +is_a: CL:0000680 ! muscle precursor cell + +[Term] +id: CL:0000057 +name: fibroblast +def: "A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped." [http://en.wikipedia.org/wiki/Fibroblast, ISBN:0517223651, MESH:A11.329.228, MESH:D005347] +xref: BTO:0000452 +xref: CALOHA:TS-0362 +xref: FMA:63877 +xref: VHOG:0001482 +is_a: CL:0002320 ! connective tissue cell + +[Term] +id: CL:0000058 +name: chondroblast +def: "Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell." [GO_REF:0000034, GOC:tfm, ISBN:0618947256] +synonym: "chrondoplast" EXACT [] +xref: BTO:0003607 +xref: FMA:66783 +is_a: CL:0000055 ! non-terminally differentiated cell +is_a: CL:0002320 ! connective tissue cell + +[Term] +id: CL:0000066 +name: epithelial cell +def: "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina." [FB:ma, GOC:tfm, MESH:A11.436] +synonym: "epitheliocyte" EXACT [] +xref: BTO:0000414 +xref: CALOHA:TS-2026 +xref: CARO:0000077 +xref: FBbt:00000124 +xref: FMA:66768 +xref: WBbt:0003672 +is_a: CL:0000548 ! animal cell +relationship: BFO:0000050 UBERON:0000483 ! part of epithelium + +[Term] +id: CL:0000071 +name: blood vessel endothelial cell +def: "An endothelial cell that lines the vasculature." [GOC:tfm] +synonym: "cuboidal endothelial cell of vascular tree" EXACT [] +is_a: CL:0000076 ! squamous epithelial cell +is_a: CL:0002139 ! endothelial cell of vascular tree +relationship: BFO:0000050 UBERON:0004638 ! part of blood vessel endothelium + +[Term] +id: CL:0000075 +name: columnar/cuboidal epithelial cell +def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [GO:0002065, https://orcid.org/0000-0001-5208-3432] +is_a: CL:0000066 ! epithelial cell +is_a: CL:0002371 ! somatic cell + +[Term] +id: CL:0000076 +name: squamous epithelial cell +xref: CALOHA:TS-1249 +is_a: CL:0000066 ! epithelial cell + +[Term] +id: CL:0000077 +name: mesothelial cell +def: "A flattened epithelial cell of mesenchymal origin that lines the serous cavity." [GOC:tfm, ISBN:0721662544] +synonym: "mesotheliocyte" EXACT [] +xref: FMA:66773 +is_a: CL:0000076 ! squamous epithelial cell +is_a: CL:0000213 ! lining cell +is_a: CL:0002078 ! meso-epithelial cell + +[Term] +id: CL:0000079 +name: stratified epithelial cell +is_a: CL:0000066 ! epithelial cell +is_a: CL:0002371 ! somatic cell + +[Term] +id: CL:0000081 +name: blood cell +def: "A cell found predominately in the blood." [GOC:add, GOC:tfm] +xref: FMA:62844 +is_a: CL:0000988 ! hematopoietic cell + +[Term] +id: CL:0000094 +name: granulocyte +def: "A leukocyte with abundant granules in the cytoplasm." [GOC:amm, GOC:tfm, http://en.wikipedia.org/wiki/Granulocyte, MESH:A11.118.637.415, MESH:D006098] +synonym: "granular leucocyte" EXACT [] +synonym: "granular leukocyte" EXACT [] +synonym: "polymorphonuclear leukocyte" EXACT [] +xref: BTO:0000539 +xref: BTO:0001026 +xref: CALOHA:TS-0422 +xref: FMA:62854 +is_a: CL:0000081 ! blood cell +is_a: CL:0000766 ! myeloid leukocyte + +[Term] +id: CL:0000095 +name: neuron associated cell +is_a: CL:0002319 ! neural cell + +[Term] +id: CL:0000099 +name: interneuron +def: "Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions." [GOC:tfm, MESH:A08.663.358] +xref: BTO:0003811 +xref: FBbt:00005125 +xref: FMA:67313 +xref: WBbt:0005113 +is_a: CL:0000540 ! neuron + +[Term] +id: CL:0000100 +name: motor neuron +def: "An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement." [MESH:A08.663.655.500, PMID:16875686] +synonym: "motoneuron" EXACT [] +xref: BTO:0000312 +xref: FMA:83617 +xref: WBbt:0005409 +is_a: CL:0000527 ! efferent neuron + +[Term] +id: CL:0000114 +name: surface ectodermal cell +synonym: "cell of surface ectoderm" EXACT [] +synonym: "surface ectoderm cell" EXACT [] +xref: FMA:72552 +is_a: CL:0000221 ! ectodermal cell + +[Term] +id: CL:0000115 +name: endothelial cell +def: "An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm." [GOC:tfm, http://en.wikipedia.org/wiki/Endothelial_cell, https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3364936&group_id=36855, MESH:D042783, PMID:21275341] +synonym: "endotheliocyte" EXACT [] +xref: BTO:0001176 +xref: CALOHA:TS-0278 +xref: FMA:66772 +is_a: CL:0000213 ! lining cell +is_a: CL:0002078 ! meso-epithelial cell + +[Term] +id: CL:0000117 +name: CNS neuron (sensu Vertebrata) +is_a: CL:0000540 ! neuron +relationship: BFO:0000050 UBERON:0001017 ! part of central nervous system + +[Term] +id: CL:0000125 +name: glial cell +def: "A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons." [MESH:A08.637] +synonym: "neuroglia" RELATED [] +synonym: "neuroglial cell" EXACT [] +xref: BTO:0002606 +xref: CALOHA:TS-0415 +xref: FMA:54536 +is_a: CL:0000095 ! neuron associated cell + +[Term] +id: CL:0000133 +name: neurectodermal cell +def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] +synonym: "neurectoderm cell" EXACT [] +is_a: CL:0000221 ! ectodermal cell + +[Term] +id: CL:0000134 +name: mesenchymal stem cell +def: "A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs." [FB:ma, GOC:dsd, http://en.wikipedia.org/wiki/Mesenchymal_stem_cell, http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells, PMCID:PMC2613570, PMID:10102814j, PMID:16923606, PMID:17986482, PMID:19960544] +synonym: "BMSC" NARROW [] +synonym: "bone marrow stromal cells" NARROW [] +synonym: "CFU-F" RELATED [] +synonym: "colony-forming unit-fibroblast" NARROW [] +synonym: "marrow stromal cells" NARROW [PMID:11378515] +synonym: "mesenchymal precursor cell" RELATED [] +synonym: "mesenchymal progenitor cells" RELATED [MESH:D044982] +synonym: "mesenchymal stem cell" RELATED [] +synonym: "mesenchymal stromal cell" RELATED [] +synonym: "mesenchymal stromal cells" RELATED [] +synonym: "MSC" RELATED [PMID:11378515] +synonym: "stem cells, mesenchymal" RELATED [MESH:D044982] +xref: BTO:0002625 +xref: BTO:0003298 +xref: FMA:70546 +is_a: CL:0000048 ! multi fate stem cell +is_a: CL:0002320 ! connective tissue cell + +[Term] +id: CL:0000136 +name: fat cell +def: "A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides." [MESH:A11.329.114] +synonym: "adipocyte" EXACT [] +synonym: "adipose cell" EXACT [] +xref: BTO:0000443 +xref: CALOHA:TS-0012 +xref: FMA:63880 +is_a: CL:0000325 ! stuff accumulating cell +is_a: CL:0002320 ! connective tissue cell + +[Term] +id: CL:0000138 +name: chondrocyte +def: "Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell." [GO_REF:0000034, MESH:A11.329.171] +synonym: "cartilage cell" EXACT [] +xref: BTO:0000249 +xref: CALOHA:TS-0138 +xref: FMA:66782 +is_a: CL:0000153 ! glycosaminoglycan secreting cell +is_a: CL:0000667 ! collagen secreting cell + +[Term] +id: CL:0000151 +name: secretory cell +def: "A cell that specializes in controlled release of one or more substances." [GOC:tfm, ISBN:0721662544] +xref: BTO:0003659 +xref: FMA:86916 +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0000153 +name: glycosaminoglycan secreting cell +def: "A cell that secretes glycosaminoglycans." [GOC:tfm] +synonym: "GAG secreting cell" EXACT [] +synonym: "hyaluronic acid secreting cell" NARROW [] +is_a: CL:0000327 ! extracellular matrix secreting cell +is_a: CL:0000447 ! carbohydrate secreting cell + +[Term] +id: CL:0000159 +name: seromucus secreting cell +is_a: CL:0000151 ! secretory cell + +[Term] +id: CL:0000183 +name: contractile cell +def: "A cell whose primary function is to shorten." [FB:ma] +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0000187 +name: muscle cell +def: "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns." [MESH:A11.620] +synonym: "muscle fiber" EXACT [] +synonym: "myocyte" EXACT [] +xref: BTO:0000888 +xref: BTO:0000902 +xref: CALOHA:TS-2032 +xref: FBbt:00005074 +xref: FMA:67328 +xref: WBbt:0003675 +is_a: CL:0000183 ! contractile cell +is_a: CL:0000393 ! electrically responsive cell +is_a: CL:0000548 ! animal cell +is_a: CL:0002371 ! somatic cell + +[Term] +id: CL:0000188 +name: cell of skeletal muscle +def: "A somatic cell located in skeletal muscle." [GOC:tfm] +synonym: "skeletal muscle cell" EXACT [] +xref: BTO:0004392 +xref: CALOHA:TS-2158 +xref: FMA:9727 +is_a: CL:0002371 ! somatic cell +relationship: BFO:0000050 UBERON:0001134 ! part of skeletal muscle tissue + +[Term] +id: CL:0000192 +name: smooth muscle cell +def: "A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast)." [http://en.wikipedia.org/wiki/Smooth_muscle_cell, MESH:A11.620.520, MESH:D032389, PMID:9315361] +synonym: "myocytes, smooth muscle" EXACT [MESH:D032389] +synonym: "non-striated muscle cell" BROAD [] +synonym: "SMCs" EXACT [PMID:9315361] +synonym: "smooth muscle fiber" EXACT [] +xref: BTO:0004576 +xref: CALOHA:TS-2159 +xref: FMA:14072 +is_a: CL:0008000 ! non-striated muscle cell +is_a: CL:0008007 ! visceral muscle cell + +[Term] +id: CL:0000211 +name: electrically active cell +def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0000213 +name: lining cell +def: "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [JB:jb] +synonym: "boundary cell" EXACT [] +is_a: CL:0000215 ! barrier cell + +[Term] +id: CL:0000214 +name: synovial cell +def: "A cell located in the synovial joint." [] +synonym: "synoviocyte" EXACT [] +xref: CALOHA:TS-0995 +is_a: CL:0000213 ! lining cell +is_a: CL:0002078 ! meso-epithelial cell +relationship: BFO:0000050 UBERON:0002217 ! part of synovial joint + +[Term] +id: CL:0000215 +name: barrier cell +def: "A cell whose primary function is to prevent the transport of stuff across compartments." [JB:jb] +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0000219 +name: motile cell +def: "A cell that moves by its own activities." [FB:ma] +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0000221 +name: ectodermal cell +def: "A cell of the outer of the three germ layers of the embryo." [MESH:A16.254.425.273] +synonym: "ectoderm cell" EXACT [] +xref: FMA:72549 +is_a: CL:0002321 ! embryonic cell (metazoa) +relationship: BFO:0000050 UBERON:0000924 ! part of ectoderm + +[Term] +id: CL:0000222 +name: mesodermal cell +def: "A cell of the middle germ layer of the embryo." [MESH:A16.254.425.660] +synonym: "mesoblast" EXACT [] +synonym: "mesoderm cell" EXACT [] +xref: FMA:72554 +is_a: CL:0002321 ! embryonic cell (metazoa) +relationship: BFO:0000050 UBERON:0000926 ! part of mesoderm + +[Term] +id: CL:0000223 +name: endodermal cell +def: "A cell of the inner of the three germ layers of the embryo." [MESH:A16.254.425.407] +synonym: "endoderm cell" EXACT [] +xref: FMA:72555 +is_a: CL:0002321 ! embryonic cell (metazoa) +relationship: BFO:0000050 UBERON:0000925 ! part of endoderm + +[Term] +id: CL:0000226 +name: single nucleate cell +def: "A cell with a single nucleus." [FB:ma, GOC:tfm] +is_a: CL:0002242 ! nucleate cell + +[Term] +id: CL:0000228 +name: multinucleate cell +def: "A cell with more than one nucleus." [FB:ma] +synonym: "syncitium" EXACT [] +synonym: "syncytial cell" EXACT [] +synonym: "syncytium" EXACT [] +xref: AEO:0000203 +xref: WBbt:0008074 +is_a: CL:0002242 ! nucleate cell + +[Term] +id: CL:0000232 +name: erythrocyte +def: "A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen." [GOC:tfm, MESH:A11.118.290] +synonym: "RBC" EXACT [] +synonym: "red blood cell" EXACT [] +xref: BTO:0000424 +xref: CALOHA:TS-0290 +xref: FMA:81100 +is_a: CL:0000081 ! blood cell +is_a: CL:0000329 ! oxygen accumulating cell +is_a: CL:0000764 ! erythroid lineage cell + +[Term] +id: CL:0000237 +name: keratinizing barrier epithelial cell +is_a: CL:0000240 ! stratified squamous epithelial cell +is_a: CL:0000311 ! keratin accumulating cell +is_a: CL:0002077 ! ecto-epithelial cell + +[Term] +id: CL:0000240 +name: stratified squamous epithelial cell +is_a: CL:0000076 ! squamous epithelial cell +is_a: CL:0000079 ! stratified epithelial cell + +[Term] +id: CL:0000255 +name: eukaryotic cell +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0000311 +name: keratin accumulating cell +is_a: CL:0000325 ! stuff accumulating cell + +[Term] +id: CL:0000312 +name: keratinocyte +def: "An epidermal cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell." [GOC:dsd, http://en.wikipedia.org/wiki/Keratinocyte, MESH:A11.436.397, MESH:D015603, PMID:15582983, PMID:15749908, PMID:19727116] +synonym: "keratinized cell of epidermis" EXACT [] +synonym: "malpighian cell" EXACT [] +xref: BTO:0000667 +xref: CALOHA:TS-0500 +xref: FMA:62879 +is_a: CL:0000237 ! keratinizing barrier epithelial cell +is_a: CL:0000362 ! epidermal cell +relationship: BFO:0000050 UBERON:0001003 ! part of skin epidermis + +[Term] +id: CL:0000313 +name: serous secreting cell +def: "Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid." [GOC:tfm, ISBN:0517223651, ISBN:0721662544] +synonym: "serous cell" EXACT [] +xref: BTO:0003687 +xref: FMA:62511 +is_a: CL:0000159 ! seromucus secreting cell + +[Term] +id: CL:0000325 +name: stuff accumulating cell +def: "A cell that is specialised to accumulate a particular substance(s)." [FB:ma] +subset: prefixes.ttl:upper_level +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0000327 +name: extracellular matrix secreting cell +is_a: CL:0000499 ! stromal cell + +[Term] +id: CL:0000329 +name: oxygen accumulating cell +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0000333 +name: migratory neural crest cell +def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [MESH:A16.254.600] +xref: FMA:86667 +is_a: CL:0000219 ! motile cell +is_a: CL:0011012 ! neural crest cell +is_a: CL:0011026 ! progenitor cell + +[Term] +id: CL:0000335 +name: mesenchyme condensation cell +def: "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [GOC:tfm, PMID:5025404] +is_a: CL:0008019 ! mesenchymal cell + +[Term] +id: CL:0000352 +name: epiblast cell +def: "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation." [GOC:tfm, ISBN:0618947256] +is_a: CL:0000052 ! totipotent stem cell + +[Term] +id: CL:0000354 +name: blastemal cell +synonym: "blastema cell" EXACT [] +xref: ncithesaurus:Blastemal_Cell +is_a: CL:0000048 ! multi fate stem cell + +[Term] +id: CL:0000355 +name: multi-potent skeletal muscle stem cell +def: "A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell." [PMID:18282570] +xref: FMA:86767 +is_a: CL:0000048 ! multi fate stem cell +is_a: CL:0000188 ! cell of skeletal muscle + +[Term] +id: CL:0000357 +name: stratified epithelial stem cell +is_a: CL:0000036 ! epithelial fate stem cell + +[Term] +id: CL:0000362 +name: epidermal cell +def: "An epithelial cell of the integument (the outer layer of an organism)." [Flybase:dsj, MA:ma] +synonym: "cell of epidermis" EXACT [FMA:62411] +synonym: "epithelial cell of skin" NARROW [FMA:62411] +xref: BTO:0001470 +xref: CALOHA:TS-0283 +xref: FMA:62411 +is_a: CL:0002159 ! general ecto-epithelial cell +relationship: BFO:0000050 UBERON:0007376 ! part of outer epithelium + +[Term] +id: CL:0000365 +name: animal zygote +def: "Diploid cell produced by the fusion of sperm cell nucleus and egg cell." [ISBN:0471245208] +synonym: "zygote" BROAD [] +xref: BTO:0000854 +xref: EHDAA2:0004546 +xref: FMA:72395 +is_a: CL:0000007 ! early embryonic cell (metazoa) +is_a: CL:0010017 ! zygote + +[Term] +id: CL:0000393 +name: electrically responsive cell +def: "A cell whose function is determined by its response to an electric signal." [FB:ma] +is_a: CL:0000211 ! electrically active cell + +[Term] +id: CL:0000402 +name: CNS interneuron +is_a: CL:0000099 ! interneuron +is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) +is_a: CL:2000029 ! central nervous system neuron + +[Term] +id: CL:0000404 +name: electrically signaling cell +def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] +is_a: CL:0000211 ! electrically active cell + +[Term] +id: CL:0000447 +name: carbohydrate secreting cell +is_a: CL:0000151 ! secretory cell + +[Term] +id: CL:0000499 +name: stromal cell +def: "A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere." [GOC:tfm, MESH:A11.329.830] +xref: BTO:0002064 +xref: FMA:83624 +is_a: CL:0002320 ! connective tissue cell + +[Term] +id: CL:0000514 +name: smooth muscle myoblast +def: "A precursor cell destined to differentiate into smooth muscle myocytes." [GOC:tfm, MESH:A11.635.510, MESH:D032390] +synonym: "myoblast, smooth muscle" EXACT [MESH:D032390] +synonym: "satellite cell" RELATED [] +xref: FMA:84798 +is_a: CL:0000056 ! myoblast + +[Term] +id: CL:0000515 +name: skeletal muscle myoblast +def: "A myoblast that differentiates into skeletal muscle fibers." [SANBI:mhl] +synonym: "skeletal myoblast" EXACT [] +xref: FMA:84799 +is_a: CL:0000056 ! myoblast +is_a: CL:0011026 ! progenitor cell + +[Term] +id: CL:0000527 +name: efferent neuron +def: "A neuron which sends impulses peripherally to activate muscles or secretory cells." [MESH:A08.663.655] +synonym: "output neuron" EXACT [] +is_a: CL:0000540 ! neuron + +[Term] +id: CL:0000530 +name: primary neuron +is_a: CL:0000540 ! neuron + +[Term] +id: CL:0000540 +name: neuron +def: "The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." [http://en.wikipedia.org/wiki/Neuron, MESH:A08.663, MESH:D009474] +synonym: "nerve cell" EXACT [] +xref: BTO:0000938 +xref: CALOHA:TS-0683 +xref: FBbt:00005106 +xref: FMA:54527 +xref: VHOG:0001483 +xref: WBbt:0003679 +is_a: CL:0000393 ! electrically responsive cell +is_a: CL:0000404 ! electrically signaling cell +is_a: CL:0002319 ! neural cell + +[Term] +id: CL:0000542 +name: lymphocyte +def: "A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." [GOC:add, ISBN:0683073696, ISBN:0781735149] +xref: BTO:0000775 +xref: CALOHA:TS-0583 +xref: FMA:62863 +xref: VHOG:0001535 +is_a: CL:0000842 ! mononuclear cell + +[Term] +id: CL:0000547 +name: proerythroblast +def: "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers." [ISBN:0721601464, MESH:A11.118.290.350.200, PMID:1638021] +synonym: "pronormoblast" RELATED [] +synonym: "rubriblast" EXACT [ISBN:0721601464] +xref: FMA:83518 +is_a: CL:0000764 ! erythroid lineage cell +is_a: CL:0002242 ! nucleate cell + +[Term] +id: CL:0000548 +name: animal cell +subset: prefixes.ttl:upper_level +is_a: CL:0000255 ! eukaryotic cell + +[Term] +id: CL:0000549 +name: basophilic erythroblast +def: "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers." [GOC:tfm, ISBN:0721601464] +synonym: "basophilic normoblast" EXACT [ISBN:0721601464] +synonym: "early erythroblast" EXACT [ISBN:0721601464] +synonym: "early normoblast" EXACT [ISBN:0721601464] +synonym: "prorubricyte" EXACT [ISBN:0721601464] +xref: FMA:83505 +is_a: CL:0000765 ! erythroblast + +[Term] +id: CL:0000550 +name: polychromatophilic erythroblast +def: "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers." [ISBN:0721601464] +synonym: "intermediate erythroblast" EXACT [ISBN:0721601464] +synonym: "intermediate normoblast" EXACT [ISBN:0721601464] +synonym: "polychromatic erythroblast" EXACT [ISBN:0721601464] +synonym: "polychromatic normoblast" EXACT [ISBN:0721601464] +synonym: "polychromatophilic normoblast" EXACT [ISBN:0721601464] +synonym: "rubricyte" EXACT [ISBN:0721601464] +xref: FMA:83506 +is_a: CL:0000765 ! erythroblast + +[Term] +id: CL:0000552 +name: orthochromatic erythroblast +def: "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated." [ISBN:0721601464] +synonym: "acidophilic erythroblast" EXACT [ISBN:0721601464] +synonym: "eosinophilic erythroblast" EXACT [ISBN:0721601464] +synonym: "late erythoblast" EXACT [] +synonym: "orthochromatic normoblast" EXACT [ISBN:0721601464] +synonym: "pyknotic eto enrythroblast" EXACT [ISBN:0721601464] +xref: FMA:84646 +is_a: CL:0000765 ! erythroblast + +[Term] +id: CL:0000553 +name: megakaryocyte progenitor cell +def: "The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative)." [GOC:dsd, GOC:tfm, ISBN:0721601464] +synonym: "CFU-Meg" EXACT [PMID:11722431, PMID:12482498] +synonym: "colony-forming unit-megakaryocyte" EXACT [] +synonym: "Meg-CFC" EXACT [PMCID:PMC1794060] +synonym: "megacaryoblast" EXACT [] +synonym: "megacaryocyte progenitor cell" EXACT [] +synonym: "megakaryoblast" EXACT [] +synonym: "megakaryocytic progenitor cell" EXACT [PMID:12482498] +synonym: "MkP" EXACT [PMID:21116988] +synonym: "promegacaryocyte" RELATED [] +synonym: "promegakaryocyte" RELATED [] +xref: BTO:0001164 +xref: CALOHA:TS-0610 +xref: FMA:84235 +is_a: CL:0000763 ! myeloid cell +is_a: CL:0000839 ! myeloid lineage restricted progenitor cell + +[Term] +id: CL:0000556 +name: megakaryocyte +def: "A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm." [http://en.wikipedia.org/wiki/Megakaryocyte, ISBN:0721601464, MESH:D008533] +synonym: "megacaryocyte" EXACT [] +synonym: "megalocaryocyte" EXACT [] +synonym: "megalokaryocyte" EXACT [] +xref: BTO:0000843 +xref: CALOHA:TS-0611 +xref: FMA:83555 +is_a: CL:0000763 ! myeloid cell +is_a: CL:1001610 ! bone marrow hematopoietic cell + +[Term] +id: CL:0000558 +name: reticulocyte +def: "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds." [GOC:add, GOC:tfm, PMID:15946868, PMID:2037622] +xref: BTO:0001173 +xref: CALOHA:TS-0864 +is_a: CL:0000764 ! erythroid lineage cell + +[Term] +id: CL:0000566 +name: angioblastic mesenchymal cell +def: "A mesenchymal stem cell capable of developing into blood vessel endothelium." [GOC:dsd, GOC:tfm, PMID:12768659] +synonym: "angioblast" EXACT [] +synonym: "chondroplast" EXACT [] +is_a: CL:0000134 ! mesenchymal stem cell +is_a: CL:0011026 ! progenitor cell + +[Term] +id: CL:0000586 +name: germ cell +def: "The reproductive cell in multicellular organisms." [MESH:A05.360.490] +xref: BTO:0000535 +xref: VHOG:0001534 +xref: WBbt:0006796 +is_a: CL:0000039 ! germ line cell + +[Term] +id: CL:0000646 +name: basal cell +def: "Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament." [GOC:tfm, ISBN:0517223651] +xref: BTO:0000939 +xref: FMA:62516 +is_a: CL:0000036 ! epithelial fate stem cell + +[Term] +id: CL:0000667 +name: collagen secreting cell +def: "An extracellular matrix secreting cell that secretes collagen." [GOC:tfm] +is_a: CL:0000327 ! extracellular matrix secreting cell + +[Term] +id: CL:0000680 +name: muscle precursor cell +def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] +is_a: CL:0000055 ! non-terminally differentiated cell +is_a: CL:0002371 ! somatic cell + +[Term] +id: CL:0000723 +name: somatic stem cell +def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] +xref: CALOHA:TS-2086 +xref: FMA:63368 +is_a: CL:0000034 ! stem cell +is_a: CL:0002371 ! somatic cell + +[Term] +id: CL:0000737 +name: striated muscle cell +def: "Muscle cell which has as its direct parts myofilaments organized into sarcomeres." [GOC:tfm, ISBN:0721662544] +xref: BTO:0002916 +xref: CALOHA:TS-2157 +xref: FMA:86936 +is_a: CL:0000187 ! muscle cell + +[Term] +id: CL:0000738 +name: leukocyte +def: "An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue." [GOC:add, GOC:tfm, ISBN:978-0-323-05290-0] +synonym: "immune cell" EXACT [] +synonym: "leucocyte" EXACT [] +synonym: "white blood cell" EXACT [] +xref: BTO:0000751 +xref: CALOHA:TS-0549 +xref: FMA:62852 +is_a: CL:0000219 ! motile cell +is_a: CL:0000988 ! hematopoietic cell +is_a: CL:0002242 ! nucleate cell +relationship: BFO:0000050 UBERON:0002405 ! part of immune system + +[Term] +id: CL:0000763 +name: myeloid cell +def: "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage." [GOC:add] +xref: BTO:0001441 +xref: CALOHA:TS-0647 +is_a: CL:0000988 ! hematopoietic cell + +[Term] +id: CL:0000764 +name: erythroid lineage cell +def: "A immature or mature cell in the lineage leading to and including erythrocytes." [GOC:add, GOC:tfm] +synonym: "erythropoietic cell" EXACT [] +xref: CALOHA:TS-0290 +xref: FMA:62845 +xref: FMA:83516 +is_a: CL:0000763 ! myeloid cell + +[Term] +id: CL:0000765 +name: erythroblast +def: "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers." [GOC:add, ISBN:0721601464, PMID:18174176] +synonym: "normoblast" EXACT [] +xref: BTO:0001571 +xref: CALOHA:TS-0289 +xref: FMA:83504 +is_a: CL:0000764 ! erythroid lineage cell +is_a: CL:0011026 ! progenitor cell + +[Term] +id: CL:0000766 +name: myeloid leukocyte +def: "A cell of the monocyte, granulocyte, or mast cell lineage." [GOC:add] +is_a: CL:0000738 ! leukocyte +is_a: CL:0000763 ! myeloid cell + +[Term] +id: CL:0000775 +name: neutrophil +def: "Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes." [GOC:add, GOC:amm, GOC:tfm, ISBN:0721601464] +synonym: "neutrocyte" EXACT [] +synonym: "neutrophil leucocyte" EXACT [] +synonym: "neutrophil leukocyte" EXACT [] +synonym: "neutrophilic leucocyte" EXACT [] +synonym: "neutrophilic leukocyte" EXACT [] +synonym: "PMN" BROAD [] +synonym: "poly" BROAD [] +synonym: "polymorphonuclear leucocyte" BROAD [] +synonym: "polymorphonuclear leukocyte" BROAD [] +synonym: "polymorphonuclear neutrophil" BROAD [] +synonym: "polynuclear neutrophilic leucocyte" BROAD [] +synonym: "polynuclear neutrophilic leukocyte" BROAD [] +xref: BTO:0000130 +xref: CALOHA:TS-0688 +xref: FMA:62860 +is_a: CL:0000094 ! granulocyte + +[Term] +id: CL:0000837 +name: hematopoietic multipotent progenitor cell +def: "A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans." [GOC:add, GOC:tfm, PMID:19022770] +synonym: "hemopoietic progenitor cell" EXACT [] +synonym: "MPP" EXACT [] +xref: BTO:0000725 +xref: CALOHA:TS-0448 +is_a: CL:0008001 ! hematopoietic precursor cell + +[Term] +id: CL:0000839 +name: myeloid lineage restricted progenitor cell +def: "A progenitor cell restricted to the myeloid lineage." [GOC:add, GOC:tfm, PMID:19022770] +synonym: "myeloid progenitor cell" BROAD [] +xref: BTO:0004730 +xref: CALOHA:TS-2099 +xref: FMA:70339 +is_a: CL:0002031 ! hematopoietic lineage restricted progenitor cell +is_a: CL:0011026 ! progenitor cell + +[Term] +id: CL:0000842 +name: mononuclear cell +def: "A leukocyte with a single non-segmented nucleus in the mature form." [GOC:add] +synonym: "mononuclear leukocyte" EXACT [] +synonym: "peripheral blood mononuclear cell" NARROW [] +xref: BTO:0000878 +xref: CALOHA:TS-0768 +xref: FMA:86713 +is_a: CL:0000226 ! single nucleate cell +is_a: CL:0000738 ! leukocyte + +[Term] +id: CL:0000988 +name: hematopoietic cell +def: "A cell of a hematopoietic lineage." [GO_REF:0000031, GOC:add] +synonym: "haematopoietic cell" EXACT [] +synonym: "haemopoietic cell" EXACT [] +synonym: "hemopoietic cell" EXACT [] +xref: BTO:0000574 +xref: CALOHA:TS-2017 +xref: FMA:70366 +xref: FMA:83598 +is_a: CL:0000548 ! animal cell +is_a: CL:0002371 ! somatic cell + +[Term] +id: CL:0001035 +name: bone cell +def: "A connective tissue cell found in bone." [GO_REF:0000034, GOC:add] +is_a: CL:0000548 ! animal cell +relationship: BFO:0000050 UBERON:0001474 ! part of bone element + +[Term] +id: CL:0002031 +name: hematopoietic lineage restricted progenitor cell +def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] +is_a: CL:0008001 ! hematopoietic precursor cell + +[Term] +id: CL:0002032 +name: hematopoietic oligopotent progenitor cell +def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] +is_a: CL:0008001 ! hematopoietic precursor cell + +[Term] +id: CL:0002077 +name: ecto-epithelial cell +def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] +xref: FMA:69074 +is_a: CL:0000066 ! epithelial cell +is_a: CL:0002371 ! somatic cell + +[Term] +id: CL:0002078 +name: meso-epithelial cell +def: "Epithelial cell derived from mesoderm or mesenchyme." [FMA:69076, GOC:tfm] +synonym: "epithelial mesenchymal cell" EXACT [] +xref: FMA:69076 +is_a: CL:0000066 ! epithelial cell +is_a: CL:0002371 ! somatic cell + +[Term] +id: CL:0002092 +name: bone marrow cell +def: "A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells." [GOC:tfm, ISBN:0618947256] +xref: BTO:0004850 +xref: FMA:83621 +is_a: CL:0001035 ! bone cell +relationship: BFO:0000050 UBERON:0002371 ! part of bone marrow + +[Term] +id: CL:0002139 +name: endothelial cell of vascular tree +def: "An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels." [GOC:dsd, GOC:tfm, PMID:12768659] +synonym: "cubodial endothelial cell of vascular tree" NARROW [] +synonym: "vascular endothelial cell" EXACT [] +xref: BTO:0001854 +xref: CALOHA:TS-1106 +xref: FMA:67755 +is_a: CL:0000115 ! endothelial cell + +[Term] +id: CL:0002159 +name: general ecto-epithelial cell +def: "Epithelial cells derived from general body ectoderm and ectoderm placodes." [GOC:tfm] +xref: FMA:70556 +is_a: CL:0002077 ! ecto-epithelial cell + +[Term] +id: CL:0002187 +name: basal cell of epidermis +def: "A basally situated, mitotically active, columnar-shaped keratinocyte attached to the basement membrane." [GOC:tfm, ISBN:0517223651] +xref: FMA:70571 +is_a: CL:0000312 ! keratinocyte +is_a: CL:0000646 ! basal cell +is_a: CL:0011026 ! progenitor cell +is_a: CL:1000428 ! stem cell of epidermis + +[Term] +id: CL:0002242 +name: nucleate cell +def: "A cell containing at least one nucleus." [GOC:tfm] +xref: FMA:67513 +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0002305 +name: epithelial cell of distal tubule +def: "An epithelial cell of the distal convoluted tubule of the kidney that helps regulate systemic levels of potassium, sodium, calcium, and pH." [GOC:tfm, ISBN:0517223651] +synonym: "kidney distal tubule epithelial cell" EXACT [] +xref: FMA:62125 +xref: FMA:70981 +xref: KUPO:0001055 +is_a: CL:0002078 ! meso-epithelial cell +is_a: CL:1000494 ! nephron tubule epithelial cell +is_a: CL:1000615 ! kidney cortex tubule cell +relationship: BFO:0000050 UBERON:0004135 ! part of distal tubule + +[Term] +id: CL:0002319 +name: neural cell +def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] +xref: CALOHA:TS-2040 +xref: FMA:70333 +is_a: CL:0000548 ! animal cell +is_a: CL:0002371 ! somatic cell +relationship: BFO:0000050 UBERON:0001016 ! part of nervous system + +[Term] +id: CL:0002320 +name: connective tissue cell +def: "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone." [GOC:tfm, ISBN:0618947256] +xref: CALOHA:TS-2096 +xref: FMA:63875 +is_a: CL:0000548 ! animal cell +is_a: CL:0002371 ! somatic cell +relationship: BFO:0000050 UBERON:0002384 ! part of connective tissue + +[Term] +id: CL:0002321 +name: embryonic cell (metazoa) +def: "A cell of the embryo." [FMA:0618947256] +xref: CALOHA:TS-0263 +xref: FMA:82840 +xref: FMA:82841 +xref: WBbt:0007028 +is_a: CL:0000548 ! animal cell + +[Term] +id: CL:0002371 +name: somatic cell +def: "A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell)." [GOC:tfm, ISBN:0721662544] +subset: prefixes.ttl:upper_level +xref: BTO:0001268 +xref: FMA:72300 +xref: WBbt:0008378 +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0002372 +name: myotube +def: "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts." [GOC:dos, GOC:tfm, ISBN:0323052908, PMID:22274696] +synonym: "myotubule" EXACT [] +synonym: "single cell sarcomere" EXACT [] +is_a: CL:0000228 ! multinucleate cell +is_a: CL:0000737 ! striated muscle cell + +[Term] +id: CL:0002494 +name: cardiocyte +def: "A cell located in the heart, including both muscle and non muscle cells." [GOC:tfm] +synonym: "heart cell" EXACT [] +xref: BTO:0001539 +xref: CALOHA:TS-0115 +xref: FMA:83808 +xref: FMA:84791 +is_a: CL:0000548 ! animal cell +is_a: CL:0002371 ! somatic cell +relationship: BFO:0000050 UBERON:0007100 ! part of primary circulatory organ + +[Term] +id: CL:0002518 +name: kidney epithelial cell +def: "An epithelial cell of the kidney." [GOC:tfm, KUPO:SJ] +xref: KUPO:0001019 +is_a: CL:0000066 ! epithelial cell +is_a: CL:1000497 ! kidney cell + +[Term] +id: CL:0002543 +name: vein endothelial cell +def: "An endothelial cell that is part of the vein." [GOC:tfm] +synonym: "endothelial cell of vein" EXACT [] +synonym: "venous endothelial cell" EXACT [] +xref: FMA:62104 +xref: KUPO:0001099 +is_a: CL:0000071 ! blood vessel endothelial cell +relationship: BFO:0000050 UBERON:0001638 ! part of vein + +[Term] +id: CL:0002546 +name: embryonic blood vessel endothelial progenitor cell +def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] +is_a: CL:0000222 ! mesodermal cell +is_a: CL:0002371 ! somatic cell + +[Term] +id: CL:0002584 +name: renal cortical epithelial cell +def: "An epithelial cell of the kidney cortex." [GOC:tfm] +xref: KUPO:0001016 +is_a: CL:0002518 ! kidney epithelial cell +is_a: CL:0002681 ! kidney cortical cell + +[Term] +id: CL:0002681 +name: kidney cortical cell +is_a: CL:1000497 ! kidney cell +relationship: BFO:0000050 UBERON:0001225 ! part of cortex of kidney + +[Term] +id: CL:0005000 +name: spinal cord interneuron +def: "A CNS interneuron located in the spinal cord." [CL:CVS] +is_a: CL:0000402 ! CNS interneuron + +[Term] +id: CL:0005009 +name: renal principal cell +def: "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the cells apical membrane is regulated by aldosterone and vasopressin. In mammals these cells are located in the renal collecting ducts." [CL:CVS] +is_a: CL:0000075 ! columnar/cuboidal epithelial cell +is_a: CL:0002518 ! kidney epithelial cell + +[Term] +id: CL:0007001 +name: skeletogenic cell +def: "Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized)." [GO_REF:0000034] +synonym: "scleroblast" EXACT [GO_REF:0000034] +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0007004 +name: premigratory neural crest cell +def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] +is_a: CL:0011012 ! neural crest cell +relationship: BFO:0000050 UBERON:0002342 ! part of neural crest + +[Term] +id: CL:0007009 +name: prechondroblast +def: "Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells." [GO_REF:0000034] +is_a: CL:0000055 ! non-terminally differentiated cell + +[Term] +id: CL:0008000 +name: non-striated muscle cell +def: "Any muscle cell in which the fibers are not organised into sarcomeres." [GOC:DOS] +is_a: CL:0000187 ! muscle cell + +[Term] +id: CL:0008001 +name: hematopoietic precursor cell +def: "Any hematopoietic cell that is a precursor of some other hematopoietic cell type." [GOC:dos] +is_a: CL:0000988 ! hematopoietic cell + +[Term] +id: CL:0008002 +name: skeletal muscle fiber +def: "A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." [GOC:tfm, ISBN:0323052908] +is_a: CL:0000188 ! cell of skeletal muscle +is_a: CL:0002372 ! myotube + +[Term] +id: CL:0008007 +name: visceral muscle cell +def: "A muscle cell that is part of some visceral muscle" [GOC:dos] +is_a: CL:0000187 ! muscle cell + +[Term] +id: CL:0008019 +name: mesenchymal cell +def: "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." [] +synonym: "mesenchyme cell" EXACT [] +is_a: CL:0000219 ! motile cell +is_a: CL:0002371 ! somatic cell +relationship: BFO:0000050 UBERON:0003104 ! part of mesenchyme + +[Term] +id: CL:0010017 +name: zygote +def: "A zygote in a plant or an animal." [] +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0011012 +name: neural crest cell +def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] +is_a: CL:0000048 ! multi fate stem cell +is_a: CL:0002321 ! embryonic cell (metazoa) + +[Term] +id: CL:0011026 +name: progenitor cell +def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] +is_a: CL:0011115 ! precursor cell + +[Term] +id: CL:0011115 +name: precursor cell +def: "A cell that, by division or terminal differentiation, can give rise to other cell types." [GOC:dos] +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0017500 +name: neutrophillic cytoplasm +def: "Cytoplasm that exhibits a characteristic staining and color, pale-pink, with Wright-Giemsa stain." [GOC:add] + +[Term] +id: CL:0017502 +name: acidophilic cytoplasm +def: "Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain." [GOC:add] +synonym: "eosinophilic" NARROW [] + +[Term] +id: CL:0017503 +name: basophilic cytoplasm +def: "Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions." [GOC:tfm] + +[Term] +id: CL:0017504 +name: polychromatophilic cytoplasm +def: "Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions." [GOC:tfm] + +[Term] +id: CL:0017505 +name: increased nucleus size +def: "A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell." [GOC:tfm] + +[Term] +id: CL:1000428 +name: stem cell of epidermis +def: "A somatic stem cell that is part of the epidermis." [GOC:tfm] +synonym: "epidermal stem cell" EXACT [FMA:70541] +xref: FMA:70541 +is_a: CL:0000723 ! somatic stem cell +relationship: BFO:0000050 UBERON:0001003 ! part of skin epidermis + +[Term] +id: CL:1000449 +name: epithelial cell of nephron +def: "An epithelial cell that is part of the nephron." [GOC:tfm] +xref: FMA:70965 +is_a: CL:0002518 ! kidney epithelial cell +relationship: BFO:0000050 UBERON:0001285 ! part of nephron + +[Term] +id: CL:1000453 +name: epithelial cell of intermediate tubule +def: "An epithelial cell that is part of the intermediate tubule." [GOC:tfm] +xref: FMA:70980 +is_a: CL:1000909 ! kidney loop of Henle epithelial cell +relationship: BFO:0000050 UBERON:0004136 ! part of intermediate tubule + +[Term] +id: CL:1000494 +name: nephron tubule epithelial cell +def: "An epithelial cell that is part of a nephron tubule." [GOC:tfm] +synonym: "kidney tubule epithelial cell" EXACT [] +xref: FMA:86785 +xref: KUPO:0001022 +is_a: CL:1000449 ! epithelial cell of nephron +is_a: CL:1000507 ! kidney tubule cell +relationship: BFO:0000050 UBERON:0004810 ! part of nephron tubule epithelium + +[Term] +id: CL:1000497 +name: kidney cell +xref: KUPO:0001010 +is_a: CL:0000548 ! animal cell +is_a: CL:0002371 ! somatic cell +relationship: BFO:0000050 UBERON:0002113 ! part of kidney + +[Term] +id: CL:1000504 +name: kidney medulla cell +xref: KUPO:0001017 +is_a: CL:1000497 ! kidney cell +relationship: BFO:0000050 UBERON:0000362 ! part of renal medulla + +[Term] +id: CL:1000507 +name: kidney tubule cell +xref: KUPO:0001020 +is_a: CL:1000497 ! kidney cell +relationship: BFO:0000050 UBERON:0001231 ! part of nephron tubule + +[Term] +id: CL:1000615 +name: kidney cortex tubule cell +xref: KUPO:0001024 +is_a: CL:0002584 ! renal cortical epithelial cell +is_a: CL:1000449 ! epithelial cell of nephron +is_a: CL:1000507 ! kidney tubule cell +relationship: BFO:0000050 UBERON:0006853 ! part of renal cortex tubule + +[Term] +id: CL:1000616 +name: kidney outer medulla cell +xref: KUPO:0001025 +is_a: CL:1000504 ! kidney medulla cell +relationship: BFO:0000050 UBERON:0001293 ! part of outer medulla of kidney + +[Term] +id: CL:1000617 +name: kidney inner medulla cell +xref: KUPO:0001026 +is_a: CL:1000504 ! kidney medulla cell +relationship: BFO:0000050 UBERON:0001294 ! part of inner medulla of kidney + +[Term] +id: CL:1000854 +name: kidney blood vessel cell +xref: KUPO:0001014 +is_a: CL:0002584 ! renal cortical epithelial cell +is_a: CL:1000504 ! kidney medulla cell +relationship: BFO:0000050 UBERON:0003517 ! part of kidney blood vessel + +[Term] +id: CL:1000892 +name: kidney capillary endothelial cell +xref: KUPO:0001030 +is_a: CL:0000071 ! blood vessel endothelial cell +is_a: CL:1000854 ! kidney blood vessel cell +relationship: BFO:0000050 UBERON:0003527 ! part of kidney capillary + +[Term] +id: CL:1000893 +name: kidney venous blood vessel cell +xref: KUPO:0001031 +is_a: CL:1000854 ! kidney blood vessel cell +relationship: BFO:0000050 UBERON:0001140 ! part of renal vein + +[Term] +id: CL:1000909 +name: kidney loop of Henle epithelial cell +xref: KUPO:0001047 +is_a: CL:1000494 ! nephron tubule epithelial cell +relationship: BFO:0000050 UBERON:0001288 ! part of loop of Henle + +[Term] +id: CL:1001016 +name: kidney loop of Henle ascending limb epithelial cell +xref: KUPO:0001048 +is_a: CL:0002305 ! epithelial cell of distal tubule +is_a: CL:1000909 ! kidney loop of Henle epithelial cell +relationship: BFO:0000050 UBERON:0005164 ! part of ascending limb of loop of Henle + +[Term] +id: CL:1001021 +name: kidney loop of Henle descending limb epithelial cell +xref: KUPO:0001053 +is_a: CL:1000909 ! kidney loop of Henle epithelial cell +relationship: BFO:0000050 UBERON:0001289 ! part of descending limb of loop of Henle + +[Term] +id: CL:1001036 +name: vasa recta cell +xref: KUPO:0001068 +is_a: CL:0002543 ! vein endothelial cell +is_a: CL:1000892 ! kidney capillary endothelial cell +is_a: CL:1000893 ! kidney venous blood vessel cell +relationship: BFO:0000050 UBERON:0004726 ! part of vasa recta + +[Term] +id: CL:1001106 +name: kidney loop of Henle thick ascending limb epithelial cell +xref: KUPO:0001049 +is_a: CL:1000504 ! kidney medulla cell +is_a: CL:1001016 ! kidney loop of Henle ascending limb epithelial cell +relationship: BFO:0000050 UBERON:0001291 ! part of thick ascending limb of loop of Henle + +[Term] +id: CL:1001107 +name: kidney loop of Henle thin ascending limb epithelial cell +xref: KUPO:0001050 +is_a: CL:1000617 ! kidney inner medulla cell +is_a: CL:1001016 ! kidney loop of Henle ascending limb epithelial cell +relationship: BFO:0000050 UBERON:0004193 ! part of loop of Henle ascending limb thin segment + +[Term] +id: CL:1001108 +name: kidney loop of Henle medullary thick ascending limb epithelial cell +xref: KUPO:0001051 +is_a: CL:1000616 ! kidney outer medulla cell +is_a: CL:1001106 ! kidney loop of Henle thick ascending limb epithelial cell +relationship: BFO:0000050 UBERON:0006376 ! part of premacula segment of distal straight tubule + +[Term] +id: CL:1001109 +name: kidney loop of Henle cortical thick ascending limb epithelial cell +xref: KUPO:0001052 +is_a: CL:1001106 ! kidney loop of Henle thick ascending limb epithelial cell +relationship: BFO:0000050 UBERON:0006854 ! part of distal straight tubule postmacula segment + +[Term] +id: CL:1001111 +name: kidney loop of Henle thin descending limb epithelial cell +xref: KUPO:0001054 +is_a: CL:1000453 ! epithelial cell of intermediate tubule +is_a: CL:1000616 ! kidney outer medulla cell +is_a: CL:1001021 ! kidney loop of Henle descending limb epithelial cell +relationship: BFO:0000050 UBERON:0005096 ! part of descending thin limb + +[Term] +id: CL:1001126 +name: inner renal medulla vasa recta cell +xref: KUPO:0001069 +is_a: CL:1000617 ! kidney inner medulla cell +is_a: CL:1001036 ! vasa recta cell +relationship: BFO:0000050 UBERON:0004776 ! part of inner renal medulla vasa recta + +[Term] +id: CL:1001127 +name: outer renal medulla vasa recta cell +xref: KUPO:0001070 +is_a: CL:1000616 ! kidney outer medulla cell +is_a: CL:1001036 ! vasa recta cell +relationship: BFO:0000050 UBERON:0004775 ! part of outer renal medulla vasa recta + +[Term] +id: CL:1001131 +name: vasa recta ascending limb cell +xref: KUPO:0001074 +is_a: CL:1001036 ! vasa recta cell +relationship: BFO:0000050 UBERON:0009091 ! part of vasa recta ascending limb + +[Term] +id: CL:1001209 +name: inner medulla vasa recta ascending limb cell +xref: KUPO:0001075 +is_a: CL:1001126 ! inner renal medulla vasa recta cell +is_a: CL:1001131 ! vasa recta ascending limb cell +relationship: BFO:0000050 UBERON:0009092 ! part of inner medulla vasa recta ascending limb + +[Term] +id: CL:1001210 +name: outer medulla vasa recta ascending limb cell +xref: KUPO:0001076 +is_a: CL:1001127 ! outer renal medulla vasa recta cell +is_a: CL:1001131 ! vasa recta ascending limb cell +relationship: BFO:0000050 UBERON:0009093 ! part of outer medulla vasa recta ascending limb + +[Term] +id: CL:1001285 +name: vasa recta descending limb cell +xref: KUPO:0001071 +is_a: CL:1001036 ! vasa recta cell +relationship: BFO:0000050 UBERON:0009202 ! part of vasa recta descending limb + +[Term] +id: CL:1001286 +name: inner medulla vasa recta descending limb cell +xref: KUPO:0001072 +is_a: CL:1001126 ! inner renal medulla vasa recta cell +is_a: CL:1001285 ! vasa recta descending limb cell +relationship: BFO:0000050 UBERON:0009089 ! part of inner medulla vasa recta descending limb + +[Term] +id: CL:1001287 +name: outer medulla vasa recta descending limb cell +xref: KUPO:0001073 +is_a: CL:1001127 ! outer renal medulla vasa recta cell +is_a: CL:1001285 ! vasa recta descending limb cell +relationship: BFO:0000050 UBERON:0009090 ! part of outer medulla vasa recta descending limb + +[Term] +id: CL:1001610 +name: bone marrow hematopoietic cell +def: "Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes." [NPX:PDR] +synonym: "bone marrow hematopoietic cells" RELATED [CALOHA:TS-2109] +synonym: "bone marrow poietic cells" RELATED [CALOHA:TS-2109] +xref: CALOHA:TS-2109 +is_a: CL:0000988 ! hematopoietic cell +is_a: CL:0002092 ! bone marrow cell +relationship: BFO:0000050 UBERON:0012429 ! part of hematopoietic tissue + +[Term] +id: CL:2000029 +name: central nervous system neuron +def: "Any neuron that is part of a central nervous system." [GOC:TermGenie] +is_a: CL:0000540 ! neuron + +[Term] +id: CL:2000033 +name: limb basal cell of epidermis +def: "Any basal cell of epidermis that is part of a limb." [GOC:TermGenie] +is_a: CL:0002187 ! basal cell of epidermis +relationship: BFO:0000050 UBERON:0002101 ! part of limb + +[Term] +id: CL:2000076 +name: hindlimb stylopod vein endothelial cell +def: "Any vein endothelial cell that is part of a hindlimb stylopod." [GOC:TermGenie] +is_a: CL:0002543 ! vein endothelial cell +relationship: BFO:0000050 UBERON:0000376 ! part of hindlimb stylopod + +[Term] +id: UBERON:0000000 +name: processual entity +def: "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity." [span:ProcessualEntity] +subset: upper_level + +[Term] +id: UBERON:0000010 +name: peripheral nervous system +def: "A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands." [GO:0007422] +subset: cumbo +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "pars peripherica" EXACT [FMA:9903, FMA:TA, Wikipedia:Peripheral_nervous_system] +synonym: "PNS" BROAD [] +synonym: "systema nervosum periphericum" EXACT [FMA:9903, FMA:TA, Wikipedia:Peripheral_nervous_system] +xref: AAO:0000429 +xref: BAMS:PNS +xref: BILA:0000081 +xref: BIRNLEX:1111 +xref: BTO:0001028 +xref: CALOHA:TS-0808 +xref: EFO:0000891 +xref: EHDAA2:0001445 +xref: EHDAA:2893 +xref: EMAPA:16665 +xref: EV:0100335 +xref: FBbt:00005098 +xref: FMA:9903 +xref: GAID:715 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=3232 +xref: MA:0000218 +xref: MAT:0000338 +xref: MESH:D017933 +xref: MIAA:0000338 +xref: NCIT:C12465 +xref: SCTID:362292005 +xref: TAO:0000142 +xref: UMLS:C0206417 +xref: UMLS:C1305921 +xref: VHOG:0000399 +xref: Wikipedia:Peripheral_nervous_system +xref: XAO:0000178 +xref: ZFA:0000142 +is_a: UBERON:0011216 ! organ system subdivision +relationship: BFO:0000050 UBERON:0001016 ! part of nervous system + +[Term] +id: UBERON:0000014 +name: zone of skin +def: "Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Skin] +subset: pheno_slim +synonym: "portion of skin" EXACT [] +synonym: "region of skin" EXACT [] +synonym: "skin" EXACT [MA:0000151] +synonym: "skin region" EXACT [] +synonym: "skin zone" EXACT [] +xref: EHDAA2:0001844 +xref: EHDAA:6530 +xref: EMAPA:17525 +xref: EV:0100152 +xref: FMA:86166 +xref: GAID:933 +xref: MA:0000151 +xref: MAT:0000284 +xref: MESH:D012867 +xref: MIAA:0000284 +xref: OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA +xref: SCTID:20795001 +xref: VHOG:0000860 +xref: Wikipedia:Skin +is_a: UBERON:0034944 ! zone of organ +relationship: BFO:0000050 UBERON:0002097 ! part of skin of body + +[Term] +id: UBERON:0000015 +name: non-material anatomical boundary +def: "A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures." [CARO:0000010] +subset: upper_level +synonym: "anatomical boundary" EXACT [CARO:0000010] +xref: AEO:0000192 +xref: CARO:0000010 +xref: FMA:50705 +is_a: UBERON:0000466 ! immaterial anatomical entity + +[Term] +id: UBERON:0000020 +name: sense organ +def: "An organ that is capable of transducing sensory stimulus to the nervous system." [https://github.com/obophenotype/uberon/issues/549, https://orcid.org/0000-0002-6601-2165] +subset: uberon_slim +synonym: "organ of sense organ system" EXACT [OBOL:accepted] +synonym: "organ of sensory organ system" EXACT [OBOL:accepted] +synonym: "organ of sensory system" EXACT [OBOL:accepted] +synonym: "sense organ system organ" EXACT [OBOL:automatic] +synonym: "sensillum" NARROW [WBbt:0006929] +synonym: "sensor" RELATED [] +synonym: "sensory organ" EXACT [] +synonym: "sensory organ system organ" EXACT [OBOL:automatic] +synonym: "sensory system organ" EXACT [OBOL:accepted] +synonym: "Sinnesorgan" RELATED [BTO:0000202] +xref: AEO:0000094 +xref: BSA:0000121 +xref: BTO:0000202 +xref: CALOHA:TS-2043 +xref: EHDAA2:0001824 +xref: EHDAA:500 +xref: EMAPA:35955 +xref: FBbt:00005155 +xref: GAID:63 +xref: HAO:0000930 +xref: MA:0000017 +xref: MESH:D012679 +xref: NCIT:C33224 +xref: SCTID:244485009 +xref: UMLS:C0935626 +xref: VHOG:0001407 +xref: WBbt:0006929 +is_a: UBERON:0000062 ! organ +relationship: BFO:0000050 UBERON:0001032 ! part of sensory system + +[Term] +id: UBERON:0000021 +name: cutaneous appendage +def: "Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales." [https://orcid.org/0000-0002-6601-2165] +subset: uberon_slim +synonym: "epidermal appendage" NARROW [] +synonym: "epidermal growth" RELATED [] +synonym: "skin appendage" EXACT [FMA:71012] +xref: CALOHA:TS-0051 +xref: FMA:71012 +xref: SCTID:276160000 +is_a: UBERON:0013703 ! integumentary projection + +[Term] +id: UBERON:0000025 +name: tube +def: "Any hollow cylindrical anatomical structure containing a lumen through which substances are transported." [http://orcid.org/0000-0002-6601-2165] +synonym: "anatomical tube" EXACT [] +synonym: "duct" NARROW [] +xref: galen:Tube +is_a: UBERON:0004111 ! anatomical conduit + +[Term] +id: UBERON:0000026 +name: appendage +def: "Major subdivision of an organism that protrudes from the body[DOS, CARO]." [CARO:DOS] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "appendages" RELATED [XAO:0000218] +synonym: "extremitaet" RELATED [BTO:0001492] +synonym: "extremity" RELATED [] +synonym: "limbs/digits/tail" RELATED [MP:0000001] +xref: AEO:0000193 +xref: BILA:0000018 +xref: BTO:0001492 +xref: CARO:0010003 +xref: EFO:0000799 +xref: EHDAA2:0003193 +xref: EMAPA:37283 +xref: EV:0100155 +xref: FBbt:00007000 +xref: HAO:0000144 +xref: MAT:0000023 +xref: MESH:D005121 +xref: MIAA:0000023 +xref: NCIT:C61460 +xref: OpenCyc:Mx4rvViC-JwpEbGdrcN5Y29ycA +xref: UMLS:C0598782 +xref: VSAO:0000075 +xref: Wikipedia:Appendage +xref: XAO:0000218 +is_a: UBERON:0000475 ! organism subdivision + +[Term] +id: UBERON:0000029 +name: lymph node +def: "Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph." [BTO:0000784] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "lymph gland" RELATED [VHOG:0001273] +synonym: "nodus lymphaticus" RELATED [Wikipedia:Lymph_node] +xref: BTO:0000784 +xref: CALOHA:TS-0579 +xref: EFO:0000872 +xref: EMAPA:35523 +xref: EV:0100050 +xref: FMA:5034 +xref: GAID:947 +xref: galen:Lymphnode +xref: MA:0000139 +xref: MAT:0000442 +xref: MESH:D008198 +xref: NCIT:C12745 +xref: NCIT:C33027 +xref: OpenCyc:Mx4rwLPqLpwpEbGdrcN5Y29ycA +xref: SCTID:181756000 +xref: TAO_RETIRED:0005318 +xref: UMLS:C0024204 +xref: VHOG:0001273 +xref: Wikipedia:Lymph_node +xref: ZFA_RETIRED:0005318 +is_a: UBERON:0005057 ! immune organ +relationship: BFO:0000050 UBERON:0002465 ! part of lymphoid system + +[Term] +id: UBERON:0000033 +name: head +def: "The head is the anterior-most division of the body [GO]." [GO:0060322, Wikipedia:Head] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "adult head" NARROW [] +synonym: "cephalic area" RELATED [SPD:0000016] +synonym: "head (volume)" EXACT [FMA:7154] +xref: AAO:0010335 +xref: AEO:0000106 +xref: BILA:0000115 +xref: BIRNLEX:1230 +xref: BTO:0000282 +xref: CALOHA:TS-0436 +xref: EFO:0000964 +xref: EHDAA2:0003106 +xref: EMAPA:31858 +xref: FBbt:00000004 +xref: FMA:7154 +xref: GAID:61 +xref: galen:Head +xref: HAO:0000397 +xref: MA:0000023 +xref: MAT:0000294 +xref: MESH:D006257 +xref: MIAA:0000294 +xref: NCIT:C12419 +xref: OpenCyc:Mx4rEOLm4rgPEdmAAAACs6hRjg +xref: OpenCyc:Mx4rvVi6YJwpEbGdrcN5Y29ycA +xref: SCTID:302548004 +xref: SPD:0000016 +xref: TAO:0001114 +xref: TGMA:0000002 +xref: UMLS:C0018670 +xref: VHOG:0001644 +xref: WBbt:0005739 +xref: Wikipedia:Head +xref: XAO:0003024 +xref: ZFA:0001114 +is_a: UBERON:0011676 ! subdivision of organism along main body axis +relationship: BFO:0000050 UBERON:0007811 ! part of craniocervical region + +[Term] +id: UBERON:0000042 +name: serous membrane +def: "Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer." [https://github.com/obophenotype/uberon/issues/86, Wikipedia:Serous_membrane] +subset: uberon_slim +subset: vertebrate_core +synonym: "serosa" RELATED [Wikipedia:Serous_membrane] +synonym: "tunica serosa" EXACT [FMA:9581] +synonym: "wall of serous sac" EXACT [FMA:9581] +xref: FMA:9581 +xref: GAID:19 +xref: MESH:D012704 +xref: NCIT:C13169 +xref: SCTID:362878009 +xref: TAO:0005425 +xref: UMLS:C0036760 +xref: Wikipedia:Serous_membrane +xref: ZFA:0005425 +is_a: UBERON:0000481 ! multi-tissue structure +is_a: UBERON:0004120 ! mesoderm-derived structure +relationship: BFO:0000050 UBERON:0000060 ! part of anatomical wall + +[Term] +id: UBERON:0000043 +name: tendon +def: "Dense regular connective tissue that connects muscle to bone[VSAO]." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000073, Wikipedia:Tendon] +subset: pheno_slim +subset: uberon_slim +synonym: "sinew" RELATED [Wikipedia:Tendon] +synonym: "tendo" RELATED [Wikipedia:Tendon] +xref: AEO:0000091 +xref: BTO:0001356 +xref: CALOHA:TS-1021 +xref: EHDAA2:0003091 +xref: EMAPA:35854 +xref: EV:0100149 +xref: FMA:9721 +xref: GAID:276 +xref: galen:Tendon +xref: MA:0000115 +xref: MESH:D013710 +xref: NCIT:C13045 +xref: OpenCyc:Mx4rvVjefJwpEbGdrcN5Y29ycA +xref: SCTID:256667004 +xref: UMLS:C0039508 +xref: VHOG:0001286 +xref: VSAO:0000073 +xref: Wikipedia:Tendon +xref: XAO:0000173 +xref: ZFA:0005647 +is_a: UBERON:0007846 ! dense regular connective tissue +relationship: BFO:0000050 UBERON:0002204 ! part of musculoskeletal system + +[Term] +id: UBERON:0000045 +name: ganglion +def: "A biological tissue mass, most commonly a mass of nerve cell bodies." [https://github.com/obophenotype/uberon/issues/300, Wikipedia:Ganglion] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "ganglia" RELATED [] +synonym: "neural ganglion" RELATED [BTO:0000497] +xref: AAO:0010426 +xref: AEO:0000135 +xref: BAMS:G +xref: BTO:0000497 +xref: CALOHA:TS-0397 +xref: EFO:0000899 +xref: EHDAA2:0003135 +xref: EHDAA:2897 +xref: EHDAA:4662 +xref: EHDAA:5621 +xref: EHDAA:918 +xref: EMAPA:32846 +xref: EV:0100372 +xref: FBbt:00005137 +xref: FMA:5884 +xref: MA:0002406 +xref: MAT:0000207 +xref: MAT:0000343 +xref: MESH:D005724 +xref: MIAA:0000207 +xref: MIAA:0000343 +xref: NCIT:C12719 +xref: NLXANAT:100302 +xref: TAO:0000190 +xref: TGMA:0001016 +xref: UMLS:C0017067 +xref: VHOG:0000156 +xref: WBbt:0005189 +xref: Wikipedia:Ganglion +xref: XAO:0000209 +xref: ZFA:0000190 +is_a: UBERON:0010001 ! cell cluster organ +relationship: BFO:0000050 UBERON:0001016 ! part of nervous system + +[Term] +id: UBERON:0000055 +name: vessel +def: "A tubular structure that contains, conveys body fluid, such as blood or lymph." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +subset: pheno_slim +is_a: UBERON:0004111 ! anatomical conduit + +[Term] +id: UBERON:0000056 +name: ureter +def: "Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs." [GO:0090189, Wikipedia:Ureter] +subset: efo_slim +subset: major_organ +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +synonym: "metanephric duct" RELATED [ISBN:0073040584, VHOG:0000605] +xref: AAO:0010254 +xref: BTO:0001409 +xref: CALOHA:TS-1084 +xref: EFO:0000930 +xref: EHDAA2:0002139 +xref: EHDAA:9341 +xref: EMAPA:17950 +xref: EV:0100097 +xref: FMA:9704 +xref: GAID:438 +xref: galen:Ureter +xref: MA:0000378 +xref: MAT:0000120 +xref: MESH:D014513 +xref: MIAA:0000120 +xref: NCIT:C12416 +xref: OpenCyc:Mx4rvhmm6JwpEbGdrcN5Y29ycA +xref: SCTID:302511008 +xref: UMLS:C0041951 +xref: VHOG:0000605 +xref: Wikipedia:Ureter +xref: XAO:0000144 +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005179 ! pelvic region element +is_a: UBERON:0006555 ! excretory tube +is_a: UBERON:0015212 ! lateral structure +relationship: BFO:0000050 UBERON:0036295 ! part of renal pelvis/ureter + +[Term] +id: UBERON:0000057 +name: urethra +def: "The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening." [MGI:anna, MP:0000537] +subset: efo_slim +subset: major_organ +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +xref: BTO:0001426 +xref: CALOHA:TS-1132 +xref: EFO:0000931 +xref: EMAPA:30901 +xref: EV:0100099 +xref: FMA:19667 +xref: GAID:390 +xref: galen:Urethra +xref: MA:0000379 +xref: MAT:0000121 +xref: MESH:D014521 +xref: MIAA:0000121 +xref: NCIT:C12417 +xref: OpenCyc:Mx4rvVjkypwpEbGdrcN5Y29ycA +xref: SCTID:302513006 +xref: UMLS:C0041967 +xref: VHOG:0001264 +xref: Wikipedia:Urethra +xref: XAO:0000153 +is_a: UBERON:0000062 ! organ +is_a: UBERON:0004111 ! anatomical conduit +is_a: UBERON:0004120 ! mesoderm-derived structure +relationship: BFO:0000050 UBERON:0001556 ! part of lower urinary tract + +[Term] +id: UBERON:0000058 +name: duct +def: "A tubular structure that transports secreted or excreted substances." [http://orcid.org/0000-0002-6601-2165, http://www.siumed.edu/~dking2/intro/glands.htm#ducts] +subset: grouping_class +synonym: "anatomical duct" EXACT [] +synonym: "ducts" RELATED [XAO:0004000] +synonym: "exocrine duct" NARROW [] +synonym: "exocrine gland duct" NARROW [] +xref: AAO:0011123 +xref: FBbt:00100314 +xref: FMA:30320 +xref: galen:Duct +xref: NCIT:C12948 +xref: SCTID:91726008 +xref: TAO:0005171 +xref: UMLS:C0687028 +xref: Wikipedia:Duct_(anatomy) +xref: XAO:0004000 +xref: ZFA:0005171 +is_a: UBERON:0000063 ! organ subunit + +[Term] +id: UBERON:0000060 +name: anatomical wall +def: "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers." [FMA:82482] +subset: upper_level +synonym: "organ wall" RELATED [FMA:82482] +synonym: "wall" BROAD [] +synonym: "wall of organ" EXACT [FMA:82482] +xref: EMAPA:25036 +xref: FMA:82482 +xref: galen:Wall +is_a: UBERON:0000064 ! organ part + +[Term] +id: UBERON:0000061 +name: anatomical structure +def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [CARO:0000003] +subset: upper_level +synonym: "biological structure" EXACT [] +synonym: "connected biological structure" EXACT [CARO:0000003] +xref: AAO:0010825 +xref: AEO:0000003 +xref: BILA:0000003 +xref: CARO:0000003 +xref: EHDAA2:0003003 +xref: EMAPA:0 +xref: FBbt:00007001 +xref: FMA:305751 +xref: FMA:67135 +xref: GAID:781 +xref: HAO:0000003 +xref: http://dbpedia.org/ontology/AnatomicalStructure +xref: MA:0003000 +xref: MESH:D000825 +xref: SCTID:362889002 +xref: TAO:0000037 +xref: TGMA:0001823 +xref: VHOG:0001759 +xref: XAO:0003000 +xref: ZFA:0000037 +is_a: UBERON:0000465 ! material anatomical entity + +[Term] +id: UBERON:0000062 +name: organ +def: "Anatomical structure that performs a specific function or group of functions [WP]." [Wikipedia:Organ_(anatomy)] +subset: upper_level +synonym: "anatomical unit" RELATED [] +synonym: "body organ" RELATED [] +synonym: "element" RELATED [http://orcid.org/0000-0002-6601-2165] +xref: BIRNLEX:4 +xref: CARO:0020004 +xref: EFO:0000634 +xref: EMAPA:35949 +xref: ENVO:01000162 +xref: FMA:67498 +xref: MA:0003001 +xref: NCIT:C13018 +xref: OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA +xref: OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA +xref: SCTID:272625005 +xref: UMLS:C0178784 +xref: WBbt:0003760 +xref: Wikipedia:Organ_(anatomy) +is_a: UBERON:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 UBERON:0000467 ! part of anatomical system + +[Term] +id: UBERON:0000063 +name: organ subunit +def: "A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity." [http://orcid.org/0000-0002-6601-2165] +subset: upper_level +synonym: "organ region with fixed fiat boundary" RELATED [FMA:86140] +synonym: "organ segment" RELATED [FMA:86140] +synonym: "segment of organ" RELATED [FMA:86140] +xref: FMA:86140 +is_a: UBERON:0000064 ! organ part + +[Term] +id: UBERON:0000064 +name: organ part +def: "A multicellular structure that is a part of an organ." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: non_informative +subset: upper_level +synonym: "cardinal organ part" EXACT [FMA:82472] +synonym: "regional part of organ" RELATED [BIRNLEX:16] +xref: AAO:0011124 +xref: BIRNLEX:16 +xref: EFO:0000635 +xref: FMA:82472 +xref: SCTID:113343008 +xref: SCTID:91717005 +is_a: UBERON:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 UBERON:0000062 ! part of organ + +[Term] +id: UBERON:0000066 +name: fully formed stage +def: "The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage." [https://orcid.org/0000-0002-6601-2165] +subset: efo_slim +synonym: "adult stage" BROAD [] +synonym: "fully formed animal stage" EXACT [] +synonym: "juvenile-adult stage" EXACT [] +xref: BilaDO:0000004 +xref: BTO:0001043 +xref: EFO:0001272 +xref: FBdv:00005369 +xref: WBls:0000041 +xref: XtroDO:0000084 +is_a: UBERON:0000105 ! life cycle stage +relationship: BFO:0000050 UBERON:0000092 ! part of post-embryonic stage + +[Term] +id: UBERON:0000068 +name: embryo stage +def: "A life cycle stage that starts with fertilization and ends with the fully formed embryo." [http://orcid.org/0000-0002-6601-2165] +synonym: "embryogenesis" RELATED [] +synonym: "embryonic stage" EXACT [] +xref: BilaDO:0000002 +xref: EV:0300001 +xref: FBdv:00005289 +xref: FMA:72652 +xref: HsapDv:0000002 +xref: MmusDv:0000002 +xref: OGES:000000 +xref: OGES:000022 +xref: SCTID:296280003 +xref: WBls:0000003 +xref: WBls:0000092 +xref: WBls:0000102 +xref: XAO:1000012 +is_a: UBERON:0000105 ! life cycle stage + +[Term] +id: UBERON:0000071 +name: death stage +def: "End of the life of an organism." [XAO:0000437] +synonym: "death" RELATED [] +xref: XAO:0000437 +xref: XtroDO:0000085 +is_a: UBERON:0000105 ! life cycle stage + +[Term] +id: UBERON:0000073 +name: regional part of nervous system +def: "Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS." [BIRNLEX:1157] +subset: non_informative +subset: upper_level +synonym: "part of nervous system" EXACT [BIRNLEX:1157] +xref: BIRNLEX:1157 +xref: NCIT:C13040 +xref: SCTID:25087005 +xref: UMLS:C1518256 +is_a: UBERON:0000481 ! multi-tissue structure +relationship: BFO:0000050 UBERON:0001016 ! part of nervous system + +[Term] +id: UBERON:0000074 +name: renal glomerulus +def: "A capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney[GO]." [MP:0005325, Wikipedia:Glomerulus] +subset: efo_slim +subset: pheno_slim +subset: vertebrate_core +synonym: "glomerular capillary tuft" RELATED [ZFA:0001288] +synonym: "glomerular tuft" RELATED INCONSISTENT [] +synonym: "glomerulus" BROAD [] +synonym: "glomerulus renis" RELATED [Wikipedia:Glomerulus] +synonym: "Malphigian glomerulus" RELATED MISSPELLING [BTO:0000530] +synonym: "Malpighian glomerulus" RELATED [http://medical-dictionary.thefreedictionary.com/malpighian+glomerulus] +synonym: "Malpighian tuft" RELATED [http://medical-dictionary.thefreedictionary.com/malpighian+glomerulus] +synonym: "renal corpuscle" RELATED INCONSISTENT [] +synonym: "renal glomeruli" EXACT [TAO:0001288] +xref: BTO:0000530 +xref: CALOHA:TS-0862 +xref: EFO:0003667 +xref: EMAPA:28329 +xref: EV:0100386 +xref: FMA:15624 +xref: MA:0001657 +xref: MESH:D007678 +xref: NCIT:C13250 +xref: SCTID:362217000 +xref: TAO:0001288 +xref: UMLS:C0022663 +xref: Wikipedia:Glomerulus +xref: ZFA:0001288 +is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure +relationship: BFO:0000050 UBERON:0001229 ! part of renal corpuscle + +[Term] +id: UBERON:0000075 +name: subdivision of skeletal system +def: "Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] +subset: non_informative +synonym: "skeletal system part" RELATED [] +synonym: "skeletal system subdivision" EXACT [FMA:85544] +xref: FMA:85544 +xref: galen:ComplexSkeletalStructure +xref: NCIT:C34076 +xref: SCTID:118966000 +xref: UMLS:C1519343 +is_a: UBERON:0011216 ! organ system subdivision +relationship: BFO:0000050 UBERON:0001434 ! part of skeletal system + +[Term] +id: UBERON:0000076 +name: external ectoderm +def: "The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm." [MGI:anna, MP:0012532] +subset: pheno_slim +synonym: "surface (external) ectoderm" EXACT [] +synonym: "surface ectoderm" EXACT [MP:0012532] +xref: EHDAA2:0001968 +xref: EHDAA:1494 +xref: EHDAA:350 +xref: EHDAA:4784 +xref: EHDAA:4790 +xref: EHDAA:4796 +xref: EHDAA:7860 +xref: EMAPA:16096 +xref: FMA:87656 +xref: NCIT:C34309 +xref: UMLS:C1515087 +xref: Wikipedia:External_ectoderm +is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0005291 ! embryonic tissue +relationship: BFO:0000050 UBERON:0000924 ! part of ectoderm + +[Term] +id: UBERON:0000080 +name: mesonephros +def: "The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo." [GO:0001823, Wikipedia:Mesonephros] +subset: efo_slim +subset: organ_slim +subset: pheno_slim +subset: vertebrate_core +synonym: "amphibian adult kidney" RELATED [XAO:0000141] +synonym: "corpus Wolffi" RELATED [BTO:0001542] +synonym: "mesonephric kidney" EXACT [XAO:0000141] +synonym: "mesonephroi" EXACT [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] +synonym: "middle kidney" RELATED [BTO:0001542] +synonym: "opisthonephros" RELATED [VHOG:0000038, XAO:0000141] +synonym: "opisto nephros" RELATED [] +synonym: "opistonephros" RELATED [http://www.usm.maine.edu/bio/courses/bio205/bio205_26_sex.html] +synonym: "Wolffian body" EXACT [BTO:0001542, GOC:yaf, MESH:A16.254.500, Wikipedia:Mesonephros] +xref: AAO:0010384 +xref: BTO:0001542 +xref: CALOHA:TS-0624 +xref: EFO:0000928 +xref: EHDAA2:0001130 +xref: EHDAA:1581 +xref: EHDAA:5903 +xref: EMAPA:16744 +xref: FMA:72171 +xref: GAID:1308 +xref: MESH:D001755 +xref: NCIT:C26467 +xref: SCTID:308799002 +xref: TAO:0000529 +xref: UMLS:C0025492 +xref: VHOG:0000038 +xref: Wikipedia:Mesonephros +xref: XAO:0000141 +xref: ZFA:0000529 +is_a: UBERON:0002113 ! kidney +is_a: UBERON:0004120 ! mesoderm-derived structure + +[Term] +id: UBERON:0000081 +name: metanephros +def: "In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO]." [GO:0001656, Wikipedia:Metanephros#Metanephros] +subset: organ_slim +subset: pheno_slim +synonym: "definite kidney" RELATED [BTO:0001543] +synonym: "definitive kidney" RELATED [BTO:0001543] +synonym: "hind kidney" RELATED [BTO:0001543] +synonym: "metanephric kidney" RELATED [VHOG:0000039] +synonym: "metanephron" EXACT [BTO:0001543] +xref: BTO:0001543 +xref: EHDAA2:0001137 +xref: EHDAA:3089 +xref: EHDAA:5911 +xref: EMAPA:17373 +xref: EMAPA_RETIRED:17207 +xref: FMA:72172 +xref: NCIT:C34209 +xref: SCTID:308797000 +xref: UMLS:C0231049 +xref: VHOG:0000039 +xref: Wikipedia:Metanephros#Metanephros +is_a: UBERON:0002113 ! kidney +is_a: UBERON:0004120 ! mesoderm-derived structure + +[Term] +id: UBERON:0000083 +name: mesonephric tubule +def: "A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]." [Wikipedia:Mesonephric_tubules] +synonym: "renal tubules" RELATED [VHOG:0000500] +synonym: "tubuli mesonephrici" RELATED [Wikipedia:Mesonephric_tubules] +xref: AAO:0010389 +xref: EHDAA2:0001134 +xref: EMAPA:16747 +xref: VHOG:0000500 +xref: Wikipedia:Mesonephric_tubules +xref: XAO:0000148 +is_a: UBERON:0003914 ! epithelial tube +is_a: UBERON:0005103 ! mesonephric epithelium +is_a: UBERON:0006555 ! excretory tube + +[Term] +id: UBERON:0000084 +name: ureteric bud +def: "An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]." [MP:0010979, PMID:19828308] +subset: pheno_slim +synonym: "diverticulum" RELATED [BTO:0001646] +synonym: "diverticulum metanephricum" RELATED [Wikipedia:Ureteric_bud] +synonym: "gemma ureterica" RELATED [Wikipedia:Ureteric_bud] +synonym: "metanephric bud" RELATED [BTO:0001646] +synonym: "metanephric diverticulum" RELATED [Wikipedia:Metanephros#Metanephros] +synonym: "ureteric ampulla" RELATED [] +synonym: "ureteric diverticulum" RELATED [VHOG:0000541] +xref: BTO:0001646 +xref: EHDAA2:0002140 +xref: EHDAA:3091 +xref: EHDAA:5917 +xref: EMAPA:17209 +xref: NCIT:C34207 +xref: SCTID:361528000 +xref: UMLS:C1284058 +xref: VHOG:0000541 +xref: Wikipedia:Ureteric_bud +is_a: UBERON:0000083 ! mesonephric tubule +is_a: UBERON:0007499 ! epithelial sac +is_a: UBERON:0012275 ! meso-epithelium +is_a: UBERON:0034969 ! epithelial layer of duct +relationship: BFO:0000050 UBERON:0003074 ! part of mesonephric duct + +[Term] +id: UBERON:0000092 +name: post-embryonic stage +def: "Stage succeeding embryo, including mature structure." [https://orcid.org/0000-0002-6601-2165] +synonym: "post-hatching stage" NARROW [] +synonym: "postembryonic" RELATED [] +synonym: "postembryonic stage" EXACT [] +xref: BilaDO:0000003 +xref: OGES:000010 +xref: OGES:000014 +xref: OGES:000024 +xref: WBls:0000022 +xref: WBls:0000093 +xref: WBls:0000103 +is_a: UBERON:0000105 ! life cycle stage + +[Term] +id: UBERON:0000094 +name: membrane organ +def: "Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]." [FMA:7145] +synonym: "membrane" BROAD [] +synonym: "membrane of organ" EXACT [] +xref: FMA:7145 +is_a: UBERON:0000062 ! organ + +[Term] +id: UBERON:0000104 +name: life cycle +def: "An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism." [https://orcid.org/0000-0002-6601-2165] +subset: upper_level +synonym: "entire life cycle" EXACT [] +synonym: "entire lifespan" EXACT [] +synonym: "life" EXACT [] +synonym: "lifespan" EXACT [] +xref: FBdv:00000000 +xref: HsapDv:0000001 +xref: MmusDv:0000001 +xref: ncithesaurus:Life +xref: OGES:000011 +is_a: UBERON:0000000 ! processual entity + +[Term] +id: UBERON:0000105 +name: life cycle stage +def: "A spatiotemporal region encompassing some part of the life cycle of an organism." [https://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: upper_level +synonym: "developmental stage" NARROW [] +synonym: "stage" NARROW [] +xref: BILS:0000105 +xref: EFO:0000399 +xref: FBdv:00007012 +xref: FMA:24120 +xref: HsapDv:0000000 +xref: MmusDv:0000000 +xref: ncithesaurus:Developmental_Stage +xref: OlatDv:0000010 +xref: PdumDv:0000090 +xref: WBls:0000002 +xref: XAO:1000000 +xref: ZFS:0000000 +xref: ZFS:0100000 +is_a: UBERON:0000000 ! processual entity +relationship: BFO:0000050 UBERON:0000104 ! part of life cycle + +[Term] +id: UBERON:0000106 +name: zygote stage +def: "A stage at which the organism is a single cell produced by means of sexual reproduction." [Wikipedia:Zygote] +subset: efo_slim +synonym: "1-cell stage" EXACT [] +synonym: "fertilized egg stage" EXACT [BTO:0000854] +synonym: "fertilized egg stage" RELATED [] +synonym: "one cell stage" EXACT [] +synonym: "one-cell stage" RELATED [VHOG:0000745] +synonym: "zygote" RELATED [VHOG:0000745] +synonym: "zygotum" RELATED [Wikipedia:Zygote] +xref: BilaDO:0000005 +xref: BILS:0000106 +xref: EFO:0001322 +xref: EHDAA:27 +xref: FBdv:00005288 +xref: NCIT:C12601 +xref: PdumDv:0000100 +xref: VHOG:0000745 +xref: Wikipedia:Zygote +xref: XAO:1000001 +xref: ZFS:0000001 +is_a: UBERON:0000105 ! life cycle stage +relationship: BFO:0000050 UBERON:0000068 ! part of embryo stage + +[Term] +id: UBERON:0000107 +name: cleavage stage +def: "The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula." [GO:0040016, Wikipedia:Cleavage_(embryo)] +subset: efo_slim +xref: BilaDO:0000006 +xref: BILS:0000107 +xref: EFO:0001290 +xref: FBdv:00000054 +xref: MESH:A16.254.270 +xref: MmusDv:0000004 +xref: OGES:000015 +xref: OGES:000020 +xref: PdumDv:0000200 +xref: Wikipedia:Cleavage_(embryo) +xref: XAO:1000004 +xref: ZFS:0000046 +is_a: UBERON:0000105 ! life cycle stage +relationship: BFO:0000050 UBERON:0000068 ! part of embryo stage + +[Term] +id: UBERON:0000108 +name: blastula stage +def: "An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [Wikipedia:Blastula] +subset: efo_slim +xref: BilaDO:0000007 +xref: BILS:0000108 +xref: EFO:0001282 +xref: HsapDv:0000006 +xref: MmusDv:0000007 +xref: OGES:000003 +xref: OGES:000016 +xref: OGES:000021 +xref: OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg +xref: WBls:0000005 +xref: Wikipedia:Blastula +xref: XAO:1000003 +xref: ZFS:0000045 +is_a: UBERON:0000105 ! life cycle stage +relationship: BFO:0000050 UBERON:0000068 ! part of embryo stage + +[Term] +id: UBERON:0000109 +name: gastrula stage +def: "A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm." [GO:0007369] +subset: efo_slim +synonym: "blastocystis trilaminaris stage" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar blastocyst stage" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar blastoderm stage" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar disk stage" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar germ stage" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar stage" RELATED [https://orcid.org/0000-0002-6601-2165] +xref: BilaDO:0000008 +xref: BILS:0000109 +xref: EFO:0001296 +xref: FBdv:00005317 +xref: HsapDv:0000010 +xref: MmusDv:0000013 +xref: OGES:000004 +xref: OGES:000019 +xref: WBls:0000010 +xref: XAO:1000005 +xref: ZFS:0000047 +is_a: UBERON:0000105 ! life cycle stage +relationship: BFO:0000050 UBERON:0000068 ! part of embryo stage + +[Term] +id: UBERON:0000110 +name: neurula stage +def: "Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." [GO:0001841] +xref: BilaDO:0000009 +xref: BILS:0000110 +xref: HsapDv:0000012 +xref: MmusDv:0000017 +xref: XAO:1000006 +is_a: UBERON:0000105 ! life cycle stage +relationship: BFO:0000050 UBERON:0000068 ! part of embryo stage + +[Term] +id: UBERON:0000111 +name: organogenesis stage +def: "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism." [Wikipedia:Organogenesis] +synonym: "segmentation stage" RELATED [] +xref: BilaDO:0000010 +xref: BILS:0000111 +xref: HsapDv:0000015 +xref: MmusDv:0000018 +xref: OGES:000005 +xref: OGES:000032 +xref: Wikipedia:Organogenesis +is_a: UBERON:0000105 ! life cycle stage +relationship: BFO:0000050 UBERON:0000068 ! part of embryo stage + +[Term] +id: UBERON:0000122 +name: neuron projection bundle +def: "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." [CARO:0001001, FBbt:00005099, FBC:DOS] +synonym: "funiculus" EXACT [] +synonym: "nerve fiber bundle" EXACT [FBbt:00005099] +synonym: "neural fiber bundle" EXACT [] +xref: CARO:0001001 +xref: FBbt:00005099 +xref: NLX:147821 +is_a: UBERON:0005162 ! multi cell part structure +relationship: BFO:0000050 UBERON:0001016 ! part of nervous system + +[Term] +id: UBERON:0000153 +name: anterior region of body +is_a: UBERON:0000475 ! organism subdivision + +[Term] +id: UBERON:0000154 +name: posterior region of body +is_a: UBERON:0000475 ! organism subdivision + +[Term] +id: UBERON:0000158 +name: membranous layer +synonym: "membrane" BROAD [] +synonym: "membranous organ component" EXACT [FMA:82500] +xref: FMA:30322 +xref: FMA:82500 +xref: MESH:D008566 +xref: NCIT:C12749 +is_a: UBERON:0004923 ! organ component layer + +[Term] +id: UBERON:0000161 +name: orifice +def: "Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]." [FMA:3724] +synonym: "anatomical orifice" EXACT [FMA:3724] +synonym: "anatomical ostium" BROAD [FMA:3724] +synonym: "hilum" NARROW [] +synonym: "ostium" BROAD [] +xref: FMA:3724 +xref: SCTID:91837002 +is_a: UBERON:0004111 ! anatomical conduit + +[Term] +id: UBERON:0000162 +name: cloaca +def: "Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures." [ISBN:0073040584, Wikipedia:Cloaca] +synonym: "cloacal chamber" RELATED [AAO:0000095] +synonym: "vent" RELATED [XAO:0000244] +xref: AAO:0000095 +xref: GAID:1206 +xref: MESH:D002988 +xref: NCIT:C34127 +xref: SCTID:362857006 +xref: SCTID:370631000 +xref: UMLS:C0008987 +xref: VHOG:0001186 +xref: Wikipedia:Cloaca +xref: XAO:0000244 +xref: ZFA:0005781 +is_a: UBERON:0013522 ! subdivision of tube +relationship: BFO:0000050 UBERON:0001555 ! part of digestive tract +relationship: BFO:0000050 UBERON:0004122 ! part of genitourinary system + +[Term] +id: UBERON:0000163 +name: embryonic cloaca +def: "Endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]." [MP:0010115, Wikipedia:Cloaca_(embryology)] +subset: pheno_slim +synonym: "cloaca" RELATED SENSU [] +xref: EHDAA2:0000256 +xref: EHDAA:4895 +xref: EMAPA:27573 +xref: Wikipedia:Cloaca_(embryology) +is_a: UBERON:0000162 ! cloaca +relationship: BFO:0000050 UBERON:0000922 ! part of embryo +relationship: BFO:0000050 UBERON:0001008 ! part of renal system +relationship: BFO:0000050 UBERON:0012361 ! part of internal anal region + +[Term] +id: UBERON:0000164 +name: primitive urogenital sinus +def: "The ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females." [ISBN:0-683-40008-8, MP:0010116] +subset: pheno_slim +synonym: "fetal UGS" EXACT [PMID:18977204] +synonym: "sinus urogenitalis" EXACT [] +synonym: "UGS" EXACT [MP:0010116] +synonym: "urogenital sinus" BROAD [MP:0010116] +xref: EHDAA2:0004060 +xref: EHDAA:5029 +xref: EHDAA:5919 +xref: EMAPA:17379 +xref: NCIT:C34322 +xref: SCTID:50961009 +xref: UMLS:C0231057 +xref: VHOG:0000414 +xref: Wikipedia:Definitive_urogenital_sinus +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0000163 ! part of embryonic cloaca + +[Term] +id: UBERON:0000165 +name: mouth +def: "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks)." [https://github.com/obophenotype/uberon/wiki/The-digestive-tract, Wikipedia:Mouth] +subset: efo_slim +subset: major_organ +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "adult mouth" NARROW [] +synonym: "cavital oralis" RELATED [Wikipedia:Mouth] +synonym: "cavitas oris" RELATED [BTO:0001090] +synonym: "cavum oris" RELATED [BTO:0001090] +synonym: "mouth cavity" RELATED [BTO:0001090] +synonym: "oral region" RELATED [EHDAA2:0001326] +synonym: "oral vestibule" RELATED [BTO:0001090] +synonym: "regio oralis" EXACT [BTO:0004698, FMA:49184, FMA:TA] +synonym: "rima oris" RELATED [BTO:0001090] +synonym: "stoma" RELATED [] +synonym: "stomatodaeum" RELATED [VHOG:0000812] +synonym: "trophic apparatus" RELATED [http://orcid.org/0000-0002-6601-2165] +synonym: "vestibule of mouth" RELATED [BTO:0001090] +synonym: "vestibulum oris" RELATED [BTO:0001090] +xref: AAO:0010355 +xref: BTO:0001090 +xref: BTO:0004698 +xref: CALOHA:TS-1315 +xref: EFO:0000825 +xref: EHDAA2:0001326 +xref: EHDAA:542 +xref: EMAPA:16262 +xref: FBbt:00003126 +xref: FMA:49184 +xref: GAID:75 +xref: galen:Mouth +xref: http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg +xref: MA:0000341 +xref: MA:0002474 +xref: MAT:0000038 +xref: MESH:D009055 +xref: MIAA:0000038 +xref: OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA +xref: SCTID:21082005 +xref: TADS:0000040 +xref: TAO:0000547 +xref: TAO:0000590 +xref: TGMA:0000131 +xref: VHOG:0000280 +xref: VHOG:0000812 +xref: Wikipedia:Mouth +xref: XAO:0003029 +xref: ZFA:0000547 +xref: ZFA:0000590 +is_a: UBERON:0004921 ! subdivision of digestive tract +relationship: BFO:0000050 UBERON:0000033 ! part of head + +[Term] +id: UBERON:0000166 +name: oral opening +def: "The orifice that connects the mouth to the exterior of the body." [https://github.com/obophenotype/uberon/wiki/The-digestive-tract] +subset: uberon_slim +subset: vertebrate_core +synonym: "mouth" RELATED INCONSISTENT [] +synonym: "oral fissure" EXACT [FMA:59806] +synonym: "oral orifice" EXACT [FMA:59806] +synonym: "oral part of face" RELATED [] +xref: FMA:59806 +is_a: UBERON:0000161 ! orifice +relationship: BFO:0000050 UBERON:0000165 ! part of mouth + +[Term] +id: UBERON:0000174 +name: excreta +def: "A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity." [GO:0007588, http://orcid.org/0000-0002-6601-2165] +synonym: "excreted substance" EXACT [] +synonym: "excretion" RELATED [BTO:0000491] +synonym: "portion of excreted substance" EXACT [FMA:9674] +synonym: "waste substance" EXACT [AEO:0000184] +xref: AEO:0000184 +xref: BTO:0000491 +xref: EHDAA2_RETIRED:0003184 +xref: ENVO:02000022 +xref: FMA:9674 +xref: galen:Excretion +is_a: UBERON:0000463 ! organism substance + +[Term] +id: UBERON:0000178 +name: blood +def: "A fluid that is composed of blood plasma and erythrocytes." [FMA:9670, http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/9, Wikipedia:Blood] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "portion of blood" EXACT [] +synonym: "vertebrate blood" EXACT [] +synonym: "whole blood" RELATED [BTO:0000089] +xref: AAO:0000046 +xref: BTO:0000089 +xref: CALOHA:TS-0079 +xref: EFO:0000296 +xref: EHDAA2:0000176 +xref: EHDAA:418 +xref: EMAPA:16332 +xref: ENVO:02000027 +xref: EV:0100047 +xref: FMA:9670 +xref: GAID:965 +xref: galen:Blood +xref: MA:0000059 +xref: MESH:D001769 +xref: MIAA:0000315 +xref: NCIT:C12434 +xref: OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA +xref: TAO:0000007 +xref: UMLS:C0005767 +xref: VHOG:0000224 +xref: Wikipedia:Blood +xref: XAO:0000124 +xref: ZFA:0000007 +is_a: UBERON:0000179 ! haemolymphatic fluid +relationship: BFO:0000050 UBERON:0002390 ! part of hematopoietic system + +[Term] +id: UBERON:0000179 +name: haemolymphatic fluid +def: "Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs." [http://orcid.org/0000-0002-6601-2165] +synonym: "blood or blood analog" RELATED [] +synonym: "circulating fluid" RELATED [] +xref: CARO:0000081 +is_a: UBERON:0006314 ! bodily fluid +relationship: BFO:0000050 UBERON:0002193 ! part of hemolymphoid system + +[Term] +id: UBERON:0000203 +name: pallium +def: "Dorsal part (roof region) of the telencephalon[GO]." [GO:0021543, https://github.com/obophenotype/uberon/issues/287, ISBN:0471888893, Wikipedia:Pallium_(neuroanatomy)] +subset: developmental_classification +subset: efo_slim +synonym: "area dorsalis telencephali" EXACT [ZFA:0000505] +synonym: "dorsal part of telencephalon" EXACT [ISBN:0471888893] +synonym: "dorsal telencephalic area" EXACT [ZFA:0000505] +synonym: "dorsal telencephalon" EXACT [ZFA:0000505] +xref: BTO:0003399 +xref: DMBA:15903 +xref: EFO:0003534 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=3240 +xref: SCTID:369224000 +xref: TAO:0000505 +xref: TAO:0007007 +xref: Wikipedia:Avian_pallium +xref: Wikipedia:Pallium_(neuroanatomy) +xref: ZFA:0000505 +is_a: UBERON:0002616 ! regional part of brain +relationship: BFO:0000050 UBERON:0001893 ! part of telencephalon + +[Term] +id: UBERON:0000307 +name: blastula +def: "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [Wikipedia:Blastula] +subset: inconsistent_with_fma +synonym: "blastosphere" RELATED [Wikipedia:Blastula] +synonym: "blastula embryo" EXACT [BILA:0000059] +xref: BILA:0000059 +xref: BTO:0000128 +xref: GAID:1294 +xref: MESH:A16.254.270.274 +xref: OGEM:000006 +xref: OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg +xref: Wikipedia:Blastula +is_a: UBERON:0000922 ! embryo + +[Term] +id: UBERON:0000309 +name: body wall +def: "The external portion of an animal body derived from ectoderm and mesoderm layers that encloses the body cavity." [MP:0003385] +subset: pheno_slim +synonym: "trunk wall" NARROW [FMA:10427] +synonym: "wall fo trunk" EXACT [FMA:10427] +synonym: "wall of trunk" NARROW [FMA:10427] +xref: BTO:0000139 +xref: EMAPA:32761 +xref: FMA:10427 +xref: galen:BodyWall +xref: SCTID:281483004 +is_a: UBERON:0000475 ! organism subdivision + +[Term] +id: UBERON:0000349 +name: limbic system +def: "A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex]." [BIRNLEX:Limbic_system, Wikipedia:Limbic_system] +subset: non_informative +subset: pheno_slim +synonym: "visceral brain" RELATED [ISBN:0123813611] +xref: BTO:0000928 +xref: CALOHA:TS-1307 +xref: FMA:242000 +xref: GAID:615 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2055 +xref: MESH:A08.186.211.577 +xref: NCIT:C94541 +xref: OpenCyc:Mx4rwAeba5wpEbGdrcN5Y29ycA +xref: SCTID:361342009 +xref: UMLS:C0023715 +xref: Wikipedia:Limbic_system +is_a: UBERON:0011216 ! organ system subdivision +relationship: BFO:0000050 UBERON:0001890 ! part of forebrain + +[Term] +id: UBERON:0000353 +name: parenchyma +def: "Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues." [Wikipedia:Parenchyma] +xref: EHDAA:3015 +xref: EHDAA:3905 +xref: EHDAA:3999 +xref: EHDAA:4005 +xref: EHDAA:6899 +xref: EHDAA:6903 +xref: EHDAA:6994 +xref: EHDAA:8086 +xref: EHDAA:9182 +xref: EHDAA:9190 +xref: EHDAA:9196 +xref: EHDAA:9202 +xref: FMA:45732 +xref: NCIT:C74601 +xref: UMLS:C0933845 +xref: Wikipedia:Parenchyma +is_a: UBERON:0000064 ! organ part + +[Term] +id: UBERON:0000362 +name: renal medulla +def: "The inner portion of the kidney consisting of the renal pyramids." [ISBN:0-683-40008-8, MGI:smb, MP:0003014] +subset: pheno_slim +synonym: "kidney medulla" EXACT [OBOL:automatic] +synonym: "medulla of kidney" EXACT [OBOL:automatic] +synonym: "medulla renalis" EXACT [FMA:74268, FMA:TA] +synonym: "medullary pyramids" RELATED [FMA:74268] +synonym: "pyramides renales" EXACT [FMA:74268, FMA:TA] +synonym: "renal marrow" RELATED [BTO:0001167] +synonym: "renal medullae" EXACT [FMA:86327] +synonym: "renal medullae set" EXACT [FMA:86327] +synonym: "renal pyramids" EXACT [FMA:74268] +synonym: "renal pyramids set" EXACT [FMA:74268] +xref: BTO:0001167 +xref: CALOHA:TS-1157 +xref: EMAPA:19279 +xref: GAID:425 +xref: galen:MedullaOfKidney +xref: MA:0000373 +xref: MESH:D007679 +xref: NCIT:C12740 +xref: SCTID:30737000 +xref: UMLS:C0022664 +xref: Wikipedia:Renal_medulla +is_a: UBERON:0000958 ! medulla of organ +relationship: BFO:0000050 UBERON:0002113 ! part of kidney + +[Term] +id: UBERON:0000376 +name: hindlimb stylopod +def: "The part of the hindlimb between pelvis and the knee, corresponding to the femur." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: pheno_slim +synonym: "femur" RELATED [Wikipedia:Thigh] +synonym: "hind limb stylopod" EXACT [OBOL:automatic] +synonym: "hind limb stylopodium" EXACT [VHOG:0000349] +synonym: "hind propodium" EXACT [AAO:0000887] +synonym: "hindlimb propodium" EXACT [AAO:0000887] +synonym: "hindlimb stylopod" EXACT [OBOL:automatic] +synonym: "hindlimb stylopodium" EXACT [OBOL:automatic] +synonym: "proximal segment of free lower limb" EXACT [FMA:24967] +synonym: "stylopod of hind limb" EXACT [OBOL:automatic] +synonym: "stylopod of hindlimb" EXACT [OBOL:automatic] +synonym: "stylopod of lower limb" EXACT [] +synonym: "thigh" EXACT [] +synonym: "upper leg" EXACT HUMAN_PREFERRED [MA:0000052] +xref: BTO:0001376 +xref: CALOHA:TS-2039 +xref: EFO:0001943 +xref: EHDAA2:0002130 +xref: EHDAA:5171 +xref: EHDAA:6200 +xref: EMAPA:17499 +xref: FMA:24967 +xref: GAID:50 +xref: galen:Thigh +xref: MA:0000052 +xref: MESH:D013848 +xref: NCIT:C33763 +xref: OpenCyc:Mx4rvVjN7JwpEbGdrcN5Y29ycA +xref: SCTID:302544002 +xref: UMLS:C0039866 +xref: VHOG:0000349 +xref: Wikipedia:Thigh +is_a: UBERON:0002472 ! stylopod +is_a: UBERON:0008784 ! lower limb segment +relationship: BFO:0000050 UBERON:0000978 ! part of leg + +[Term] +id: UBERON:0000383 +name: musculature of body +def: "The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]." [VSAO:0000033] +subset: efo_slim +subset: pheno_slim +synonym: "muscle system" EXACT [] +synonym: "muscle system of body" EXACT [] +synonym: "muscular system" EXACT [FMA:72954] +synonym: "musculature system" EXACT [BILA:0000088] +synonym: "muskelsystem" RELATED [BTO:0001485] +synonym: "set of all muscles" EXACT [FMA:72954] +synonym: "set of muscles of body" EXACT [FMA:72954] +synonym: "vertebrate muscular system" EXACT [BTO:0001369] +xref: AAO:0000307 +xref: BILA:0000088 +xref: BTO:0001369 +xref: BTO:0001485 +xref: EFO:0000801 +xref: EMAPA:35578 +xref: FBbt:00005069 +xref: FMA:72954 +xref: MA:0002888 +xref: MAT:0000025 +xref: MIAA:0000025 +xref: VSAO:0000033 +xref: XAO:0004042 +is_a: UBERON:0011216 ! organ system subdivision + +[Term] +id: UBERON:0000409 +name: serous gland +def: "A gland in which the principal secretory cells are serous secreting cells." [http://orcid.org/0000-0002-6601-2165, http://www.siumed.edu/~dking2/intro/glands.htm] +subset: organ_slim +subset: pheno_slim +xref: BTO:0001837 +xref: EMAPA:37950 +xref: FMA:62889 +xref: Wikipedia:Serous_gland +is_a: UBERON:0002365 ! exocrine gland + +[Term] +id: UBERON:0000456 +name: secretion of exocrine gland +def: "A portion of organism substance that is produced by exocrine glands." [http://orcid.org/0000-0002-6601-2165] +synonym: "bodily secretion" EXACT [MESH:D012634] +synonym: "exocrine gland fluid" RELATED [] +synonym: "exocrine gland fluid or secretion" RELATED [] +synonym: "exocrine gland fluid/secretion" EXACT [MA:0002504] +synonym: "exocrine gland secretion" RELATED [] +synonym: "external secretion" RELATED [BTO:0002977] +synonym: "secreted substance" EXACT [] +synonym: "secretion" BROAD [FMA:9675] +xref: AEO:0001005 +xref: BTO:0002977 +xref: BTO:0002979 +xref: EMAPA:36535 +xref: FMA:9675 +xref: galen:Secretion +xref: MA:0002504 +xref: MESH:D012634 +xref: NCIT:C34062 +xref: UMLS:C1516992 +is_a: UBERON:0000463 ! organism substance + +[Term] +id: UBERON:0000463 +name: organism substance +def: "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body." [http://orcid.org/0000-0001-9114-8737] +subset: pheno_slim +subset: upper_level +synonym: "body fluid or substance" EXACT [MA:0002450] +synonym: "body substance" EXACT [FMA:9669] +synonym: "organism substance" EXACT [CARO:0000004] +synonym: "portion of body substance" EXACT [FMA:9669] +synonym: "portion of organism substance" EXACT [ZFA:0001487] +xref: AAO:0010839 +xref: AEO:0000004 +xref: BILA:0000004 +xref: CALOHA:TS-2101 +xref: CARO:0000004 +xref: EHDAA2:0003004 +xref: EMAPA:35178 +xref: FBbt:00007019 +xref: FMA:9669 +xref: galen:BodySubstance +xref: HAO:0000004 +xref: MA:0002450 +xref: NCIT:C13236 +xref: SPD:0000008 +xref: TAO:0001487 +xref: TGMA:0001824 +xref: VHOG:0001726 +xref: XAO:0004001 +xref: ZFA:0001487 +is_a: UBERON:0000465 ! material anatomical entity +relationship: BFO:0000050 UBERON:0000468 ! part of multicellular organism + +[Term] +id: UBERON:0000464 +name: anatomical space +def: "Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures." [http://orcid.org/0000-0001-9114-8737] +subset: upper_level +synonym: "anatomical spaces" RELATED [ZFA:0001643] +synonym: "lumen" BROAD [] +synonym: "lumen space" EXACT [] +synonym: "space" BROAD [] +xref: AAO:0010110 +xref: AEO:0000005 +xref: BILA:0000005 +xref: CARO:0000005 +xref: EHDAA2:0003005 +xref: FBbt:00007017 +xref: FMA:5897 +xref: HAO:0000005 +xref: NCIT:C94478 +xref: TAO:0001668 +xref: TGMA:0001825 +xref: UMLS:C0524461 +xref: VHOG:0001728 +xref: XAO:0003190 +xref: ZFA:0001643 +is_a: UBERON:0000466 ! immaterial anatomical entity + +[Term] +id: UBERON:0000465 +name: material anatomical entity +def: "Anatomical entity that has mass." [http://orcid.org/0000-0001-9114-8737] +subset: upper_level +xref: AAO:0010264 +xref: AEO:0000006 +xref: BILA:0000006 +xref: CARO:0000006 +xref: EHDAA2:0003006 +xref: FBbt:00007016 +xref: FMA:67165 +xref: HAO:0000006 +xref: TAO:0001836 +xref: TGMA:0001826 +xref: VHOG:0001721 +is_a: UBERON:0001062 ! anatomical entity + +[Term] +id: UBERON:0000466 +name: immaterial anatomical entity +def: "Anatomical entity that has no mass." [http://orcid.org/0000-0001-9114-8737] +subset: upper_level +synonym: "immaterial physical anatomical entity" EXACT [FMA:67112] +xref: AAO:0010265 +xref: AEO:0000007 +xref: BILA:0000007 +xref: CARO:0000007 +xref: EHDAA2:0003007 +xref: FBbt:00007015 +xref: FMA:67112 +xref: HAO:0000007 +xref: TAO:0001835 +xref: TGMA:0001827 +xref: VHOG:0001727 +is_a: UBERON:0001062 ! anatomical entity + +[Term] +id: UBERON:0000467 +name: anatomical system +def: "Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function." [CARO:0000011] +subset: pheno_slim +subset: uberon_slim +subset: upper_level +synonym: "anatomical systems" RELATED [ZFA:0001439] +synonym: "body system" EXACT [BIRNLEX:14] +synonym: "connected anatomical system" EXACT [CARO:0000011] +synonym: "organ system" EXACT [] +synonym: "system" BROAD [GO:0048731] +xref: AAO:0000007 +xref: AEO:0000011 +xref: BILA:0000011 +xref: BIRNLEX:14 +xref: BSA:0000049 +xref: CALOHA:TS-2088 +xref: CARO:0000011 +xref: EHDAA2:0003011 +xref: EHDAA:392 +xref: EMAPA:16103 +xref: EV:0100000 +xref: FBbt:00004856 +xref: FMA:7149 +xref: galen:AnatomicalSystem +xref: HAO:0000011 +xref: MA:0000003 +xref: NCIT:C12919 +xref: OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ +xref: SCTID:278195005 +xref: TAO:0001439 +xref: TGMA:0001831 +xref: UMLS:C0460002 +xref: VHOG:0001725 +xref: WBbt:0005746 +xref: WBbt:0005763 +xref: Wikipedia:Organ_system +xref: XAO:0003002 +xref: ZFA:0001439 +is_a: UBERON:0000061 ! anatomical structure +relationship: BFO:0000050 UBERON:0000468 ! part of multicellular organism + +[Term] +id: UBERON:0000468 +name: multicellular organism +def: "Anatomical structure that is an individual member of a species and consists of more than one cell." [CARO:0000012, http://orcid.org/0000-0001-9114-8737, Wikipedia:Multi-cellular_organism] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: upper_level +synonym: "animal" NARROW [BTO:0000042] +synonym: "body" RELATED [AEO:0000103, BIRNLEX:18, FMA:256135, NCIT:C13041] +synonym: "Koerper" RELATED [BTO:0001489] +synonym: "multi-cellular organism" EXACT [CARO:0000012] +synonym: "organism" BROAD [FBbt:00000001, VHOG:0000671, WBbt:0007833] +synonym: "whole body" RELATED [BTO:0001489] +synonym: "whole organism" RELATED [FBbt:00000001] +xref: AAO:0010026 +xref: AEO:0000191 +xref: BILA:0000012 +xref: BIRNLEX:18 +xref: BSA:0000038 +xref: BTO:0000042 +xref: CARO:0000012 +xref: EFO:0002906 +xref: EHDAA2:0003103 +xref: EHDAA2:0003191 +xref: EHDAA:1 +xref: EMAPA:25765 +xref: EV:0100016 +xref: FBbt:00000001 +xref: FMA:256135 +xref: galen:Organism +xref: HAO:0000012 +xref: NCIT:C13041 +xref: ncithesaurus:Whole_Organism +xref: SCTID:243928005 +xref: TADS:0000001 +xref: TAO:0001094 +xref: TGMA:0001832 +xref: VHOG:0000671 +xref: WBbt:0007833 +xref: Wikipedia:Multi-cellular_organism +xref: XAO:0003004 +xref: ZFA:0001094 +is_a: UBERON:0010000 ! multicellular anatomical structure + +[Term] +id: UBERON:0000471 +name: compound organ component +def: "Multi-tissue structure that is part of a compound organ." [CARO:0000019, http://orcid.org/0000-0001-9114-8737] +subset: upper_level +synonym: "compound organ components" RELATED [ZFA:0001489] +xref: AAO:0010017 +xref: AEO:0000019 +xref: BILA:0000019 +xref: CARO:0000019 +xref: EHDAA2:0003019 +xref: HAO:0000019 +xref: TAO:0001489 +xref: TGMA:0001835 +xref: XAO:0003039 +xref: ZFA:0001489 +is_a: UBERON:0000481 ! multi-tissue structure +relationship: BFO:0000050 UBERON:0003103 ! part of compound organ + +[Term] +id: UBERON:0000475 +name: organism subdivision +def: "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument." [CARO:0000032, CARO:DOS, http://orcid.org/0000-0001-9114-8737] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: upper_level +synonym: "anatomic region" EXACT [MA:0002433] +synonym: "body part" RELATED [] +synonym: "body region" RELATED [FMA:7153] +synonym: "cardinal body part" RELATED [FMA:7153] +xref: AAO:0010053 +xref: AEO:0000032 +xref: BILA:0000032 +xref: BIRNLEX:7 +xref: CALOHA:TS-2084 +xref: CARO:0000032 +xref: EFO:0000808 +xref: EHDAA2:0003032 +xref: EMAPA:36031 +xref: FBbt:00007009 +xref: FMA:7153 +xref: galen:BodyPart +xref: HAO:0000032 +xref: MA:0002433 +xref: MAT:0000293 +xref: MESH:D001829 +xref: MIAA:0000293 +xref: NCIT:C32221 +xref: OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA +xref: TAO:0001308 +xref: TGMA:0001840 +xref: UMLS:C0229962 +xref: VHOG:0001758 +xref: Wikipedia:Body_part +xref: XAO:0003013 +xref: ZFA:0001308 +is_a: UBERON:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 UBERON:0000468 ! part of multicellular organism + +[Term] +id: UBERON:0000476 +name: acellular anatomical structure +def: "Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue." [http://orcid.org/0000-0001-9114-8737] +subset: vertebrate_core +synonym: "acellular anatomical structures" RELATED [ZFA:0000382] +xref: AAO:0010268 +xref: AEO:0000040 +xref: BILA:0000040 +xref: CARO:0000040 +xref: EHDAA2:0003040 +xref: FBbt:00007013 +xref: FMA:63863 +xref: HAO:0000040 +xref: TAO:0000382 +xref: TGMA:0001841 +xref: XAO:0003162 +xref: ZFA:0000382 +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0000477 +name: anatomical cluster +def: "Anatomical group that has its parts adjacent to one another." [http://orcid.org/0000-0001-9114-8737] +subset: upper_level +xref: AAO:0010009 +xref: AEO:0000041 +xref: BILA:0000041 +xref: CARO:0000041 +xref: EHDAA2:0003041 +xref: FBbt:00007277 +xref: FMA:49443 +xref: HAO:0000041 +xref: TADS:0000605 +xref: TAO:0001478 +xref: TGMA:0001842 +xref: VHOG:0001737 +xref: XAO:0003160 +xref: ZFA:0001478 +is_a: UBERON:0001062 ! anatomical entity + +[Term] +id: UBERON:0000479 +name: tissue +def: "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation." [CARO:0000043] +subset: pheno_slim +subset: upper_level +synonym: "portion of tissue" EXACT [CARO:0000043] +synonym: "simple tissue" NARROW [AEO:0000043] +synonym: "tissue portion" EXACT [] +xref: AAO:0000607 +xref: AAO:0010054 +xref: AEO:0000043 +xref: BILA:0000043 +xref: BIRNLEX:19 +xref: CALOHA:TS-2090 +xref: CARO:0000043 +xref: EHDAA2:0003043 +xref: EMAPA:35868 +xref: FBbt:00007003 +xref: FMA:9637 +xref: galen:Tissue +xref: HAO:0000043 +xref: MA:0003002 +xref: MESH:D014024 +xref: NCIT:C12801 +xref: TAO:0001477 +xref: TGMA:0001844 +xref: UMLS:C0040300 +xref: VHOG:0001757 +xref: WBbt:0005729 +xref: XAO:0003040 +xref: ZFA:0001477 +is_a: UBERON:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 UBERON:0000468 ! part of multicellular organism + +[Term] +id: UBERON:0000481 +name: multi-tissue structure +def: "Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types." [CARO:0000055, http://orcid.org/0000-0001-9114-8737] +subset: upper_level +synonym: "multi-tissue structures" RELATED [ZFA:0001488] +xref: AAO:0010048 +xref: AEO:0000055 +xref: BILA:0000055 +xref: CARO:0000055 +xref: EHDAA2:0003055 +xref: FBbt:00007010 +xref: HAO:0000055 +xref: TAO:0001488 +xref: TGMA:0001847 +xref: VHOG:0001762 +xref: XAO:0003037 +xref: ZFA:0001488 +is_a: UBERON:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 NCBITaxon:6072 ! part of Eumetazoa + +[Term] +id: UBERON:0000483 +name: epithelium +def: "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]." [http://orcid.org/0000-0001-9114-8737, Wikipedia:Epithelium] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "epithelial tissue" EXACT [] +synonym: "portion of epithelium" EXACT [FMA:9639] +xref: AAO:0000144 +xref: AAO:0010055 +xref: AEO:0000066 +xref: BILA:0000066 +xref: BTO:0000416 +xref: CALOHA:TS-0288 +xref: CARO:0000066 +xref: EHDAA2:0003066 +xref: EMAPA:32738 +xref: FBbt:00007005 +xref: FMA:9639 +xref: GAID:402 +xref: HAO:0000066 +xref: MA:0003060 +xref: MESH:D004848 +xref: NCIT:C12710 +xref: SCTID:31610004 +xref: TAO:0001486 +xref: UMLS:C0014609 +xref: VHOG:0000387 +xref: Wikipedia:Epithelium +xref: XAO:0003045 +xref: ZFA:0001486 +is_a: UBERON:0000479 ! tissue + +[Term] +id: UBERON:0000485 +name: simple columnar epithelium +def: "Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]." [FMA:FMA, http://orcid.org/0000-0001-9114-8737, Wikipedia:Simple_columnar_epithelium] +subset: uberon_slim +subset: vertebrate_core +synonym: "columnar epithelium" BROAD [EHDAA2:0003068] +synonym: "columnar epithlium" BROAD [AEO:0000068] +synonym: "epithelium simplex columnare" EXACT [] +synonym: "simple columnar epithelia" RELATED [ZFA:0001496] +synonym: "simple columnar epithelium" EXACT [] +xref: AAO:0010063 +xref: AEO:0000068 +xref: BILA:0000068 +xref: CARO:0000068 +xref: EHDAA2_RETIRED:0003068 +xref: FBbt:00007027 +xref: FMA:45567 +xref: HAO:0000068 +xref: NCIT:C33552 +xref: SCTID:32210007 +xref: TAO:0001496 +xref: UMLS:C0836135 +xref: Wikipedia:Simple_columnar_epithelium +xref: XAO:0004008 +xref: ZFA:0001496 +is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0012274 ! columnar epithelium + +[Term] +id: UBERON:0000486 +name: multilaminar epithelium +def: "Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]." [FMA:FMA, http://orcid.org/0000-0001-9114-8737, Wikipedia:Stratified_epithelium] +subset: uberon_slim +subset: vertebrate_core +synonym: "laminated epithelium" RELATED [BTO:0002074] +synonym: "stratified epithelium" EXACT [] +xref: AAO:0010059 +xref: AEO:0000069 +xref: BILA:0000069 +xref: BTO:0002074 +xref: CARO:0000069 +xref: EHDAA2:0003069 +xref: FMA:45562 +xref: HAO:0000069 +xref: NCIT:C33622 +xref: SCTID:309044005 +xref: TAO:0001494 +xref: UMLS:C0682575 +xref: Wikipedia:Stratified_epithelium +xref: XAO:0004006 +xref: ZFA:0001494 +is_a: UBERON:0000483 ! epithelium + +[Term] +id: UBERON:0000487 +name: simple squamous epithelium +def: "Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]." [FMA:45565, http://orcid.org/0000-0001-9114-8737, Wikipedia:Simple_squamous_epithelium] +subset: uberon_slim +subset: vertebrate_core +synonym: "epithelium simplex squamosum" EXACT [] +synonym: "simple squamous epithelia" RELATED [ZFA:0001498] +xref: AAO:0010066 +xref: AEO:0000070 +xref: BILA:0000070 +xref: BTO:0002073 +xref: CARO:0000070 +xref: EHDAA2:0003070 +xref: FMA:45565 +xref: HAO:0000070 +xref: NCIT:C13178 +xref: TAO:0001498 +xref: UMLS:C0836133 +xref: Wikipedia:Simple_squamous_epithelium +xref: XAO:0004010 +xref: ZFA:0001498 +is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0006914 ! squamous epithelium + +[Term] +id: UBERON:0000489 +name: cavitated compound organ +def: "Compound organ that contains one or more macroscopic anatomical spaces." [http://orcid.org/0000-0001-9114-8737] +subset: organ_slim +subset: upper_level +synonym: "cavitated compound organs" RELATED [ZFA:0001490] +synonym: "cavitated organ" EXACT [FMA:55671] +xref: AAO:0010016 +xref: AEO:0000072 +xref: BILA:0000072 +xref: CARO:0000072 +xref: EHDAA2:0003072 +xref: FMA:55671 +xref: HAO:0000072 +xref: TAO:0001490 +xref: TGMA:0001857 +xref: VHOG:0001730 +xref: XAO:0003165 +xref: ZFA:0001490 +is_a: UBERON:0003103 ! compound organ + +[Term] +id: UBERON:0000490 +name: unilaminar epithelium +def: "Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]." [FMA:45561, http://orcid.org/0000-0001-9114-8737] +subset: vertebrate_core +synonym: "simple epithelium" EXACT [FMA:45561] +synonym: "unilaminar epithelia" RELATED [ZFA:0001495] +xref: AAO:0010062 +xref: AEO:0000073 +xref: BILA:0000073 +xref: BTO:0002073 +xref: CARO:0000073 +xref: EHDAA2:0003073 +xref: FMA:45561 +xref: HAO:0000073 +xref: NCIT:C33554 +xref: SCTID:309043004 +xref: TAO:0001495 +xref: UMLS:C0682574 +xref: XAO:0004007 +xref: ZFA:0001495 +is_a: UBERON:0000483 ! epithelium + +[Term] +id: UBERON:0000913 +name: interstitial fluid +def: "Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid." [Wikipedia:Interstitial_fluid] +subset: pheno_slim +synonym: "intercellular fluid" EXACT [ENVO:02000042] +synonym: "tissue fluid" EXACT [ENVO:02000042] +xref: ENVO:02000042 +xref: FMA:9673 +xref: NCIT:C120839 +xref: Wikipedia:Interstitial_fluid +is_a: UBERON:0000463 ! organism substance +relationship: BFO:0000050 UBERON:0000479 ! part of tissue + +[Term] +id: UBERON:0000915 +name: thoracic segment of trunk +def: "Subdivision of trunk that lies between the head and the abdomen." [http://orcid.org/0000-0002-6601-2165] +subset: uberon_slim +synonym: "anterior subdivision of trunk" RELATED [] +synonym: "thorax" EXACT [MA:0000022] +synonym: "upper body" RELATED [] +synonym: "upper trunk" RELATED [FMA:259209] +xref: EMAPA:35862 +xref: FMA:259209 +xref: MA:0000022 +xref: SCTID:302551006 +xref: Wikipedia:Thorax +is_a: UBERON:0009569 ! subdivision of trunk +is_a: UBERON:0011676 ! subdivision of organism along main body axis + +[Term] +id: UBERON:0000916 +name: abdomen +def: "The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "abdominopelvic region" EXACT [FMA:9577] +synonym: "abdominopelvis" EXACT [FMA:9577] +synonym: "adult abdomen" RELATED [] +synonym: "belly" RELATED [] +synonym: "celiac region" RELATED [] +xref: BTO:0000020 +xref: CALOHA:TS-0001 +xref: EFO:0000968 +xref: EMAPA:35102 +xref: EV:0100011 +xref: FMA:9577 +xref: GAID:16 +xref: galen:Abdomen +xref: MA:0000029 +xref: MAT:0000298 +xref: MESH:A01.047 +xref: MIAA:0000298 +xref: OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA +xref: SCTID:302553009 +xref: Wikipedia:Abdomen +is_a: UBERON:0009569 ! subdivision of trunk +relationship: BFO:0000050 UBERON:0002417 ! part of abdominal segment of trunk + +[Term] +id: UBERON:0000922 +name: embryo +def: "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [BTO:0000379, FB:FBrf0039741, FB:FBrf0041814, GO:0009790, Wikipedia:Embryo] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "developing organism" RELATED [BILA:0000056] +synonym: "developmental tissue" RELATED [] +synonym: "embryonic organism" EXACT [BILA:0000056] +xref: AAO:0011035 +xref: AEO:0000169 +xref: BILA:0000056 +xref: BSA:0000039 +xref: BTO:0000379 +xref: CALOHA:TS-0229 +xref: EFO:0001367 +xref: EHDAA2:0000002 +xref: EHDAA2_RETIRED:0003236 +xref: EHDAA:38 +xref: EMAPA:16039 +xref: FBbt:00000052 +xref: FMA:69068 +xref: GAID:963 +xref: http://neurolex.org/wiki/Category\:Embryonic_organism +xref: MAT:0000226 +xref: MESH:D004622 +xref: MIAA:0000019 +xref: NCIT:C28147 +xref: OGEM:000001 +xref: OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA +xref: SCTID:57991002 +xref: UMLS:C0013935 +xref: VHOG:0001766 +xref: Wikipedia:Embryo +xref: XAO:0000113 +xref: ZFA:0000103 +is_a: UBERON:0000468 ! multicellular organism + +[Term] +id: UBERON:0000923 +name: germ layer +def: "A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm." [https://github.com/obophenotype/uberon/issues/203, Wikipedia:Germ_layer] +subset: uberon_slim +subset: vertebrate_core +synonym: "embryonic germ layer" RELATED [] +synonym: "embryonic germ layers" RELATED [] +synonym: "embryonic tissue" BROAD [FMA:69069] +synonym: "germinal layer" EXACT [ncithesaurus:Germinal_Layer] +synonym: "primary germ layer" NARROW [GO:0001704, ZFA:0001122] +xref: AAO:0000480 +xref: BILA:0000035 +xref: BTO:0000556 +xref: EMAPA:36033 +xref: FBbt:00000110 +xref: FMA:69069 +xref: GAID:1303 +xref: MESH:A16.254.425 +xref: NCIT:C12950 +xref: NCIT:C54105 +xref: TAO:0001122 +xref: UMLS:C0920502 +xref: UMLS:C1708239 +xref: VHOG:0001223 +xref: Wikipedia:Germ_layer +xref: XAO:0003011 +xref: ZFA:0001122 +is_a: UBERON:0010316 ! germ layer / neural crest + +[Term] +id: UBERON:0000924 +name: ectoderm +def: "Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue." [Wikipedia:Ectoderm] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "embryonic ectoderm" EXACT [VHOG:0000153] +xref: AAO:0000137 +xref: BILA:0000036 +xref: BTO:0000315 +xref: CALOHA:TS-0216 +xref: EFO:0000414 +xref: EHDAA2:0000428 +xref: EMAPA:16069 +xref: EV:0100003 +xref: FBbt:00000111 +xref: FMA:69070 +xref: GAID:1304 +xref: MAT:0000155 +xref: MAT:0000173 +xref: MESH:A16.254.425.273 +xref: MIAA:0000173 +xref: NCIT:C12703 +xref: SCTID:362851007 +xref: TAO:0000016 +xref: UMLS:C0013574 +xref: VHOG:0000153 +xref: Wikipedia:Ectoderm +xref: XAO:0000001 +xref: ZFA:0000016 +is_a: UBERON:0000923 ! germ layer + +[Term] +id: UBERON:0000925 +name: endoderm +def: "Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut." [Wikipedia:Endoderm] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "entoderm" RELATED DEPRECATED [DOI:10.5962/bhl.title.1013] +xref: AAO:0000139 +xref: BILA:0000038 +xref: BTO:0000800 +xref: CALOHA:TS-0273 +xref: EFO:0002545 +xref: EHDAA2:0000436 +xref: EMAPA:16062 +xref: EV:0100005 +xref: FBbt:00000125 +xref: FMA:69071 +xref: GAID:1305 +xref: MAT:0000175 +xref: MESH:A16.254.425.407 +xref: MIAA:0000175 +xref: NCIT:C12706 +xref: SCTID:362855003 +xref: TAO:0000017 +xref: UMLS:C0014144 +xref: VHOG:0000154 +xref: Wikipedia:Endoderm +xref: XAO:0000090 +xref: ZFA:0000017 +is_a: UBERON:0000923 ! germ layer + +[Term] +id: UBERON:0000926 +name: mesoderm +def: "The middle germ layer of the embryo, between the endoderm and ectoderm." [Wikipedia:Mesoderm] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "embryonic mesoderm" RELATED [VHOG:0000152] +synonym: "entire mesoderm" RELATED [https://orcid.org/0000-0002-6601-2165, SCTID:362854004] +synonym: "mesodermal mantle" RELATED [] +xref: AAO:0000304 +xref: BILA:0000037 +xref: BTO:0000839 +xref: CALOHA:TS-0623 +xref: EFO:0001981 +xref: EHDAA2:0001128 +xref: EHDAA:124 +xref: EHDAA:160 +xref: EHDAA:183 +xref: EMAPA:16083 +xref: EV:0100006 +xref: FBbt:00000126 +xref: FMA:69072 +xref: GAID:522 +xref: MAT:0000174 +xref: MESH:A16.254.425.660 +xref: MIAA:0000174 +xref: NCIT:C12750 +xref: SCTID:362854004 +xref: TAO:0000041 +xref: UMLS:C0025485 +xref: VHOG:0000152 +xref: Wikipedia:Mesoderm +xref: XAO:0000050 +xref: ZFA:0000041 +is_a: UBERON:0000923 ! germ layer + +[Term] +id: UBERON:0000930 +name: stomodeum +def: "Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity." [http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/326, Wikipedia:Stomodeum] +subset: grouping_class +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "mouth pit" RELATED [EMAPA:16263] +synonym: "mouth primordium" EXACT [XAO:0000269] +synonym: "oral ectoderm" RELATED [ZFA:0001290, ZFIN:ZDB-PUB-100726-23] +synonym: "oral pit" RELATED [EMAPA:16263] +synonym: "primitive oral cavity" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "stomatodeum" EXACT [Wikipedia:Stomodeum] +synonym: "stomodaeum" EXACT [] +synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] +xref: BTO:0004224 +xref: EHDAA2:0001929 +xref: EMAPA:16263 +xref: FBbt:00000439 +xref: FMA:295846 +xref: NCIT:C34306 +xref: TAO:0001290 +xref: TGMA:0000135 +xref: UMLS:C1514977 +xref: Wikipedia:Stomodeum +xref: XAO:0000269 +xref: ZFA:0001290 +is_a: UBERON:0013522 ! subdivision of tube +relationship: BFO:0000050 UBERON:0000924 ! part of ectoderm +relationship: BFO:0000050 UBERON:0035804 ! part of future mouth + +[Term] +id: UBERON:0000931 +name: proctodeum +def: "Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract." [https://github.com/obophenotype/uberon/issues/685, https://sourceforge.net/p/fbbtdv/tickets/52, ZFA:0000066] +subset: uberon_slim +synonym: "amnioproctodeal invagination" NARROW [FBbt:00000123] +synonym: "anal pit" RELATED [VHOG:0000139] +synonym: "anus porus" RELATED [XAO:0001019] +synonym: "embryonic proctodaeum" EXACT [] +synonym: "proctodaeum" EXACT [] +xref: AAO:0011087 +xref: EHDAA2:0000121 +xref: EMAPA:25038 +xref: FBbt:00000123 +xref: NCIT:C34278 +xref: TAO:0000066 +xref: UMLS:C0231054 +xref: VHOG:0000139 +xref: Wikipedia:Proctodeum +xref: XAO:0001019 +xref: ZFA:0000066 +is_a: UBERON:0016566 ! pit +relationship: BFO:0000050 UBERON:0007026 ! part of presumptive gut + +[Term] +id: UBERON:0000948 +name: heart +def: "A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Heart] +subset: efo_slim +subset: major_organ +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "branchial heart" NARROW SENSU [] +synonym: "cardium" RELATED [EMAPA:16105] +synonym: "chambered heart" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "vertebrate heart" EXACT [] +xref: AAO:0010210 +xref: BILA:0000020 +xref: BTO:0000562 +xref: CALOHA:TS-0445 +xref: EFO:0000815 +xref: EHDAA2:0000738 +xref: EHDAA:420 +xref: EMAPA:16105 +xref: EV:0100018 +xref: FMA:7088 +xref: GAID:174 +xref: galen:Heart +xref: MA:0000072 +xref: MAT:0000036 +xref: MESH:D006321 +xref: MIAA:0000036 +xref: NCIT:C12727 +xref: OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA +xref: SCTID:302509004 +xref: TAO:0000114 +xref: UMLS:C0018787 +xref: VHOG:0000276 +xref: Wikipedia:Heart +xref: XAO:0000064 +xref: ZFA:0000114 +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005181 ! thoracic segment organ +is_a: UBERON:0007100 ! primary circulatory organ +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: BFO:0000050 UBERON:0015410 ! part of heart plus pericardium + +[Term] +id: UBERON:0000955 +name: brain +def: "The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]." [https://github.com/obophenotype/uberon/issues/300, Wikipedia:Brain] +subset: cumbo +subset: efo_slim +subset: major_organ +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "encephalon" RELATED [BTO:0000142] +synonym: "suprasegmental levels of nervous system" RELATED [NeuroNames:21] +synonym: "suprasegmental structures" RELATED [NeuroNames:21] +synonym: "synganglion" RELATED [] +synonym: "the brain" RELATED [NeuroNames:21] +xref: AAO:0010478 +xref: ABA:Brain +xref: BAMS:Br +xref: BAMS:Brain +xref: BILA:0000135 +xref: BIRNLEX:796 +xref: BTO:0000142 +xref: CALOHA:TS-0095 +xref: DHBA:10155 +xref: EFO:0000302 +xref: EHDAA2:0000183 +xref: EHDAA:2641 +xref: EHDAA:6485 +xref: EMAPA:16894 +xref: EV:0100164 +xref: FBbt:00005095 +xref: FMA:50801 +xref: GAID:571 +xref: galen:Brain +xref: HBA:4005 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 +xref: MA:0000168 +xref: MAT:0000098 +xref: MBA:8 +xref: MBA:997 +xref: MESH:D001921 +xref: MIAA:0000098 +xref: NCIT:C12439 +xref: OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA +xref: PBA:3999 +xref: SCTID:258335003 +xref: TAO:0000008 +xref: UMLS:C0006104 +xref: UMLS:C1269537 +xref: VHOG:0000157 +xref: Wikipedia:Brain +xref: XAO:0000010 +xref: ZFA:0000008 +is_a: UBERON:0000062 ! organ +is_a: UBERON:0004121 ! ectoderm-derived structure +relationship: BFO:0000050 UBERON:0001017 ! part of central nervous system + +[Term] +id: UBERON:0000956 +name: cerebral cortex +def: "The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex." [BIRNLEX:1494] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "brain cortex" RELATED [BTO:0000233] +synonym: "cortex cerebralis" RELATED [NeuroNames:39] +synonym: "cortex cerebri" RELATED [Wikipedia:Cerebral_cortex] +synonym: "cortex of cerebral hemisphere" EXACT [BTO:0000233, FMA:61830] +synonym: "cortical plate (areas)" RELATED [NeuroNames:39] +synonym: "cortical plate (CTXpl)" RELATED [NeuroNames:39] +synonym: "pallium of the brain" RELATED [BTO:0000233] +xref: BAMS:C +xref: BAMS:Cerebral_cortex +xref: BAMS:CTX +xref: BAMS:Cx +xref: BIRNLEX:1494 +xref: BM:Tel-Cx +xref: BTO:0000233 +xref: CALOHA:TS-0091 +xref: DHBA:10159 +xref: EFO:0000328 +xref: EHDAA2:0000234 +xref: EHDAA:5464 +xref: EMAPA:17544 +xref: EV:0100166 +xref: FMA:61830 +xref: GAID:629 +xref: HBA:4008 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=39 +xref: MA:0000185 +xref: MAT:0000108 +xref: MBA:688 +xref: MESH:A08.186.211.730.885.213 +xref: MIAA:0000108 +xref: NCIT:C12443 +xref: PBA:128011354 +xref: SCTID:362880003 +xref: UMLS:C0007776 +xref: VHOG:0000722 +xref: Wikipedia:Cerebral_cortex +is_a: UBERON:0011215 ! central nervous system cell part cluster +is_a: UBERON:0016548 ! central nervous system gray matter layer +relationship: BFO:0000050 UBERON:0000203 ! part of pallium +relationship: BFO:0000050 UBERON:0005401 ! part of cerebral hemisphere gray matter + +[Term] +id: UBERON:0000958 +name: medulla of organ +def: "Middle part of an organ, surrounded by the cortex." [http://orcid.org/0000-0002-6601-2165] +subset: upper_level +synonym: "medulla" EXACT [FMA:61108] +xref: FMA:61108 +xref: galen:Medulla +is_a: UBERON:0000471 ! compound organ component + +[Term] +id: UBERON:0000976 +name: humerus +def: "Paired endochondral long bone that extends between the pectoral girdle and the skeletal parts of the forelimb. [PHENOSCAPE:mah]." [AAO:0000679, https://github.com/obophenotype/uberon/issues/106, PHENOSCAPE:mah] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "humeri" EXACT [PHENOSCAPE:ad] +synonym: "humerus bone" EXACT [] +synonym: "mesomere 1 of pectoral appendage" RELATED HOMOLOGY [ISBN:0226313409] +synonym: "proximal metapterygial mesomere of pectoral appendage" RELATED HOMOLOGY [ISBN:0226313409] +synonym: "proximal metapterygial mesomere of pectoral fin" RELATED HOMOLOGY [ISBN:0226313409] +xref: AAO:0000679 +xref: CALOHA:TS-2202 +xref: EFO:0001398 +xref: EMAPA:19106 +xref: FMA:13303 +xref: GAID:183 +xref: galen:Humerus +xref: MA:0001356 +xref: MESH:A02.835.232.087.412 +xref: NCIT:C12731 +xref: SCTID:181923006 +xref: UMLS:C0020164 +xref: VHOG:0001158 +xref: Wikipedia:Humerus +xref: XAO:0003210 +is_a: UBERON:0003461 ! shoulder bone +is_a: UBERON:0003607 ! forelimb long bone +is_a: UBERON:0004250 ! upper arm bone +is_a: UBERON:0015053 ! humerus endochondral element + +[Term] +id: UBERON:0000978 +name: leg +def: "The portion of the hindlimb that contains both the stylopod and zeugopod." [Wikipedia:Leg#Limb] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "lower extremity" RELATED [MESH:A01.378.610] +synonym: "tetrapod leg" EXACT [] +xref: BTO:0000721 +xref: CALOHA:TS-2206 +xref: EFO:0001411 +xref: EHDAA2:0000972 +xref: EHDAA:5151 +xref: EHDAA:6176 +xref: EHDAA:8289 +xref: EMAPA:17489 +xref: GAID:49 +xref: MA:0000047 +xref: MESH:D035002 +xref: OpenCyc:Mx4rvViYzZwpEbGdrcN5Y29ycA +xref: VHOG:0000345 +xref: Wikipedia:Leg#Limb +is_a: UBERON:0006058 ! multi-limb segment region +is_a: UBERON:0008784 ! lower limb segment + +[Term] +id: UBERON:0000981 +name: femur +def: "Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified]." [VSAO:0000186, Wikipedia:Femur] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "femoral bone" RELATED [BTO:0001284] +synonym: "mesomere 1 of pevlic appendage" RELATED HOMOLOGY [ISBN:0226313409] +synonym: "os femorale" RELATED [BTO:0001284] +synonym: "os femoris" RELATED [BTO:0001284] +synonym: "os longissimum" RELATED [Wikipedia:Femur] +synonym: "proximal metapterygial mesomere of pelvic appendage" RELATED HOMOLOGY [ISBN:0226313409] +synonym: "proximal metapterygial mesomere of pelvic fin" RELATED HOMOLOGY [ISBN:0226313409] +synonym: "thigh bone" EXACT [] +xref: AAO:0000887 +xref: AAO:0000889 +xref: BTO:0001284 +xref: CALOHA:TS-0322 +xref: EFO:0001396 +xref: EMAPA:19143 +xref: FMA:9611 +xref: GAID:199 +xref: galen:Femur +xref: MA:0001359 +xref: MESH:A02.835.232.500.247 +xref: NCIT:C12717 +xref: OpenCyc:Mx4rvVjOJJwpEbGdrcN5Y29ycA +xref: SCTID:182046008 +xref: UMLS:C0015811 +xref: VHOG:0001159 +xref: VSAO:0000186 +xref: Wikipedia:Femur +xref: XAO:0003214 +is_a: UBERON:0003608 ! hindlimb long bone +is_a: UBERON:0003826 ! upper leg bone +is_a: UBERON:0008202 ! bone of hip region +is_a: UBERON:0015052 ! femur endochondral element + +[Term] +id: UBERON:0000982 +name: skeletal joint +def: "Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000101, Wikipedia:Joint] +subset: efo_slim +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "articular joint" RELATED [BTO:0001686] +synonym: "articulation" BROAD [VSAO:0000101] +synonym: "joint" BROAD [FMA:7490, VSAO:0000101] +synonym: "joints" RELATED [ZFA:0001596] +xref: AEO:0000182 +xref: BTO:0001686 +xref: CALOHA:TS-2023 +xref: EFO:0000948 +xref: EMAPA:35456 +xref: FMA:7490 +xref: GAID:102 +xref: galen:Joint +xref: MA:0000319 +xref: MAT:0000188 +xref: MESH:D007596 +xref: MIAA:0000188 +xref: NCIT:C13044 +xref: OpenCyc:Mx4rvVjjdpwpEbGdrcN5Y29ycA +xref: RETIRED_EHDAA2:0003182 +xref: SCTID:302536002 +xref: TAO:0000367 +xref: UMLS:C0022417 +xref: VHOG:0001276 +xref: VSAO:0000101 +xref: Wikipedia:Joint +xref: XAO:0000171 +xref: ZFA:0001596 +is_a: UBERON:0004905 ! articulation + +[Term] +id: UBERON:0000990 +name: reproductive system +def: "Anatomical system that has as its parts the organs concerned with reproduction." [Wikipedia:Reproductive_system] +subset: efo_slim +subset: functional_classification +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "animal reproductive system" RELATED [BTO:0000081] +synonym: "genital system" RELATED [] +synonym: "genital tract" RELATED [] +synonym: "genitalia" RELATED [] +synonym: "Geschlechtsorgan" RELATED [BTO:0000081] +synonym: "organa genitalia" RELATED [BTO:0000081] +synonym: "reproductive tissue" RELATED [BTO:0000081] +synonym: "reproductive tract" RELATED [] +synonym: "systemata genitalia" RELATED [Wikipedia:Reproductive_system] +xref: AAO:0010258 +xref: BILA:0000103 +xref: BTO:0000081 +xref: CALOHA:TS-1318 +xref: EFO:0000809 +xref: EHDAA2:0001603 +xref: EHDAA:5923 +xref: EMAPA:17381 +xref: EV:0100100 +xref: FBbt:00004857 +xref: FMA:7160 +xref: GAID:363 +xref: HAO:0000374 +xref: HAO:0000895 +xref: MA:0000326 +xref: MIAA:0000305 +xref: NCIT:C12841 +xref: OpenCyc:Mx4rvVja4ZwpEbGdrcN5Y29ycA +xref: SCTID:278875001 +xref: TAO:0000632 +xref: UMLS:C1261210 +xref: VHOG:0000182 +xref: WBbt:0005747 +xref: Wikipedia:Reproductive_system +xref: XAO:0000142 +xref: ZFA:0000632 +is_a: UBERON:0000467 ! anatomical system + +[Term] +id: UBERON:0000991 +name: gonad +def: "Reproductive organ that produces and releases eggs (ovary) or sperm (testis)." [ISBN:0140512888, Wikipedia:Gonad, ZFA:0000413, ZFIN:curator] +subset: major_organ +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "gonada" EXACT [] +synonym: "gonads" RELATED [ZFA:0000413] +xref: AAO:0000213 +xref: BILA:0000123 +xref: BSA:0000079 +xref: BTO:0000534 +xref: EMAPA:17383 +xref: FBbt:00004858 +xref: FMA:18250 +xref: GAID:368 +xref: HAO:0000379 +xref: MA:0002420 +xref: MESH:D006066 +xref: NCIT:C12725 +xref: OpenCyc:Mx4rwQvdiZwpEbGdrcN5Y29ycA +xref: SCTID:304623008 +xref: TAO:0000413 +xref: UMLS:C0018067 +xref: VHOG:0000397 +xref: WBbt:0005175 +xref: Wikipedia:Gonad +xref: XAO:0003146 +xref: ZFA:0000413 +is_a: UBERON:0003133 ! reproductive organ + +[Term] +id: UBERON:0001003 +name: skin epidermis +def: "The outer epithelial layer of the skin that is superficial to the dermis." [http://orcid.org/0000-0002-6601-2165, ISBN:0073040584] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "epidermis" BROAD [] +synonym: "skin" BROAD [] +synonym: "vertebrate epidermis" EXACT [] +xref: AAO:0000143 +xref: BTO:0000404 +xref: CALOHA:TS-0283 +xref: EFO:0000954 +xref: EMAPA:17528 +xref: EV:0100153 +xref: FMA:70596 +xref: GAID:932 +xref: MA:0000153 +xref: MAT:0000154 +xref: MESH:D004817 +xref: MIAA:0000154 +xref: NCIT:C12708 +xref: SCTID:361694003 +xref: TAO:0000105 +xref: UMLS:C0014520 +xref: VHOG:0000077 +xref: Wikipedia:Epidermis_(skin) +xref: XAO:0000028 +xref: ZFA:0000105 +is_a: UBERON:0007376 ! outer epithelium +is_a: UBERON:3000961 ! external integument structure +relationship: BFO:0000050 UBERON:0002097 ! part of skin of body + +[Term] +id: UBERON:0001004 +name: respiratory system +def: "Functional system which consists of structures involved in respiration." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Respiratory_system] +subset: efo_slim +subset: functional_classification +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "apparatus respiratorius" EXACT [] +synonym: "apparatus respiratorius" RELATED [BTO:0000203] +synonym: "Atmungssystem" RELATED [BTO:0000203] +synonym: "respiratory system" EXACT [] +synonym: "systema respiratorium" RELATED [Wikipedia:Respiratory_system] +xref: AAO:0000541 +xref: BTO:0000203 +xref: CALOHA:TS-1319 +xref: EFO:0000804 +xref: EHDAA2:0001604 +xref: EHDAA:2203 +xref: EMAPA:16727 +xref: EV:0100036 +xref: FMA:7158 +xref: GAID:78 +xref: MA:0000327 +xref: MAT:0000030 +xref: MESH:D012137 +xref: MIAA:0000030 +xref: NCIT:C12779 +xref: OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA +xref: SCTID:278197002 +xref: TAO:0000272 +xref: UMLS:C0035237 +xref: VHOG:0000202 +xref: Wikipedia:Respiratory_system +xref: XAO:0000117 +xref: ZFA:0000272 +is_a: UBERON:0000467 ! anatomical system + +[Term] +id: UBERON:0001007 +name: digestive system +def: "Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes." [FB:gg, NLM:alimentary+system, Wikipedia:Digestive_system] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "alimentary system" RELATED [] +synonym: "alimentary tract" RELATED [] +synonym: "gastrointestinal system" RELATED [] +synonym: "gut" RELATED [] +xref: AAO:0000129 +xref: BILA:0000082 +xref: BTO:0000058 +xref: CALOHA:TS-1293 +xref: EFO:0000793 +xref: EV:0100056 +xref: FBbt:00005055 +xref: FMA:7152 +xref: GAID:278 +xref: galen:DigestiveSystem +xref: MA:0002431 +xref: MAT:0000018 +xref: MESH:D004064 +xref: MIAA:0000018 +xref: ncithesaurus:Digestive_System +xref: SCTID:278859004 +xref: TADS:0000170 +xref: TAO:0000339 +xref: WBbt:0005748 +xref: Wikipedia:Digestive_system +xref: XAO:0000125 +xref: ZFA:0000339 +is_a: UBERON:0000467 ! anatomical system + +[Term] +id: UBERON:0001008 +name: renal system +def: "The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.." [DOI:10.1371/journal.pone.0099864, GO:0072001] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "excretory system" EXACT [] +synonym: "renal or urinary system" RELATED [EHDAA:5901] +synonym: "renal system" EXACT [GO:0001977] +synonym: "renal/urinary system" RELATED [] +synonym: "systema urinaria" EXACT [FMA:7159] +synonym: "systema urinarium" EXACT [BTO:0003092] +synonym: "urinary system" EXACT [] +synonym: "urinary tract" EXACT [] +xref: AAO:0010257 +xref: BILA:0000015 +xref: BTO:0001244 +xref: BTO:0003092 +xref: CALOHA:TS-1323 +xref: EFO:0000803 +xref: EHDAA2:0001601 +xref: EHDAA:5901 +xref: EMAPA:17366 +xref: EV:0100095 +xref: FBbt:00005056 +xref: FMA:7159 +xref: GAID:391 +xref: galen:UrinaryTract +xref: MA:0000325 +xref: MAT:0000027 +xref: MESH:D014551 +xref: MIAA:0000027 +xref: NCIT:C12413 +xref: SCTID:362204003 +xref: TADS:0000162 +xref: TAO:0000163 +xref: UMLS:C1508753 +xref: VHOG:0000723 +xref: WBbt:0005736 +xref: Wikipedia:Excretory_system +xref: XAO:0000143 +xref: ZFA:0000163 +is_a: UBERON:0000467 ! anatomical system + +[Term] +id: UBERON:0001009 +name: circulatory system +def: "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]." [Wikipedia:Circulatory_system] +subset: uberon_slim +synonym: "systema cardiovasculare" RELATED [Wikipedia:Circulatory_system] +xref: AAO:0000959 +xref: CALOHA:TS-2103 +xref: FBbt:00005057 +xref: OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA +xref: VHOG:0001248 +xref: Wikipedia:Circulatory_system +is_a: UBERON:0000467 ! anatomical system + +[Term] +id: UBERON:0001013 +name: adipose tissue +def: "Portion of connective tissue composed of adipocytes enmeshed in areolar tissue." [http://orcid.org/0000-0002-6601-2165, MESH:A10.165.114, MGI:cwg, MP:0000003, Wikipedia:Adipose_tissue] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "adipose" RELATED [BTO:0001487] +synonym: "bodyfat" RELATED [BTO:0001487] +synonym: "fat" EXACT [MA:0000009] +synonym: "fat tissue" EXACT [] +synonym: "fatty depot" RELATED [] +synonym: "fatty tissue" EXACT [] +xref: AAO:0000001 +xref: AEO:000020 +xref: BTO:0001487 +xref: CALOHA:TS-0013 +xref: EFO:0000790 +xref: EHDAA2:0003120 +xref: EMAPA:35112 +xref: EV:0100381 +xref: FMA:20110 +xref: GAID:920 +xref: galen:FattyTissue +xref: MA:0000009 +xref: MAT:0000015 +xref: MESH:D000273 +xref: MIAA:0000015 +xref: NCIT:C12472 +xref: OpenCyc:Mx4rvVjc_ZwpEbGdrcN5Y29ycA +xref: SCTID:55603005 +xref: TAO:0002134 +xref: UMLS:C0001527 +xref: VHOG:0001284 +xref: Wikipedia:Adipose_tissue +xref: XAO:0003049 +xref: ZFA:0005345 +is_a: UBERON:0011822 ! dense irregular connective tissue + +[Term] +id: UBERON:0001015 +name: musculature +def: "A subdivision of the muscular system corresponding to a subdisivision of an organism." [https://orcid.org/0000-0002-6601-2165, Wikipedia:Muscular_system] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "muscle group" EXACT [] +synonym: "muscle system" RELATED [] +synonym: "muscles" RELATED [] +synonym: "muscles set" EXACT [] +synonym: "musculature" EXACT [] +synonym: "musculature system" RELATED [] +synonym: "musculi" EXACT [FMA:32558, FMA:TA] +synonym: "set of muscles" EXACT [FMA:32558] +synonym: "set of skeletal muscles" EXACT [MA:0000165] +xref: AAO:0011066 +xref: BTO:0000887 +xref: EFO:0001949 +xref: EMAPA:32715 +xref: EMAPA:35577 +xref: FMA:32558 +xref: MA:0000165 +xref: NCIT:C13056 +xref: OpenCyc:Mx4rvVjmr5wpEbGdrcN5Y29ycA +xref: TAO:0000548 +xref: UMLS:C0026845 +xref: VSAO:0005038 +xref: WBbt:0005737 +xref: Wikipedia:Muscular_system +xref: ZFA:0000548 +is_a: UBERON:0011216 ! organ system subdivision +relationship: BFO:0000050 UBERON:0000383 ! part of musculature of body + +[Term] +id: UBERON:0001016 +name: nervous system +def: "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]." [BIRNLEX:844, ISBN:0-14-051288-8, ISBN:3110148986, NLM:nervous+system, WB:rynl, Wikipedia:Nervous_system, ZFIN:curator] +subset: cumbo +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "nerve net" NARROW [Wikipedia:Nerve_net] +synonym: "neurological system" EXACT [GO:0050877] +synonym: "systema nervosum" RELATED [Wikipedia:Nervous_system] +xref: AAO:0000324 +xref: BILA:0000079 +xref: BIRNLEX:844 +xref: BTO:0001484 +xref: CALOHA:TS-1313 +xref: EFO:0000802 +xref: EHDAA2:0001246 +xref: EHDAA:826 +xref: EMAPA:16469 +xref: EV:0100162 +xref: FBbt:00005093 +xref: FMA:7157 +xref: GAID:466 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=3236 +xref: MA:0000016 +xref: MAT:0000026 +xref: MESH:D009420 +xref: MIAA:0000026 +xref: NCIT:C12755 +xref: OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA +xref: SCTID:278196006 +xref: TAO:0000396 +xref: UMLS:C0027763 +xref: VHOG:0000402 +xref: WBbt:0005735 +xref: Wikipedia:Nervous_system +xref: XAO:0000177 +xref: ZFA:0000396 +is_a: UBERON:0000467 ! anatomical system + +[Term] +id: UBERON:0001017 +name: central nervous system +def: "The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord." [GO:0021551, http://www.frontiersinzoology.com/content/7/1/29, https://sourceforge.net/p/geneontology/ontology-requests/11422/] +subset: cumbo +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "cerebrospinal axis" NARROW [FMA:55675] +synonym: "CNS" EXACT [] +synonym: "neuraxis" RELATED [FMA:55675] +synonym: "systema nervosum centrale" EXACT [FMA:55675, FMA:TA] +xref: AAO:0000090 +xref: BAMS:CNS +xref: BILA:0000080 +xref: BIRNLEX:1099 +xref: BTO:0000227 +xref: CALOHA:TS-0150 +xref: EFO:0000908 +xref: EHDAA2:0000225 +xref: EHDAA:828 +xref: EMAPA:16470 +xref: EMAPA:16754 +xref: EV:0100163 +xref: FBbt:00005094 +xref: FMA:55675 +xref: GAID:570 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=854 +xref: MA:0000167 +xref: MAT:0000457 +xref: MESH:D002490 +xref: NCIT:C12438 +xref: OpenCyc:Mx4rvzYt3pwpEbGdrcN5Y29ycA +xref: SCTID:278199004 +xref: TAO:0000012 +xref: UMLS:C0927232 +xref: VHOG:0000293 +xref: Wikipedia:Central_nervous_system +xref: XAO:0000215 +xref: ZFA:0000012 +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0011216 ! organ system subdivision +relationship: BFO:0000050 UBERON:0001016 ! part of nervous system + +[Term] +id: UBERON:0001019 +name: nerve fasciculus +def: "A slender neuron projection bundle[FBbt]; A bundle of anatomical fibers, as of muscle or nerve (American Heritage Dictionary 4th ed)." [BIRNLEX:872, FBbt:00005101] +subset: uberon_slim +synonym: "fascicle" BROAD [FBbt:00005101] +synonym: "fasciculus" EXACT [] +synonym: "nerve bundle" EXACT [FMA:12235] +synonym: "nerve fasciculus" EXACT [FMA:12235] +synonym: "nerve fiber tract" RELATED [BTO:0002191] +synonym: "neural fasciculus" EXACT [FMA:12235] +xref: BIRNLEX:872 +xref: BTO:0002191 +xref: EMAPA:36605 +xref: FMA:12235 +xref: NCIT:C32586 +xref: TGMA:0000088 +xref: UMLS:C1185741 +xref: Wikipedia:Nervous_system_fascicle +is_a: UBERON:0000122 ! neuron projection bundle + +[Term] +id: UBERON:0001021 +name: nerve +def: "An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures." [FBbt:00005105, http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "nerves" EXACT [TAO:0007009] +synonym: "neural subtree" RELATED [FMA:65132] +synonym: "peripheral nerve" EXACT [http://orcid.org/0000-0002-6601-2165] +xref: AAO:0011070 +xref: AEO:0000137 +xref: BAMS:n +xref: BIRNLEX:1615 +xref: BSA:0000098 +xref: BTO:0000925 +xref: BTO:0001027 +xref: CALOHA:TS-0772 +xref: EHDAA2:0003137 +xref: EHDAA:2851 +xref: EHDAA:3776 +xref: EHDAA:4657 +xref: EMAPA:32808 +xref: EMAPA:32815 +xref: EV:0100371 +xref: FBbt:00005105 +xref: FMA:65132 +xref: FMA:65239 +xref: GAID:747 +xref: GAID:758 +xref: galen:Nerve +xref: MA:0000217 +xref: MA:0000228 +xref: MESH:D010525 +xref: NCIT:C12466 +xref: NCIT:C12768 +xref: NLX:147826 +xref: OpenCyc:Mx4rwP3lkpwpEbGdrcN5Y29ycA +xref: SCTID:244457007 +xref: SCTID:256864008 +xref: TAO:0007009 +xref: UMLS:C0027740 +xref: UMLS:C0031119 +xref: VHOG:0000901 +xref: Wikipedia:Nervous_system +xref: XAO:0000204 +xref: XAO:0003047 +xref: ZFA:0007009 +is_a: UBERON:0000122 ! neuron projection bundle +relationship: BFO:0000050 UBERON:0000010 ! part of peripheral nervous system + +[Term] +id: UBERON:0001032 +name: sensory system +def: "Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information." [Wikipedia:Sensory_system] +subset: efo_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "organa sensuum" EXACT [FMA:75259, FMA:TA] +synonym: "organa sensuum" RELATED [Wikipedia:Sensory_system] +synonym: "sense organ subsystem" EXACT [] +synonym: "sense organs" EXACT [FMA:75259] +synonym: "sense organs set" EXACT [FMA:75259] +synonym: "sensory organ system" RELATED [] +synonym: "sensory subsystem" EXACT [] +synonym: "sensory systems" EXACT [TAO:0000282] +synonym: "set of sense organs" RELATED [FMA:75259] +xref: AAO:0000555 +xref: BAMS:SEN +xref: BILA:0000099 +xref: EFO:0000805 +xref: EHDAA2:0003094 +xref: EMAPA:16192 +xref: FBbt:00007692 +xref: FMA:75259 +xref: MA:0002442 +xref: MAT:0000031 +xref: MIAA:0000031 +xref: NLXANAT:090816 +xref: TAO:0000282 +xref: VHOG:0001674 +xref: Wikipedia:Sensory_system +xref: XAO:0003194 +xref: ZFA:0000282 +is_a: UBERON:0000467 ! anatomical system +relationship: BFO:0000050 UBERON:0004456 ! part of entire sense organ system + +[Term] +id: UBERON:0001037 +name: strand of hair +def: "A filament, mostly protein, that grows from follicles found in the dermis[WP]." [Wikipedia:Hair] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "coat hair" RELATED [] +synonym: "coat/ hair" RELATED [] +synonym: "fur" RELATED [] +synonym: "hair" EXACT [] +synonym: "microchaeta" RELATED [] +synonym: "quill" RELATED SENSU [] +synonym: "setulae" RELATED [] +synonym: "vibrissa" RELATED SENSU [] +synonym: "whisker" RELATED SENSU [] +xref: BTO:0001501 +xref: CALOHA:TS-0430 +xref: EFO:0000958 +xref: EMAPA:18769 +xref: EV:0100157 +xref: FMA:53667 +xref: GAID:71 +xref: MA:0000155 +xref: MAT:0000160 +xref: MESH:D006197 +xref: MIAA:0000160 +xref: NCIT:C32705 +xref: OpenCyc:Mx4rvVjOX5wpEbGdrcN5Y29ycA-Mp88EdaAAACgycbRww +xref: SCTID:361702001 +xref: UMLS:C0018494 +xref: VHOG:0001191 +xref: Wikipedia:Hair +is_a: UBERON:0000021 ! cutaneous appendage +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: BFO:0000050 UBERON:0001003 ! part of skin epidermis +relationship: BFO:0000050 UBERON:0011932 ! part of pilosebaceous unit + +[Term] +id: UBERON:0001041 +name: foregut +def: "Anterior subdivision of a digestive tract." [http://orcid.org/0000-0002-6601-2165] +subset: developmental_classification +subset: pheno_slim +subset: uberon_slim +synonym: "praeenteron" RELATED [Wikipedia:Foregut] +synonym: "proenteron" RELATED [Wikipedia:Foregut] +xref: AAO:0011042 +xref: BILA:0000085 +xref: BTO:0000507 +xref: EHDAA2:0000557 +xref: EHDAA:520 +xref: EMAPA:16548 +xref: FBbt:00005379 +xref: FMA:45616 +xref: MA:0001526 +xref: NCIT:C34180 +xref: SCTID:361409009 +xref: TGMA:0001014 +xref: UMLS:C0231051 +xref: VHOG:0000285 +xref: Wikipedia:Foregut +xref: XAO:0000232 +is_a: UBERON:0004921 ! subdivision of digestive tract + +[Term] +id: UBERON:0001045 +name: midgut +def: "Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]." [GO:0007494, Wikipedia:Midgut] +subset: developmental_classification +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "mesenteron" RELATED [Wikipedia:Midgut] +xref: BILA:0000086 +xref: BTO:0000863 +xref: EFO:0001950 +xref: EHDAA2:0001185 +xref: EHDAA:983 +xref: EMAPA:16255 +xref: FBbt:00005383 +xref: FMA:45617 +xref: MA:0001564 +xref: NCIT:C34210 +xref: SCTID:361410004 +xref: TGMA:0001036 +xref: UMLS:C0231052 +xref: VHOG:0000290 +xref: Wikipedia:Midgut +xref: XAO:0000103 +is_a: UBERON:0004921 ! subdivision of digestive tract + +[Term] +id: UBERON:0001046 +name: hindgut +def: "The caudalmost subdivision of a digestive tract." [http://orcid.org/0000-0002-6601-2165] +subset: developmental_classification +subset: pheno_slim +subset: uberon_slim +synonym: "metenteron" RELATED [Wikipedia:Hindgut] +xref: AAO:0011052 +xref: BILA:0000087 +xref: BTO:0000510 +xref: EHDAA2:0000779 +xref: EHDAA:975 +xref: EMAPA:16715 +xref: FBbt:00005384 +xref: FMA:45618 +xref: MA:0001527 +xref: NCIT:C34188 +xref: SCTID:362856002 +xref: TGMA:0001020 +xref: UMLS:C0231053 +xref: VHOG:0000459 +xref: Wikipedia:Hindgut +xref: XAO:0000104 +is_a: UBERON:0004921 ! subdivision of digestive tract + +[Term] +id: UBERON:0001048 +name: primordium +def: "Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]." [BTO:0001886, FB:DJS, FB:FBrf0089570, http://flybase.org/reports/FBrf0178740.html] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "bud" RELATED [] +synonym: "future organ" RELATED [] +synonym: "placode" RELATED [FBbt:00005495] +synonym: "primordia" RELATED [XAO:0003043] +synonym: "rudiment" RELATED [] +xref: AEO:0000171 +xref: BTO:0001886 +xref: EFO:0001652 +xref: EHDAA2:0003171 +xref: FBbt:00005495 +xref: FMA:86589 +xref: MAT:0000482 +xref: NCIT:C34275 +xref: UMLS:C0678727 +xref: Wikipedia:Primordium +xref: XAO:0003043 +is_a: UBERON:0005423 ! developing anatomical structure +relationship: BFO:0000050 UBERON:0000468 ! part of multicellular organism + +[Term] +id: UBERON:0001049 +name: neural tube +def: "In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]." [Wikipedia:Neural_tube] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "neural primordium" RELATED [] +synonym: "presumptive central nervous system" RELATED [] +synonym: "tubus neuralis" RELATED [Wikipedia:Neural_tube] +xref: AAO:0010617 +xref: BTO:0001057 +xref: CALOHA:TS-2371 +xref: DHBA:10154 +xref: EHDAA2:0001254 +xref: EHDAA:2869 +xref: EHDAA:908 +xref: EMAPA:16164 +xref: EMAPA:16757 +xref: FMA:293882 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1365 +xref: MAT:0000069 +xref: MIAA:0000069 +xref: NCIT:C34226 +xref: SCTID:362852000 +xref: TAO:0001135 +xref: UMLS:C0231024 +xref: VHOG:0000307 +xref: Wikipedia:Neural_tube +xref: XAO:0003204 +xref: ZFA:0001135 +is_a: UBERON:0003914 ! epithelial tube +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium +is_a: UBERON:0016879 ! future central nervous system + +[Term] +id: UBERON:0001062 +name: anatomical entity +def: "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." [FMA:62955, http://orcid.org/0000-0001-9114-8737] +subset: upper_level +xref: AAO:0010841 +xref: AEO:0000000 +xref: BILA:0000000 +xref: BIRNLEX:6 +xref: CARO:0000000 +xref: EHDAA2:0002229 +xref: FBbt:10000000 +xref: FMA:62955 +xref: HAO:0000000 +xref: MA:0000001 +xref: NCIT:C12219 +xref: TAO:0100000 +xref: TGMA:0001822 +xref: UMLS:C1515976 +xref: WBbt:0000100 +xref: XAO:0000000 +xref: ZFA:0100000 + +[Term] +id: UBERON:0001072 +name: posterior vena cava +def: "A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Inferior_vena_cava] +subset: pheno_slim +subset: uberon_slim +synonym: "caudal vena cava" RELATED [VHOG:0001194] +synonym: "inferior caval vein" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "inferior vena cava" EXACT [Wikipedia:Venae_cavae] +synonym: "postcava" RELATED [] +synonym: "posterior vena cava" EXACT [Wikipedia:Venae_cavae] +synonym: "vena cava inferior" RELATED [BTO:0002682, Wikipedia:Inferior_vena_cava] +xref: AAO:0011083 +xref: BTO:0002682 +xref: EHDAA2:0000611 +xref: EMAPA:18416 +xref: FMA:10951 +xref: GAID:548 +xref: galen:InferiorVenaCava +xref: MA:0000480 +xref: MESH:D014682 +xref: NCIT:C12815 +xref: SCTID:181369003 +xref: UMLS:C0042458 +xref: VHOG:0001194 +xref: Wikipedia:Inferior_vena_cava +xref: XAO:0000388 +is_a: UBERON:0004087 ! vena cava + +[Term] +id: UBERON:0001088 +name: urine +def: "Excretion that is the output of a kidney." [https://github.com/geneontology/go-ontology/issues/11025, Wikipedia:Urine] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +xref: BTO:0001419 +xref: CALOHA:TS-1092 +xref: EFO:0001939 +xref: EMAPA:36554 +xref: ENVO:00002047 +xref: FMA:12274 +xref: GAID:1189 +xref: galen:Urine +xref: MA:0002545 +xref: MAT:0000058 +xref: MESH:D014556 +xref: MIAA:0000058 +xref: NCIT:C13283 +xref: OpenCyc:Mx4rvVjGppwpEbGdrcN5Y29ycA +xref: UMLS:C0042036 +xref: Wikipedia:Urine +is_a: UBERON:0000174 ! excreta + +[Term] +id: UBERON:0001090 +name: synovial fluid +def: "Joint fluid is a transudate of plasma that is actively secreted by synovial cells." [https://www.ncbi.nlm.nih.gov/books/NBK274/] +subset: uberon_slim +subset: vertebrate_core +synonym: "joint fluid" EXACT [https://www.ncbi.nlm.nih.gov/books/NBK274/] +xref: BTO:0001339 +xref: CALOHA:TS-0996 +xref: ENVO:02000039 +xref: FMA:12277 +xref: GAID:265 +xref: galen:SynovialFluid +xref: MA:0002544 +xref: MESH:D013582 +xref: NCIT:C33718 +xref: TAO:0005154 +xref: UMLS:C0039097 +xref: Wikipedia:Synovial_fluid +xref: ZFA:0005154 +is_a: UBERON:0007779 ! transudate +is_a: UBERON:0007794 ! secretion of serous gland + +[Term] +id: UBERON:0001134 +name: skeletal muscle tissue +def: "Muscle tissue that consists primarily of skeletal muscle fibers." [https://github.com/obophenotype/uberon/issues/324] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "skeletal muscle" BROAD [] +synonym: "skeletal muscle system" RELATED [BTO:0001103] +synonym: "somatic muscle" RELATED [BTO:0001103] +xref: EMAPA:32716 +xref: FMA:14069 +xref: MA:0002439 +xref: NCIT:C13050 +xref: SCTID:426215008 +xref: UMLS:C0242692 +xref: Wikipedia:Skeletal_striated_muscle +is_a: UBERON:0002036 ! striated muscle tissue +relationship: BFO:0000050 UBERON:0014892 ! part of skeletal muscle organ + +[Term] +id: UBERON:0001135 +name: smooth muscle tissue +def: "Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]." [GO:0006939, Wikipedia:Smooth_muscle_tissue] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "involuntary muscle" EXACT [] +synonym: "non-striated muscle" EXACT [] +synonym: "smooth muscle" EXACT [] +synonym: "textus muscularis levis; textus muscularis nonstriatus" RELATED [Wikipedia:Smooth_muscle_tissue] +synonym: "textus muscularis nonstriatus" EXACT [FMA:14070, FMA:TA] +synonym: "visceral muscle" NARROW SENSU [] +synonym: "visceral muscle tissue" NARROW SENSU [] +xref: AAO:0010244 +xref: AEO:0000141 +xref: BTO:0001260 +xref: CALOHA:TS-0943 +xref: EFO:0000889 +xref: EHDAA2:0003141 +xref: EMAPA:32717 +xref: EV:0100378 +xref: FBbt:00003525 +xref: FMA:14070 +xref: GAID:167 +xref: galen:SmoothMuscle +xref: galen:SmoothMuscleTissue +xref: MA:0000166 +xref: MAT:0000303 +xref: MESH:D009130 +xref: MIAA:0000303 +xref: NCIT:C12437 +xref: OpenCyc:Mx4rvvSS3pwpEbGdrcN5Y29ycA +xref: TAO:0005274 +xref: UMLS:C1267092 +xref: VHOG:0001246 +xref: WBbt:0005781 +xref: Wikipedia:Smooth_muscle_tissue +xref: XAO:0000175 +xref: ZFA:0005274 +is_a: UBERON:0002385 ! muscle tissue + +[Term] +id: UBERON:0001136 +name: mesothelium +def: "Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri)." [FMA:14074, Wikipedia:Mesothelium] +subset: uberon_slim +xref: AEO:0000111 +xref: BTO:0002422 +xref: CALOHA:TS-1183 +xref: EHDAA2_RETIRED:0003111 +xref: EHDAA:2331 +xref: EHDAA:2349 +xref: EHDAA:295 +xref: EHDAA:6073 +xref: EHDAA:640 +xref: EHDAA:646 +xref: EMAPA:32856 +xref: FMA:14074 +xref: MA:0000565 +xref: NCIT:C33105 +xref: SCTID:361918002 +xref: UMLS:C0086610 +xref: Wikipedia:Mesothelium +is_a: UBERON:0000487 ! simple squamous epithelium +is_a: UBERON:0012275 ! meso-epithelium +relationship: BFO:0000050 UBERON:0000042 ! part of serous membrane + +[Term] +id: UBERON:0001137 +name: dorsum +def: "A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.." [BSPO:0000063, UBERONREF:0000006, Wikipedia:Dorsum_(anatomy)] +subset: efo_slim +subset: uberon_slim +synonym: "back" EXACT [FMA:14181] +synonym: "back of body proper" EXACT [FMA:14181] +synonym: "dorsal part of organism" EXACT [] +xref: BTO:0001713 +xref: CALOHA:TS-2223 +xref: EFO:0001405 +xref: FMA:14181 +xref: GAID:30 +xref: galen:Back +xref: MESH:A01.176 +xref: NCIT:C13062 +xref: OpenCyc:Mx4rvVkEU5wpEbGdrcN5Y29ycA +xref: SCTID:123961009 +xref: UMLS:C0004600 +xref: Wikipedia:Dorsum_(anatomy) +is_a: UBERON:0000475 ! organism subdivision + +[Term] +id: UBERON:0001140 +name: renal vein +def: "Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava." [ISBN:0-683-40008-8, MGI:csmith, MP:0011323] +subset: pheno_slim +subset: uberon_slim +synonym: "kidney vein" EXACT [OBOL:automatic] +synonym: "renal venous tree" EXACT [] +synonym: "vein of kidney" EXACT [OBOL:automatic] +synonym: "venae renales" RELATED [Wikipedia:Renal_vein] +xref: BTO:0002681 +xref: EHDAA2:0001602 +xref: EHDAA:8722 +xref: EMAPA:28376 +xref: FMA:14334 +xref: GAID:544 +xref: galen:RenalVein +xref: MA:0002210 +xref: MESH:D012082 +xref: NCIT:C33462 +xref: OpenCyc:Mx4rvdUXKJwpEbGdrcN5Y29ycA +xref: SCTID:116358006 +xref: UMLS:C0035092 +xref: Wikipedia:Renal_vein +is_a: UBERON:0001638 ! vein + +[Term] +id: UBERON:0001224 +name: renal pelvis +def: "A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]." [MP:0004194] +subset: pheno_slim +subset: uberon_slim +synonym: "kidney pelvis" EXACT [] +synonym: "p. renallis" RELATED [Wikipedia:Renal_pelvis] +synonym: "pelvis of ureter" EXACT [] +synonym: "pyelum" RELATED [MP:0004194] +xref: CALOHA:TS-2230 +xref: EMAPA:17948 +xref: FMA:15575 +xref: GAID:426 +xref: galen:RenalPelvis +xref: MA:0000374 +xref: MESH:D007682 +xref: NCIT:C12887 +xref: SCTID:362221007 +xref: UMLS:C0227666 +xref: Wikipedia:Renal_pelvis +is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004111 ! anatomical conduit +relationship: BFO:0000050 UBERON:0002113 ! part of kidney +relationship: BFO:0000050 UBERON:0036295 ! part of renal pelvis/ureter + +[Term] +id: UBERON:0001225 +name: cortex of kidney +def: "Outer cortical portion of the kidney, between the renal capsule and the renal medulla." [Wikipedia:Renal_cortex] +subset: pheno_slim +subset: uberon_slim +synonym: "cortex renalis" EXACT [FMA:15581, FMA:TA] +synonym: "kidney cortex" EXACT [] +synonym: "renal cortex" EXACT [] +xref: BTO:0001166 +xref: CALOHA:TS-0503 +xref: EMAPA:17952 +xref: FMA:15581 +xref: GAID:424 +xref: galen:CortexOfKidney +xref: MA:0000372 +xref: MESH:D007672 +xref: NCIT:C12739 +xref: SCTID:362211004 +xref: UMLS:C0022655 +xref: Wikipedia:Renal_cortex +is_a: UBERON:0001851 ! cortex +relationship: BFO:0000050 UBERON:0008987 ! part of renal parenchyma + +[Term] +id: UBERON:0001229 +name: renal corpuscle +def: "The structure containing the glomerular capsule and the glomerulus that serves as the initial blood-filtering component of a nephron." [ISBN:0-683-40008-8, MP:0002827] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "corpusculum renale" EXACT [] +synonym: "corpusculum renis" RELATED [Wikipedia:Renal_corpuscle] +synonym: "cortical renal corpuscle" RELATED [MA:0000376] +synonym: "kidney corpuscle" RELATED [Wikipedia:Renal_corpuscle] +synonym: "Malphigian corpuscle" EXACT MISSPELLING [MA:0000376] +synonym: "Malpighian corpuscle" EXACT [ZFA:0005281] +xref: BTO:0000333 +xref: CALOHA:TS-1317 +xref: EMAPA:28236 +xref: EMAPA:35726 +xref: EV:0100385 +xref: FMA:15625 +xref: MA:0000376 +xref: NCIT:C33456 +xref: SCTID:361329009 +xref: TAO:0005281 +xref: UMLS:C0227635 +xref: VHOG:0001262 +xref: Wikipedia:Renal_corpuscle +xref: ZFA:0005281 +is_a: UBERON:0000063 ! organ subunit +relationship: BFO:0000050 UBERON:0001225 ! part of cortex of kidney +relationship: BFO:0000050 UBERON:0001285 ! part of nephron + +[Term] +id: UBERON:0001230 +name: glomerular capsule +def: "A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus." [MGI:pvb, MP:0002828, Wikipedia:Bowman%27s_capsule] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "Bowman's capsule" EXACT [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] +synonym: "Bowman's capsule" RELATED [TAO:0005254] +synonym: "Bowmans capsule" EXACT [KUPO:0001001] +synonym: "capsula glomerularis" EXACT [] +synonym: "capsula glomeruli" RELATED [] +synonym: "Malphigian capsule" RELATED MISSPELLING [BTO:0002297] +synonym: "Malpighian capsule" RELATED [UBERO:cjm] +synonym: "Mueller capsule" RELATED [BTO:0002297] +synonym: "Muellerian capsule" RELATED [BTO:0002297] +synonym: "pronephric glomerular capsule" RELATED [TAO:0005310] +synonym: "renal glomerular capsule" EXACT [TAO:0005254] +xref: AAO:0010526 +xref: BTO:0002297 +xref: EMAPA:27973 +xref: EMAPA:28257 +xref: FMA:15626 +xref: KUPO:0001001 +xref: MA:0001660 +xref: NCIT:C32225 +xref: SCTID:361331000 +xref: TAO:0005254 +xref: TAO:0005310 +xref: UMLS:C0524448 +xref: Wikipedia:Bowman%27s_capsule +xref: ZFA:0005254 +xref: ZFA:0005310 +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0001229 ! part of renal corpuscle + +[Term] +id: UBERON:0001231 +name: nephron tubule +def: "An epithelial tube that is part of the nephron, the functional part of the kidney." [GO:0072078, Wikipedia:Renal_tubule] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "kidney tubule" EXACT [GAID:433] +synonym: "renal tubule" BROAD [] +synonym: "tubulus renalis" EXACT [] +synonym: "uriniferous tubule" RELATED [MA:0000377] +xref: BTO:0000343 +xref: CALOHA:TS-1262 +xref: EFO:0003666 +xref: EMAPA:27782 +xref: EV:0100387 +xref: FMA:15627 +xref: GAID:433 +xref: MA:0000377 +xref: MESH:D007684 +xref: NCIT:C49274 +xref: SCTID:361332007 +xref: TAO:0001287 +xref: UMLS:C0022674 +xref: Wikipedia:Renal_tubule +xref: ZFA:0001287 +is_a: UBERON:0004211 ! nephron epithelium +is_a: UBERON:0009773 ! renal tubule + +[Term] +id: UBERON:0001232 +name: collecting duct of renal tubule +def: "The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient." [GO:0072044, Wikipedia:Collecting_tubule] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "arcuate renal tubule" RELATED [Wikipedia:Connecting_tubule] +synonym: "collecting duct" EXACT [GO:0072044] +synonym: "collecting duct system" RELATED [BTO:0000761] +synonym: "collecting tubule" RELATED [] +synonym: "junctional tube" RELATED [Wikipedia:Connecting_tubule] +synonym: "kidney collecting duct" EXACT [] +synonym: "kidney collecting tubule" RELATED [] +synonym: "renal collecting tubule" EXACT [FMA:15628] +synonym: "tubulus renalis arcuatus" EXACT [Wikipedia:Connecting_tubule] +synonym: "tubulus renalis colligens" EXACT [] +synonym: "ureteric tree" RELATED [EMAPA:28407] +xref: BTO:0000761 +xref: CALOHA:TS-0860 +xref: EMAPA:28407 +xref: EV:0100391 +xref: FMA:15628 +xref: GAID:434 +xref: MA:0000371 +xref: MESH:D007685 +xref: SCTID:28202009 +xref: TAO:0005294 +xref: Wikipedia:Collecting_tubule +xref: ZFA:0005294 +is_a: UBERON:0006555 ! excretory tube +relationship: BFO:0000050 UBERON:0001285 ! part of nephron +relationship: BFO:0000050 UBERON:0004100 ! part of renal collecting system + +[Term] +id: UBERON:0001245 +name: anus +def: "Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts." [Wikipedia:Anus, ZFIN:curator] +subset: pheno_slim +subset: uberon_slim +synonym: "anal opening" EXACT [] +synonym: "anal orifice" EXACT [] +synonym: "opening of terminal part of digestive tract" EXACT [] +synonym: "proctodeum" RELATED [] +xref: BTO:0001680 +xref: CALOHA:TS-2005 +xref: EV:0100082 +xref: FBbt:00003148 +xref: FMA:15711 +xref: GAID:312 +xref: galen:Anus +xref: MA:0000331 +xref: MESH:A03.492.411.495.767.288 +xref: NCIT:C43362 +xref: OpenCyc:Mx4rvVjaEZwpEbGdrcN5Y29ycA +xref: SCTID:181262009 +xref: TADS:0000066 +xref: TGMA:0001279 +xref: UMLS:C0003461 +xref: WBbt:0005364 +xref: Wikipedia:Anus +is_a: UBERON:0000161 ! orifice +is_a: UBERON:0004121 ! ectoderm-derived structure +relationship: BFO:0000050 UBERON:0001555 ! part of digestive tract + +[Term] +id: UBERON:0001255 +name: urinary bladder +def: "Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]." [MGI:anna, Wikipedia:Urinary_bladder] +subset: efo_slim +subset: major_organ +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +synonym: "bladder" BROAD [EHDAA2:0000174] +synonym: "urocyst" RELATED [Wikipedia:Urinary_bladder] +synonym: "vesica" RELATED [BTO:0001418] +synonym: "vesica urinaria" EXACT [Wikipedia:Urinary_bladder] +xref: AAO:0000623 +xref: BTO:0001418 +xref: CALOHA:TS-1090 +xref: EFO:0000290 +xref: EHDAA2:0000174 +xref: EHDAA:9328 +xref: EMAPA:18321 +xref: EV:0100098 +xref: FMA:15900 +xref: GAID:0000004 +xref: galen:UrinaryBladder +xref: MA:0000380 +xref: MAT:0000122 +xref: MESH:A05.810.161 +xref: MIAA:0000122 +xref: NCIT:C12414 +xref: OpenCyc:Mx4rvVjMmZwpEbGdrcN5Y29ycA +xref: SCTID:302512001 +xref: UMLS:C0005682 +xref: VHOG:0000740 +xref: Wikipedia:Urinary_bladder +xref: XAO:0000154 +is_a: UBERON:0002075 ! viscus +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0018707 ! bladder organ +relationship: BFO:0000050 UBERON:0001556 ! part of lower urinary tract + +[Term] +id: UBERON:0001271 +name: pelvic girdle region +def: "The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions." [DOI:10.1002/dvdy.22617, FMA:16581, FMA:23217, https://groups.google.com/d/topic/obo-anatomy/h4R4xKmINrw/discussion, https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] +subset: uberon_slim +subset: vertebrate_core +synonym: "girdle - pelvic" RELATED [] +synonym: "pelvic girdle" RELATED INCONSISTENT [] +xref: EMAPA:37862 +xref: FMA:16581 +xref: NCIT:C33291 +xref: SCTID:360010001 +xref: UMLS:C0684083 +xref: VSAO:0000304 +is_a: UBERON:0007823 ! appendage girdle region +is_a: UBERON:0015212 ! lateral structure +relationship: BFO:0000050 UBERON:0002355 ! part of pelvic region of trunk +relationship: BFO:0000050 UBERON:0010709 ! part of pelvic complex + +[Term] +id: UBERON:0001285 +name: nephron +def: "The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]." [PMID:9268568, Wikipedia:Nephron] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "mature nephron" NARROW [EMAPA:28491] +synonym: "nephroneum" RELATED [Wikipedia:Nephron] +synonym: "tubulus renalis" RELATED [Wikipedia:Nephron] +xref: BTO:0000924 +xref: CALOHA:TS-1312 +xref: EMAPA:28491 +xref: EMAPA:35592 +xref: EV:0100384 +xref: FMA:17640 +xref: GAID:428 +xref: MA:0000375 +xref: MESH:D009399 +xref: NCIT:C13048 +xref: SCTID:361337001 +xref: TAO:0002153 +xref: UMLS:C0027713 +xref: Wikipedia:Nephron +xref: ZFA:0005282 +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0007684 ! part of uriniferous tubule + +[Term] +id: UBERON:0001287 +name: proximal convoluted tubule +def: "The proximal convoluted tubule is the most proximal portion of the proximal tubule and extends from the glomerular capsule to the proximal straight tubule." [GO:0072019] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "1st convoluted tubule" RELATED [] +synonym: "first convoluted tubule" RELATED [] +synonym: "kidney proximal convoluted tubule" RELATED [EMAPA:28287] +synonym: "PCT" RELATED [] +synonym: "proximal convoluted renal tubule" EXACT [] +synonym: "renal proximal convoluted tubule" RELATED [http://orcid.org/0000-0002-6601-2165] +synonym: "tubulus contortus proximalis" EXACT [] +synonym: "tubulus contortus proximalis" RELATED [Wikipedia:Proximal_convoluted_tubule] +synonym: "tubulus convolutus proximalis" RELATED [] +xref: CALOHA:TS-2198 +xref: EMAPA:28287 +xref: EV:0100388 +xref: FMA:17693 +xref: MA:0001669 +xref: NCIT:C33417 +xref: SCTID:362220008 +xref: TAO:0005290 +xref: UMLS:C1514580 +xref: Wikipedia:Proximal_convoluted_tubule +xref: ZFA:0005290 +is_a: UBERON:0006534 ! renal convoluted tubule +is_a: UBERON:0006853 ! renal cortex tubule +is_a: UBERON:0012275 ! meso-epithelium +relationship: BFO:0000050 UBERON:0004134 ! part of proximal tubule + +[Term] +id: UBERON:0001288 +name: loop of Henle +def: "The section of the renal tubule in the kidney medulla with a hairpin bend; consists of a descending limb and an ascending limb, and is situated between the proximal convoluted tubule to the distal convoluted tubule; it functions to reabsorb water and ions from the urine." [MGI:csmith, MP:0004755] +subset: pheno_slim +subset: uberon_slim +synonym: "ansa nephroni" EXACT [Wikipedia:Loop_of_Henle] +synonym: "Henle loop" EXACT [] +synonym: "Henle's loop" EXACT [] +xref: BTO:0004608 +xref: EMAPA:19280 +xref: EV:0100390 +xref: FMA:17698 +xref: GAID:437 +xref: MA:0001675 +xref: MESH:D008138 +xref: NCIT:C33006 +xref: SCTID:361335009 +xref: UMLS:C0023986 +xref: VHOG:0001270 +xref: Wikipedia:Loop_of_Henle +is_a: UBERON:0007685 ! region of nephron tubule + +[Term] +id: UBERON:0001289 +name: descending limb of loop of Henle +def: "The portion of the renal tubule that constitutes the proximal part of the loop of Henle, has low permeability to ions and urea, and is highly permeable to water; it consists of an initial short thick segment lined by low simple cuboidal epithelium and a long thin segment lined by simple squamous epithelium; however, this distinction is not as important physiologically as in the ascending limb, so often the two are treated as one structure." [MGI:anna, MP:0011341] +subset: pheno_slim +subset: uberon_slim +synonym: "descending limb" BROAD [] +synonym: "descending limb of Henle's loop" EXACT [] +synonym: "loop of Henle descending limb" EXACT [] +xref: EMAPA:35511 +xref: FMA:17705 +xref: MA:0001679 +xref: NCIT:C32456 +xref: SCTID:245350001 +xref: UMLS:C0227657 +xref: Wikipedia:Descending_limb_of_loop_of_henle +is_a: UBERON:0007685 ! region of nephron tubule +relationship: BFO:0000050 UBERON:0001288 ! part of loop of Henle + +[Term] +id: UBERON:0001290 +name: proximal straight tubule +def: "The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule." [GO:0072020] +subset: uberon_slim +subset: vertebrate_core +synonym: "pars recta" RELATED [] +synonym: "pars recta tubuli renalis" RELATED [BTO:0000055] +synonym: "proximal tubule segment 3" RELATED [MA:0002614] +synonym: "S3" EXACT [GO:0072020] +synonym: "segment 3 of proximal tubule" RELATED [EMAPA:29661] +synonym: "thick descending limb of proximal tubule" EXACT [] +synonym: "tubulus rectus proximalis" EXACT [] +xref: BTO:0000055 +xref: EMAPA:29661 +xref: EMAPA:29669 +xref: FMA:17716 +xref: MA:0002614 +xref: TAO:0005291 +xref: Wikipedia:Proximal_straight_tubule +xref: ZFA:0005291 +is_a: UBERON:0006853 ! renal cortex tubule +is_a: UBERON:0009035 ! renal straight tubule +relationship: BFO:0000050 UBERON:0001289 ! part of descending limb of loop of Henle +relationship: BFO:0000050 UBERON:0004134 ! part of proximal tubule +relationship: BFO:0000050 UBERON:0006542 ! part of outer medulla outer stripe loop of Henle + +[Term] +id: UBERON:0001291 +name: thick ascending limb of loop of Henle +def: "The distal sub-portion of the ascending loop of Henle which is lined by simple cuboidal epithelium and enters the renal cortex to empty a hypotonic filtrate into the distal convoluted tubule." [MGI:anna, MP:0011344] +subset: pheno_slim +subset: uberon_slim +synonym: "ascending thick limb" EXACT [] +synonym: "distal straight tubule" EXACT [MA:0001677] +synonym: "loop of Henle ascending limb thick segment" EXACT [MA:0001677] +synonym: "straight portion of distal convoluted renal tubule" EXACT [] +synonym: "straight portion of distal convoluted tubule" EXACT [FMA:17722] +synonym: "thick ascending limb" EXACT [] +synonym: "thick ascending limb of distal tubule" EXACT [FMA:17722] +synonym: "thick ascending limb of Henle's loop" EXACT [] +synonym: "tubulus rectus distalis" EXACT [FMA:17722] +synonym: "tubulus rectus distalis" RELATED [Wikipedia:Thick_ascending_limb_of_loop_of_Henle] +xref: EMAPA:28396 +xref: EMAPA:29671 +xref: EMAPA:35512 +xref: FMA:17722 +xref: MA:0001677 +xref: SCTID:244953001 +xref: Wikipedia:Thick_ascending_limb_of_loop_of_Henle +is_a: UBERON:0009035 ! renal straight tubule +relationship: BFO:0000050 UBERON:0005164 ! part of ascending limb of loop of Henle + +[Term] +id: UBERON:0001292 +name: distal convoluted tubule +def: "The first segment of the nephron lying just downstream from the loop of Henle, immediately after the macula densa." [GO:0072025] +subset: pheno_slim +subset: uberon_slim +synonym: "distal convoluted renal tubule" EXACT [] +synonym: "second convoluted tubule" RELATED [] +synonym: "tubulus contortus distalis" EXACT [] +synonym: "tubulus contortus distalis" RELATED [Wikipedia:Distal_convoluted_tubule] +synonym: "tubulus convolutus distalis" RELATED [] +xref: EMAPA:28393 +xref: EV:0100389 +xref: FMA:17721 +xref: MA:0001666 +xref: NCIT:C32469 +xref: SCTID:361336005 +xref: UMLS:C0022676 +xref: Wikipedia:Distal_convoluted_tubule +is_a: UBERON:0006534 ! renal convoluted tubule +is_a: UBERON:0006853 ! renal cortex tubule +is_a: UBERON:0012275 ! meso-epithelium +relationship: BFO:0000050 UBERON:0004135 ! part of distal tubule + +[Term] +id: UBERON:0001293 +name: outer medulla of kidney +def: "The renal outer medulla is the region of the kidney that lies between the renal cortex and the renal inner medulla[GO]." [DOI:10.1371/journal.pone.0099864, GOC:mtg_kidney_jan10] +subset: pheno_slim +synonym: "kidney outer medulla" RELATED [BTO:0001746] +synonym: "outer renal medulla" EXACT [] +synonym: "outer zone of medulla of kidney" EXACT [] +synonym: "outer zone of renal medulla" EXACT [] +synonym: "renal outer medulla" EXACT [BTO:0001746] +synonym: "set of outer region of renal pyramids" RELATED [FMA:17733] +synonym: "zona externa (medullaris renalis)" EXACT [FMA:17733, FMA:TA] +synonym: "zona externa medullae renalis" EXACT [FMA:17733, FMA:TA] +xref: BTO:0001746 +xref: CALOHA:TS-0508 +xref: EMAPA:28310 +xref: FMA:17733 +xref: MA:0001653 +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0000362 ! part of renal medulla + +[Term] +id: UBERON:0001294 +name: inner medulla of kidney +def: "Innermost region of the mammalian kidney." [GO:0072053] +subset: pheno_slim +synonym: "inner renal medulla" EXACT [] +synonym: "inner zone of medulla of kidney" EXACT [] +synonym: "inner zone of renal medulla" EXACT [] +synonym: "kidney inner medulla" RELATED [BTO:0001745] +synonym: "renal inner medulla" EXACT [BTO:0001745] +synonym: "set of inner region of renal pyramids" EXACT [] +synonym: "zona interna (medullaris renalis)" EXACT [FMA:17734, FMA:TA] +synonym: "zona interna medullae renalis" EXACT [FMA:17734, FMA:TA] +xref: BTO:0001745 +xref: CALOHA:TS-0506 +xref: EMAPA:28349 +xref: FMA:17734 +xref: MA:0001652 +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0000362 ! part of renal medulla + +[Term] +id: UBERON:0001353 +name: anal region +def: "The anus and surrounding regions. Encompasses both internal and external regions, where present." [https://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "posterior" RELATED [] +synonym: "posterior end of organism" RELATED [] +xref: EFO:0000847 +xref: EHDAA2:0000122 +xref: EHDAA:2931 +xref: EMAPA:16831 +xref: MA:0000329 +xref: MAT:0000042 +xref: MIAA:0000042 +xref: NCIT:C32069 +xref: SCTID:362680001 +xref: UMLS:C0230120 +xref: VHOG:0000395 +xref: WBbt:0006919 +is_a: UBERON:0000475 ! organism subdivision + +[Term] +id: UBERON:0001383 +name: muscle of leg +def: "A muscle that is part of the region of the hindlimb between the pelvis and ankle." [https://orcid.org/0000-0002-6601-2165, Wikipedia:Leg_muscle] +subset: pheno_slim +subset: uberon_slim +synonym: "leg muscle" EXACT [] +synonym: "leg muscle organ" EXACT [OBOL:automatic] +synonym: "leg skeletal muscle" EXACT [OBOL:automatic] +synonym: "leg skeletal muscle tissue" EXACT [OBOL:automatic] +synonym: "muscle of hindlimb zeugopod or stylopod" EXACT [https://orcid.org/0000-0002-6601-2165, OBOL:automatic] +synonym: "muscle of thigh or crus" EXACT [https://orcid.org/0000-0002-6601-2165, OBOL:automatic] +synonym: "muscle of upper or lower hindlimb segment" EXACT [https://orcid.org/0000-0002-6601-2165, OBOL:automatic] +synonym: "muscle of upper/lower leg" EXACT [] +synonym: "muscle organ of leg" EXACT [OBOL:automatic] +synonym: "skeletal muscle of leg" EXACT [OBOL:automatic] +xref: BTO:0000722 +xref: EHDAA:8291 +xref: EMAPA:19144 +xref: EMAPA:19318 +xref: MA:0000672 +xref: RETIRED_EHDAA2:0000974 +xref: Wikipedia:Leg_muscle +is_a: UBERON:0003663 ! hindlimb muscle +relationship: BFO:0000050 UBERON:0004466 ! part of musculature of leg + +[Term] +id: UBERON:0001419 +name: skin of limb +def: "A zone of skin that is part of a limb [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "limb skin" EXACT [] +synonym: "limb zone of skin" EXACT [OBOL:automatic] +synonym: "zone of skin of limb" EXACT [OBOL:automatic] +xref: EMAPA:32726 +xref: FMA:23100 +xref: MA:0000694 +xref: NCIT:C53276 +xref: SCTID:314403009 +xref: UMLS:C1282135 +is_a: UBERON:0000014 ! zone of skin +relationship: BFO:0000050 UBERON:0002101 ! part of limb + +[Term] +id: UBERON:0001421 +name: pectoral girdle region +def: "An organism subdivision that includes the pectoral girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions." [FMA:23217, https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "cingulum membri superioris" EXACT [FMA:23217, FMA:TA] +synonym: "cingulum membri superioris" NARROW [FMA:TA] +synonym: "girdle - pectoral" EXACT [] +synonym: "pectoral girdle" RELATED [] +synonym: "pectoral region" RELATED [] +synonym: "shoulder girdle" NARROW [FMA:23217] +synonym: "upper limb girdle" NARROW [FMA:23217] +xref: EMAPA:37856 +xref: FMA:23217 +xref: galen:ShoulderGirdle +xref: SCTID:229759004 +xref: VSAO:0000305 +is_a: UBERON:0007823 ! appendage girdle region +is_a: UBERON:0015212 ! lateral structure +relationship: BFO:0000050 UBERON:0010708 ! part of pectoral complex + +[Term] +id: UBERON:0001434 +name: skeletal system +def: "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000027] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "set of all bones and joints" NARROW SENSU [] +synonym: "skeleton system" EXACT [] +synonym: "Skelettsystem" RELATED [BTO:0001486] +xref: AAO:0000566 +xref: BTO:0001486 +xref: CALOHA:TS-1320 +xref: EFO:0000806 +xref: EHDAA2:0003168 +xref: EMAPA:35773 +xref: FMA:23881 +xref: MA:0000018 +xref: NCIT:C12788 +xref: OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA +xref: TAO:0000434 +xref: UMLS:C0037253 +xref: VHOG:0001254 +xref: VSAO:0000027 +xref: XAO:0003060 +xref: ZFA:0000434 +is_a: UBERON:0011216 ! organ system subdivision +relationship: BFO:0000050 UBERON:0002204 ! part of musculoskeletal system + +[Term] +id: UBERON:0001440 +name: forelimb skeleton +def: "The collection of all skeletal elements in a free forelimb region. Excludes the pectoral girdle." [https://orcid.org/0000-0002-6601-2165] +synonym: "bones of upper limb" EXACT [] +synonym: "fore limb skeleton" EXACT [] +synonym: "forelimb skeleton" EXACT [VHOG:0001256] +synonym: "free upper limb skeleton" EXACT [FMA:24142] +synonym: "ossa membri superioris" EXACT [FMA:24139, FMA:TA] +synonym: "pectoral limb skeleton" EXACT [] +synonym: "set of bones of upper limb" EXACT [] +synonym: "skeleton of forelimb" EXACT [] +synonym: "skeleton of free upper limb" EXACT [FMA:24142] +synonym: "skeleton of pectoral limb" EXACT [] +synonym: "skeleton of upper limb" EXACT [FMA:24139] +synonym: "upper limb skeleton" EXACT [EHDAA2:0002222] +synonym: "wing skeleton" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +xref: AAO:0000202 +xref: EHDAA2:0002222 +xref: EMAPA:32623 +xref: FMA:24142 +xref: VHOG:0001256 +xref: VSAO:0000151 +xref: XAO:0003061 +is_a: UBERON:0004381 ! skeleton of limb +is_a: UBERON:0007272 ! pectoral appendage skeleton +relationship: BFO:0000050 UBERON:0002102 ! part of forelimb +relationship: BFO:0000050 UBERON:0012475 ! part of skeleton of pectoral complex + +[Term] +id: UBERON:0001441 +name: hindlimb skeleton +def: "Subdivision of skeleton consisting of all skeletal elements in an hindlimb region." [https://orcid.org/0000-0002-6601-2165] +subset: uberon_slim +synonym: "bones of lower limb" EXACT [] +synonym: "free lower limb skeleton" EXACT [FMA:24144] +synonym: "hind limb skeleton" EXACT [XAO:0003062] +synonym: "hind-limb skeleton" EXACT [VSAO:0000152] +synonym: "hindlimb skeleton" EXACT [VHOG:0001255] +synonym: "lower limb skeleton" EXACT [] +synonym: "ossa membri inferioris" EXACT [FMA:24140, FMA:TA] +synonym: "set of bones of lower limb" EXACT [] +synonym: "skeleton of free lower limb" EXACT [FMA:24144] +synonym: "skeleton of lower limb" EXACT [FMA:24140] +xref: AAO:0000217 +xref: EHDAA2:0002226 +xref: EMAPA:32633 +xref: FMA:24144 +xref: OpenCyc:Mx4rvZcKkZwpEbGdrcN5Y29ycA +xref: VHOG:0001255 +xref: VSAO:0000152 +xref: XAO:0003062 +is_a: UBERON:0004381 ! skeleton of limb +is_a: UBERON:0007273 ! pelvic appendage skeleton +relationship: BFO:0000050 UBERON:0002103 ! part of hindlimb +relationship: BFO:0000050 UBERON:0012476 ! part of skeleton of pelvic complex + +[Term] +id: UBERON:0001442 +name: skeleton of manus +def: "Subdivision of skeleton that is the collection of all skeletal elements in a manus, which is the distal section of the anterior forelimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the wrist, palm, and fingers)[Phenoscape]." [https://github.com/obophenotype/uberon/issues/74, https://orcid.org/0000-0002-6601-2165, PHENOSCAPE:MAH] +subset: pheno_slim +synonym: "anterior autopodium" RELATED [VSAO:0005020, VSAO:NI] +synonym: "anterior autopodium skeleton" EXACT [] +synonym: "bones of hand" EXACT [FMA:24159] +synonym: "fore autopod skeleton" EXACT [] +synonym: "forelimb autopod skeleton" EXACT [] +synonym: "hand region skeleton" EXACT [EHDAA2:0002227] +synonym: "hand skeleton" EXACT [FMA:24159] +synonym: "manual skeleton" EXACT [] +synonym: "manus" RELATED [VSAO:0005020, VSAO:NI] +synonym: "manus skeleton" EXACT [] +synonym: "ossa manus" EXACT [FMA:24159, FMA:TA] +synonym: "set of bones of hand" EXACT [FMA:24159] +synonym: "skeleton of hand" EXACT [FMA:24159] +xref: EHDAA2:0002227 +xref: EMAPA:32643 +xref: FMA:24159 +xref: OpenCyc:Mx4rvdHPJJwpEbGdrcN5Y29ycA +xref: VSAO:0005020 +is_a: UBERON:0006717 ! autopodial skeleton +relationship: BFO:0000050 UBERON:0001440 ! part of forelimb skeleton +relationship: BFO:0000050 UBERON:0002398 ! part of manus + +[Term] +id: UBERON:0001444 +name: subdivision of head +subset: non_informative +synonym: "head region" RELATED [] +synonym: "head subdivision" EXACT [] +synonym: "region of head" RELATED [] +xref: FMA:24218 +xref: SCTID:123852005 +xref: XAO:0000040 +is_a: UBERON:0000475 ! organism subdivision +relationship: BFO:0000050 UBERON:0000033 ! part of head + +[Term] +id: UBERON:0001445 +name: skeleton of pes +def: "Subdivision of skeleton that is the collection of all skeletal elements in a pes, which is the distal section of the posterior hindlimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the ankle, sole, and toes)[Phenoscape]." [https://github.com/obophenotype/uberon/issues/75, https://orcid.org/0000-0002-6601-2165, PHENOSCAPE:MAH] +subset: pheno_slim +synonym: "foot region skeleton" EXACT [EHDAA2:0002228] +synonym: "foot skeleton" EXACT [FMA:24222] +synonym: "pedal skeleton" EXACT [] +synonym: "pes" RELATED INCONSISTENT [VSAO:0005021, VSAO:NI] +synonym: "pes skeleton" EXACT [] +synonym: "posterior autopodium" RELATED [VSAO:0005021, VSAO:NI] +synonym: "posterior autopodium skeleton" EXACT [] +synonym: "set of bones of foot" EXACT [FMA:24222] +synonym: "skeleton of foot" EXACT [FMA:24222] +xref: EHDAA2:0002228 +xref: FMA:24222 +xref: VSAO:0005021 +is_a: UBERON:0006717 ! autopodial skeleton +relationship: BFO:0000050 UBERON:0001441 ! part of hindlimb skeleton +relationship: BFO:0000050 UBERON:0002387 ! part of pes + +[Term] +id: UBERON:0001456 +name: face +def: "A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc)." [http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +subset: uberon_slim +synonym: "facia/facies" RELATED [Wikipedia:Face] +synonym: "visage" RELATED [BTO:0003369] +xref: BTO:0003369 +xref: CALOHA:TS-2216 +xref: EMAPA:32763 +xref: FMA:24728 +xref: GAID:64 +xref: galen:Face +xref: HAO:0000316 +xref: MA:0002473 +xref: MESH:D005145 +xref: NCIT:C13071 +xref: OpenCyc:Mx4rvVi5GZwpEbGdrcN5Y29ycA +xref: SCTID:302549007 +xref: UMLS:C0015450 +xref: Wikipedia:Face +is_a: UBERON:0001444 ! subdivision of head + +[Term] +id: UBERON:0001460 +name: arm +def: "The part of the forelimb extending from the shoulder to the autopod[cjm]." [Wikipedia:Arm] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "brachium" RELATED [Wikipedia:Arm] +synonym: "upper extremity" RELATED [MESH:A01.378.800] +xref: BTO:0001435 +xref: CALOHA:TS-2204 +xref: EFO:0001410 +xref: EHDAA2:0000140 +xref: EHDAA:4164 +xref: EHDAA:6210 +xref: EHDAA:8275 +xref: EMAPA:17413 +xref: GAID:52 +xref: MA:0000033 +xref: MESH:A01.378.800 +xref: MESH:D001132 +xref: OpenCyc:Mx4rvVjp5ZwpEbGdrcN5Y29ycA +xref: VHOG:0000339 +xref: Wikipedia:Arm +is_a: UBERON:0006058 ! multi-limb segment region +is_a: UBERON:0008785 ! upper limb segment + +[Term] +id: UBERON:0001464 +name: hip +def: "The hip region is located lateral to the gluteal region (i.e. the buttock), inferior to the iliac crest, and overlying the greater trochanter of the thigh bone. In adults, three of the bones of the pelvis have fused into the hip bone which forms part of the hip region. The hip joint, scientifically referred to as the acetabulofemoral joint (art. coxae), is the joint between the femur and acetabulum of the pelvis and its primary function is to support the weight of the body in both static (e.g. standing) and dynamic (e.g. walking or running) postures. [WP,modified]." [Wikipedia:Hip] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "coxa" RELATED [Wikipedia:Hip] +synonym: "hip region" EXACT [FMA:24964] +synonym: "regio coxae" EXACT [FMA:24964] +xref: BTO:0001457 +xref: CALOHA:TS-2226 +xref: EFO:0001929 +xref: EHDAA2:0000783 +xref: EHDAA:5153 +xref: EHDAA:6178 +xref: EMAPA:17490 +xref: FMA:24964 +xref: GAID:47 +xref: galen:Hip +xref: MA:0000045 +xref: MESH:D006615 +xref: NCIT:C64193 +xref: OpenCyc:Mx4rvVjhy5wpEbGdrcN5Y29ycA +xref: SCTID:302543008 +xref: UMLS:C0019552 +xref: VHOG:0000346 +xref: Wikipedia:Hip +is_a: UBERON:0000475 ! organism subdivision +relationship: BFO:0000050 UBERON:0010709 ! part of pelvic complex + +[Term] +id: UBERON:0001467 +name: shoulder +def: "A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle)." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "articulatio humeri" RELATED [Wikipedia:Shoulder] +synonym: "shoulder region" EXACT [] +xref: CALOHA:TS-2229 +xref: EFO:0003068 +xref: EHDAA2:0001834 +xref: EHDAA:4180 +xref: EHDAA:6228 +xref: EMAPA:17421 +xref: FMA:25202 +xref: GAID:60 +xref: galen:Shoulder +xref: MA:0000038 +xref: MESH:D012782 +xref: NCIT:C25203 +xref: OpenCyc:Mx4rvViCM5wpEbGdrcN5Y29ycA +xref: SCTID:361103004 +xref: UMLS:C0037004 +xref: VHOG:0000342 +xref: Wikipedia:Shoulder +is_a: UBERON:0000475 ! organism subdivision +relationship: BFO:0000050 UBERON:0010708 ! part of pectoral complex + +[Term] +id: UBERON:0001470 +name: glenohumeral joint +def: "The glenohumeral joint, commonly known as the shoulder joint, is a multiaxial synovial ball and socket joint and involves articulation between the glenoid fossa of the scapula (shoulder blade) and the head of the humerus (upper arm bone). [WP,unvetted]." [Wikipedia:Glenohumeral_joint] +subset: uberon_slim +synonym: "articulatio humeri" EXACT [FMA:25912, FMA:TA] +synonym: "humeral joint" EXACT [FMA:25912] +synonym: "humeroscapular joint" RELATED [Wikipedia:Glenohumeral_joint] +synonym: "joint of shoulder" BROAD [OBOL:automatic] +synonym: "shoulder joint" BROAD [MA:0000459] +xref: EMAPA:19105 +xref: FMA:25912 +xref: GAID:269 +xref: galen:ShoulderJoint +xref: MA:0000459 +xref: MESH:D012785 +xref: NCIT:C33548 +xref: OpenCyc:Mx4rwP32BZwpEbGdrcN5Y29ycA +xref: SCTID:182168000 +xref: UMLS:C0037009 +xref: VHOG:0001002 +xref: Wikipedia:Glenohumeral_joint +is_a: UBERON:0011108 ! synovial joint of pectoral girdle +is_a: UBERON:0011139 ! synovial limb joint +is_a: UBERON:0016884 ! shoulder joint +relationship: BFO:0000050 UBERON:0004753 ! part of scapulocoracoid + +[Term] +id: UBERON:0001473 +name: lymphatic vessel +def: "A vessel that contains or conveys lymph, that originates as an interfibrillar or intercellular cleft or space in a tissue or organ, and that if small has no distinct walls or walls composed only of endothelial cells and if large resembles a vein in structure[BTO]." [BTO:0000752, Wikipedia:Lymphatic_vessel] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "lymph vessel" EXACT [] +synonym: "vas lymphaticum" RELATED [Wikipedia:Lymphatic_vessel] +xref: AAO:0011005 +xref: BTO:0000752 +xref: CALOHA:TS-2102 +xref: EFO:0000873 +xref: EMAPA:35532 +xref: FMA:30315 +xref: MA:0000138 +xref: MAT:0000443 +xref: NCIT:C33038 +xref: OpenCyc:Mx4rwA1fYZwpEbGdrcN5Y29ycA +xref: SCTID:279089004 +xref: TAO:0005105 +xref: UMLS:C0229889 +xref: VHOG:0001249 +xref: Wikipedia:Lymphatic_vessel +xref: XAO:0000375 +is_a: UBERON:0000055 ! vessel +relationship: BFO:0000050 UBERON:0004536 ! part of lymph vasculature + +[Term] +id: UBERON:0001474 +name: bone element +def: "Skeletal element that is composed of bone tissue." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, https://github.com/obophenotype/uberon/issues/277, PSPUB:0000170, VSAO:0000057] +subset: efo_slim +subset: major_organ +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "bone" RELATED [AEO:0000082, BTO:0000140, MA:0001459, VHOG:0001190] +synonym: "bone organ" EXACT [FMA:5018] +synonym: "bones" RELATED [ZFA:0001514] +xref: AAO:0000047 +xref: AEO:0000082 +xref: BTO:0000140 +xref: CALOHA:TS-0088 +xref: EFO:0000298 +xref: EHDAA2:0003082 +xref: EMAPA:32782 +xref: ENVO:00002039 +xref: EV:0100140 +xref: FMA:30317 +xref: FMA:5018 +xref: GAID:92 +xref: galen:Bone +xref: MA:0001459 +xref: MAT:0000299 +xref: MIAA:0000299 +xref: NCIT:C12366 +xref: OpenCyc:Mx4rvViDlpwpEbGdrcN5Y29ycA +xref: OpenCyc:Mx4rvVkCG5wpEbGdrcN5Y29ycA +xref: SCTID:90780006 +xref: TAO:0001514 +xref: UMLS:C0262950 +xref: VHOG:0001190 +xref: VSAO:0000057 +xref: Wikipedia:Bone +xref: XAO:0000169 +xref: ZFA:0001514 +is_a: UBERON:0004765 ! skeletal element + +[Term] +id: UBERON:0001484 +name: articular capsule +def: "An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]." [Wikipedia:Articular_capsule] +subset: organ_slim +subset: uberon_slim +synonym: "capsula articularis" EXACT [FMA:34836, FMA:TA] +synonym: "capsulae articulares" RELATED [Wikipedia:Articular_capsule] +synonym: "fibrous capsule of joint" EXACT [] +synonym: "joint capsule" EXACT [] +synonym: "joint fibrous capsule" EXACT [] +xref: EMAPA:37621 +xref: FMA:34836 +xref: GAID:263 +xref: galen:JointCapsule +xref: MA:0001519 +xref: MESH:D017746 +xref: NCIT:C32259 +xref: NCIT:C84388 +xref: SCTID:182238002 +xref: UMLS:C0206207 +xref: Wikipedia:Articular_capsule +is_a: UBERON:0000094 ! membrane organ + +[Term] +id: UBERON:0001499 +name: muscle of arm +def: "A muscle organ that is part of an arm [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "arm muscle" EXACT [MA:0000594] +synonym: "arm muscle system" RELATED [EHDAA2:0000141] +synonym: "arm skeletal muscle" EXACT [OBOL:automatic] +synonym: "arm skeletal muscle tissue" EXACT [OBOL:automatic] +synonym: "muscle of upper arm or lower arm" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "upper arm / lower arm muscle" EXACT [https://orcid.org/0000-0002-6601-2165] +xref: EHDAA:8277 +xref: EMAPA:36053 +xref: MA:0000594 +xref: RETIRED_EHDAA2:0000142 +is_a: UBERON:0003662 ! forelimb muscle +relationship: BFO:0000050 UBERON:0004474 ! part of musculature of arm + +[Term] +id: UBERON:0001555 +name: digestive tract +def: "A tube extending from the mouth to the anus." [https://github.com/geneontology/go-ontology/issues/7549, Wikipedia:Talk\:Human_gastrointestinal_tract] +subset: uberon_slim +subset: vertebrate_core +synonym: "alimentary canal" NARROW [] +synonym: "alimentary tract" NARROW [] +synonym: "digestive canal" RELATED [BTO:0000058] +synonym: "digestive tube" EXACT [] +synonym: "enteric tract" EXACT [ZFA:0000112] +synonym: "gut" BROAD [] +synonym: "gut tube" RELATED [] +xref: AAO:0010023 +xref: BILA:0000083 +xref: BTO:0000511 +xref: BTO:0000545 +xref: EHDAA2:0000726 +xref: EHDAA:518 +xref: EMAPA:16247 +xref: FBbt:00003125 +xref: FMA:45615 +xref: galen:AlimentaryTract +xref: MA:0000917 +xref: NCIT:C34082 +xref: OpenCyc:Mx4rvVi0GpwpEbGdrcN5Y29ycA +xref: TAO:0000112 +xref: TGMA:0001819 +xref: UMLS:C0017189 +xref: VHOG:0000309 +xref: WBbt:0005743 +xref: ZFA:0000112 +is_a: UBERON:0000025 ! tube +relationship: BFO:0000050 UBERON:0001007 ! part of digestive system + +[Term] +id: UBERON:0001556 +name: lower urinary tract +def: "Subdivision of urinary system which consists of the urinary bladder and the urethra." [FMA:45659] +subset: pheno_slim +subset: uberon_slim +xref: FMA:45659 +xref: galen:LowerUrinaryTract +xref: MA:0002636 +xref: SCTID:181420004 +is_a: UBERON:0000477 ! anatomical cluster +relationship: BFO:0000050 UBERON:0001008 ! part of renal system + +[Term] +id: UBERON:0001630 +name: muscle organ +def: "Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]." [GO:0007517] +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "muscle" BROAD [ZFA:0005145] +xref: AAO:0011066 +xref: EMAPA:32715 +xref: EMAPA:37474 +xref: EV:0100146 +xref: FMA:5022 +xref: GAID:131 +xref: galen:Muscle +xref: MA:0000015 +xref: OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA +xref: SCTID:71616004 +xref: TAO:0005145 +xref: VHOG:0001245 +xref: XAO:0000172 +xref: ZFA:0005145 +is_a: UBERON:0000062 ! organ +is_a: UBERON:0005090 ! muscle structure +relationship: BFO:0000050 UBERON:0001015 ! part of musculature + +[Term] +id: UBERON:0001637 +name: artery +def: "An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]." [AEO:JB] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "arterial subtree" EXACT [] +synonym: "arterial system" RELATED [] +synonym: "arterial tree organ part" EXACT [] +synonym: "arterial vessel" RELATED [] +synonym: "arteries" EXACT [TAO:0000005] +xref: AAO:0010211 +xref: AEO:0000208 +xref: BTO:0000573 +xref: CALOHA:TS-0054 +xref: EFO:0000814 +xref: EHDAA2:0000143 +xref: EHDAA2:0003253 +xref: EMAPA:35147 +xref: EV:0100026 +xref: FMA:50720 +xref: GAID:468 +xref: galen:Artery +xref: MA:0000064 +xref: MAT:0000034 +xref: MESH:D001158 +xref: MIAA:0000034 +xref: NCIT:C12372 +xref: OpenCyc:Mx4rvVjknZwpEbGdrcN5Y29ycA +xref: SCTID:362877004 +xref: TAO:0000005 +xref: UMLS:C0003842 +xref: VHOG:0001251 +xref: Wikipedia:Artery +xref: XAO:0000114 +xref: ZFA:0000005 +is_a: UBERON:0003509 ! arterial blood vessel + +[Term] +id: UBERON:0001638 +name: vein +def: "Any of the tubular branching vessels that carry blood from the capillaries toward the heart." [Wikipedia:Vein] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "vascular element" RELATED [EMAPA:th] +synonym: "vena" RELATED [Wikipedia:Vein] +synonym: "venae" RELATED [VHOG:0001743] +synonym: "venous subtree" BROAD [] +synonym: "venous tree organ part" EXACT [] +synonym: "venous vessel" BROAD [] +xref: AAO:0010212 +xref: AEO:0000209 +xref: BTO:0000234 +xref: CALOHA:TS-1108 +xref: EFO:0000816 +xref: EHDAA2:0003254 +xref: EMAPA:35906 +xref: EV:0100031 +xref: FMA:50723 +xref: GAID:492 +xref: galen:Vein +xref: MA:0000067 +xref: MAT:0000037 +xref: MESH:D014680 +xref: MIAA:0000037 +xref: NCIT:C12814 +xref: OpenCyc:Mx4rvVjkWpwpEbGdrcN5Y29ycA +xref: SCTID:181367001 +xref: TAO:0000082 +xref: UMLS:C0042449 +xref: VHOG:0001743 +xref: Wikipedia:Vein +xref: XAO:0000115 +xref: ZFA:0000082 +is_a: UBERON:0003920 ! venous blood vessel + +[Term] +id: UBERON:0001678 +name: temporal bone +def: "The large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous." [ISBN:0-683-40008-8, MP:0005272] +subset: pheno_slim +subset: uberon_slim +synonym: "os temporale" RELATED [Wikipedia:Temporal_bone] +xref: EHDAA:6035 +xref: EMAPA:17682 +xref: FMA:52737 +xref: GAID:232 +xref: MA:0001476 +xref: MESH:D013701 +xref: NCIT:C12797 +xref: OpenCyc:Mx4rvbkAk5wpEbGdrcN5Y29ycA +xref: SCTID:181795004 +xref: UMLS:C0039484 +xref: VHOG:0000800 +xref: Wikipedia:Temporal_bone +is_a: UBERON:0008193 ! pneumatized bone + +[Term] +id: UBERON:0001690 +name: ear +def: "Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals." [GO:0042471, Wikipedia:Ear] +subset: efo_slim +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +synonym: "auditory apparatus" RELATED [] +synonym: "auris" RELATED [BTO:0000368] +xref: AAO:0011014 +xref: BIRNLEX:1062 +xref: BTO:0000368 +xref: CALOHA:TS-1165 +xref: EFO:0000826 +xref: EHDAA2:0000423 +xref: EHDAA:502 +xref: EMAPA:16193 +xref: EV:0100353 +xref: FMA:52780 +xref: GAID:62 +xref: galen:Ear +xref: MA:0000236 +xref: MAT:0000138 +xref: MESH:D004423 +xref: MIAA:0000138 +xref: NCIT:C12394 +xref: OpenCyc:Mx4rvViXS5wpEbGdrcN5Y29ycA +xref: OpenCyc:Mx4rvVjL05wpEbGdrcN5Y29ycA +xref: SCTID:1910005 +xref: UMLS:C0013443 +xref: UMLS:C0521421 +xref: VHOG:0000330 +xref: Wikipedia:Ear +xref: XAO:0000189 +is_a: UBERON:0000020 ! sense organ +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: BFO:0000050 UBERON:0000033 ! part of head +relationship: BFO:0000050 UBERON:0002105 ! part of vestibulo-auditory system + +[Term] +id: UBERON:0001694 +name: petrous part of temporal bone +def: "The petrous portion of the temporal bone or pyramid is pyramidal and is wedged in at the base of the skull between the sphenoid and occipital bones. Directed medially, forward, and a little upward, it presents for examination a base, an apex, three surfaces, and three angles, and contains, in its interior, the essential parts of the organ of hearing. The petrous portion is among the most basal elements of the skull and forms part of the endocranium.[WP,unvetted]." [Wikipedia:Petrous_part_of_the_temporal_bone] +subset: uberon_slim +synonym: "pars petrosa (os temporale)" EXACT [FMA:52871] +synonym: "pars petrosa ossis temporalis" EXACT [] +synonym: "petromastoid part of temporal bone" EXACT [FMA:52871] +synonym: "petrosal" BROAD [VHOG:0001553] +synonym: "petrosal bone" RELATED [FMA:52871] +synonym: "petrous bone" RELATED [FMA:52871] +synonym: "temporal bone petrous part" EXACT [] +xref: EHDAA2:0001452 +xref: EMAPA:17683 +xref: FMA:52871 +xref: GAID:234 +xref: MA:0001477 +xref: MESH:D010579 +xref: NCIT:C32316 +xref: SCTID:361733004 +xref: UMLS:C1261761 +xref: VHOG:0001553 +xref: Wikipedia:Petrous_part_of_the_temporal_bone +is_a: UBERON:0005913 ! zone of bone organ +relationship: BFO:0000050 UBERON:0001678 ! part of temporal bone +relationship: BFO:0000050 UBERON:0002517 ! part of basicranium + +[Term] +id: UBERON:0001703 +name: neurocranium +def: "Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof." [PMID:11523816, TAO:MAH, Wikipedia:Neuroranium, ZFA:0001580] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "brain box" EXACT [] +synonym: "brain case" RELATED [ZFA:0001580] +synonym: "brain pan" RELATED [http://www.thefreedictionary.com/braincase] +synonym: "braincase" RELATED [ZFA:0001580] +xref: AAO:0010153 +xref: EHDAA2:0000243 +xref: EMAPA:17681 +xref: FMA:53672 +xref: MA:0000317 +xref: SCTID:361731002 +xref: TAO:0001580 +xref: Wikipedia:Neuroranium +xref: XAO:0003170 +xref: ZFA:0001580 +is_a: UBERON:0011158 ! primary subdivision of skull +relationship: BFO:0000050 UBERON:0003128 ! part of cranium + +[Term] +id: UBERON:0001708 +name: jaw skeleton +def: "Subdivision of skeleton which includes upper and lower jaw skeletons." [https://orcid.org/0000-0002-6601-2165, Wikipedia:Jaw] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "anterior splanchnocranium" RELATED [] +synonym: "jaw" EXACT [MA:0001905] +synonym: "jaw cartilage" EXACT [ZFA:0001227] +synonym: "jaws" RELATED [] +synonym: "mandibular arch" RELATED [TAO:0001227] +synonym: "mandibular arch skeleton" EXACT [ZFA:0001227] +synonym: "oral jaw skeleton" RELATED [] +synonym: "pharyngeal arch 1 skeleton" RELATED [] +synonym: "visceral arch 1" RELATED [] +xref: AAO:0000988 +xref: BTO:0001749 +xref: EMAPA:35455 +xref: FMA:54396 +xref: GAID:214 +xref: galen:Jaw +xref: MA:0001905 +xref: MESH:D007568 +xref: NCIT:C48821 +xref: OpenCyc:Mx4rvVjjEZwpEbGdrcN5Y29ycA +xref: SCTID:181811001 +xref: TAO:0001227 +xref: UMLS:C0022359 +xref: Wikipedia:Jaw +xref: ZFA:0001227 +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: UBERON:0010912 ! subdivision of skeleton +relationship: BFO:0000050 UBERON:0011156 ! part of facial skeleton +relationship: BFO:0000050 UBERON:0011595 ! part of jaw region + +[Term] +id: UBERON:0001710 +name: lower jaw region +def: "Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]." [Wikipedia:Lower_jaw] +subset: efo_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "lower part of mouth" RELATED [] +synonym: "mandibular part of mouth" EXACT [FMA:59398] +synonym: "mandibular series" RELATED [] +xref: AAO:0000272 +xref: EFO:0003660 +xref: EHDAA2:0001018 +xref: EHDAA:7995 +xref: EMAPA:17906 +xref: FMA:59398 +xref: MESH:D008334 +xref: ncithesaurus:Lower_Jaw +xref: SCTID:362637005 +xref: VHOG:0000453 +xref: Wikipedia:Lower_jaw +is_a: UBERON:0000475 ! organism subdivision +relationship: BFO:0000050 UBERON:0011595 ! part of jaw region + +[Term] +id: UBERON:0001714 +name: cranial ganglion +def: "The groups of nerve cell bodies associated with the twelve cranial nerves." [ISBN:0-683-40008-8, MGI:csmith, MP:0001081, PMID:9362461] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "cranial ganglia" RELATED [] +synonym: "cranial ganglion" EXACT [] +synonym: "cranial ganglion part of peripheral nervous system" EXACT [BIRNLEX:2597] +synonym: "cranial ganglion/nerve" EXACT [] +synonym: "cranial nerve ganglion" EXACT [] +synonym: "cranial neural ganglion" EXACT [] +synonym: "cranial neural tree organ ganglion" EXACT [OBOL:automatic] +synonym: "ganglion of cranial nerve" EXACT [FMA:54502] +synonym: "ganglion of cranial neural tree organ" EXACT [OBOL:automatic] +synonym: "head ganglion" RELATED [] +synonym: "presumptive cranial ganglia" RELATED [ZFA:0000013] +xref: BIRNLEX:2597 +xref: BTO:0000106 +xref: EFO:0000902 +xref: EMAPA:16659 +xref: FMA:54502 +xref: MA:0000213 +xref: MA:0000214 +xref: MAT:0000200 +xref: MIAA:0000200 +xref: SCTID:244448001 +xref: TAO:0000013 +xref: VHOG:0000076 +xref: Wikipedia:Cranial_nerve_ganglion +xref: XAO:0000027 +xref: ZFA:0000013 +is_a: UBERON:0000045 ! ganglion +relationship: BFO:0000050 UBERON:0000033 ! part of head + +[Term] +id: UBERON:0001744 +name: lymphoid tissue +def: "Portion of connective tissue with various types of white blood cells enmeshed in it, most numerous being the lymphocytes[WP]." [Wikipedia:Lymphoid_tissue] +subset: pheno_slim +subset: uberon_slim +synonym: "lymphatic tissue" EXACT [] +synonym: "lymphocytic tissue" EXACT [] +xref: BTO:0000753 +xref: CALOHA:TS-0584 +xref: FMA:55220 +xref: GAID:342 +xref: galen:LymphoidTissue +xref: MA:0002436 +xref: MESH:D008221 +xref: NCIT:C13049 +xref: SCTID:181768009 +xref: UMLS:C0024296 +xref: Wikipedia:Lymphoid_tissue +is_a: UBERON:0034769 ! lymphomyeloid tissue +relationship: BFO:0000050 UBERON:0002465 ! part of lymphoid system + +[Term] +id: UBERON:0001780 +name: spinal nerve +def: "The any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified]." [MESH:A08.800.800.720, MP:0001077] +subset: pheno_slim +subset: uberon_slim +synonym: "backbone nerve" EXACT [OBOL:automatic] +synonym: "nerve of backbone" EXACT [OBOL:automatic] +synonym: "nerve of spinal column" EXACT [OBOL:automatic] +synonym: "nerve of spine" EXACT [OBOL:automatic] +synonym: "nerve of vertebral column" EXACT [OBOL:automatic] +synonym: "nervi spinales" RELATED [Wikipedia:Spinal_nerve] +synonym: "spinal column nerve" EXACT [OBOL:automatic] +synonym: "spinal nerve tree" EXACT [] +synonym: "spinal nerves" RELATED [BAMS:spin] +synonym: "spine nerve" EXACT [OBOL:automatic] +synonym: "vertebral column nerve" EXACT [OBOL:automatic] +xref: AAO:0011101 +xref: BAMS:spin +xref: BTO:0000870 +xref: EHDAA2:0001898 +xref: EMAPA:16989 +xref: FMA:5858 +xref: GAID:841 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1228 +xref: MA:0000233 +xref: MESH:D013127 +xref: NCIT:C12792 +xref: OpenCyc:Mx4rwK_iFJwpEbGdrcN5Y29ycA +xref: SCTID:361099009 +xref: UMLS:C0037941 +xref: VHOG:0000824 +xref: Wikipedia:Spinal_nerve +xref: XAO:0003101 +is_a: UBERON:0001021 ! nerve + +[Term] +id: UBERON:0001785 +name: cranial nerve +def: "Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord." [Wikipedia:Cranial_nerve] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "cranial nerves" RELATED [] +synonym: "cranial neural tree organ" EXACT [] +synonym: "nervus cranialis" RELATED [Wikipedia:Cranial_nerve] +xref: AAO:0000108 +xref: BAMS:cran +xref: BIRNLEX:1623 +xref: BTO:0001104 +xref: EHDAA2:0000323 +xref: EMAPA:17264 +xref: FMA:5865 +xref: GAID:802 +xref: HBA:9299 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1227 +xref: MA:0000215 +xref: MBA:967 +xref: MESH:D003391 +xref: NCIT:C12700 +xref: OpenCyc:Mx4rvWvJVpwpEbGdrcN5Y29ycA +xref: SCTID:244447006 +xref: TAO:0000641 +xref: UMLS:C0010268 +xref: UMLS:C1269897 +xref: VHOG:0000279 +xref: Wikipedia:Cranial_nerve +xref: XAO:0000429 +xref: XAO:0003089 +xref: ZFA:0000641 +is_a: UBERON:0011779 ! nerve of head region +is_a: UBERON:0034713 ! cranial neuron projection bundle + +[Term] +id: UBERON:0001821 +name: sebaceous gland +def: "A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP]." [MP:0000647, Wikipedia:Sebaceous_gland] +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +synonym: "glandula sebacea" RELATED [Wikipedia:Sebaceous_gland] +synonym: "glandula sebaceae" RELATED [BTO:0001980] +synonym: "sebaceous follicle" RELATED [BTO:0001980] +xref: BTO:0001980 +xref: CALOHA:TS-2384 +xref: EMAPA:35754 +xref: EV:0100161 +xref: FMA:59160 +xref: GAID:900 +xref: MA:0002565 +xref: MESH:D012627 +xref: NCIT:C33519 +xref: SCTID:361697005 +xref: UMLS:C0036505 +xref: VHOG:0001468 +xref: Wikipedia:Sebaceous_gland +is_a: UBERON:0007771 ! epidermis gland +is_a: UBERON:0012344 ! holocrine gland +is_a: UBERON:0019319 ! exocrine gland of integumental system +relationship: BFO:0000050 UBERON:0011932 ! part of pilosebaceous unit + +[Term] +id: UBERON:0001839 +name: bony labyrinth +def: "A system of fluid passages in the inner ear, including both the cochlea, which is part of the auditory system, and the vestibular system, which provides the sense of balance. The bony labyrinth, or osseous labyrinth, is the network of passages with bony walls lined with periosteum. The bony labyrinth is lined with the membranous labyrinth. There is a layer of perilymph between them. The three parts of the bony labyrinth are the vestibule of the ear, the semicircular canals, and the cochlea. The vestibular system is the region of the inner ear where the semicircular canals converge, close to the cochlea (the hearing organ). The vestibular system works with the visual system to keep objects in focus when the head is moving. Joint and muscle receptors also are important in maintaining balance. The brain receives, interprets, and processes the information from these systems that control our balance. [WP,unvetted]." [Wikipedia:Bony_labyrinth] +subset: pheno_slim +subset: uberon_slim +synonym: "labyrinthus osseus" RELATED [Wikipedia:Bony_labyrinth] +synonym: "osseous labyrinth" EXACT [] +synonym: "osseus labyrinth" RELATED [] +xref: AAO:0011078 +xref: BTO:0004685 +xref: CALOHA:TS-2080 +xref: EMAPA:36580 +xref: EV:0100362 +xref: FMA:60179 +xref: MA:0000238 +xref: NCIT:C33227 +xref: SCTID:279727008 +xref: UMLS:C0458699 +xref: VHOG:0001219 +xref: Wikipedia:Bony_labyrinth +xref: XAO:0000193 +is_a: UBERON:0034921 ! multi organ part structure +relationship: BFO:0000050 UBERON:0001694 ! part of petrous part of temporal bone +relationship: BFO:0000050 UBERON:0001846 ! part of internal ear +relationship: BFO:0000050 UBERON:0004681 ! part of vestibular system + +[Term] +id: UBERON:0001844 +name: cochlea +def: "The spiral-shaped bony canal in the inner ear containing the hair cells that transduce sound. Its core component is the Organ of Corti, the sensory organ of hearing, which is distributed along the partition separating fluid chambers in the coiled tapered tube of the cochlea. [WP,modified]." [ISBN:0-683-40008-8, MP:0000031, Wikipedia:Cochlea] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "cochleae" RELATED [] +synonym: "cochlear duct" RELATED [] +synonym: "cochlear organ" RELATED [BTO:0000267] +synonym: "cochlear part of bony labyrinth" EXACT [] +synonym: "lagena" EXACT SENSU [XAO:0000197] +synonym: "lagenas" RELATED [ZFA:0000374] +xref: AAO:0000253 +xref: BIRNLEX:1190 +xref: BTO:0000267 +xref: CALOHA:TS-0151 +xref: EFO:0000357 +xref: EMAPA:17597 +xref: EV:0100363 +xref: FMA:60201 +xref: GAID:724 +xref: MA:0000240 +xref: MAT:0000144 +xref: MESH:D003051 +xref: MIAA:0000144 +xref: NCIT:C12395 +xref: NIFSTD_RETIRED:birnlex_883 +xref: OpenCyc:Mx4rvqfJmJwpEbGdrcN5Y29ycA +xref: SCTID:181187008 +xref: TAO:0000374 +xref: UMLS:C0009195 +xref: UMLS:C1278895 +xref: VHOG:0000691 +xref: Wikipedia:Cochlea +xref: XAO:0000197 +xref: ZFA:0000374 +is_a: UBERON:0034921 ! multi organ part structure +relationship: BFO:0000050 UBERON:0001839 ! part of bony labyrinth + +[Term] +id: UBERON:0001846 +name: internal ear +def: "Complex labyrinthine structure that comprises sensory endorgans specialized for vestibular, auditory, and acoustico-vestibular sensation." [PMID:16217737, Wikipedia:Internal_ear, ZFIN:curator] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "auris interna" RELATED [BTO:0000630] +synonym: "inner ear" EXACT [] +synonym: "labyrinth" RELATED [] +synonym: "otocyst" RELATED [] +xref: AAO:0000238 +xref: BIRNLEX:1196 +xref: BTO:0000630 +xref: CALOHA:TS-0478 +xref: EFO:0001363 +xref: EHDAA2:0000831 +xref: EHDAA:504 +xref: EMAPA:16194 +xref: EV:0100361 +xref: FMA:60909 +xref: GAID:871 +xref: galen:InnerEar +xref: MA:0000237 +xref: MAT:0000145 +xref: MESH:D007758 +xref: MIAA:0000145 +xref: NCIT:C12499 +xref: OpenCyc:Mx4rwJ8SsJwpEbGdrcN5Y29ycA +xref: SCTID:181189006 +xref: SCTID:304982002 +xref: TAO:0000217 +xref: UMLS:C0022889 +xref: UMLS:C1268973 +xref: VHOG:0000284 +xref: Wikipedia:Internal_ear +xref: XAO:0000192 +xref: ZFA:0000217 +is_a: UBERON:0034921 ! multi organ part structure +relationship: BFO:0000050 UBERON:0001690 ! part of ear + +[Term] +id: UBERON:0001849 +name: membranous labyrinth +def: "Organ with organ cavity which consists of the vestibular labyrinth and the cochlear labyrinth. The membranous labyrinth is lodged within the bony labyrinth and has the same general form; it is, however, considerably smaller and is partly separated from the bony walls by a quantity of fluid, the perilymph.[FMA, WP]." [FMA:61022, Wikipedia:Membranous_labyrinth] +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +synonym: "labyrinthus membranaceus" EXACT [Wikipedia:Membranous_labyrinth] +xref: AAO:0011060 +xref: EHDAA2:0000899 +xref: EHDAA:4698 +xref: EMAPA:17815 +xref: EV:0100367 +xref: FMA:61022 +xref: MA:0000242 +xref: NCIT:C33090 +xref: SCTID:263790009 +xref: UMLS:C0458700 +xref: VHOG:0000729 +xref: Wikipedia:Membranous_labyrinth +xref: XAO:0000194 +is_a: UBERON:0000062 ! organ +relationship: BFO:0000050 UBERON:0001846 ! part of internal ear + +[Term] +id: UBERON:0001851 +name: cortex +def: "Outermost layer of an organ[WP]." [Wikipedia:Cortex_(anatomy)] +subset: pheno_slim +subset: uberon_slim +subset: upper_level +synonym: "cortex" EXACT [FMA:61109] +synonym: "cortex of organ" EXACT [] +xref: EFO:0000383 +xref: EHDAA:9344 +xref: FMA:61109 +xref: galen:Cortex +xref: Wikipedia:Cortex_(anatomy) +is_a: UBERON:0000064 ! organ part + +[Term] +id: UBERON:0001855 +name: cochlear duct of membranous labyrinth +def: "An endolymph filled cavity inside the cochlea, located in between the scala tympani and the scala vestibuli, separated by the basilar membrane and Reissner's membrane (the vestibular membrane) respectively. Houses the organ of Corti[WP]." [Wikipedia:Cochlear_duct] +subset: pheno_slim +subset: uberon_slim +synonym: "cochlea duct" EXACT [BIRNLEX:2562] +synonym: "cochlear aqueduct" RELATED [] +synonym: "cochlear duct" EXACT [] +synonym: "ductus cochlearis" RELATED [BTO:0001692, Wikipedia:Cochlear_duct] +synonym: "membranous cochlea" RELATED [BTO:0001692] +synonym: "Reissner's canal" EXACT [FMA:61119] +synonym: "Reissners canal" EXACT [BIRNLEX:2562] +synonym: "scala media" RELATED [Wikipedia:Cochlear_duct] +synonym: "scala medias" EXACT [BIRNLEX:2562] +synonym: "scala of Loewenberg" RELATED [BTO:0001692] +xref: BIRNLEX:2562 +xref: BTO:0001692 +xref: CALOHA:TS-0152 +xref: EHDAA2:0000262 +xref: EHDAA:4718 +xref: EMAPA:17598 +xref: FMA:61119 +xref: GAID:874 +xref: MA:0000243 +xref: MESH:D003053 +xref: NCIT:C32335 +xref: SCTID:279849006 +xref: UMLS:C1281166 +xref: UMLS:C1323110 +xref: VHOG:0000507 +xref: Wikipedia:Cochlear_duct +is_a: UBERON:0000025 ! tube +relationship: BFO:0000050 UBERON:0002499 ! part of cochlear labyrinth + +[Term] +id: UBERON:0001866 +name: sebum +def: "Fatty lubricant matter secreted by sebaceous glands, and made of made of triglyceride oils, wax, squalene, and metabolytes of fat-producing cells[BTO,WP]." [BTO:0001981, Wikipedia:Sebaceous_glands#Sebum] +subset: uberon_slim +xref: BTO:0001981 +xref: ENVO:02000037 +xref: FMA:61304 +xref: GAID:1168 +xref: MA:0002538 +xref: MESH:D012629 +xref: NCIT:C13276 +xref: UMLS:C0036511 +xref: Wikipedia:Sebaceous_glands#Sebum +is_a: UBERON:0000456 ! secretion of exocrine gland + +[Term] +id: UBERON:0001869 +name: cerebral hemisphere +def: "One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.[FMA]." [FMA:61817, Wikipedia:Cerebral_hemisphere] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "cerebrum" RELATED [https://github.com/obophenotype/uberon/issues/1208, MA:0000133, VHOG:0001639] +synonym: "hemisphere" RELATED [VHOG:0001639] +synonym: "hemispheric regions" RELATED [BAMS:HEM] +synonym: "hemispherium cerebri" RELATED [Wikipedia:Cerebral_hemisphere] +synonym: "medial amygdalar nucleus" RELATED [NeuroNames:241] +synonym: "nucleus amygdaloideus medialis" RELATED [NeuroNames:241] +synonym: "nucleus medialis amygdalae" RELATED [NeuroNames:241] +xref: AAO:0010480 +xref: BAMS:HEM +xref: BIRNLEX:1042 +xref: BTO:0000231 +xref: CALOHA:TS-2007 +xref: DMBA:15739 +xref: EFO:0002521 +xref: EMAPA:16653 +xref: FMA:61817 +xref: galen:CerebralHemisphere +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=241 +xref: MA:0000133 +xref: MBA:403 +xref: NCIT:C12351 +xref: OpenCyc:Mx4rvigx5ZwpEbGdrcN5Y29ycA +xref: SCTID:278251007 +xref: UMLS:C0228174 +xref: UMLS:C0242202 +xref: VHOG:0001639 +xref: Wikipedia:Cerebral_hemisphere +is_a: UBERON:0000064 ! organ part +is_a: UBERON:0015212 ! lateral structure +relationship: BFO:0000050 UBERON:0001893 ! part of telencephalon + +[Term] +id: UBERON:0001890 +name: forebrain +def: "The most anterior region of the brain including both the telencephalon and diencephalon." [Wikipedia:Forebrain, ZFIN:ZDB-PUB-961014-576] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "FB" BROAD [BIRNLEX:1509, NIFSTD:NeuroNames_abbrevSource] +synonym: "prosencephalon" RELATED [] +xref: AAO:0010147 +xref: BAMS:FB +xref: BAMS:Forebrain +xref: BIRNLEX:1509 +xref: BTO:0000478 +xref: CALOHA:TS-0380 +xref: DHBA:10156 +xref: DMBA:15566 +xref: EFO:0000909 +xref: EHDAA2:0000556 +xref: EHDAA:3470 +xref: EMAPA:16895 +xref: FMA:61992 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=27 +xref: MA:0000170 +xref: MAT:0000105 +xref: MESH:D016548 +xref: MIAA:0000105 +xref: NCIT:C40185 +xref: SCTID:362291003 +xref: TAO:0000109 +xref: UMLS:C0085140 +xref: VHOG:0000383 +xref: Wikipedia:Forebrain +xref: XAO:0000011 +xref: ZFA:0000109 +is_a: UBERON:0002616 ! regional part of brain +is_a: UBERON:0004121 ! ectoderm-derived structure + +[Term] +id: UBERON:0001891 +name: midbrain +def: "The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]." [GO:0030901] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "MB" BROAD [BIRNLEX:1667, NIFSTD:NeuroNames_abbrevSource] +synonym: "mesencephalon" RELATED [Wikipedia:Midbrain] +xref: AAO:0010149 +xref: BAMS:MES +xref: BIRNLEX:1667 +xref: BM:MB +xref: BTO:0000138 +xref: CALOHA:TS-0630 +xref: DHBA:10648 +xref: DMBA:16649 +xref: EFO:0000919 +xref: EHDAA2:0001162 +xref: EHDAA:3694 +xref: EMAPA:16974 +xref: EV:0100242 +xref: FMA:61993 +xref: HBA:9001 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462 +xref: MA:0000207 +xref: MAT:0000106 +xref: MBA:313 +xref: MESH:D008636 +xref: MIAA:0000106 +xref: NCIT:C12510 +xref: OpenCyc:Mx4rvsBUqpwpEbGdrcN5Y29ycA +xref: RETIRED_EHDAA2:0001104 +xref: SCTID:279099009 +xref: TAO:0000128 +xref: UMLS:C0025462 +xref: VHOG:0000069 +xref: Wikipedia:Midbrain +xref: XAO:0000014 +xref: ZFA:0000128 +is_a: UBERON:0002616 ! regional part of brain +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest + +[Term] +id: UBERON:0001893 +name: telencephalon +def: "Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres." [AAO:0010479, XAO:0000012] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "cerebrum" EXACT [BTO:0000239, EMAPA:16910, FMA:62000, https://github.com/obophenotype/uberon/issues/1208, Wikipedia:Talk\:Cerebrum/Archive_1] +synonym: "endbrain" EXACT [http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=31, Swanson:2004] +synonym: "supratentorial region" BROAD [Wikipedia:Tentorium_cerebelli] +xref: AAO:0010479 +xref: BAMS:CB +xref: BAMS:CH +xref: BAMS:IV +xref: BAMS:Tel +xref: BIRNLEX:1115 +xref: BM:Tel +xref: BTO:0000239 +xref: CALOHA:TS-1018 +xref: DHBA:10158 +xref: EFO:0000912 +xref: EHDAA2:0001982 +xref: EMAPA:16910 +xref: EV:0100165 +xref: FMA:62000 +xref: GAID:621 +xref: HBA:4007 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=31 +xref: MA:0000183 +xref: MAT:0000421 +xref: MBA:567 +xref: MESH:D013687 +xref: MIAA:0000421 +xref: PBA:128011350 +xref: SCTID:263353005 +xref: TAO:0000079 +xref: UMLS:C0039452 +xref: VHOG:0000283 +xref: Wikipedia:Telencephalon +xref: XAO:0000012 +xref: ZFA:0000079 +is_a: UBERON:0002616 ! regional part of brain +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: BFO:0000050 UBERON:0001890 ! part of forebrain + +[Term] +id: UBERON:0001896 +name: medulla oblongata +def: "Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]." [FMA:62004, GO:0021550, Wikipedia:Bone_marrow_of_ovary_oblongata] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "bulb" BROAD [] +synonym: "bulbus" EXACT [FMA:62004, FMA:TA] +synonym: "medulla" BROAD [ABA:MY] +synonym: "medulla oblonzata" RELATED [Wikipedia:Medulla_oblongata] +synonym: "metepencephalon" RELATED [FMA:62004] +xref: AAO:0010486 +xref: BAMS:Md +xref: BAMS:MY +xref: BIRNLEX:957 +xref: BM:Me +xref: BTO:0000041 +xref: CALOHA:TS-0607 +xref: DMBA:17352 +xref: EFO:0000924 +xref: EHDAA2:0001088 +xref: EHDAA:7588 +xref: EMAPA:17550 +xref: EV:0100275 +xref: FMA:62004 +xref: GAID:590 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698 +xref: MA:0000206 +xref: MAT:0000111 +xref: MAT:0000367 +xref: MBA:354 +xref: MESH:D008526 +xref: MIAA:0000111 +xref: NCIT:C12442 +xref: OpenCyc:Mx4rvVjxSJwpEbGdrcN5Y29ycA +xref: OpenCyc:Mx4rwCqnXJwpEbGdrcN5Y29ycA +xref: SCTID:279104005 +xref: TAO:0000545 +xref: UMLS:C0025148 +xref: UMLS:C1269575 +xref: VHOG:0000181 +xref: Wikipedia:Bone_marrow_of_ovary_oblongata +xref: XAO:0003100 +xref: ZFA:0000545 +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0002298 ! part of brainstem +relationship: BFO:0000050 UBERON:0005290 ! part of myelencephalon + +[Term] +id: UBERON:0001943 +name: midbrain tegmentum +def: "Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]." [FMA:FMA, ISBN:0471888893, Wikipedia:Midbrain_tegmentum] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "mesencephalic tegmentum" RELATED [VHOG:0001367] +synonym: "MTg" BROAD [BIRNLEX:1200, NIFSTD:NeuroNames_abbrevSource] +synonym: "tegmentum" BROAD [ISBN:0471888893] +synonym: "tegmentum mesencephali" EXACT [Wikipedia:Midbrain_tegmentum] +synonym: "tegmentum mesencephalicum" RELATED [NeuroNames:491] +synonym: "tegmentum of midbrain" EXACT [] +xref: BAMS:MTg +xref: BIRNLEX:1200 +xref: BTO:0003388 +xref: DHBA:12195 +xref: EFO:0000921 +xref: EHDAA2:0004475 +xref: EMAPA:18215 +xref: FMA:62393 +xref: HBA:9002 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 +xref: MA:0000212 +xref: MAT:0000452 +xref: SCTID:362392007 +xref: TAO:0000160 +xref: UMLS:C0039441 +xref: VHOG:0001367 +xref: Wikipedia:Midbrain_tegmentum +xref: XAO:0004271 +xref: ZFA:0000160 +is_a: UBERON:0002616 ! regional part of brain +relationship: BFO:0000050 UBERON:0001891 ! part of midbrain +relationship: BFO:0000050 UBERON:0002298 ! part of brainstem + +[Term] +id: UBERON:0001950 +name: neocortex +def: "An area of cerebral cortex defined on the basis of cytoarchitecture that have six layers. Starting from the cortical surface the layers are: molecular layer (I), external granular layer (II), external pyramidal layer (III), internal granular layer (IV), internal pyramidal layer (V), and multiform layer (VI). Neocortex is most prominent in the frontal lobe, the parietal lobe, the temporal lobe and the occipital lobe, less so in the cingulate gyrus, the parahippocampal gyrus and the insula. It is composed of two subdivisions: true isocortex and proisocortex (Carpenter-83)(NN)." [BIRNLEX:2547, OldNeuroNames:754] +subset: pheno_slim +subset: uberon_slim +synonym: "cerebral neocortex" EXACT [] +synonym: "homogenetic cortex" EXACT DEPRECATED [ISBN:0471888893] +synonym: "homotypical cortex" EXACT [BIRNLEX:2547] +synonym: "iso-cortex" RELATED [BAMS:iso-cortex] +synonym: "isocortex" NARROW [BRAINSPAN:BRAINSPAN] +synonym: "isocortex (sensu lato)" EXACT [FMA:62429] +synonym: "neocortex (isocortex)" EXACT [DHBA:10160] +synonym: "neopallial cortex" EXACT [] +synonym: "neopallium" EXACT [] +synonym: "nonolfactory cortex" RELATED [BTO:0000920] +synonym: "nucleus hypoglossalis" RELATED [NeuroNames:757] +xref: BAMS:ISO +xref: BAMS:Iso-cortex +xref: BAMS:NCX +xref: BIRNLEX:2547 +xref: BTO:0000920 +xref: DHBA:10160 +xref: EHDAA2:0004662 +xref: EMAPA:32842 +xref: EMAPA:35589 +xref: FMA:62429 +xref: GAID:677 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=757 +xref: MA:0002754 +xref: MBA:315 +xref: MESH:A08.186.211.730.885.213.420 +xref: PBA:294021746 +xref: UMLS:C0175173 +xref: Wikipedia:Neocortex +is_a: UBERON:0002616 ! regional part of brain +relationship: BFO:0000050 UBERON:0000956 ! part of cerebral cortex + +[Term] +id: UBERON:0001969 +name: blood plasma +def: "The liquid component of blood, in which erythrocytes are suspended." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "blood plasm" EXACT [] +synonym: "plasma" BROAD [MA:0002501] +synonym: "portion of blood plasma" EXACT [] +synonym: "portion of plasma" BROAD [FMA:62970] +xref: BTO:0000131 +xref: CALOHA:TS-0800 +xref: EFO:0001905 +xref: EMAPA:35690 +xref: FMA:62970 +xref: GAID:1178 +xref: MA:0002501 +xref: MAT:0000052 +xref: MESH:D010949 +xref: MIAA:0000052 +xref: NCIT:C13356 +xref: OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw +xref: UMLS:C0032105 +xref: Wikipedia:Blood_plasma +is_a: UBERON:0000179 ! haemolymphatic fluid +relationship: BFO:0000050 UBERON:0000178 ! part of blood + +[Term] +id: UBERON:0001979 +name: venule +def: "One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins." [MESH:A07.231.432.952, MP:0004125] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "venula" RELATED [Wikipedia:Venule] +xref: BTO:0002626 +xref: EMAPA:35917 +xref: FMA:63130 +xref: MA:0000071 +xref: MESH:A07.231.432.952 +xref: NCIT:C12818 +xref: SCTID:341687009 +xref: TAO:0005315 +xref: UMLS:C0042520 +xref: VHOG:0001765 +xref: Wikipedia:Venule +xref: ZFA:0005315 +is_a: UBERON:0003920 ! venous blood vessel + +[Term] +id: UBERON:0001980 +name: arteriole +def: "The smallest division of the artery located between the muscular arteries and the capillaries[GO]." [GO:0014830] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "arteriola" RELATED [Wikipedia:Arteriole] +xref: AAO:0010253 +xref: BTO:0001997 +xref: EMAPA:35146 +xref: FMA:63182 +xref: MA:0000063 +xref: MESH:D001160 +xref: NCIT:C12672 +xref: SCTID:337724002 +xref: TAO:0002138 +xref: UMLS:C0003847 +xref: VHOG:0001763 +xref: Wikipedia:Arteriole +xref: ZFA:0005255 +is_a: UBERON:0003509 ! arterial blood vessel + +[Term] +id: UBERON:0001981 +name: blood vessel +def: "A vessel through which blood circulates in the body." [BTO:0001102, Wikipedia:Blood_vessel] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "region of vascular tree organ" EXACT [FMA:50722] +synonym: "vas sanguineum" RELATED [Wikipedia:Blood_vessel] +synonym: "vascular element" BROAD [EMAPA:35993] +synonym: "vascular tree organ region" EXACT [FMA:50722] +xref: AAO:0011004 +xref: AEO:0000207 +xref: BTO:0001102 +xref: CALOHA:TS-0080 +xref: EFO:0000817 +xref: EHDAA2:0003252 +xref: EHDAA:240 +xref: EMAPA:32743 +xref: EMAPA:35993 +xref: FMA:50722 +xref: FMA:63183 +xref: GAID:169 +xref: MA:0000060 +xref: MAT:0000393 +xref: MESH:D001808 +xref: NCIT:C12679 +xref: NLXANAT:090901 +xref: OpenCyc:Mx4rvVjxlpwpEbGdrcN5Y29ycA +xref: SCTID:361097006 +xref: TAO:0002137 +xref: UMLS:C0005847 +xref: VHOG:0001250 +xref: Wikipedia:Blood_vessel +xref: XAO:0001011 +xref: ZFA:0005314 +is_a: UBERON:0000055 ! vessel +relationship: BFO:0000050 UBERON:0004537 ! part of blood vasculature + +[Term] +id: UBERON:0001982 +name: capillary +def: "Any of the smallest blood vessels connecting arterioles with venules." [https://github.com/obophenotype/uberon/issues/137, ISBN:0073040584, Wikipedia:Capillary] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "blood capillary" EXACT [] +synonym: "capillary vessel" EXACT [] +xref: AAO:0010252 +xref: BTO:0002045 +xref: CALOHA:TS-2006 +xref: EFO:0001906 +xref: EMAPA:35198 +xref: EV:0100035 +xref: FMA:63194 +xref: MA:0000065 +xref: MESH:A07.231.432.410 +xref: NCIT:C12685 +xref: NLXANAT:090902 +xref: OpenCyc:Mx4rvWEU-5wpEbGdrcN5Y29ycA +xref: TAO:0005250 +xref: UMLS:C0935624 +xref: VHOG:0001253 +xref: Wikipedia:Capillary +xref: XAO:0000116 +xref: ZFA:0005250 +is_a: UBERON:0001981 ! blood vessel +is_a: UBERON:0010523 ! microcirculatory vessel + +[Term] +id: UBERON:0001986 +name: endothelium +def: "A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]." [FMA:63916, https://github.com/obophenotype/uberon/issues/225, MESH:A10.272.491] +subset: efo_slim +subset: uberon_slim +xref: BTO:0000393 +xref: CALOHA:TS-0278 +xref: EFO:0002548 +xref: FMA:63916 +xref: GAID:520 +xref: galen:Endothelium +xref: MESH:D004727 +xref: NCIT:C12481 +xref: SCTID:27168002 +xref: UMLS:C0014257 +is_a: UBERON:0000487 ! simple squamous epithelium +is_a: UBERON:0012275 ! meso-epithelium + +[Term] +id: UBERON:0002006 +name: cortex of lymph node +def: "Peripheral portion of the lymph node, underneath the capsule[WP]." [Wikipedia:Cortex_of_lymph_node] +subset: pheno_slim +subset: uberon_slim +synonym: "cortex nodi lymphoidei" RELATED [Wikipedia:Cortex_of_lymph_node] +synonym: "lymph node cortex" EXACT [] +xref: EMAPA:35525 +xref: FMA:66253 +xref: MA:0000740 +xref: NCIT:C33029 +xref: UMLS:C0933402 +xref: Wikipedia:Cortex_of_lymph_node +is_a: UBERON:0001851 ! cortex +relationship: BFO:0000050 UBERON:0000029 ! part of lymph node + +[Term] +id: UBERON:0002007 +name: medulla of lymph node +def: "The medullary portion of the lymph node, which contains large blood vessels, sinuses and medullary cords that contain antibody-secreting plasma cells." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Lymph_node#Medulla] +subset: pheno_slim +subset: uberon_slim +synonym: "lymph node medulla" EXACT [] +synonym: "medulla nodi lymphoidei" RELATED [Wikipedia:Medulla_of_lymph_node] +xref: EMAPA:35529 +xref: FMA:66254 +xref: MA:0000745 +is_a: UBERON:0000958 ! medulla of organ +relationship: BFO:0000050 UBERON:0000029 ! part of lymph node + +[Term] +id: UBERON:0002020 +name: gray matter +def: "A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Gray_matter] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "gray mater" RELATED [ZFA:0001681] +synonym: "gray matter" EXACT [] +synonym: "gray matter of neuraxis" EXACT [FMA:67242] +synonym: "grey matter" EXACT [] +synonym: "grey matter of neuraxis" EXACT [] +synonym: "grey substance" EXACT [] +synonym: "grisea" RELATED [] +synonym: "neuronal grey matter" EXACT [AEO:0001012] +synonym: "substantia grisea" EXACT [FMA:67242, FMA:TA] +xref: AEO:0001012 +xref: EHDAA2:0003136 +xref: EHDAA2_RETIRED:0004658 +xref: EMAPA:37596 +xref: FMA:67242 +xref: HBA:4006 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2869 +xref: MA:0001112 +xref: NCIT:C32695 +xref: OpenCyc:Mx4rwDdKMpwpEbGdrcN5Y29ycA +xref: TAO:0002197 +xref: UMLS:C0018220 +xref: VHOG:0001768 +xref: Wikipedia:Gray_matter +xref: ZFA:0001681 +is_a: UBERON:0011215 ! central nervous system cell part cluster + +[Term] +id: UBERON:0002028 +name: hindbrain +def: "The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]." [Wikipedia:Rhombencephalon, ZFA:0000029, ZFIN:curator] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "rhombencephalon" RELATED [] +xref: AAO:0010150 +xref: BAMS:HB +xref: BIRNLEX:942 +xref: BTO:0000672 +xref: CALOHA:TS-0457 +xref: DHBA:10653 +xref: DMBA:16808 +xref: EFO:0000923 +xref: EHDAA2:0000746 +xref: EHDAA:3514 +xref: EHDAA:6487 +xref: EMAPA:16916 +xref: FMA:67687 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540 +xref: MA:0000195 +xref: MAT:0000107 +xref: MBA:1065 +xref: MESH:D012249 +xref: MIAA:0000107 +xref: NCIT:C40336 +xref: SCTID:303456008 +xref: TAO:0000029 +xref: UMLS:C0035507 +xref: UMLS:C1522180 +xref: VHOG:0000070 +xref: Wikipedia:Rhombencephalon +xref: XAO:0000015 +xref: ZFA:0000029 +is_a: UBERON:0002616 ! regional part of brain +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest + +[Term] +id: UBERON:0002033 +name: arrector muscle of hair +def: "A tiny smooth muscle that connects the hair follicle with the dermis." [DOI:10.1016/j.cub.2008.12.005] +subset: pheno_slim +subset: uberon_slim +synonym: "arectores pilorum" RELATED [BTO:0005132] +synonym: "arrector pili" EXACT [FMA:67821, MA:0000778] +synonym: "arrector pili muscle" EXACT [EMAPA:26779, MP:0010679] +synonym: "arrector pili smooth muscle" EXACT [MA:0000778] +synonym: "arrector pilli" EXACT [MP:0010679] +synonym: "arrector pilli muscle" EXACT [MP:0010679] +synonym: "arrector pilorum" EXACT [ISBN:0123813611] +synonym: "arrector pilorum muscle of hair" EXACT [ISBN:0123813611] +synonym: "erector pili" RELATED [BTO:0005132] +synonym: "erectores pilorum" RELATED [BTO:0005132] +synonym: "pilomotor muscle" RELATED [BTO:0005132] +xref: BTO:0005132 +xref: EMAPA:26775 +xref: FMA:67821 +xref: MA:0000778 +xref: SCTID:319910005 +xref: Wikipedia:Arrector_pili_muscle +is_a: UBERON:0001135 ! smooth muscle tissue +relationship: BFO:0000050 UBERON:0011932 ! part of pilosebaceous unit + +[Term] +id: UBERON:0002036 +name: striated muscle tissue +def: "Muscle tissue that contains fibers that are divided by transverse bands into striations." [CL:0000737, GOC:dph, GOC:mtg_muscle] +subset: pheno_slim +subset: uberon_slim +synonym: "striated muscle" EXACT [] +xref: AAO:0010762 +xref: AEO:0000140 +xref: CALOHA:TS-2047 +xref: EHDAA2:0003140 +xref: EMAPA:36390 +xref: FMA:67905 +xref: galen:StriatedMuscle +xref: MA:0002438 +xref: NCIT:C12436 +xref: OpenCyc:Mx4rwAoze5wpEbGdrcN5Y29ycA +xref: UMLS:C1331262 +xref: WBbt:0005779 +xref: Wikipedia:Striated_muscle +is_a: UBERON:0002385 ! muscle tissue + +[Term] +id: UBERON:0002049 +name: vasculature +def: "An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face." [ZFA:0005249] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "vascular network" EXACT [FMA:69050] +xref: BTO:0003718 +xref: FMA:69050 +xref: TAO:0005249 +xref: ZFA:0005249 +is_a: UBERON:0000477 ! anatomical cluster +relationship: BFO:0000050 UBERON:0007798 ! part of vascular system + +[Term] +id: UBERON:0002050 +name: embryonic structure +def: "Anatomical structure that is part of an embryo." [BTO:0000174, ZFIN:curator] +subset: efo_slim +subset: inconsistent_with_fma +subset: vertebrate_core +synonym: "developing embryonic structure" EXACT [FBbt:00004208] +synonym: "developing structure" RELATED [] +synonym: "embryonale Struktur" RELATED [BTO:0000174] +synonym: "embryonic anatomical structure" EXACT [RETIRED_EHDAA2:0003169] +synonym: "embryonic structures" RELATED [ZFA:0001105] +xref: AAO:0000138 +xref: BILA:0000034 +xref: BTO:0000174 +xref: CALOHA:TS-2110 +xref: EFO:0000461 +xref: FBbt:00004208 +xref: FMA:69067 +xref: GAID:407 +xref: MESH:D004628 +xref: NCIT:C13229 +xref: RETIRED_EHDAA2:0003169 +xref: SCTID:667009 +xref: TAO:0001105 +xref: UMLS:C0013948 +xref: VSAO:0000178 +xref: XAO:0003042 +xref: ZFA:0001105 +is_a: UBERON:0005423 ! developing anatomical structure +relationship: BFO:0000050 UBERON:0000922 ! part of embryo + +[Term] +id: UBERON:0002067 +name: dermis +def: "The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]." [Wikipedia:Dermis, ZFIN:curator] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "corium" RELATED [BTO:0000294, Wikipedia:Dermis] +synonym: "cutis" RELATED [BTO:0000294] +synonym: "vertebrate dermis" EXACT [] +xref: AAO:0000128 +xref: BTO:0000294 +xref: CALOHA:TS-2076 +xref: EFO:0000953 +xref: EMAPA:17527 +xref: EV:0100154 +xref: FMA:70323 +xref: GAID:1321 +xref: MA:0000152 +xref: MAT:0000153 +xref: MESH:D020405 +xref: MIAA:0000153 +xref: NCIT:C12701 +xref: SCTID:361696001 +xref: TAO:0001119 +xref: UMLS:C0011646 +xref: VHOG:0000108 +xref: Wikipedia:Dermis +xref: XAO:0000217 +xref: ZFA:0001119 +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: UBERON:0013754 ! integumentary system layer +relationship: BFO:0000050 UBERON:0002097 ! part of skin of body + +[Term] +id: UBERON:0002072 +name: hypodermis +def: "Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]." [Wikipedia:Hypodermis] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "hypoderm" EXACT [] +synonym: "sub-tegumental tissue" RELATED [BTO:0004525] +synonym: "subcutaneous tissue" RELATED [Wikipedia:Hypodermis] +synonym: "subcutis" RELATED [] +synonym: "subtegumental tissue" RELATED [BTO:0004525] +synonym: "superficial fascia" RELATED INCONSISTENT [] +synonym: "tela subcutanea" RELATED [Wikipedia:Hypodermis] +synonym: "vertebrate hypodermis" EXACT [] +xref: BTO:0001314 +xref: CALOHA:TS-2366 +xref: EMAPA:37505 +xref: FMA:70544 +xref: NCIT:C33645 +xref: TAO:0001136 +xref: UMLS:C0278403 +xref: Wikipedia:Hypodermis +xref: ZFA:0001136 +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0013754 ! integumentary system layer +relationship: BFO:0000050 UBERON:0002199 ! part of integument + +[Term] +id: UBERON:0002073 +name: hair follicle +def: "A tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open[GO]." [Wikipedia:Hair_follicle] +subset: efo_slim +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +synonym: "folliculus pili" RELATED [Wikipedia:Hair_follicle] +xref: BTO:0000554 +xref: CALOHA:TS-0432 +xref: EFO:0002464 +xref: EMAPA:18771 +xref: EMAPA:29741 +xref: EV:0100156 +xref: FMA:70660 +xref: GAID:934 +xref: MA:0000154 +xref: MESH:D018859 +xref: NCIT:C13317 +xref: OpenCyc:Mx4rvVjOI5wpEbGdrcN5Y29ycA +xref: SCTID:280830006 +xref: UMLS:C0221971 +xref: VHOG:0001268 +xref: Wikipedia:Hair_follicle +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: UBERON:0036150 ! skin appendage follicle +relationship: BFO:0000050 UBERON:0001003 ! part of skin epidermis +relationship: BFO:0000050 UBERON:0011932 ! part of pilosebaceous unit + +[Term] +id: UBERON:0002075 +name: viscus +def: "An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen." [BTO:0001491, https://github.com/obophenotype/mouse-anatomy-ontology/issues/14, Wikipedia:Viscus] +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +subset: upper_level +synonym: "splanchnic tissue" RELATED [BTO:0001491] +synonym: "viscera" RELATED [] +synonym: "visceral organ" EXACT [RETIRED_EHDAA2:0002201] +synonym: "visceral organ system" EXACT [MA:0000019] +synonym: "visceral tissue" RELATED [BTO:0001491] +xref: AAO:0010386 +xref: BTO:0001491 +xref: EHDAA:512 +xref: EMAPA:16245 +xref: FMA:7085 +xref: MA:0000019 +xref: MESH:D014781 +xref: NCIT:C28287 +xref: RETIRED_EHDAA2:0002201 +xref: SCTID:118760003 +xref: UMLS:C0042779 +xref: Wikipedia:Viscus +xref: XAO:0003034 +is_a: UBERON:0005177 ! trunk region element + +[Term] +id: UBERON:0002090 +name: postcranial axial skeleton +def: "The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]." [https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957, https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834, ZFA:0000317] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "axial skeleton" BROAD [FMA:71221, https://github.com/obophenotype/uberon/wiki/The-axial-skeleton] +synonym: "post-cranial axial skeleton" EXACT [] +xref: AAO:0000034 +xref: EFO:0000942 +xref: EHDAA2:0000161 +xref: EHDAA:5049 +xref: EMAPA:17214 +xref: EMAPA:37721 +xref: FMA:71221 +xref: MA:0002986 +xref: MAT:0000148 +xref: MIAA:0000148 +xref: TAO:0000317 +xref: VHOG:0000317 +xref: VSAO:0000093 +xref: XAO:0003073 +xref: ZFA:0000317 +is_a: UBERON:0010912 ! subdivision of skeleton +relationship: BFO:0000050 UBERON:0005944 ! part of axial skeleton plus cranial skeleton +relationship: BFO:0000050 UBERON:0011138 ! part of postcranial axial skeletal system + +[Term] +id: UBERON:0002091 +name: appendicular skeleton +def: "Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003, Wikipedia:Appendicular_skeleton] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "appendicular skeleton" EXACT [] +synonym: "entire appendicular skeleton" EXACT [https://github.com/obophenotype/uberon/issues/59] +synonym: "paired fin skeleton" NARROW SENSU [] +synonym: "skeleton appendiculare" RELATED [Wikipedia:Appendicular_skeleton] +xref: AAO:0000747 +xref: EFO:0000951 +xref: EMAPA:32729 +xref: FMA:71222 +xref: MA:0000290 +xref: MAT:0000278 +xref: MIAA:0000278 +xref: NCIT:C49477 +xref: SCTID:322050006 +xref: UMLS:C0222646 +xref: VHOG:0001666 +xref: VSAO:0000076 +xref: Wikipedia:Appendicular_skeleton +xref: XAO:0003166 +is_a: UBERON:0010912 ! subdivision of skeleton +relationship: BFO:0000050 UBERON:0011249 ! part of appendicular skeletal system + +[Term] +id: UBERON:0002097 +name: skin of body +def: "The organ covering the body that consists of the dermis and epidermis." [UBERON:cjm] +subset: efo_slim +subset: major_organ +subset: pheno_slim +subset: uberon_slim +synonym: "entire integument" RELATED [] +synonym: "entire skin" EXACT [] +synonym: "integument" RELATED [] +synonym: "integumental organ" RELATED [] +synonym: "pelt" RELATED [] +synonym: "skin" RELATED [] +synonym: "skin organ" EXACT [] +xref: BTO:0001253 +xref: CALOHA:TS-0934 +xref: EFO:0000962 +xref: EHDAA2:0001844 +xref: EMAPA:17525 +xref: FMA:7163 +xref: galen:Skin +xref: MESH:D012867 +xref: MFMO:0000099 +xref: NCIT:C12470 +xref: OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA +xref: SCTID:181469002 +xref: UMLS:C1123023 +xref: Wikipedia:Skin +xref: XAO:0000023 +is_a: UBERON:0000062 ! organ +relationship: BFO:0000050 UBERON:0002199 ! part of integument + +[Term] +id: UBERON:0002100 +name: trunk +def: "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present." [TAO:0001115, UBERONREF:0000006, Wikipedia:Torso] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "Rumpf" RELATED [BTO:0001493] +synonym: "thoracolumbar region" EXACT [] +synonym: "torso" EXACT [] +synonym: "trunk region" EXACT [XAO:0000054] +xref: AAO:0010339 +xref: BILA:0000116 +xref: BTO:0001493 +xref: CALOHA:TS-1071 +xref: EFO:0000966 +xref: EMAPA:31857 +xref: FMA:7181 +xref: galen:Trunk +xref: MA:0000004 +xref: MAT:0000296 +xref: MIAA:0000296 +xref: NCIT:C33816 +xref: OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA +xref: SCTID:262225004 +xref: TAO:0001115 +xref: UMLS:C0460005 +xref: Wikipedia:Torso +xref: XAO:0000054 +xref: XAO:0003025 +xref: ZFA:0001115 +is_a: UBERON:0011676 ! subdivision of organism along main body axis +relationship: BFO:0000050 UBERON:0013702 ! part of body proper + +[Term] +id: UBERON:0002101 +name: limb +def: "A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts." [UBERONREF:0000003] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "extremities" RELATED [] +synonym: "extremity" RELATED [] +synonym: "flipper" NARROW SENSU [] +synonym: "free limb" EXACT [FMA:24875] +synonym: "limb sensu Vertebrata" EXACT [MAT:0000090] +synonym: "pentadactyl limb" EXACT [] +synonym: "tetrapod limb" EXACT [] +xref: AAO:0010336 +xref: AEO:0000172 +xref: CALOHA:TS-0552 +xref: EFO:0000876 +xref: EHDAA2:0003172 +xref: EHDAA:1697 +xref: EHDAA:8273 +xref: EMAPA:16405 +xref: FMA:24875 +xref: GAID:36 +xref: galen:Extremity +xref: MA:0000007 +xref: MAT:0000090 +xref: MIAA:0000090 +xref: NCIT:C12429 +xref: OpenCyc:Mx4rvn1uSZwpEbGdrcN5Y29ycA +xref: SCTID:243996003 +xref: UMLS:C0015385 +xref: VHOG:0000336 +xref: VSAO:0000121 +xref: Wikipedia:Limb +xref: XAO:0003027 +is_a: UBERON:0004708 ! paired limb/fin + +[Term] +id: UBERON:0002102 +name: forelimb +def: "A (free) limb that is connected to a pectoral girdle. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pectoral girdle and its parts." [UBERONREF:0000003] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "anteriormost limb" EXACT [] +synonym: "fore limb" EXACT [] +synonym: "foreleg" RELATED [] +synonym: "forelimb" EXACT [] +synonym: "free part of upper limb" EXACT [FMA:24878] +synonym: "free upper limb" EXACT [FMA:24878, UBERONREF:0000003] +synonym: "membrum superius" EXACT [FMA:7183, FMA:TA] +synonym: "pectoral flipper" NARROW SENSU [] +synonym: "pectoral limb" EXACT [] +synonym: "superior member" EXACT [] +synonym: "upper extremity" EXACT [] +synonym: "upper limb" EXACT [] +xref: AAO:0000205 +xref: BTO:0001729 +xref: CALOHA:TS-2214 +xref: EFO:0000882 +xref: EHDAA2:0002133 +xref: EHDAA:6208 +xref: EMAPA:17412 +xref: EV:0100014 +xref: FMA:24878 +xref: GAID:1215 +xref: GAID:51 +xref: galen:UpperExtremity +xref: MA:0000025 +xref: MAT:0000394 +xref: MESH:D005552 +xref: MIAA:0000394 +xref: NCIT:C12671 +xref: SCTID:182245002 +xref: UMLS:C1140618 +xref: VHOG:0000338 +xref: VSAO:0000148 +xref: Wikipedia:Forelimb +xref: XAO:0003030 +is_a: UBERON:0002101 ! limb +is_a: UBERON:0004710 ! pectoral appendage +relationship: BFO:0000050 UBERON:0000153 ! part of anterior region of body + +[Term] +id: UBERON:0002103 +name: hindlimb +def: "A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts." [UBERONREF:0000003, Wikipedia:Hindlimb, Wikipedia:Lower_limb] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "free lower limb" EXACT [FMA:24879, UBERONREF:0000003] +synonym: "free part of lower limb" RELATED [FMA:24879] +synonym: "hind limb" EXACT [] +synonym: "hind-limb" EXACT [VSAO:0000150] +synonym: "hindlimb" EXACT [] +synonym: "inferior member" EXACT [] +synonym: "lower extremity" RELATED [] +synonym: "lower limb" EXACT [] +synonym: "membrum inferius" EXACT [FMA:7184, FMA:TA] +synonym: "membrum inferius" RELATED [Wikipedia:Lower_limb] +synonym: "pelvic appendage" RELATED [] +xref: AAO:0000219 +xref: BTO:0002345 +xref: CALOHA:TS-2215 +xref: EFO:0000883 +xref: EHDAA2:0001033 +xref: EHDAA:6094 +xref: EMAPA:17458 +xref: EV:0100015 +xref: FMA:24879 +xref: GAID:1221 +xref: GAID:38 +xref: galen:LowerExtremity +xref: MA:0000026 +xref: MAT:0000395 +xref: MESH:D006614 +xref: MIAA:0000395 +xref: NCIT:C12742 +xref: NCIT:C77625 +xref: SCTID:182281004 +xref: UMLS:C0023216 +xref: UMLS:C1522391 +xref: VHOG:0000337 +xref: VSAO:0000150 +xref: Wikipedia:Hindlimb +xref: XAO:0003031 +is_a: UBERON:0002101 ! limb +is_a: UBERON:0004709 ! pelvic appendage +relationship: BFO:0000050 UBERON:0000154 ! part of posterior region of body + +[Term] +id: UBERON:0002105 +name: vestibulo-auditory system +def: "Sensory system responsible for the perception of spatial orientation and auditory stimuli." [ZFA:0001138] +subset: functional_classification +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "auditory organ system" EXACT [] +synonym: "auditory system" RELATED [] +synonym: "auditory/vestibular system" RELATED [] +synonym: "vestibuloauditory system" EXACT [] +synonym: "vestibuloauditory system" RELATED [] +xref: AAO:0000631 +xref: EMAPA:36002 +xref: EMAPA:37985 +xref: FMA:78500 +xref: TAO:0001138 +xref: XAO:0003195 +xref: ZFA:0001138 +is_a: UBERON:0001032 ! sensory system + +[Term] +id: UBERON:0002113 +name: kidney +def: "A paired organ of the urinary tract which has the production of urine as its primary function." [http://anatomy.uams.edu/anatomyhtml/kidney.html, Wikipedia:Kidney] +subset: efo_slim +subset: major_organ +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "reniculate kidney" NARROW SENSU [Wikipedia:Reniculate_kidney] +xref: AAO:0000250 +xref: BTO:0000671 +xref: CALOHA:TS-0510 +xref: EFO:0000929 +xref: EMAPA:17373 +xref: EV:0100096 +xref: FMA:7203 +xref: GAID:423 +xref: galen:Kidney +xref: MA:0000368 +xref: MAT:0000119 +xref: MESH:D007668 +xref: MIAA:0000119 +xref: NCIT:C12415 +xref: OpenCyc:Mx4rvVjlYpwpEbGdrcN5Y29ycA +xref: SCTID:181414000 +xref: UMLS:C0022646 +xref: Wikipedia:Kidney +xref: XAO:0003267 +is_a: UBERON:0000489 ! cavitated compound organ +is_a: UBERON:0005172 ! abdomen element +is_a: UBERON:0015212 ! lateral structure +relationship: BFO:0000050 UBERON:0011143 ! part of upper urinary tract + +[Term] +id: UBERON:0002120 +name: pronephros +def: "In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]." [GO:0048793, Wikipedia:Pronephros] +subset: efo_slim +subset: organ_slim +subset: uberon_slim +synonym: "archinephron" RELATED [BTO:0001541] +synonym: "embryonic kidney" RELATED [BTO:0001541] +synonym: "pronephric kidney" EXACT [XAO:0002000] +synonym: "pronephron" RELATED [BTO:0001541] +xref: AAO:0011089 +xref: BTO:0001541 +xref: EFO:0000927 +xref: EHDAA2:0001570 +xref: EHDAA:1017 +xref: EMAPA:16579 +xref: FMA:72170 +xref: MAT:0000117 +xref: MIAA:0000117 +xref: NCIT:C34280 +xref: SCTID:308804007 +xref: TAO:0000151 +xref: UMLS:C0231048 +xref: VHOG:0000037 +xref: Wikipedia:Pronephros +xref: XAO:0002000 +xref: ZFA:0000151 +is_a: UBERON:0002113 ! kidney +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005423 ! developing anatomical structure + +[Term] +id: UBERON:0002193 +name: hemolymphoid system +def: "Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs." [http://orcid.org/0000-0002-6601-2165] +synonym: "haemolymphoid system" RELATED [] +synonym: "hematolymphoid system" EXACT [] +synonym: "lymphomyeloid complex" EXACT [] +xref: CALOHA:TS-2018 +xref: EHDAA2:0004615 +xref: EMAPA:18765 +xref: FMA:74562 +xref: MA:0000013 +is_a: UBERON:0000467 ! anatomical system + +[Term] +id: UBERON:0002194 +name: capsule of lymph node +def: "Capsule surrounding lymph node composed of connective tissue with some plain muscle fibers." [Wikipedia:Lymph_node#Capsule] +subset: uberon_slim +synonym: "capsula nodi lymphoidei" EXACT [FMA:74604, FMA:TA] +synonym: "lymph node capsule" EXACT [] +xref: EMAPA:35524 +xref: FMA:74604 +xref: MA:0000739 +xref: NCIT:C33028 +xref: SCTID:327532004 +xref: UMLS:C0229699 +xref: Wikipedia:Lymph_node_capsule +is_a: UBERON:0003893 ! capsule + +[Term] +id: UBERON:0002199 +name: integument +def: "The dermis, epidermis and hypodermis." [Wikipedia:Integument] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "dermal system" RELATED [BTO:0000634] +synonym: "dermis plus epidermis plus hypodermis" EXACT [] +synonym: "dermoid system" RELATED [BTO:0000634] +synonym: "integumentum commune" EXACT [FMA:74657, FMA:TA] +synonym: "skin" RELATED [] +synonym: "skin and subcutaneous tissue" EXACT [] +synonym: "skin plus hypodermis" EXACT [] +synonym: "tegument" RELATED [BTO:0000634] +synonym: "the integument" EXACT [FMA:74657] +synonym: "vertebrate integument" RELATED [] +xref: AAO:0000239 +xref: BTO:0000634 +xref: EMAPA:37504 +xref: FMA:74657 +xref: galen:Integument +xref: TAO:0000368 +xref: VSAO:0000029 +xref: Wikipedia:Integument +xref: ZFA:0000368 +is_a: UBERON:0011216 ! organ system subdivision +relationship: BFO:0000050 UBERON:0002416 ! part of integumental system + +[Term] +id: UBERON:0002201 +name: vasculature of trunk +def: "A vasculature that is part of a trunk [Automatically generated definition]." [OBOL:automatic] +subset: vertebrate_core +synonym: "torso vascular network" EXACT [OBOL:automatic] +synonym: "torso vasculature" EXACT [OBOL:automatic] +synonym: "trunk vascular network" EXACT [OBOL:automatic] +synonym: "trunk vasculature" EXACT [] +synonym: "vascular network of torso" EXACT [OBOL:automatic] +synonym: "vascular network of trunk" EXACT [OBOL:automatic] +synonym: "vasculature of torso" EXACT [OBOL:automatic] +xref: FMA:74712 +xref: TAO:0005024 +xref: ZFA:0005024 +is_a: UBERON:0002049 ! vasculature +relationship: BFO:0000050 UBERON:0002100 ! part of trunk + +[Term] +id: UBERON:0002204 +name: musculoskeletal system +def: "Anatomical system that consists of the muscular and skeletal systems." [https://github.com/obophenotype/uberon/issues/77, VSAO:0000031, VSAO:curator] +subset: uberon_slim +synonym: "musculo-skeletal system" EXACT [] +xref: AAO:0010546 +xref: CALOHA:TS-1311 +xref: EMAPA:32714 +xref: EV:0100139 +xref: FMA:7482 +xref: GAID:98 +xref: MA:0002418 +xref: MESH:D009141 +xref: NCIT:C12754 +xref: OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g +xref: SCTID:278858007 +xref: UMLS:C0026860 +xref: VHOG:0001275 +xref: VSAO:0000031 +xref: Wikipedia:Musculoskeletal_system +xref: XAO:0000168 +is_a: UBERON:0000467 ! anatomical system + +[Term] +id: UBERON:0002217 +name: synovial joint +def: "Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]." [FMA:7501, Wikipedia:Synovial_joint] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "articulatio synoviale" EXACT [] +synonym: "diarthrodial joints" RELATED [ZFA:0005153] +synonym: "diarthroses" EXACT [ZFA:0005153] +synonym: "diarthrosis" EXACT [] +synonym: "diarthrosis joint" EXACT [] +xref: AEO:0000183 +xref: CALOHA:TS-2138 +xref: EHDAA2:0003183 +xref: FMA:7501 +xref: galen:SynovialJoint +xref: MA:0000322 +xref: NCIT:C32461 +xref: OpenCyc:Mx4rv2bBV5wpEbGdrcN5Y29ycA +xref: SCTID:113234001 +xref: TAO:0005153 +xref: Wikipedia:Synovial_joint +xref: ZFA:0005153 +is_a: UBERON:0000982 ! skeletal joint + +[Term] +id: UBERON:0002224 +name: thoracic cavity +def: "The part of the coelemic cavity lumen that is enclosed by the walls of the thorax." [UBERON:cjm, Wikipedia:Thoracic_cavity] +subset: pheno_slim +subset: uberon_slim +synonym: "cavitas thoracis" EXACT [Wikipedia:Thoracic_cavity] +synonym: "cavity of chest" EXACT [] +synonym: "cavity of thorax" EXACT [] +synonym: "chest cavity" EXACT [] +synonym: "pectoral cavity" EXACT [] +synonym: "space of thoracic compartment" EXACT [FMA:7565] +synonym: "thoracic lumen" EXACT [] +xref: EMAPA:36497 +xref: FMA:7565 +xref: GAID:93 +xref: MA:0000032 +xref: MESH:A01.911.800 +xref: NCIT:C12905 +xref: OpenCyc:Mx4rmvyleLfEEduAAAACs6hRXg +xref: OpenCyc:Mx4rvhU_TpwpEbGdrcN5Y29ycA +xref: SCTID:243949006 +xref: UMLS:C0230139 +xref: Wikipedia:Thoracic_cavity +is_a: UBERON:0000464 ! anatomical space +relationship: BFO:0000050 UBERON:0002323 ! part of coelemic cavity lumen + +[Term] +id: UBERON:0002240 +name: spinal cord +def: "Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO)." [BIRNLEX:1709] +subset: cumbo +subset: efo_slim +subset: major_organ +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "cerebro-cerebellar fissure" RELATED [NeuroNames:22] +synonym: "cerebrocerebellar fissure" RELATED [NeuroNames:22] +synonym: "fissura cerebro-cerebellaris" RELATED [NeuroNames:22] +synonym: "fissura cerebrocerebellaris" RELATED [NeuroNames:22] +synonym: "medulla spinalis" RELATED [BTO:0001279, Wikipedia:Spinal_cord] +synonym: "SpC" RELATED [] +synonym: "spinal cord structure" RELATED [ZFA:0000075] +synonym: "spinal medulla" RELATED [BTO:0001279] +xref: AAO:0010151 +xref: BAMS:SP +xref: BAMS:Spinal +xref: BIRNLEX:1709 +xref: BM:SpC +xref: BTO:0001279 +xref: CALOHA:TS-0953 +xref: DHBA:12890 +xref: DMBA:17651 +xref: EFO:0000110 +xref: EHDAA2:0001255 +xref: EHDAA:2863 +xref: EMAPA:17577 +xref: EV:0100316 +xref: FMA:7647 +xref: GAID:695 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22 +xref: MA:0000216 +xref: MAT:0000183 +xref: MESH:D013116 +xref: MIAA:0000183 +xref: NCIT:C12464 +xref: OpenCyc:Mx4rvVjjk5wpEbGdrcN5Y29ycA +xref: SCTID:180959008 +xref: TAO:0000075 +xref: UMLS:C0037925 +xref: VHOG:0000601 +xref: Wikipedia:Spinal_cord +xref: XAO:0000020 +xref: ZFA:0000075 +is_a: UBERON:0000489 ! cavitated compound organ +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0005174 ! dorsal region element +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: BFO:0000050 UBERON:0001017 ! part of central nervous system + +[Term] +id: UBERON:0002241 +name: chondrocranium +def: "Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD]." [http://medical-dictionary.thefreedictionary.com/chondrocranium, Wikipedia:Chondrocranium] +subset: vertebrate_core +synonym: "calvarium" RELATED [MA:0000317] +synonym: "neurocranium" RELATED INCONSISTENT [MA:0000317] +xref: AAO:0010169 +xref: EHDAA2:0000243 +xref: EMAPA:17681 +xref: TAO:0001424 +xref: VHOG:0000288 +xref: Wikipedia:Chondrocranium +xref: ZFA:0001424 +is_a: UBERON:0011159 ! primary subdivision of cranial skeletal system + +[Term] +id: UBERON:0002276 +name: lamina of spiral limbus +def: "The osseous spiral lamina consists of two plates of bone, and between these are the canals for the transmission of the filaments of the acoustic nerve. On the upper plate of that part of the lamina which is outside the vestibular membrane, the periosteum is thickened to form the limbus spiralis (or limbus laminæ spiralis), this ends externally in a concavity, the sulcus spiralis internus, which represents, on section, the form of the letter C. [WP,unvetted]." [Wikipedia:Limbus_laminae_spiralis] +subset: pheno_slim +subset: uberon_slim +synonym: "limbus lamina spiralis" EXACT [MA:0001191] +synonym: "limbus laminae spiralis" EXACT [FMA:77721] +synonym: "limbus laminae spiralis osseae" EXACT [] +synonym: "spiral limbus" RELATED [] +synonym: "spiral limbus lamina" EXACT [FMA:77721] +xref: EMAPA:35496 +xref: FMA:77721 +xref: MA:0001191 +xref: Wikipedia:Limbus_laminae_spiralis +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0001855 ! part of cochlear duct of membranous labyrinth + +[Term] +id: UBERON:0002298 +name: brainstem +def: "Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]." [ISBN:0471888893, MP:0005277, Wikipedia:Brainstem, ZFA:0001707] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "accessory medullary lamina of pallidum" RELATED [NeuroNames:236] +synonym: "brain stem" EXACT [ABA:BS] +synonym: "lamella pallidi incompleta" RELATED [NeuroNames:236] +synonym: "lamina medullaris accessoria" RELATED [NeuroNames:236] +synonym: "lamina medullaris incompleta pallidi" RELATED [NeuroNames:236] +synonym: "lamina pallidi incompleta" RELATED [NeuroNames:236] +synonym: "truncus encephali" EXACT [Wikipedia:Brainstem] +synonym: "truncus encephalicus" RELATED [BTO:0000146] +xref: BAMS:BS +xref: BIRNLEX:1565 +xref: BTO:0000146 +xref: CALOHA:TS-0093 +xref: EFO:0001962 +xref: EMAPA:32678 +xref: EV:0100241 +xref: FMA:79876 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236 +xref: MA:0000169 +xref: MBA:343 +xref: MESH:D001933 +xref: NCIT:C12441 +xref: SCTID:180925009 +xref: TAO:0002156 +xref: UMLS:C0006121 +xref: VHOG:0001457 +xref: Wikipedia:Brainstem +xref: ZFA:0001707 +is_a: UBERON:0002616 ! regional part of brain + +[Term] +id: UBERON:0002316 +name: white matter +def: "Neural tissue consisting of myelinated axons connecting grey matter areas of the central nervous system." [https://orcid.org/0000-0002-6601-2165, Wikipedia:White_matter] +subset: uberon_slim +subset: vertebrate_core +synonym: "CNS tract/commissure" EXACT [ZFA:0001682] +synonym: "CNS tracts and commissures" RELATED [TAO:0000145] +synonym: "CNS white matter" RELATED [TAO:0002143] +synonym: "neuronal white matter" EXACT [AEO:0001011] +synonym: "substantia alba" RELATED [Wikipedia:White_matter] +synonym: "white mater" RELATED [VHOG:0001764] +synonym: "white matter of neuraxis" EXACT [FMA:83929] +synonym: "white substance" EXACT [] +xref: AEO:0000139 +xref: AEO:0001011 +xref: EMAPA:35927 +xref: FMA:83929 +xref: HBA:9218 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2870 +xref: MA:0001135 +xref: NCIT:C33892 +xref: NLX:412 +xref: NLXANAT:101177 +xref: OpenCyc:Mx4rwOAsDZwpEbGdrcN5Y29ycA +xref: PBA:294022044 +xref: TAO:0000145 +xref: TAO:0002142 +xref: TAO:0002143 +xref: UMLS:C0682708 +xref: VHOG:0001764 +xref: Wikipedia:White_matter +xref: ZFA:0001682 +is_a: UBERON:0011215 ! central nervous system cell part cluster + +[Term] +id: UBERON:0002323 +name: coelemic cavity lumen +def: "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities." [BTO:0001707] +subset: uberon_slim +subset: vertebrate_core +synonym: "body cavity" BROAD [BTO:0001707] +synonym: "celom" RELATED [BTO:0001707] +synonym: "coelom" RELATED [] +synonym: "coelome" RELATED [BTO:0001707] +synonym: "coelomic cavity" EXACT [EHDAA2:0000267] +synonym: "coelomic cavity lumen" EXACT [EHDAA2:0000267] +synonym: "hemocoel" RELATED [FBbt:00005060] +synonym: "main body cavity" EXACT [] +synonym: "space of body compartment" EXACT [FMA:85006] +synonym: "ventral body cavity" NARROW [NCBITaxon:7742] +xref: AEO:0000186 +xref: BTO:0001707 +xref: EHDAA2:0000267 +xref: FBbt:00005060 +xref: FMA:85006 +xref: galen:BodyCavity +xref: NCIT:C25444 +xref: RETIRED_EHDAA2:0003186 +xref: SCTID:361348008 +xref: TAO:0001438 +xref: UMLS:C0333343 +xref: ZFA:0001438 +is_a: UBERON:0002553 ! anatomical cavity + +[Term] +id: UBERON:0002328 +name: notochord +def: "A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube." [http://tolweb.org/Chordata/2499, https://github.com/obophenotype/uberon/issues/25, https://github.com/obophenotype/uberon/issues/271, ISBN:0815318960, Wikipedia:Notochord] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "embryonic notocord" EXACT [] +synonym: "notochorda" RELATED [Wikipedia:Notochord] +synonym: "notocord" EXACT [ZFA:0000135] +xref: AAO:0000327 +xref: BTO:0001768 +xref: CALOHA:TS-0690 +xref: EHDAA2:0001277 +xref: EHDAA:1241 +xref: EHDAA:6021 +xref: EMAPA:16191 +xref: EV:0100002 +xref: FMA:85521 +xref: GAID:1311 +xref: http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg +xref: MAT:0000281 +xref: MESH:A16.254.610 +xref: NCIT:C12463 +xref: SCTID:308820002 +xref: TAO:0000135 +xref: UMLS:C0028439 +xref: VHOG:0000199 +xref: VSAO:0000032 +xref: Wikipedia:Notochord +xref: XAO:0000055 +xref: ZFA:0000135 +is_a: UBERON:0000481 ! multi-tissue structure +is_a: UBERON:0004121 ! ectoderm-derived structure +relationship: BFO:0000050 UBERON:0011137 ! part of axial skeletal system + +[Term] +id: UBERON:0002329 +name: somite +def: "Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm." [DOI:10.1111/j.1439-0426.2012.01987.x, Wikipedia:Somite] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "epimere" RELATED [ISBN:0073040584] +synonym: "epimere mesoderm" RELATED [] +synonym: "epithelial somite" RELATED [https://github.com/obophenotype/uberon/wiki/The-neural-crest] +synonym: "mesodermal cluster" BROAD [GO:0001756] +synonym: "somites" RELATED [] +synonym: "somitic mesoderm" RELATED [] +synonym: "somitus" RELATED [Wikipedia:Somite] +xref: AAO:0010569 +xref: AEO:0001015 +xref: BTO:0001558 +xref: EHDAA2:0003436 +xref: EHDAA:366 +xref: EHDAA:699 +xref: EMAPA:31169 +xref: FMA:85522 +xref: GAID:1306 +xref: MAT:0000068 +xref: MESH:A16.254.425.660.750 +xref: MIAA:0000068 +xref: NCIT:C34302 +xref: TAO:0000155 +xref: UMLS:C0376449 +xref: VHOG:0000191 +xref: Wikipedia:Somite +xref: XAO:0000058 +xref: ZFA:0000155 +is_a: UBERON:0005423 ! developing anatomical structure +is_a: UBERON:0007503 ! epithelial vesicle + +[Term] +id: UBERON:0002330 +name: exocrine system +def: "Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]." [Wikipedia:Exocrine_gland] +subset: pheno_slim +subset: uberon_slim +synonym: "exocrine glandular system" EXACT [EHDAA2:0002225] +xref: CALOHA:TS-2057 +xref: EHDAA2:0002225 +xref: EMAPA:35329 +xref: FMA:85539 +xref: MA:0002411 +xref: NCIT:C12957 +xref: UMLS:C1516995 +xref: Wikipedia:Exocrine_gland +xref: WikipediaCategory:Exocrine_system +is_a: UBERON:0000467 ! anatomical system + +[Term] +id: UBERON:0002342 +name: neural crest +def: "A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]." [MP:0009846] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "crista neuralis" RELATED [Wikipedia:Neural_crest] +synonym: "NC" EXACT [XAO:0000048] +synonym: "neural crest material" RELATED [VHOG:0000057] +xref: AAO:0010578 +xref: BTO:0001764 +xref: CALOHA:TS-0676 +xref: EHDAA2:0004419 +xref: EMAPA:32737 +xref: FMA:86666 +xref: GAID:1310 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1366 +xref: MAT:0000066 +xref: MESH:A16.254.600 +xref: MIAA:0000066 +xref: NCIT:C34222 +xref: SCTID:361462002 +xref: TAO:0000045 +xref: UMLS:C0027789 +xref: VHOG:0000057 +xref: Wikipedia:Neural_crest +xref: XAO:0000048 +xref: ZFA:0000045 +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010316 ! germ layer / neural crest +relationship: BFO:0000050 UBERON:0002346 ! part of neurectoderm + +[Term] +id: UBERON:0002346 +name: neurectoderm +def: "Embryonic ectoderm that gives rise to nervous tissue." [Wikipedia:Neuroectoderm] +subset: uberon_slim +subset: vertebrate_core +synonym: "epithelium tubi neuralis; neuroectoderma" RELATED [Wikipedia:Neuroectoderm] +synonym: "neuaral ectoderm" RELATED [] +synonym: "neural ectoderm" EXACT [] +synonym: "neuroectoderm" EXACT [] +synonym: "presumptive central nervous system" RELATED [] +synonym: "ventral neurogenic region" RELATED [VHOG:0000150] +xref: AAO:0011074 +xref: BILA:0000039 +xref: CALOHA:TS-1212 +xref: EHDAA2:0001248 +xref: EHDAA:1498 +xref: EHDAA:255 +xref: EMAPA:16073 +xref: EV:0100004 +xref: FBbt:00001061 +xref: FMA:87657 +xref: MAT:0000176 +xref: MIAA:0000176 +xref: NCIT:C34228 +xref: TAO:0001120 +xref: UMLS:C1518271 +xref: VHOG:0000150 +xref: Wikipedia:Neuroectoderm +xref: XAO:0000042 +xref: ZFA:0001120 +is_a: UBERON:0000923 ! germ layer +is_a: UBERON:0004121 ! ectoderm-derived structure + +[Term] +id: UBERON:0002355 +name: pelvic region of trunk +def: "The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs." [http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/720, Wikipedia:Pelvis] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "lesser pelvis" EXACT [FMA:9578] +synonym: "pelvic region" EXACT [] +synonym: "pelvis" EXACT [FMA:9578, MA:0000030] +synonym: "pelvis region" EXACT [] +synonym: "true pelvis" EXACT [FMA:9578] +xref: BTO:0001006 +xref: CALOHA:TS-2227 +xref: EFO:0002805 +xref: EMAPA:35931 +xref: EV:0100012 +xref: FMA:9578 +xref: GAID:87 +xref: galen:Pelvis +xref: MA:0000030 +xref: MESH:A01.673 +xref: NCIT:C12767 +xref: OpenCyc:Mx4rvVjiTJwpEbGdrcN5Y29ycA +xref: SCTID:229765004 +xref: UMLS:C0030797 +xref: Wikipedia:Pelvis +is_a: UBERON:0000475 ! organism subdivision +relationship: BFO:0000050 UBERON:0002417 ! part of abdominal segment of trunk + +[Term] +id: UBERON:0002365 +name: exocrine gland +def: "A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas." [Wikipedia:Exocrine_gland] +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +synonym: "ducted gland" EXACT [AEO:0000097] +synonym: "glandula exocrina" EXACT [Wikipedia:Exocrine_gland] +xref: AEO:0000097 +xref: BTO:0000765 +xref: CALOHA:TS-2012 +xref: EHDAA2:0003097 +xref: EMAPA:35327 +xref: FMA:9596 +xref: GAID:34 +xref: MA:0002564 +xref: MESH:D005088 +xref: NCIT:C12712 +xref: SCTID:115976003 +xref: UMLS:C0015282 +xref: Wikipedia:Exocrine_gland +is_a: UBERON:0002530 ! gland +relationship: BFO:0000050 UBERON:0002330 ! part of exocrine system + +[Term] +id: UBERON:0002371 +name: bone marrow +def: "The soft tissue that fills the cavities of bones." [MGI:cwg, MP:0002397] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "medulla of bone" RELATED [BTO:0000141] +synonym: "medulla ossea" EXACT [BTO:0000141, FMA:9608] +synonym: "medulla ossium" EXACT [BTO:0000141, Wikipedia:Bone_marrow] +synonym: "medullary bone" RELATED [] +xref: AAO:0011007 +xref: BTO:0000141 +xref: BTO:0000829 +xref: CALOHA:TS-0087 +xref: EFO:0000868 +xref: EMAPA:32760 +xref: EV:0100046 +xref: FMA:9608 +xref: GAID:1287 +xref: galen:BoneMarrow +xref: MA:0000134 +xref: MAT:0000084 +xref: MESH:D001853 +xref: MIAA:0000084 +xref: NCIT:C12431 +xref: OpenCyc:Mx4rvVm-FpwpEbGdrcN5Y29ycA +xref: SCTID:421320006 +xref: UMLS:C0005953 +xref: VHOG:0001218 +xref: Wikipedia:Bone_marrow +xref: XAO:0000123 +is_a: UBERON:0000479 ! tissue +relationship: BFO:0000050 UBERON:0001474 ! part of bone element +relationship: BFO:0000050 UBERON:0002390 ! part of hematopoietic system +relationship: BFO:0000050 UBERON:0002405 ! part of immune system + +[Term] +id: UBERON:0002384 +name: connective tissue +def: "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, https://github.com/obophenotype/uberon/issues/23, PSPUB:0000170, VSAO:0000017] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "Bindegewebe" RELATED [BTO:0000421] +synonym: "portion of connective tissue" EXACT [FMA:9640] +synonym: "textus connectivus" EXACT [] +xref: AAO:0000098 +xref: BTO:0000421 +xref: CALOHA:TS-2009 +xref: EFO:0000952 +xref: EMAPA:35251 +xref: FMA:9640 +xref: GAID:100 +xref: galen:ConnectiveTissue +xref: MA:0000011 +xref: MAT:0000301 +xref: MESH:D003238 +xref: MIAA:0000301 +xref: NCIT:C12374 +xref: OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA +xref: SCTID:361919005 +xref: TAO:0001641 +xref: UMLS:C0009780 +xref: VSAO:0000017 +xref: XAO:0001017 +xref: ZFA:0001632 +is_a: UBERON:0000479 ! tissue + +[Term] +id: UBERON:0002385 +name: muscle tissue +def: "Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]." [GO:0060537, https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764, Wikipedia:Muscle_tissue] +subset: uberon_slim +synonym: "muscular tissue" EXACT SENSU [] +synonym: "portion of muscle tissue" EXACT [FMA:9641] +synonym: "textus muscularis" EXACT [] +xref: AAO:0000306 +xref: AEO:0000122 +xref: CALOHA:TS-0642 +xref: EHDAA2:0003122 +xref: EMAPA:32715 +xref: FMA:9641 +xref: galen:MuscleTissue +xref: MA:0002437 +xref: MESH:D009132 +xref: NCIT:C12435 +xref: SCTID:91727004 +xref: UMLS:C2328219 +xref: Wikipedia:Muscle_tissue +is_a: UBERON:0000479 ! tissue +is_a: UBERON:0004120 ! mesoderm-derived structure +relationship: BFO:0000050 UBERON:0001015 ! part of musculature + +[Term] +id: UBERON:0002386 +name: forelimb zeugopod +def: "The middle limb segment of the pectoral free limb, between the autopod and stylopod segments. Includes as parts the forelimb zeugopodial skeleton, which includes as parts the radius and ulna, or their cartilage precursors, or evolutionary variants." [PHENOSCAPE:curators] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "antebrachial region" EXACT [] +synonym: "antebrachium" EXACT [VSAO:0005058, Wikipedia:Forearm] +synonym: "antebrachium" RELATED [Wikipedia:Forearm] +synonym: "antibrachium" EXACT [] +synonym: "arm middle limb segment" EXACT [OBOL:automatic] +synonym: "arm zeugopod" EXACT [OBOL:automatic] +synonym: "brachial region middle limb segment" EXACT [OBOL:automatic] +synonym: "brachial region zeugopod" EXACT [OBOL:automatic] +synonym: "fore epipodium" RELATED [] +synonym: "forearm" EXACT [] +synonym: "forelimb epipodium" EXACT [] +synonym: "forelimb zeugopodium" EXACT [] +synonym: "forelimb zygopod" EXACT [] +synonym: "intermediate segment of free upper limb" EXACT [] +synonym: "lower arm" EXACT HUMAN_PREFERRED [MA:0000034] +synonym: "lower segment of arm" EXACT [] +synonym: "middle limb segment of arm" EXACT [OBOL:automatic] +synonym: "middle limb segment of brachial region" EXACT [OBOL:automatic] +synonym: "middle limb segment of forelimb" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "middle limb segment of proximal segment of free upper limb" EXACT [OBOL:automatic] +synonym: "regio antebrachialis" EXACT [FMA:9663, FMA:TA] +synonym: "wing zeugopod" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +synonym: "zeugopod of arm" EXACT [] +synonym: "zeugopod of brachial region" EXACT [OBOL:automatic] +synonym: "zeugopod of forelimb" EXACT [] +synonym: "zeugopod of proximal segment of free upper limb" EXACT [OBOL:automatic] +xref: BTO:0001447 +xref: CALOHA:TS-2205 +xref: EFO:0003053 +xref: EHDAA2:0000553 +xref: EHDAA:4172 +xref: EHDAA:6218 +xref: EMAPA:17417 +xref: FMA:9663 +xref: GAID:55 +xref: galen:Forearm +xref: MA:0000034 +xref: MESH:D005542 +xref: NCIT:C32628 +xref: OpenCyc:Mx4rvVjnmpwpEbGdrcN5Y29ycA +xref: SCTID:362741001 +xref: UMLS:C0016536 +xref: VHOG:0000341 +xref: VSAO:0005058 +xref: Wikipedia:Forearm +is_a: UBERON:0002471 ! zeugopod +is_a: UBERON:0008785 ! upper limb segment +relationship: BFO:0000050 UBERON:0001460 ! part of arm + +[Term] +id: UBERON:0002387 +name: pes +def: "Distal portion of the hind limb, including tarsal region, metatarsal region and digits." [Wikipedia:Foot, Wikipedia:Pes_(anatomy)] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "foot" EXACT HUMAN_PREFERRED [MA:0000044] +synonym: "hind foot" NARROW [] +synonym: "hind limb autopodium" RELATED [VHOG:0000350] +synonym: "hind paw" NARROW SENSU [EMAPA:17428, OBOL:automatic] +synonym: "hind-paw" NARROW SENSU [EMAPA:17428] +synonym: "hindfeet" NARROW [] +synonym: "hindfoot" NARROW [] +synonym: "hindfoot of quadruped" NARROW [] +synonym: "hindlimb autopod" EXACT [OBOL:automatic] +synonym: "hindlimb autopodium" EXACT [OBOL:automatic] +synonym: "hindlimb distal free limb segment" EXACT [OBOL:automatic] +synonym: "hindpaw" NARROW SENSU [MA:0000044] +synonym: "pes" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "terminal segment of free lower limb" EXACT [] +xref: BTO:0000476 +xref: CALOHA:TS-0377 +xref: EFO:0003065 +xref: EHDAA2:0000546 +xref: EMAPA:17459 +xref: FMA:9664 +xref: GAID:40 +xref: galen:Foot +xref: MA:0000044 +xref: MESH:D005528 +xref: NCIT:C32622 +xref: OpenCyc:Mx4rvVi-k5wpEbGdrcN5Y29ycA +xref: SCTID:302545001 +xref: UMLS:C0016504 +xref: VHOG:0000350 +xref: Wikipedia:Pes_(anatomy) +is_a: UBERON:0002470 ! autopod region +is_a: UBERON:0008784 ! lower limb segment + +[Term] +id: UBERON:0002389 +name: manual digit +def: "A digit that is part of a manus (hand)." [http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +subset: uberon_slim +synonym: "digit of hand" EXACT [FMA:9666] +synonym: "digit of manus" EXACT [] +synonym: "digitus manus" EXACT [] +synonym: "finger" EXACT [FMA:9666] +synonym: "fore digit" EXACT [AAO:0000857, XAO:0003036] +synonym: "forelimb digit" EXACT [] +synonym: "hand digit" EXACT [MA:0000041] +synonym: "manual digit (phalangeal portion) plus soft tissue" EXACT COMPARATIVE_PREFERRED [http://orcid.org/0000-0002-6601-2165] +xref: AAO:0000857 +xref: BTO:0004669 +xref: EHDAA2:0000404 +xref: EMAPA:32642 +xref: FMA:9666 +xref: GAID:57 +xref: galen:Finger +xref: MA:0000041 +xref: MESH:D005385 +xref: NCIT:C32608 +xref: NLXANAT:20090602 +xref: OpenCyc:Mx4rvVi_f5wpEbGdrcN5Y29ycA +xref: SCTID:283992002 +xref: UMLS:C0016129 +xref: Wikipedia:Finger +xref: XAO:0003036 +is_a: UBERON:0002544 ! digit +relationship: BFO:0000050 UBERON:0012141 ! part of manual digitopodium region +relationship: BFO:0000050 UBERON:5002389 ! part of manual digit plus metapodial segment + +[Term] +id: UBERON:0002390 +name: hematopoietic system +def: "Anatomical system that is involved in the production of hematopoietic cells." [Wikipedia:Haematopoiesis] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "Blutbildungssystem" RELATED [BTO:0000570] +synonym: "haematological system" EXACT [] +synonym: "haematopoietic system" RELATED [] +synonym: "haemopoietic system" EXACT [] +synonym: "hematological system" RELATED [] +synonym: "hematolymphoid system" RELATED [] +synonym: "hemopoietic system" RELATED [] +synonym: "organa haemopoietica" EXACT [] +xref: AAO:0011002 +xref: BTO:0000570 +xref: CALOHA:TS-0449 +xref: EFO:0000798 +xref: EMAPA:35402 +xref: EV:0100045 +xref: FMA:9667 +xref: GAID:1008 +xref: MA:0002434 +xref: MAT:0000022 +xref: MESH:D006413 +xref: MIAA:0000022 +xref: NCIT:C12909 +xref: SCTID:362587009 +xref: TAO:0005023 +xref: UMLS:C0018957 +xref: VHOG:0001624 +xref: Wikipedia:Haematopoiesis +xref: XAO:0000122 +xref: ZFA:0005023 +is_a: UBERON:0000467 ! anatomical system +is_a: UBERON:0004120 ! mesoderm-derived structure +relationship: BFO:0000050 UBERON:0002193 ! part of hemolymphoid system + +[Term] +id: UBERON:0002391 +name: lymph +def: "Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]." [Wikipedia:Lymph] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "lympha" RELATED [Wikipedia:Lymph] +xref: BTO:0000855 +xref: CALOHA:TS-0580 +xref: EFO:0000871 +xref: ENVO:02000041 +xref: EV:0100049 +xref: FMA:9671 +xref: GAID:1186 +xref: galen:Lymph +xref: MA:0002520 +xref: MAT:0000055 +xref: MESH:A12.207.630 +xref: MIAA:0000055 +xref: NCIT:C13252 +xref: OpenCyc:Mx4rvpDOU5wpEbGdrcN5Y29ycA +xref: UMLS:C0024202 +xref: VHOG:0001590 +xref: Wikipedia:Lymph +xref: ZFA:0005658 +is_a: UBERON:0000179 ! haemolymphatic fluid +relationship: BFO:0000050 UBERON:0006558 ! part of lymphatic part of lymphoid system + +[Term] +id: UBERON:0002398 +name: manus +def: "Distal segment of the fore limb, including carpal region, metacarpal region and digits." [Wikipedia:Hand, Wikipedia:Manus_(anatomy)] +subset: pheno_slim +subset: uberon_slim +synonym: "fore foot" NARROW INCONSISTENT [] +synonym: "fore paw" NARROW SENSU [EMAPA:17428, OBOL:automatic] +synonym: "fore-paw" NARROW SENSU [EMAPA:17428] +synonym: "forefeet" NARROW [] +synonym: "forefoot" NARROW INCONSISTENT [] +synonym: "forefoot of quadruped" NARROW [] +synonym: "forelimb autopod" EXACT [OBOL:automatic] +synonym: "forelimb autopodium" EXACT [OBOL:automatic] +synonym: "forepaw" NARROW SENSU [MA:0000037] +synonym: "hand" EXACT HUMAN_PREFERRED [MA:0000037] +synonym: "hand region" EXACT [EHDAA2:0000728] +synonym: "terminal segment of free upper limb" EXACT [] +xref: AAO:0010803 +xref: BTO:0004668 +xref: CALOHA:TS-2213 +xref: EHDAA2:0000728 +xref: EMAPA:17428 +xref: FMA:9712 +xref: GAID:56 +xref: galen:Hand +xref: MA:0000037 +xref: MESH:D006225 +xref: NCIT:C32712 +xref: NLXANAT:20090603 +xref: OpenCyc:Mx4rvViGVZwpEbGdrcN5Y29ycA +xref: SCTID:302539009 +xref: UMLS:C0018563 +xref: VHOG:0000344 +xref: Wikipedia:Manus_(anatomy) +is_a: UBERON:0002470 ! autopod region +is_a: UBERON:0008785 ! upper limb segment + +[Term] +id: UBERON:0002405 +name: immune system +def: "Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies." [Wikipedia:Immune_system] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +xref: AAO:0011003 +xref: BILA:0000104 +xref: BTO:0005810 +xref: FMA:9825 +xref: GAID:328 +xref: MA:0002711 +xref: MESH:D007107 +xref: NCIT:C12735 +xref: OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA +xref: SCTID:362590003 +xref: TAO:0001159 +xref: UMLS:C0020962 +xref: VHOG:0001247 +xref: Wikipedia:Immune_system +xref: XAO:0003152 +xref: ZFA:0001159 +is_a: UBERON:0000467 ! anatomical system + +[Term] +id: UBERON:0002410 +name: autonomic nervous system +def: "The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO]." [GO:0048483] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "ANS" RELATED [] +synonym: "autonomic division of peripheral nervous system" EXACT [FMA:65553] +synonym: "autonomic part of peripheral nervous system" EXACT [FMA:65553] +synonym: "divisio autonomica systematis nervosi peripherici" EXACT [FMA:TA] +synonym: "divisio autonomica systematis nervosi peripherici" RELATED [Wikipedia:Autonomic_nervous_system] +synonym: "pars autonomica systematis nervosi peripherici" EXACT [FMA:TA] +synonym: "peripheral autonomic nervous system" EXACT [FMA:65553] +synonym: "visceral nervous system" EXACT [] +xref: AAO:0000033 +xref: BIRNLEX:1123 +xref: BTO:0002507 +xref: CALOHA:TS-2001 +xref: EHDA:10095 +xref: EHDAA2:0000158 +xref: EHDAA:3767 +xref: EMAPA:16984 +xref: FMA:65553 +xref: GAID:706 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2054 +xref: MA:0000219 +xref: MESH:D001341 +xref: NCIT:C12673 +xref: SCTID:362481007 +xref: TAO:0001574 +xref: UMLS:C0004388 +xref: UMLS:C1305381 +xref: VHOG:0000396 +xref: Wikipedia:Autonomic_nervous_system +xref: ZFA:0001574 +is_a: UBERON:0011216 ! organ system subdivision +relationship: BFO:0000050 UBERON:0000010 ! part of peripheral nervous system + +[Term] +id: UBERON:0002416 +name: integumental system +def: "Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle." [CARO:0002001, http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/29] +subset: efo_slim +subset: grouping_class +subset: pheno_slim +synonym: "body surface" RELATED [] +synonym: "dermal system" RELATED [MIAA:0000033] +synonym: "external covering of organism" RELATED [] +synonym: "integumentary system" EXACT [FMA:72979] +synonym: "integumentum commune" RELATED [Wikipedia:Integumentary_system] +synonym: "organism surface" RELATED [EHDAA2:0003154] +synonym: "surface" RELATED [BILA:0000118] +xref: AEO:0000154 +xref: BILA:0000118 +xref: CALOHA:TS-1299 +xref: CARO:0002001 +xref: EFO:0000807 +xref: EHDAA2:0000836 +xref: EHDAA2_RETIRED:0003154 +xref: EHDAA:6520 +xref: EMAPA:17524 +xref: EV:0100151 +xref: FBbt:00004969 +xref: FMA:72979 +xref: galen:Surface +xref: HAO:0000421 +xref: MA:0000014 +xref: MAT:0000033 +xref: MESH:D034582 +xref: MIAA:0000033 +xref: NCIT:C12907 +xref: SCTID:361692004 +xref: TADS:0000108 +xref: UMLS:C0037267 +xref: VHOG:0000403 +xref: Wikipedia:Integumentary_system +xref: XAO:0000176 +is_a: UBERON:0000467 ! anatomical system + +[Term] +id: UBERON:0002417 +name: abdominal segment of trunk +def: "The abdominal segment of the torso." [Wikipedia:Lumbar] +synonym: "abdomen/pelvis/perineum" RELATED [MA:0000021] +synonym: "lower body" RELATED [MA:0000021] +synonym: "lower trunk" RELATED [FMA:259211] +synonym: "lumbar region" RELATED [https://orcid.org/0000-0002-6601-2165] +xref: EMAPA:35104 +xref: FMA:259211 +xref: MA:0000021 +xref: SCTID:362875007 +xref: Wikipedia:Lumbar +is_a: UBERON:0009569 ! subdivision of trunk +is_a: UBERON:0011676 ! subdivision of organism along main body axis + +[Term] +id: UBERON:0002418 +name: cartilage tissue +def: "Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, https://github.com/obophenotype/uberon/issues/37, https://sourceforge.net/p/obo/vertebrate-skeletal-anatomy-vsao-term-requests/5, PSPUB:0000170, VSAO:0000040] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "cartilage" RELATED [] +synonym: "cartilage tissue" EXACT [FMA:37377] +synonym: "cartilages" RELATED [VHOG:0001207] +synonym: "cartilaginous tissue" EXACT [] +synonym: "chondrogenic tissue" EXACT [VSAO:0000040] +synonym: "portion of cartilage tissue" RELATED [FMA:37377] +xref: AAO:0000060 +xref: AEO:0000087 +xref: BTO:0000206 +xref: EFO:0000949 +xref: EHDAA2:0003087 +xref: EMAPA:32730 +xref: EV:0100141 +xref: FMA:37377 +xref: GAID:99 +xref: galen:Cartilage +xref: MA:0000104 +xref: MAT:0000189 +xref: MESH:D002356 +xref: MIAA:0000189 +xref: NCIT:C12373 +xref: NCIT:C32268 +xref: OpenCyc:Mx4rvVjeOZwpEbGdrcN5Y29ycA +xref: SCTID:309312004 +xref: TAO:0001501 +xref: UMLS:C0007301 +xref: VHOG:0001207 +xref: VSAO:0000040 +xref: Wikipedia:Cartilage +xref: XAO:0000170 +xref: ZFA:0005622 +is_a: UBERON:0004755 ! skeletal tissue + +[Term] +id: UBERON:0002419 +name: skin gland +def: "A gland that is part of a skin of body [Automatically generated definition]." [OBOL:automatic] +subset: organ_slim +synonym: "glandulae cutis" EXACT [FMA:71878, FMA:TA] +synonym: "set of skin glands" RELATED [FMA:71878] +synonym: "skin glands" RELATED [] +synonym: "skin glands set" RELATED [] +xref: EMAPA:35774 +xref: FMA:71878 +xref: MA:0000146 +xref: SCTID:110485007 +is_a: UBERON:0003297 ! gland of integumental system +is_a: UBERON:0006003 ! integumentary adnexa +relationship: BFO:0000050 UBERON:0002097 ! part of skin of body + +[Term] +id: UBERON:0002428 +name: limb bone +def: "A bone that is part of a limb [Automatically generated definition]." [OBOL:automatic] +subset: efo_slim +subset: pheno_slim +synonym: "bone of extremity" EXACT [] +synonym: "bone of limb" EXACT [OBOL:automatic] +synonym: "free limb bone" EXACT [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] +xref: EFO:0000945 +xref: MAT:0000151 +xref: MIAA:0000151 +xref: NCIT:C32223 +xref: SCTID:304149004 +xref: UMLS:C0582791 +is_a: UBERON:0002513 ! endochondral bone +is_a: UBERON:0004375 ! bone of free limb or fin +is_a: UBERON:0015061 ! limb endochondral element + +[Term] +id: UBERON:0002437 +name: cerebral hemisphere white matter +def: "White matter that is part of a cerebral hemisphere." [https://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "cerebral hemisphere white matter" EXACT [] +synonym: "cerebral white matter" EXACT [MA:0000945] +synonym: "hemisphere white matter" RELATED [] +synonym: "region of cerebral white matter" RELATED [FMA:256174] +synonym: "substantia medullaris cerebri" RELATED [NeuroNames:189] +synonym: "white matter structure of cerebral hemisphere" EXACT [FMA:61822] +xref: BAMS:cw +xref: BIRNLEX:711 +xref: BTO:0000236 +xref: CALOHA:TS-2362 +xref: EMAPA:35237 +xref: FMA:241998 +xref: FMA:256174 +xref: FMA:61822 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=189 +xref: MA:0000945 +xref: NCIT:C49347 +xref: SCTID:361691006 +xref: UMLS:C0152295 +xref: UMLS:C1284115 +is_a: UBERON:0011299 ! white matter of telencephalon +relationship: BFO:0000050 UBERON:0001869 ! part of cerebral hemisphere + +[Term] +id: UBERON:0002465 +name: lymphoid system +def: "The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP]." [Wikipedia:Lymphoid_system] +subset: uberon_slim +subset: vertebrate_core +synonym: "lymphatic circulatory system" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "lymphatic drainage system" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "lymphatic system" NARROW [ZFA:0000385] +synonym: "systema lymphoideum" RELATED [Wikipedia:Lymphoid_system] +xref: EHDAA2:0001043 +xref: EHDAA:8677 +xref: EMAPA:37664 +xref: FMA:74594 +xref: GAID:931 +xref: MA:0002435 +xref: MAT:0000197 +xref: MIAA:0000197 +xref: NCIT:C12746 +xref: OpenCyc:Mx4rwQAKT5wpEbGdrcN5Y29ycA +xref: SCTID:362589007 +xref: TAO:0000385 +xref: UMLS:C0024235 +xref: VHOG:0000842 +xref: Wikipedia:Lymphoid_system +xref: XAO:0003199 +xref: ZFA:0000385 +is_a: UBERON:0000467 ! anatomical system +relationship: BFO:0000050 UBERON:0002193 ! part of hemolymphoid system +relationship: BFO:0000050 UBERON:0002405 ! part of immune system + +[Term] +id: UBERON:0002470 +name: autopod region +def: "Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot." [https://github.com/obophenotype/uberon/issues/303, https://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "autopod" BROAD [MA:0002714] +synonym: "autopodial element" RELATED [] +synonym: "autopodial limb segment" EXACT [MA:th] +synonym: "autopodial segment" EXACT [] +synonym: "autopodium" EXACT [] +synonym: "autopodium region" EXACT [] +synonym: "distal free limb segment" EXACT [FMA:83015] +synonym: "distal segment of free limb" EXACT [FMA:83015] +synonym: "distal segment of limb" RELATED [EMAPA:32722] +synonym: "manus/pes" RELATED [] +synonym: "paw" RELATED [] +synonym: "paw/hand/foot/hoof" RELATED [] +synonym: "pod" RELATED [] +xref: BTO:0004359 +xref: EFO:0000877 +xref: EMAPA:32722 +xref: FMA:83015 +xref: MA:0002714 +xref: MAT:0000091 +xref: MIAA:0000091 +xref: NCIT:C77660 +xref: SCTID:95936004 +xref: UMLS:C0687080 +is_a: UBERON:0002529 ! limb segment + +[Term] +id: UBERON:0002471 +name: zeugopod +def: "The middle free limb segment, between the autopod and stylopod segments. Includes as parts the zeugopodial skeleton. Examples: There are two types of zeugopod: forelimb zeugopod (aka forearm), hindlimb zeugopod (aka crus)." [https://github.com/obophenotype/uberon/issues/101, PHENOSCAPE:curators] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "epipodium" EXACT [MA:th] +synonym: "middle free limb segment" EXACT [FMA:83016] +synonym: "middle limb segment" EXACT [] +synonym: "middle part of limb" BROAD [] +synonym: "middle segment of free limb" RELATED [FMA:83016] +synonym: "zeugopod limb segment" EXACT [MA:th] +synonym: "zeugopodial limb segment" EXACT [MA:th] +synonym: "zeugopodium" EXACT [] +synonym: "zygopod" EXACT [] +synonym: "zygopodium" EXACT [] +xref: EFO:0000878 +xref: FMA:83016 +xref: MA:0002716 +xref: MAT:0000092 +xref: MIAA:0000092 +is_a: UBERON:0002529 ! limb segment + +[Term] +id: UBERON:0002472 +name: stylopod +def: "The proximal free limb segment. Includes as parts the stylopod skeleton." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: uberon_slim +synonym: "propodium" EXACT [MA:th] +synonym: "proximal free limb segment" EXACT [FMA:83014] +synonym: "proximal part of limb" BROAD [] +synonym: "proximal segment of free limb" RELATED [FMA:83014] +synonym: "stylopodial limb segment" EXACT [MA:th] +synonym: "stylopodium" EXACT [] +xref: EFO:0000879 +xref: FMA:83014 +xref: MA:0002717 +xref: MAT:0000093 +xref: MIAA:0000093 +is_a: UBERON:0002529 ! limb segment + +[Term] +id: UBERON:0002481 +name: bone tissue +def: "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000047] +subset: pheno_slim +subset: uberon_slim +synonym: "bone" RELATED [MESH:A02.835.232] +synonym: "calcium tissue" EXACT [] +synonym: "mineralized bone tissue" NARROW [XAO:0004040] +synonym: "osseous tissue" EXACT [] +synonym: "osteogenic tissue" EXACT [VSAO:curator] +synonym: "portion of bone tissue" RELATED [FMA:224804] +xref: CALOHA:TS-2011 +xref: EMAPA:35179 +xref: FMA:224804 +xref: galen:BoneTissue +xref: MA:0002780 +xref: MESH:D001842 +xref: NCIT:C13076 +xref: UMLS:C0391978 +xref: VSAO:0000047 +xref: Wikipedia:Bone_tissue +xref: XAO:0004040 +xref: ZFA:0005621 +is_a: UBERON:0004755 ! skeletal tissue +relationship: BFO:0000050 UBERON:0001474 ! part of bone element + +[Term] +id: UBERON:0002495 +name: long bone +def: "A long bone is a bone that has a shaft and 2 ends and is longer than it is wide. Long bones have a thick outside layer of compact bone and an inner medullary cavity containing bone marrow. The ends of a long bone contain spongy bone and an epiphyseal plate or line depending on the stage of development. The epiphyseal plate is a hyaline cartilage, where new bone growth takes place, lengthening the bone prior to adulthood. Bone lengthening ceases when this cartilage is lost, leaving a remnant referred to as an epiphyseal line." [https://medlineplus.gov/ency/imagepages/9582.htm, Wikipedia:Long_bone] +subset: pheno_slim +subset: uberon_slim +synonym: "os longum" RELATED [BTO:0004256] +xref: BTO:0004256 +xref: EMAPA:35503 +xref: FMA:7474 +xref: galen:LongBone +xref: MA:0002802 +xref: NCIT:C33003 +xref: OpenCyc:Mx4rv6axr5wpEbGdrcN5Y29ycA +xref: SCTID:332709000 +xref: UMLS:C0222647 +xref: Wikipedia:Long_bone +is_a: UBERON:0001474 ! bone element +relationship: BFO:0000050 UBERON:0002091 ! part of appendicular skeleton + +[Term] +id: UBERON:0002499 +name: cochlear labyrinth +def: "The labyrinth is a system of fluid passages in the inner ear, including both the cochlea, which is part of the auditory system, and the vestibular system, which provides the sense of balance. It is named by analogy with the mythical maze that imprisoned the Minotaur, because of its appearance. The bony labyrinth, or osseous labyrinth, is the network of passages with bony walls lined with periosteum. The bony labyrinth is lined with the membranous labyrinth. There is a layer of perilymph between them. The three parts of the bony labyrinth are the vestibule of the ear, the semicircular canals, and the cochlea. The vestibular system is the region of the inner ear where the semicircular canals converge, close to the cochlea (the hearing organ). The vestibular system works with the visual system to keep objects in focus when the head is moving. Joint and muscle receptors also are important in maintaining balance. The brain receives, interprets, and processes the information from these systems that control our balance. [WP,unvetted]." [Wikipedia:Cochlear_labyrinth] +subset: pheno_slim +subset: uberon_slim +xref: BTO:0004686 +xref: EMAPA:36569 +xref: FMA:61259 +xref: MA:0002809 +xref: NCIT:C32336 +xref: UMLS:C0931689 +xref: Wikipedia:Cochlear_labyrinth +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0001849 ! part of membranous labyrinth + +[Term] +id: UBERON:0002513 +name: endochondral bone +def: "Replacement bone that forms within cartilage." [GO:0001958, GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, https://github.com/obophenotype/uberon/issues/54, VSAO:0000145] +subset: uberon_slim +subset: vertebrate_core +synonym: "cartilaginous bone" RELATED [BTO:0002157] +synonym: "endochondral bones" RELATED [ZFA:0001591] +synonym: "ossified chondrogenic bone" EXACT [VSAO:0000145] +xref: AAO:0010776 +xref: AEO:0000083 +xref: BTO:0002157 +xref: EHDAA2:0003083 +xref: FMA:24321 +xref: TAO:0001591 +xref: VSAO:0000145 +xref: XAO:0004018 +xref: ZFA:0001591 +is_a: UBERON:0001474 ! bone element +is_a: UBERON:0010363 ! endochondral element + +[Term] +id: UBERON:0002517 +name: basicranium +def: "The base of skull is the most inferior area of the skull, composed of the endocranium and lower parts of the skull roof." [Wikipedia:Base_of_skull] +subset: pheno_slim +subset: uberon_slim +synonym: "base of cranium" EXACT [] +synonym: "base of skull" EXACT [FMA:52801] +synonym: "basis cranii" EXACT [FMA:52801, FMA:TA, Wikipedia:Base_of_skull] +synonym: "cranial base" EXACT [FMA:52801, MA:0002840] +xref: FMA:52801 +xref: MA:0002840 +xref: MESH:D019291 +xref: MFMO:0000044 +xref: NCIT:C12493 +xref: SCTID:181890004 +xref: UMLS:C0149543 +xref: Wikipedia:Base_of_skull +is_a: UBERON:0000075 ! subdivision of skeletal system +relationship: BFO:0000050 UBERON:0001703 ! part of neurocranium +relationship: BFO:0000050 UBERON:0002241 ! part of chondrocranium + +[Term] +id: UBERON:0002529 +name: limb segment +def: "A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles." [https://orcid.org/0000-0002-6601-2165] +synonym: "extremity part" RELATED [] +synonym: "free limb segment" EXACT [FMA:241863] +synonym: "limb region" RELATED [] +synonym: "region of limb" RELATED [] +synonym: "segment of limb" EXACT [] +synonym: "subdivision of limb" EXACT [] +xref: FMA:241863 +xref: MA:0002889 +xref: NCIT:C38630 +xref: UMLS:C1268195 +is_a: UBERON:0010538 ! paired limb/fin segment +relationship: BFO:0000050 UBERON:0002101 ! part of limb + +[Term] +id: UBERON:0002530 +name: gland +def: "An organ that functions as a secretory or excretory organ." [MGI:csmith, MP:0002163] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "Druese" RELATED [BTO:0000522] +synonym: "glandula" RELATED [BTO:0000522, Wikipedia:Gland] +synonym: "glandular organ" EXACT [http://orcid.org/0000-0002-6601-2165] +xref: AAO:0000212 +xref: AEO:0000096 +xref: BTO:0000522 +xref: EFO:0000797 +xref: EHDAA2:0003096 +xref: EHDAA:2161 +xref: EHDAA:4475 +xref: EHDAA:6522 +xref: EMAPA:18425 +xref: FBbt:00100317 +xref: FMA:7146 +xref: FMA:86294 +xref: galen:Gland +xref: HAO:0000375 +xref: MA:0003038 +xref: MAT:0000021 +xref: MIAA:0000021 +xref: NCIT:C13319 +xref: OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA +xref: SCTID:134358001 +xref: UMLS:C1285092 +xref: Wikipedia:Gland +xref: WikipediaCategory:Glands +is_a: UBERON:0000062 ! organ + +[Term] +id: UBERON:0002532 +name: epiblast (generic) +def: "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]." [Wikipedia:Epiblast, ZFIN:curator] +subset: early_development +subset: grouping_class +subset: uberon_slim +subset: vertebrate_core +synonym: "blastocyst" RELATED [] +synonym: "ectoblast" RELATED [MP:0003886] +synonym: "epiblast" EXACT [VHOG:0000243] +synonym: "epiblastus" RELATED [Wikipedia:Epiblast] +synonym: "primitive ectoderm" RELATED [VHOG:0000243] +xref: BTO:0004593 +xref: FMA:296704 +xref: MAT:0000067 +xref: MIAA:0000067 +xref: VHOG:0000243 +xref: Wikipedia:Epiblast +is_a: UBERON:0002050 ! embryonic structure + +[Term] +id: UBERON:0002539 +name: pharyngeal arch +def: "One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches." [http://orcid.org/0000-0002-6601-2165, PMID:16313389, ZFA:yb] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "arcus pharyngei" RELATED [Wikipedia:Pharyngeal_arch] +synonym: "branchial arch" NARROW [BTO:0001785, MP:0002884] +synonym: "pharyngeal arches" EXACT [] +synonym: "visceral arch" RELATED [] +xref: AAO:0010359 +xref: BTO:0001785 +xref: EFO:0000959 +xref: EHDAA:571 +xref: EMAPA:16117 +xref: FMA:293015 +xref: GAID:1292 +xref: MAT:0000242 +xref: MESH:A16.254.160 +xref: MIAA:0000242 +xref: NCIT:C34249 +xref: SCTID:308766004 +xref: TAO:0001306 +xref: UMLS:C0080322 +xref: VHOG:0000155 +xref: Wikipedia:Pharyngeal_arch +xref: XAO:0000096 +xref: ZFA:0001306 +is_a: UBERON:0000481 ! multi-tissue structure +is_a: UBERON:0010188 ! protuberance +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: BFO:0000050 UBERON:0008814 ! part of pharyngeal arch system +relationship: BFO:0000050 UBERON:0008816 ! part of embryonic head + +[Term] +id: UBERON:0002544 +name: digit +def: "A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans)." [http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/420] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "acropodial unit" EXACT [] +synonym: "digit (phalangeal portion) plus soft tissue" EXACT COMPARATIVE_PREFERRED [http://orcid.org/0000-0002-6601-2165] +synonym: "limb digit" EXACT [MA:0000690] +xref: AAO:0011126 +xref: EFO:0000881 +xref: EMAPA:32725 +xref: FMA:85518 +xref: galen:Digit +xref: MA:0000690 +xref: MAT:0000285 +xref: MIAA:0000285 +xref: NCIT:C40186 +xref: OpenCyc:Mx4rvzLD_ZwpEbGdrcN5Y29ycA +xref: SCTID:361367007 +xref: UMLS:C0582802 +xref: VHOG:0000944 +xref: Wikipedia:Digit_(anatomy) +xref: XAO:0003032 +is_a: UBERON:0005881 ! autopodial extension +relationship: BFO:0000050 UBERON:0012354 ! part of acropodium region +relationship: BFO:0000050 UBERON:5002544 ! part of digit plus metapodial segment + +[Term] +id: UBERON:0002546 +name: cranial placode +def: "Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic." [http://www.ncbi.nlm.nih.gov/books/NBK53175/, https://github.com/obophenotype/uberon/issues/135, https://github.com/seger/aao/issues/4, https://orcid.org/0000-0002-6601-2165, https://sourceforge.net/p/obo/xenopus-anatomy-xao-term-requests/11/] +subset: efo_slim +synonym: "cranial placodes" RELATED [XAO:0000305] +synonym: "ectodermal cranial placode" EXACT [UBERON:cjm] +synonym: "ectodermal placode" BROAD INCONSISTENT [FMA:293966, PMID:22512454] +synonym: "placode" BROAD [Wikipedia:Placode] +xref: AAO:0010466 +xref: EFO:0001650 +xref: FMA:293966 +xref: MAT:0000369 +xref: MIAA:0000369 +xref: XAO:0000305 +is_a: UBERON:0005085 ! ectodermal placode +relationship: BFO:0000050 UBERON:0000033 ! part of head + +[Term] +id: UBERON:0002553 +name: anatomical cavity +def: "Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina." [FMA:67552] +subset: upper_level +synonym: "cavity" BROAD [] +xref: BIRNLEX:1011 +xref: EMAPA:37442 +xref: FMA:67552 +xref: galen:Cavity +xref: MA:0002447 +xref: NCIT:C34007 +is_a: UBERON:0000464 ! anatomical space + +[Term] +id: UBERON:0002558 +name: organ cavity +subset: upper_level +synonym: "cavity of organ" EXACT [FMA:12237] +xref: BIRNLEX:1019 +xref: FMA:12237 +xref: SCTID:362606005 +is_a: UBERON:0002553 ! anatomical cavity + +[Term] +id: UBERON:0002600 +name: limbic lobe +def: "Part of cerebral hemisphere located on the medial surface, forming a ring around the brain stem." [BIRNLEX:1128] +subset: pheno_slim +subset: uberon_slim +synonym: "fornicate convolution" RELATED [NeuroNames:834] +synonym: "fornicate gyrus" EXACT [FMA:72719] +synonym: "fornicate lobe" RELATED [NeuroNames:834] +synonym: "grande lobe limbique of Broca" EXACT [] +synonym: "gyrus fornicatus" RELATED [NeuroNames:834] +synonym: "limbic lobe (carpenter)" EXACT [] +synonym: "lobus limbicus" RELATED [Wikipedia:Limbic_lobe] +xref: BAMS:Limbic_lobe +xref: BAMS:LL +xref: BIRNLEX:1128 +xref: CALOHA:TS-2061 +xref: DHBA:12155 +xref: FMA:72719 +xref: HBA:4219 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=834 +xref: SCTID:279215006 +xref: UMLS:C0458337 +xref: Wikipedia:Limbic_lobe +is_a: UBERON:0016526 ! lobe of cerebral hemisphere + +[Term] +id: UBERON:0002616 +name: regional part of brain +def: "Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia." [BIRNLEX:1167] +subset: non_informative +synonym: "anatomical structure of brain" EXACT [OBOL:automatic] +synonym: "biological structure of brain" EXACT [OBOL:automatic] +synonym: "brain anatomical structure" EXACT [OBOL:automatic] +synonym: "brain biological structure" EXACT [OBOL:automatic] +synonym: "brain part" EXACT [] +synonym: "neuraxis segment" EXACT [FMA:55676] +synonym: "neuroanatomical region" EXACT [] +synonym: "segment of brain" EXACT [BIRNLEX:1167] +xref: BIRNLEX:1167 +xref: FMA:55676 +xref: NCIT:C13031 +xref: SCTID:384763002 +xref: UMLS:C0445620 +is_a: UBERON:0000073 ! regional part of nervous system +relationship: BFO:0000050 UBERON:0000955 ! part of brain + +[Term] +id: UBERON:0002804 +name: left limbic lobe +def: "A limbic lobe that is part of a left cerebral hemisphere." [OBOL:automatic] +xref: BIRNLEX:1780 +xref: FMA:72981 +is_a: UBERON:0002600 ! limbic lobe +relationship: BFO:0000050 UBERON:0002812 ! part of left cerebral hemisphere + +[Term] +id: UBERON:0002805 +name: right limbic lobe +def: "A limbic lobe that is part of a right cerebral hemisphere." [OBOL:automatic] +xref: BIRNLEX:1781 +xref: FMA:72980 +is_a: UBERON:0002600 ! limbic lobe +relationship: BFO:0000050 UBERON:0002813 ! part of right cerebral hemisphere + +[Term] +id: UBERON:0002812 +name: left cerebral hemisphere +def: "A cerebral hemisphere that is in the left side of a brain." [OBOL:automatic] +synonym: "left hemisphere" EXACT [BIRNLEX:1795] +xref: BIRNLEX:1795 +xref: FMA:61819 +xref: NCIT:C32955 +xref: SCTID:362323007 +xref: UMLS:C0228176 +is_a: UBERON:0001869 ! cerebral hemisphere + +[Term] +id: UBERON:0002813 +name: right cerebral hemisphere +def: "A cerebral hemisphere that is in the right side of a brain." [OBOL:automatic] +synonym: "right hemisphere" EXACT [BIRNLEX:1797] +xref: BIRNLEX:1797 +xref: FMA:67292 +xref: NCIT:C33472 +xref: OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvigx5ZwpEbGdrcN5Y29ycA +xref: SCTID:362322002 +xref: UMLS:C0228175 +is_a: UBERON:0001869 ! cerebral hemisphere + +[Term] +id: UBERON:0003051 +name: ear vesicle +def: "An epithelial sac of invaginated ectoderm formed from the otic placode that gives rise to the structures of the inner ear[MP]." [MP:0009806, Wikipedia:Otic_vesicle] +subset: pheno_slim +subset: vertebrate_core +synonym: "acoustic vesicle" RELATED [VHOG:0001148] +synonym: "auditory vesicle" RELATED [BTO:0002661] +synonym: "otic vesicle" EXACT [MP:0004311] +synonym: "otocyst" RELATED [MP:0004311] +synonym: "OV" RELATED [] +xref: AAO:0011080 +xref: BTO:0002661 +xref: EHDAA2:0001342 +xref: EMAPA:16669 +xref: FMA:302920 +xref: NCIT:C34240 +xref: SCTID:308792006 +xref: TAO:0000051 +xref: UMLS:C1518678 +xref: VHOG:0001148 +xref: Wikipedia:Otic_vesicle +xref: XAO:0000006 +xref: ZFA:0000051 +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0006598 ! presumptive structure +is_a: UBERON:0007499 ! epithelial sac +relationship: BFO:0000050 UBERON:0000924 ! part of ectoderm + +[Term] +id: UBERON:0003052 +name: midbrain-hindbrain boundary +def: "The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate." [GO:0021555] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "isthmic organizer territory" RELATED [XAO:0000016] +synonym: "isthmo-cerebellar region" RELATED [VHOG:0000649] +synonym: "isthmus" RELATED [] +synonym: "isthmus/MHB" RELATED [Geisha:syn, NCBITaxon:8782] +synonym: "MHB" EXACT [] +synonym: "mid-hindbrain boundary" EXACT [] +synonym: "mid-hindbrain junction" EXACT [] +synonym: "midbrain hindbrain boundary" EXACT [] +xref: AAO:0011064 +xref: DMBA:16810 +xref: EHDAA2:0004395 +xref: EHDAA:5789 +xref: EMAPA:32857 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2076 +xref: NCIT:C93172 +xref: TAO:0000042 +xref: VHOG:0000649 +xref: XAO:0000016 +xref: ZFA:0000042 +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0007651 ! anatomical junction +relationship: BFO:0000050 UBERON:0000955 ! part of brain + +[Term] +id: UBERON:0003055 +name: periderm +def: "A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis." [ISBN:9780878932504] +subset: pheno_slim +subset: uberon_slim +synonym: "epidermis epithelial layer" RELATED [] +synonym: "epidermis outer layer" RELATED [] +synonym: "epitrichium" RELATED [MP:0013530] +synonym: "EVL" RELATED [ZFA:0001185] +synonym: "periderm" RELATED [] +synonym: "skin periderm" EXACT [EHDAA2:0001846] +xref: EHDAA2:0001846 +xref: EHDAA:6538 +xref: FMA:295662 +xref: NCIT:C34247 +xref: TAO:0001185 +xref: UMLS:C1518973 +xref: VHOG:0001680 +xref: XAO:0000029 +xref: ZFA:0001185 +is_a: UBERON:0000487 ! simple squamous epithelium +relationship: BFO:0000050 UBERON:0002199 ! part of integument + +[Term] +id: UBERON:0003056 +name: pre-chordal neural plate +def: "The portion of neural plate anterior to the mid-hindbrain junction." [XB:curator] +synonym: "anterior neural plate" RELATED [] +xref: AAO:0011084 +xref: TAO:0007016 +xref: VHOG:0001200 +xref: XAO:0000045 +xref: ZFA:0007016 +is_a: UBERON:0005291 ! embryonic tissue +relationship: BFO:0000050 UBERON:0003075 ! part of neural plate + +[Term] +id: UBERON:0003057 +name: chordal neural plate +def: "The portion of neural plate posterior to the mid-hindbrain junction." [XB:curator] +synonym: "posterior neural plate" RELATED [] +xref: TAO:0007017 +xref: VHOG:0001201 +xref: XAO:0000046 +xref: ZFA:0007017 +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0003075 ! part of neural plate + +[Term] +id: UBERON:0003059 +name: presomitic mesoderm +def: "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form." [ZFIN:curator] +subset: efo_slim +subset: pheno_slim +synonym: "presumptive somite mesoderm" RELATED [] +synonym: "PSM" RELATED [] +synonym: "segmental plate" EXACT [] +synonym: "somitogenic mesoderm" RELATED [] +synonym: "somitomeric mesoderm" RELATED [GO:0002075] +synonym: "unsegmented mesenchyme" RELATED [VHOG:0000559] +synonym: "unsegmented paraxial mesoderm" EXACT [https://orcid.org/0000-0002-6601-2165] +xref: AAO:0011086 +xref: EFO:0001982 +xref: EMAPA:16189 +xref: EMAPA:16752 +xref: TAO:0000279 +xref: VHOG:0000559 +xref: XAO:0000057 +xref: ZFA:0000279 +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0003077 ! part of paraxial mesoderm + +[Term] +id: UBERON:0003060 +name: pronephric duct +def: "In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]." [Wikipedia:Pronephric_duct] +subset: uberon_slim +synonym: "archinephric duct" RELATED [VHOG:0000082] +synonym: "ductus pronephricus" RELATED [Wikipedia:Pronephric_duct] +synonym: "pronephric ducts" RELATED [ZFA:0000150] +xref: AAO:0011088 +xref: NCIT:C34279 +xref: SCTID:361406002 +xref: TAO:0000150 +xref: UMLS:C1283945 +xref: VHOG:0000082 +xref: Wikipedia:Pronephric_duct +xref: XAO:0000063 +xref: ZFA:0000150 +is_a: UBERON:0009201 ! nephric duct +is_a: UBERON:0012275 ! meso-epithelium +relationship: BFO:0000050 UBERON:0002120 ! part of pronephros + +[Term] +id: UBERON:0003061 +name: blood island +def: "Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]." [Wikipedia:Blood_island_of_umbilical_vesicle] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "blood islands" EXACT [] +synonym: "caudal hematopoietic tissue" RELATED [] +synonym: "posterior blood island" RELATED [] +synonym: "posterior ICM" RELATED [] +synonym: "VBI" RELATED [] +synonym: "ventral blood island" RELATED [] +synonym: "ventral lateral plate mesoderm" BROAD [] +xref: AAO:0011006 +xref: EFO:0003489 +xref: EHDAA:207 +xref: NCIT:C34113 +xref: TAO:0000094 +xref: TE:E5.11.2.0.0.0.4 +xref: UMLS:C1511224 +xref: VHOG:0000085 +xref: Wikipedia:Blood_island_of_umbilical_vesicle +xref: XAO:0000067 +xref: ZFA:0000094 +is_a: UBERON:0006598 ! presumptive structure + +[Term] +id: UBERON:0003064 +name: intermediate mesoderm +def: "The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads." [GOC:curators, Wikipedia:Intermediate_mesoderm] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "IM" RELATED [] +synonym: "intermediate mesenchyme" RELATED [https://github.com/obophenotype/uberon/wiki/The-neural-crest] +synonym: "intermediate plate" RELATED [EMAPA:16178] +synonym: "intermediate plate mesoderm" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "mesenchyma intermedium" RELATED [Wikipedia:Intermediate_mesoderm] +xref: AAO:0010575 +xref: EMAPA:16056 +xref: EMAPA:16178 +xref: FMA:293147 +xref: NCIT:C34193 +xref: SCTID:361476001 +xref: TAO:0001206 +xref: UMLS:C1284010 +xref: VHOG:0000087 +xref: Wikipedia:Intermediate_mesoderm +xref: XAO:0000085 +xref: ZFA:0001206 +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0000926 ! part of mesoderm +relationship: BFO:0000050 UBERON:0005256 ! part of trunk mesenchyme + +[Term] +id: UBERON:0003067 +name: dorsolateral placode +def: "Lateral neurogenic placodes positioned dorsal of the epibranchial placodes." [ZFIN:curator] +synonym: "dorsolateral placodes" EXACT [ZFA:0001310] +xref: TAO:0001310 +xref: VHOG:0000103 +xref: XAO:0000187 +xref: ZFA:0001310 +is_a: UBERON:0009955 ! neurogenic placode + +[Term] +id: UBERON:0003068 +name: axial mesoderm +def: "The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord." [GO:0048318, Wikipedia:Chordamesoderm] +subset: efo_slim +subset: uberon_slim +synonym: "chordamesoderm" RELATED [Wikipedia:Chordamesoderm] +xref: AAO:0011017 +xref: EFO:0003647 +xref: TAO:0001204 +xref: VHOG:0000107 +xref: Wikipedia:Chordamesoderm +xref: XAO:0000205 +xref: ZFA:0001204 +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0000926 ! part of mesoderm + +[Term] +id: UBERON:0003069 +name: otic placode +def: "A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK]." [NCBIBook:NBK53175, Wikipedia:Otic_placode] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "auditory placode" RELATED [] +synonym: "ear placode" RELATED [] +synonym: "ear/otic placode" RELATED [] +synonym: "octaval placode" RELATED [ISBN:0471888893] +synonym: "octaval VIII placode" RELATED [ISBN:0471888893] +synonym: "placoda otica" EXACT [] +xref: AAO:0011079 +xref: EFO:0003429 +xref: EHDAA2:0001339 +xref: EHDAA:506 +xref: EMAPA:16195 +xref: FMA:293973 +xref: NCIT:C34239 +xref: TAO:0000138 +xref: UMLS:C1518677 +xref: VHOG:0000235 +xref: Wikipedia:Otic_placode +xref: XAO:0000223 +xref: ZFA:0000138 +is_a: UBERON:0003067 ! dorsolateral placode +relationship: BFO:0000050 UBERON:0001690 ! part of ear + +[Term] +id: UBERON:0003074 +name: mesonephric duct +def: "Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]." [https://github.com/obophenotype/uberon/issues/28, Wikipedia:Mesonephric_duct, ZFIN:curator] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "archinephric duct" RELATED [VHOG:0000082, Wikipedia:Wolffian_duct] +synonym: "ductus mesonephricus; ductus Wolffi" RELATED [Wikipedia:Mesonephric_duct] +synonym: "Leydig's duct" RELATED [Wikipedia:Wolffian_duct] +synonym: "renal duct" RELATED [] +synonym: "Wolffian duct" EXACT [GOC:yaf, Wikipedia:Wolffian_duct, ZFA:0000546] +xref: AAO:0000637 +xref: EHDAA2:0001243 +xref: EHDAA:1590 +xref: EMAPA:16577 +xref: GAID:1315 +xref: MESH:A16.254.940 +xref: NCIT:C26469 +xref: SCTID:308800003 +xref: TAO:0000546 +xref: UMLS:C0043204 +xref: VHOG:0000082 +xref: Wikipedia:Mesonephric_duct +xref: XAO:0000242 +xref: ZFA:0000546 +is_a: UBERON:0000083 ! mesonephric tubule +is_a: UBERON:0009201 ! nephric duct +is_a: UBERON:0012275 ! meso-epithelium + +[Term] +id: UBERON:0003075 +name: neural plate +def: "A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]." [ISBN:0815318960, OMD:neural+plate, Wikipedia:Neural_plate, ZFIN:curator] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "lamina neuralis" RELATED [Wikipedia:Neural_plate] +synonym: "presumptive central nervous system" RELATED [] +xref: AAO:0011072 +xref: BTO:0001765 +xref: DHBA:10153 +xref: DMBA:15565 +xref: EHDAA:346 +xref: EHDAA:902 +xref: EMAPA:35593 +xref: FMA:293879 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1362 +xref: NCIT:C34225 +xref: RETIRED_EHDAA2:0001252 +xref: TAO:0000132 +xref: UMLS:C0920623 +xref: VHOG:0000068 +xref: Wikipedia:Neural_plate +xref: XAO:0000249 +xref: ZFA:0000132 +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium +is_a: UBERON:0016879 ! future central nervous system + +[Term] +id: UBERON:0003076 +name: posterior neural tube +xref: AAO:0011082 +xref: TAO:0007037 +xref: VHOG:0001383 +xref: XAO:0000250 +xref: ZFA:0007037 +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0001049 ! part of neural tube + +[Term] +id: UBERON:0003077 +name: paraxial mesoderm +def: "The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]." [GO:0048339, https://github.com/obophenotype/uberon/issues/30] +subset: efo_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "mesoderma paraxiale" RELATED [Wikipedia:Paraxial_mesoderm] +synonym: "paraxial mesenchyme" EXACT [https://github.com/obophenotype/uberon/issues/30, https://github.com/obophenotype/uberon/wiki/The-neural-crest, ZFA:0000255] +synonym: "somitic mesoderm" EXACT [ISBN:9780878932504] +xref: AAO:0010568 +xref: EFO:0003515 +xref: EMAPA:16183 +xref: EMAPA:16751 +xref: FMA:293145 +xref: NCIT:C34244 +xref: SCTID:361475002 +xref: TAO:0000255 +xref: UMLS:C1284009 +xref: VHOG:0000114 +xref: Wikipedia:Paraxial_mesoderm +xref: XAO:0000259 +xref: ZFA:0000255 +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007524 ! dense mesenchyme tissue +is_a: UBERON:0015212 ! lateral structure + +[Term] +id: UBERON:0003078 +name: epibranchial placode +def: "Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia." [VHOG:0000117] +subset: efo_slim +synonym: "epibranchial placodes" EXACT [ZFA:0001294] +synonym: "ventrolateral placode" RELATED [ISBN:0471888893] +xref: AAO:0011036 +xref: EFO:0003455 +xref: FMA:293968 +xref: TAO:0001294 +xref: VHOG:0000117 +xref: XAO:0000284 +xref: ZFA:0001294 +is_a: UBERON:0009955 ! neurogenic placode +relationship: BFO:0000050 UBERON:0000010 ! part of peripheral nervous system + +[Term] +id: UBERON:0003080 +name: anterior neural tube +xref: AAO:0011012 +xref: TAO:0007038 +xref: VHOG:0001384 +xref: XAO:0000307 +xref: ZFA:0007038 +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0001049 ! part of neural tube + +[Term] +id: UBERON:0003081 +name: lateral plate mesoderm +def: "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]." [MP:0010117, Wikipedia:Lateral_plate_mesoderm] +subset: pheno_slim +subset: uberon_slim +synonym: "lateral mesoderm" EXACT [GO:0048368] +synonym: "lateral plate" RELATED [] +synonym: "lateral plate mesenchyme" RELATED [EHDAA2:0000919] +synonym: "LPM" EXACT [ZFA:0000121] +synonym: "mesoderma laminae lateralis" RELATED [Wikipedia:Lateral_plate_mesoderm] +xref: AAO:0010574 +xref: EHDAA2:0000919 +xref: EHDAA:379 +xref: EMAPA:16179 +xref: FMA:293149 +xref: NCIT:C34199 +xref: SCTID:361477005 +xref: TAO:0000121 +xref: UMLS:C1517749 +xref: VHOG:0000118 +xref: Wikipedia:Lateral_plate_mesoderm +xref: XAO:0000311 +xref: ZFA:0000121 +is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007524 ! dense mesenchyme tissue +relationship: BFO:0000050 UBERON:0000926 ! part of mesoderm + +[Term] +id: UBERON:0003082 +name: myotome +def: "A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells." [AEO:0001018] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "muscle plate" RELATED [] +synonym: "myomere" RELATED [] +synonym: "myomeres" EXACT [TAO:0001056] +synonym: "myotome region" RELATED [] +synonym: "myotomes" RELATED [] +synonym: "myotomus" RELATED [Wikipedia:Myotome] +xref: AAO:0011067 +xref: AEO:0001018 +xref: BTO:0000742 +xref: EHDAA2_RETIRED:0003431 +xref: EHDAA:1721 +xref: EHDAA:1727 +xref: EHDAA:1733 +xref: EHDAA:1739 +xref: EMAPA:32841 +xref: FMA:295658 +xref: NCIT:C34214 +xref: SCTID:344535001 +xref: TAO:0001056 +xref: UMLS:C1513802 +xref: VHOG:0001244 +xref: Wikipedia:Myotome +xref: XAO:0000315 +xref: ZFA:0001056 +is_a: UBERON:0017650 ! developing mesenchymal structure + +[Term] +id: UBERON:0003084 +name: heart primordium +def: "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone." [ZFIN:curator] +subset: uberon_slim +synonym: "cardiac field" RELATED [ZFA:0000028] +synonym: "fused heart primordium" RELATED [] +xref: AAO:0011044 +xref: BTO:0001887 +xref: NCIT:C34276 +xref: TAO:0000028 +xref: UMLS:C1514450 +xref: XAO:0000336 +xref: ZFA:0000028 +is_a: UBERON:0001048 ! primordium +relationship: BFO:0000050 UBERON:0004535 ! part of cardiovascular system + +[Term] +id: UBERON:0003089 +name: sclerotome +def: "Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]." [https://github.com/obophenotype/uberon/issues/316, Wikipedia:Sclerotome, XB:curator] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "sclerotomes" EXACT [TAO:0001080] +synonym: "sclerotomus" RELATED [Wikipedia:Sclerotome] +xref: AAO:0010571 +xref: AEO:0000212 +xref: EHDAA2:0003439 +xref: EMAPA:31159 +xref: FMA:295652 +xref: NCIT:C34287 +xref: TAO:0001080 +xref: UMLS:C0183176 +xref: VHOG:0000680 +xref: Wikipedia:Sclerotome +xref: XAO:0000397 +xref: ZFA:0001080 +is_a: UBERON:0005856 ! developing mesenchymal condensation +is_a: UBERON:0007530 ! migrating mesenchyme population + +[Term] +id: UBERON:0003099 +name: cranial neural crest +def: "Neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage." [MGI:anna] +subset: efo_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "cephalic neural crest" EXACT [EMAPA:16091] +synonym: "CNC" EXACT [XAO:0001001] +synonym: "cranial NCC population" EXACT [] +synonym: "crista neuralis cranialis" RELATED [Wikipedia:Cranial_neural_crest] +synonym: "head crest" RELATED [] +synonym: "head NCC population" EXACT [] +synonym: "head neural crest" RELATED [] +xref: AAO:0010580 +xref: EFO:0003645 +xref: EHDAA2:0004420 +xref: EMAPA:16091 +xref: TAO:0001194 +xref: VHOG:0000063 +xref: Wikipedia:Cranial_neural_crest +xref: XAO:0001001 +xref: ZFA:0001194 +is_a: UBERON:0005291 ! embryonic tissue +relationship: BFO:0000050 UBERON:0002342 ! part of neural crest + +[Term] +id: UBERON:0003102 +name: surface structure +def: "Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism." [http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/24] +subset: upper_level +synonym: "anatomical surface feature" EXACT [EHDAA2:0003010] +synonym: "surface feature" RELATED [] +synonym: "surface region" RELATED [] +synonym: "surface structures" RELATED [ZFA:0000292] +xref: AAO:0010337 +xref: AEO_RETIRED:0000010 +xref: EHDAA2_RETIRED:0003010 +xref: galen:SurfaceRegion +xref: TAO:0000292 +xref: VSAO:0000001 +xref: Wikipedia:Surface_structure +xref: XAO:0003028 +xref: ZFA:0000292 +is_a: UBERON:0000061 ! anatomical structure +relationship: BFO:0000050 UBERON:0002416 ! part of integumental system + +[Term] +id: UBERON:0003103 +name: compound organ +def: "Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types." [CARO:0000024] +subset: organ_slim +subset: upper_level +synonym: "organ" RELATED [] +xref: AAO:0010015 +xref: AEO:0000024 +xref: BILA:0000024 +xref: CARO:0000024 +xref: EHDAA2:0003024 +xref: HAO:0000024 +xref: TADS:0000598 +xref: TAO:0000496 +xref: TGMA:0001837 +xref: VHOG:0001723 +xref: XAO:0003041 +xref: ZFA:0000496 +is_a: UBERON:0000062 ! organ + +[Term] +id: UBERON:0003104 +name: mesenchyme +def: "Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme." [https://archive.org/details/invertebratesnde00brus/page/n240/mode/2up, https://en.wikipedia.org/wiki/Mesenchyme, https://github.com/obophenotype/uberon/issues/1641] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "mesenchyma" RELATED [Wikipedia:Mesenchyme] +synonym: "mesenchymal tissue" EXACT [] +synonym: "mesenchyme tissue" EXACT [] +synonym: "portion of mesenchymal tissue" EXACT [] +synonym: "portion of mesenchyme tissue" EXACT [] +xref: AAO:0010427 +xref: AEO:0000145 +xref: BTO:0001393 +xref: CALOHA:TS-0620 +xref: EHDAA2:0003145 +xref: EV:0100007 +xref: NCIT:C13301 +xref: TAO:0000393 +xref: UMLS:C0162415 +xref: VHOG:0000170 +xref: Wikipedia:Mesenchyme +xref: XAO:0003046 +xref: ZFA:0000393 +is_a: UBERON:0000479 ! tissue + +[Term] +id: UBERON:0003110 +name: otic region +synonym: "cranial vault" RELATED [ZFA:0000189] +xref: AAO:0010208 +xref: TAO:0000189 +xref: XAO:0003175 +xref: ZFA:0000189 +is_a: UBERON:0034921 ! multi organ part structure +relationship: BFO:0000050 UBERON:0001703 ! part of neurocranium +relationship: BFO:0000050 UBERON:0002241 ! part of chondrocranium + +[Term] +id: UBERON:0003113 +name: dermatocranium +def: "Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified]." [Wikipedia:Skull_roof, ZFA:0000863] +synonym: "dendrocranium" EXACT [TAO:0000863] +synonym: "dermal bone cranium" RELATED [ZFA:0000863] +synonym: "dermal part of skull" RELATED [] +synonym: "dermal skull bones" RELATED [] +synonym: "dermal skull roof" NARROW [PMID:11523816, Wikipedia:Skull_roof] +synonym: "dermatocranial cover" NARROW [] +synonym: "exocranium" EXACT [UBERONREF:0000007] +synonym: "roof of skull" NARROW [Wikipedia:Skull_roof] +synonym: "roofing bones of the skull" RELATED [Wikipedia:Skull_roof] +synonym: "skull exoskeleton" RELATED [] +synonym: "skull roof" NARROW [PMID:11523816, Wikipedia:Skull_roof] +xref: AAO:0010154 +xref: TAO:0000863 +xref: VHOG:0001665 +xref: Wikipedia:Skull_roof +xref: XAO:0003169 +xref: ZFA:0000863 +is_a: UBERON:0011159 ! primary subdivision of cranial skeletal system +relationship: BFO:0000050 UBERON:0010364 ! part of dermal skeleton + +[Term] +id: UBERON:0003128 +name: cranium +def: "Upper portion of the skull that excludes the mandible (when present in the organism)." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Cranium_(anatomy)] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "bones of cranium" EXACT [FMA:71325] +synonym: "calvarium" RELATED [BTO:0001328] +synonym: "epicranial plate" RELATED [] +synonym: "ossa cranii" EXACT [FMA:71325, FMA:TA] +synonym: "set of bones of cranium" EXACT [FMA:71325] +synonym: "skeletal system of head" RELATED [] +synonym: "skull minus mandible" EXACT [] +synonym: "upper part of skull" EXACT [] +xref: BTO:0001328 +xref: EFO:0000831 +xref: EHDAA:6029 +xref: EMAPA:17680 +xref: FMA:71325 +xref: MA:0000316 +xref: MAT:0000340 +xref: MIAA:0000340 +xref: OpenCyc:Mx4rvVlEyJwpEbGdrcN5Y29ycA +xref: SCTID:181889008 +xref: VHOG:0000334 +xref: Wikipedia:Cranium_(anatomy) +is_a: UBERON:0000075 ! subdivision of skeletal system +relationship: BFO:0000050 UBERON:0003129 ! part of skull + +[Term] +id: UBERON:0003129 +name: skull +def: "Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]." [http://sourceforge.net/tracker/?func=detail&aid=2962656&group_id=76834&atid=1205376, PMID:11523816, Wikipedia:Skull] +subset: pheno_slim +subset: uberon_slim +synonym: "cranial skeleton" RELATED [] +synonym: "skeletal system of head" RELATED [] +xref: BTO:0001295 +xref: CALOHA:TS-2344 +xref: EHDAA2:0000325 +xref: EMAPA:17680 +xref: FMA:46565 +xref: GAID:82 +xref: galen:Skull +xref: MESH:D012886 +xref: NCIT:C12789 +xref: OpenCyc:Mx4rvVjOsZwpEbGdrcN5Y29ycA +xref: SCTID:110530005 +xref: UMLS:C0037303 +xref: Wikipedia:Skull +xref: WikipediaCategory:Skull +is_a: UBERON:0000075 ! subdivision of skeletal system +relationship: BFO:0000050 UBERON:0000033 ! part of head +relationship: BFO:0000050 UBERON:0010323 ! part of cranial skeletal system + +[Term] +id: UBERON:0003133 +name: reproductive organ +def: "An organ involved in reproduction." [UBERON:xp] +subset: functional_classification +subset: organ_slim +subset: pheno_slim +synonym: "genital organ" EXACT [] +synonym: "genitalia" RELATED [] +synonym: "reproductive system organ" EXACT [] +synonym: "sex organ" EXACT [] +xref: EMAPA:17381 +xref: EMAPA:37731 +xref: MA:0001752 +xref: MESH:D005835 +xref: NCIT:C25177 +xref: OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA +xref: SCTID:128181006 +xref: TGMA:0000591 +xref: UMLS:C0017420 +xref: WBbt:0008422 +is_a: UBERON:0000062 ! organ +is_a: UBERON:0005156 ! reproductive structure + +[Term] +id: UBERON:0003220 +name: metanephric mesenchyme +def: "One of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO]." [GO:0072075, Wikipedia:Metanephric_blastema] +subset: pheno_slim +synonym: "metanephric blastema" EXACT [Wikipedia:Metanephric_blastema] +synonym: "metanephric mesoderm" EXACT [Wikipedia:Metanephric_blastema] +synonym: "metanephrogenic mesenchyme" EXACT [EHDAA:5021] +synonym: "metanephros associated mesenchyme" EXACT [RETIRED_EHDAA2:0001139] +xref: EHDAA2:0004062 +xref: EHDAA:4041 +xref: EHDAA:5021 +xref: EHDAA:5915 +xref: EMAPA:17375 +xref: SCTID:361529008 +xref: VHOG:0000540 +xref: Wikipedia:Metanephric_blastema +is_a: UBERON:0003918 ! kidney mesenchyme +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0006598 ! presumptive structure + +[Term] +id: UBERON:0003258 +name: endoderm of foregut +def: "An endoderm that is part of a foregut [Automatically generated definition]." [OBOL:automatic] +synonym: "foregut endoderm" EXACT [OBOL:automatic] +xref: EHDAA2:0004568 +xref: EHDAA:524 +is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0005911 ! endo-epithelium +is_a: UBERON:0015833 ! foregut epithelium + +[Term] +id: UBERON:0003278 +name: skeleton of lower jaw +def: "A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage." [http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "lower jaw" BROAD [MA:0001906, ZFA:0001273] +synonym: "lower jaw skeleton" EXACT [AAO:0000274] +synonym: "mandible" BROAD [ZFA:0001273] +synonym: "mandibles" RELATED [TAO:0001273] +synonym: "mandibular series" RELATED [ZFA:0001273] +xref: AAO:0000274 +xref: EHDAA2:0004606 +xref: EHDAA:8005 +xref: EMAPA:17906 +xref: EMAPA:17910 +xref: FMA:54398 +xref: MA:0001906 +xref: TAO:0001273 +xref: VHOG:0000428 +xref: XAO:0003084 +xref: ZFA:0001273 +is_a: UBERON:0010912 ! subdivision of skeleton +relationship: BFO:0000050 UBERON:0001708 ! part of jaw skeleton +relationship: BFO:0000050 UBERON:0001710 ! part of lower jaw region + +[Term] +id: UBERON:0003297 +name: gland of integumental system +def: "A gland that is part of a integumental system [Automatically generated definition]." [OBOL:automatic] +synonym: "integumental gland" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "integumental system gland" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "integumentary gland" EXACT [http://orcid.org/0000-0002-6601-2165] +xref: EHDAA2:0000837 +xref: EHDAA:6522 +xref: EMAPA:17758 +xref: MA:0000144 +xref: VHOG:0000654 +is_a: UBERON:0002530 ! gland +relationship: BFO:0000050 UBERON:0002416 ! part of integumental system + +[Term] +id: UBERON:0003322 +name: mesenchyme of shoulder +def: "Mesenchyme that is part of a developing shoulder [Automatically generated definition]." [OBOL:automatic] +synonym: "shoulder mesenchyme" EXACT [OBOL:automatic] +xref: EHDAA2:0001837 +xref: EHDAA:4184 +xref: EHDAA:6232 +xref: EMAPA:17423 +xref: VHOG:0001035 +is_a: UBERON:0003104 ! mesenchyme +relationship: BFO:0000050 UBERON:0001467 ! part of shoulder + +[Term] +id: UBERON:0003412 +name: pelvic appendage bud mesenchyme +def: "Mesenchyme that is part of a pelvic appendage bud." [OBOL:automatic] +synonym: "hindlimb bud mesenchyme" NARROW SENSU [EMAPA:16781] +synonym: "leg mesenchyme" EXACT [OBOL:automatic] +synonym: "lower limb bud mesenchyme" EXACT [EHDAA2:0001035] +synonym: "mesoderm pelvic fin bud" NARROW SENSU [ZFA:0001386] +synonym: "pelvic fin bud mesenchyme" NARROW SENSU [] +xref: EHDAA2:0001035 +xref: EMAPA:16781 +xref: TAO:0001386 +xref: ZFA:0001386 +is_a: UBERON:0010329 ! paired limb/fin bud mesenchyme +relationship: BFO:0000050 UBERON:0005420 ! part of pelvic appendage bud + +[Term] +id: UBERON:0003413 +name: pectoral appendage bud mesenchyme +def: "Mesenchyme that is part of a pectoral appendage bud." [OBOL:automatic] +synonym: "arm mesenchyme" NARROW [OBOL:automatic] +synonym: "forelimb bud mesenchyme" NARROW SENSU [EMAPA:16408] +synonym: "mesoderm pectoral fin bud" NARROW SENSU [ZFA:0000789] +synonym: "pectoral fin bud mesenchyme" NARROW SENSU [] +synonym: "upper limb bud mesenchyme" NARROW [EHDAA2:0002135] +synonym: "wing mesenchyme" NARROW [OBOL:automatic] +xref: EHDAA2:0002135 +xref: EHDAA:1703 +xref: EMAPA:16408 +xref: TAO:0000789 +xref: ZFA:0000789 +is_a: UBERON:0010329 ! paired limb/fin bud mesenchyme +relationship: BFO:0000050 UBERON:0005419 ! part of pectoral appendage bud + +[Term] +id: UBERON:0003440 +name: limb nerve +def: "A nerve that is part of a limb [Automatically generated definition]." [OBOL:automatic] +synonym: "nerve of limb" EXACT [OBOL:automatic] +xref: EMAPA:37291 +xref: MA:0000693 +xref: SCTID:359923002 +is_a: UBERON:0001021 ! nerve +relationship: BFO:0000050 UBERON:0002101 ! part of limb + +[Term] +id: UBERON:0003441 +name: forelimb nerve +def: "A nerve that is part of a forelimb [Automatically generated definition]." [OBOL:automatic] +synonym: "fore limb nerve" EXACT [OBOL:automatic] +synonym: "nerve of fore limb" EXACT [OBOL:automatic] +synonym: "nerve of forelimb" EXACT [OBOL:automatic] +synonym: "nerve of superior member" EXACT [OBOL:automatic] +synonym: "nerve of upper extremity" EXACT [OBOL:automatic] +synonym: "wing nerve" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +xref: EMAPA:37334 +xref: MA:0000616 +is_a: UBERON:0003440 ! limb nerve +relationship: BFO:0000050 UBERON:0002102 ! part of forelimb + +[Term] +id: UBERON:0003442 +name: hindlimb nerve +def: "A nerve that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] +synonym: "hind limb nerve" EXACT [OBOL:automatic] +synonym: "nerve of hind limb" EXACT [OBOL:automatic] +synonym: "nerve of hindlimb" EXACT [OBOL:automatic] +synonym: "nerve of inferior member" EXACT [OBOL:automatic] +synonym: "nerve of lower extremity" EXACT [OBOL:automatic] +xref: EMAPA:37342 +xref: MA:0000664 +is_a: UBERON:0003440 ! limb nerve +relationship: BFO:0000050 UBERON:0002103 ! part of hindlimb + +[Term] +id: UBERON:0003455 +name: inner renal medulla loop of Henle +def: "A loop of Henle that is part of a inner medulla of kidney [Automatically generated definition]." [OBOL:automatic] +synonym: "kidney inner medulla loop of Henle" EXACT [MA:0002623] +synonym: "loop of Henle, inner medullary portion" EXACT [EMAPA:28352] +xref: EMAPA:28352 +xref: MA:0002623 +is_a: UBERON:0034997 ! renal medulla loop of Henle +relationship: BFO:0000050 UBERON:0001294 ! part of inner medulla of kidney + +[Term] +id: UBERON:0003460 +name: arm bone +def: "A bone that is part of the region of the forelimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia." [https://orcid.org/0000-0002-6601-2165] +synonym: "arm bone organ" EXACT [OBOL:automatic] +synonym: "bone of arm" EXACT [OBOL:automatic] +synonym: "bone of upper extremity" RELATED [GAID:178] +synonym: "bone organ of arm" EXACT [OBOL:automatic] +xref: EMAPA:37303 +xref: MA:0000592 +xref: OpenCyc:Mx4rwKTXoJwpEbGdrcN5Y29ycA +is_a: UBERON:0008962 ! forelimb bone +relationship: BFO:0000050 UBERON:0001460 ! part of arm + +[Term] +id: UBERON:0003461 +name: shoulder bone +def: "A bone that is connected via a shoulder joint (i.e. glenohumeral or acromioclavicular joints). The shoulder bones are the clavicle, scapula and humerus - but note that these are only considered to be shoulder bones when a true shoulder is present, as in most tetrapods." [http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "bone of shoulder" EXACT [OBOL:automatic] +synonym: "shoulder-articulating bone" EXACT [] +xref: MA:0000631 +is_a: UBERON:0010741 ! bone of pectoral complex +relationship: BFO:0000050 UBERON:0012475 ! part of skeleton of pectoral complex + +[Term] +id: UBERON:0003464 +name: hindlimb bone +def: "A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle)." [https://orcid.org/0000-0002-6601-2165] +subset: efo_slim +synonym: "bone of hind limb" EXACT [OBOL:automatic] +synonym: "bone of hindlimb" EXACT [OBOL:automatic] +synonym: "bone of inferior member" EXACT [OBOL:automatic] +synonym: "bone of lower extremity" EXACT [OBOL:automatic] +synonym: "bone organ of hind limb" EXACT [OBOL:automatic] +synonym: "bone organ of hindlimb" EXACT [OBOL:automatic] +synonym: "bone organ of lower extremity" EXACT [OBOL:automatic] +synonym: "hind limb bone" EXACT [OBOL:automatic] +synonym: "hind limb bone organ" EXACT [OBOL:automatic] +synonym: "hindlimb bone organ" EXACT [OBOL:automatic] +xref: EFO:0003842 +xref: GAID:198 +xref: NCIT:C12982 +xref: SCTID:361370006 +xref: UMLS:C0448188 +is_a: UBERON:0002428 ! limb bone +is_a: UBERON:0010742 ! bone of pelvic complex +is_a: UBERON:0015022 ! hindlimb endochondral element + +[Term] +id: UBERON:0003466 +name: forelimb zeugopod bone +def: "A bone that is part of a lower arm [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "antebrachial region bone" EXACT [OBOL:automatic] +synonym: "antebrachial region bone organ" EXACT [OBOL:automatic] +synonym: "arm zeugopod bone" EXACT [OBOL:automatic] +synonym: "arm zeugopod bone organ" EXACT [OBOL:automatic] +synonym: "lower arm bone" EXACT [MA:0000598] +synonym: "wing zeugopod bone" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +synonym: "zeugopod bone, forelimb" EXACT [OBOL:automatic] +synonym: "zeugopod bone, upper" EXACT [OBOL:automatic] +xref: EMAPA:35347 +xref: MA:0000598 +is_a: UBERON:0003460 ! arm bone +relationship: BFO:0000050 UBERON:0010703 ! part of forelimb zeugopod skeleton + +[Term] +id: UBERON:0003479 +name: thoracic cavity vein +def: "A vein that is part of a thoracic cavity [Automatically generated definition]." [OBOL:automatic] +synonym: "cavity of chest vein" EXACT [OBOL:automatic] +synonym: "cavity of thorax vein" EXACT [OBOL:automatic] +synonym: "chest cavity vein" EXACT [OBOL:automatic] +synonym: "pectoral cavity vein" EXACT [OBOL:automatic] +synonym: "vein of cavity of chest" EXACT [OBOL:automatic] +synonym: "vein of cavity of thorax" EXACT [OBOL:automatic] +synonym: "vein of chest cavity" EXACT [OBOL:automatic] +synonym: "vein of pectoral cavity" EXACT [OBOL:automatic] +synonym: "vein of thoracic cavity" EXACT [OBOL:automatic] +xref: EMAPA:37242 +xref: MA:0001903 +is_a: UBERON:0001638 ! vein +is_a: UBERON:0003519 ! thoracic cavity blood vessel + +[Term] +id: UBERON:0003497 +name: abdomen blood vessel +def: "A blood vessel that is part of an abdomen [Automatically generated definition]." [OBOL:automatic] +synonym: "blood vessel of abdomen" EXACT [OBOL:automatic] +xref: MA:0000518 +is_a: UBERON:0003835 ! abdominal segment blood vessel +relationship: BFO:0000050 UBERON:0000916 ! part of abdomen + +[Term] +id: UBERON:0003509 +name: arterial blood vessel +def: "A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta." [https://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +xref: EMAPA:35144 +xref: MA:0000061 +is_a: UBERON:0001981 ! blood vessel +relationship: BFO:0000050 UBERON:0004572 ! part of arterial system + +[Term] +id: UBERON:0003513 +name: trunk blood vessel +def: "A blood vessel that is part of a trunk [Automatically generated definition]." [OBOL:automatic] +synonym: "blood vessel of torso" EXACT [OBOL:automatic] +synonym: "blood vessel of trunk" EXACT [OBOL:automatic] +synonym: "torso blood vessel" EXACT [OBOL:automatic] +xref: EMAPA:37237 +xref: MA:0000511 +is_a: UBERON:0001981 ! blood vessel +relationship: BFO:0000050 UBERON:0002100 ! part of trunk + +[Term] +id: UBERON:0003514 +name: limb blood vessel +def: "A blood vessel that is part of a limb [Automatically generated definition]." [OBOL:automatic] +synonym: "blood vessel of limb" EXACT [OBOL:automatic] +xref: EMAPA:36598 +xref: MA:0000687 +is_a: UBERON:0007301 ! appendage blood vessel +relationship: BFO:0000050 UBERON:0002101 ! part of limb + +[Term] +id: UBERON:0003515 +name: forelimb blood vessel +def: "A blood vessel that is part of a forelimb [Automatically generated definition]." [OBOL:automatic] +synonym: "anteriormost limb blood vessel" EXACT [OBOL:automatic] +synonym: "blood vessel of anteriormost limb" EXACT [OBOL:automatic] +synonym: "blood vessel of fore limb" EXACT [OBOL:automatic] +synonym: "blood vessel of forelimb" EXACT [OBOL:automatic] +synonym: "blood vessel of upper extremity" EXACT [OBOL:automatic] +synonym: "fore limb blood vessel" EXACT [OBOL:automatic] +synonym: "wing blood vessel" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +xref: EMAPA:37292 +xref: MA:0000611 +is_a: UBERON:0003514 ! limb blood vessel +is_a: UBERON:0007300 ! pectoral appendage blood vessel +relationship: BFO:0000050 UBERON:0002102 ! part of forelimb + +[Term] +id: UBERON:0003516 +name: hindlimb blood vessel +def: "A blood vessel that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] +synonym: "blood vessel of hind limb" EXACT [OBOL:automatic] +synonym: "blood vessel of hindlimb" EXACT [OBOL:automatic] +synonym: "blood vessel of lower extremity" EXACT [OBOL:automatic] +synonym: "hind limb blood vessel" EXACT [OBOL:automatic] +xref: EMAPA:37298 +xref: MA:0000659 +is_a: UBERON:0003514 ! limb blood vessel +relationship: BFO:0000050 UBERON:0002103 ! part of hindlimb + +[Term] +id: UBERON:0003517 +name: kidney blood vessel +def: "A blood vessel that is part of a kidney [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +subset: vertebrate_core +synonym: "blood vessel of kidney" EXACT [OBOL:automatic] +synonym: "renal blood vessel" EXACT [OBOL:automatic] +xref: EMAPA:28457 +xref: MA:0001682 +xref: TAO:0005306 +xref: ZFA:0005306 +is_a: UBERON:0003497 ! abdomen blood vessel +relationship: BFO:0000050 UBERON:0006544 ! part of kidney vasculature + +[Term] +id: UBERON:0003519 +name: thoracic cavity blood vessel +def: "A blood vessel that is part of a thoracic cavity [Automatically generated definition]." [OBOL:automatic] +synonym: "blood vessel of cavity of chest" EXACT [OBOL:automatic] +synonym: "blood vessel of cavity of thorax" EXACT [OBOL:automatic] +synonym: "blood vessel of chest cavity" EXACT [OBOL:automatic] +synonym: "blood vessel of pectoral cavity" EXACT [OBOL:automatic] +synonym: "blood vessel of thoracic cavity" EXACT [OBOL:automatic] +synonym: "cavity of chest blood vessel" EXACT [OBOL:automatic] +synonym: "cavity of thorax blood vessel" EXACT [OBOL:automatic] +synonym: "chest cavity blood vessel" EXACT [OBOL:automatic] +synonym: "pectoral cavity blood vessel" EXACT [OBOL:automatic] +xref: EMAPA:37240 +xref: MA:0000554 +is_a: UBERON:0001981 ! blood vessel + +[Term] +id: UBERON:0003522 +name: manual digit blood vessel +def: "A blood vessel that is part of a finger [Automatically generated definition]." [OBOL:automatic] +synonym: "blood vessel of digit of terminal segment of free upper limb" EXACT [OBOL:automatic] +synonym: "blood vessel of terminal segment of free upper limb digit" EXACT [OBOL:automatic] +synonym: "digit of terminal segment of free upper limb blood vessel" EXACT [OBOL:automatic] +synonym: "finger blood vessel" EXACT [OBOL:automatic] +synonym: "hand digit blood vessel" EXACT [MA:0000621] +synonym: "hand digit blood vessel" NARROW SENSU [NCBITaxon:9606, OBOL:accepted] +synonym: "terminal segment of free upper limb digit blood vessel" EXACT [OBOL:automatic] +xref: EMAPA:37297 +xref: MA:0000621 +is_a: UBERON:0003523 ! manus blood vessel +relationship: BFO:0000050 UBERON:0002389 ! part of manual digit + +[Term] +id: UBERON:0003523 +name: manus blood vessel +def: "A blood vessel that is part of a manus [Automatically generated definition]." [OBOL:automatic] +synonym: "blood vessel of hand" EXACT [OBOL:automatic] +synonym: "blood vessel of manus" EXACT [OBOL:automatic] +synonym: "hand blood vessel" EXACT [MA:0000618] +xref: EMAPA:37296 +xref: MA:0000618 +is_a: UBERON:0003515 ! forelimb blood vessel +relationship: BFO:0000050 UBERON:0002398 ! part of manus + +[Term] +id: UBERON:0003527 +name: kidney capillary +def: "A capillary that is part of a kidney [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "blood capillary of kidney" EXACT [OBOL:automatic] +synonym: "capillary of kidney" EXACT [OBOL:automatic] +synonym: "capillary vessel of kidney" EXACT [OBOL:automatic] +synonym: "kidney blood capillary" EXACT [OBOL:automatic] +synonym: "kidney capillary vessel" EXACT [OBOL:automatic] +synonym: "renal capillary" EXACT [OBOL:automatic] +xref: EMAPA:31443 +xref: MA:0002586 +xref: SCTID:275409003 +is_a: UBERON:0001982 ! capillary +is_a: UBERON:0003517 ! kidney blood vessel + +[Term] +id: UBERON:0003528 +name: brain gray matter +def: "A gray matter that is part of a brain [Automatically generated definition]." [OBOL:automatic] +synonym: "brain grey matter" EXACT [MA:0000810] +synonym: "brain grey substance" EXACT [OBOL:automatic] +synonym: "gray matter of brain" EXACT [OBOL:automatic] +synonym: "grey matter of brain" EXACT [OBOL:automatic] +synonym: "grey substance of brain" EXACT [OBOL:automatic] +xref: EMAPA:35184 +xref: MA:0000810 +xref: NCIT:C49333 +xref: UMLS:C1707348 +is_a: UBERON:0002020 ! gray matter +relationship: BFO:0000050 UBERON:0000955 ! part of brain + +[Term] +id: UBERON:0003531 +name: forelimb skin +def: "A zone of skin that is part of a forelimb [Automatically generated definition]." [OBOL:automatic] +synonym: "anteriormost limb skin" EXACT [OBOL:automatic] +synonym: "fore limb skin" EXACT [OBOL:automatic] +synonym: "skin of fore limb" EXACT [OBOL:automatic] +synonym: "skin of forelimb" EXACT [OBOL:automatic] +synonym: "skin of upper limb" EXACT [FMA:23101] +synonym: "upper limb skin" EXACT [FMA:23101] +synonym: "wing skin" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +xref: EMAPA:32612 +xref: FMA:23101 +xref: MA:0000617 +xref: NCIT:C12296 +xref: SCTID:244130001 +xref: UMLS:C0222212 +is_a: UBERON:0001419 ! skin of limb +relationship: BFO:0000050 UBERON:0002102 ! part of forelimb + +[Term] +id: UBERON:0003532 +name: hindlimb skin +def: "A zone of skin that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] +synonym: "hind limb skin" EXACT [OBOL:automatic] +synonym: "lower limb skin" EXACT [FMA:23102] +synonym: "skin of hind limb" EXACT [OBOL:automatic] +synonym: "skin of hindlimb" EXACT [OBOL:automatic] +synonym: "skin of lower extremity" EXACT [OBOL:automatic] +synonym: "skin of lower limb" EXACT [FMA:23102] +xref: EMAPA:32620 +xref: FMA:23102 +xref: MA:0000665 +xref: NCIT:C12297 +xref: SCTID:181528008 +xref: UMLS:C0222268 +is_a: UBERON:0001419 ! skin of limb +relationship: BFO:0000050 UBERON:0002103 ! part of hindlimb + +[Term] +id: UBERON:0003544 +name: brain white matter +def: "The regions of the brain that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites." [MP:0008026] +subset: pheno_slim +synonym: "brain white matter of neuraxis" EXACT [OBOL:automatic] +synonym: "brain white substance" EXACT [OBOL:automatic] +synonym: "white matter of brain" EXACT [OBOL:automatic] +synonym: "white matter of neuraxis of brain" EXACT [OBOL:automatic] +synonym: "white substance of brain" EXACT [OBOL:automatic] +xref: EMAPA:35187 +xref: HBA:9218 +xref: MA:0000820 +xref: NCIT:C49334 +xref: UMLS:C1706995 +is_a: UBERON:0002316 ! white matter +relationship: BFO:0000050 UBERON:0000955 ! part of brain + +[Term] +id: UBERON:0003587 +name: limb connective tissue +def: "A portion of connective tissue that is part of a limb [Automatically generated definition]." [OBOL:automatic] +synonym: "connective tissue of limb" EXACT [OBOL:automatic] +synonym: "limb portion of connective tissue" EXACT [OBOL:automatic] +synonym: "limb textus connectivus" EXACT [OBOL:automatic] +synonym: "portion of connective tissue of limb" EXACT [OBOL:automatic] +synonym: "textus connectivus of limb" EXACT [OBOL:automatic] +xref: EMAPA:37313 +xref: MA:0000689 +is_a: UBERON:0002384 ! connective tissue +relationship: BFO:0000050 UBERON:0002101 ! part of limb + +[Term] +id: UBERON:0003588 +name: forelimb connective tissue +def: "A portion of connective tissue that is part of a forelimb [Automatically generated definition]." [OBOL:automatic] +synonym: "connective tissue of anteriormost limb" EXACT [OBOL:automatic] +synonym: "connective tissue of fore limb" EXACT [OBOL:automatic] +synonym: "connective tissue of forelimb" EXACT [OBOL:automatic] +synonym: "connective tissue of superior member" EXACT [OBOL:automatic] +synonym: "connective tissue of upper extremity" EXACT [OBOL:automatic] +synonym: "wing connective tissue" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +xref: EMAPA:37314 +xref: MA:0000613 +is_a: UBERON:0003587 ! limb connective tissue +relationship: BFO:0000050 UBERON:0002102 ! part of forelimb + +[Term] +id: UBERON:0003589 +name: hindlimb connective tissue +def: "A portion of connective tissue that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] +synonym: "connective tissue of hind limb" EXACT [OBOL:automatic] +synonym: "connective tissue of hindlimb" EXACT [OBOL:automatic] +synonym: "connective tissue of inferior member" EXACT [OBOL:automatic] +synonym: "connective tissue of lower extremity" EXACT [OBOL:automatic] +synonym: "hind limb connective tissue" EXACT [OBOL:automatic] +xref: EMAPA:37322 +xref: MA:0000661 +is_a: UBERON:0003587 ! limb connective tissue +relationship: BFO:0000050 UBERON:0002103 ! part of hindlimb + +[Term] +id: UBERON:0003606 +name: limb long bone +def: "A long bone that is part of a limb [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "long bone of limb" EXACT [OBOL:automatic] +xref: EMAPA:35495 +xref: MA:0000298 +is_a: UBERON:0002428 ! limb bone +is_a: UBERON:0002495 ! long bone + +[Term] +id: UBERON:0003607 +name: forelimb long bone +def: "A long bone that is part of a forelimb [Automatically generated definition]." [OBOL:automatic] +synonym: "anteriormost limb long bone" EXACT [OBOL:automatic] +synonym: "fore limb long bone" EXACT [OBOL:automatic] +synonym: "long bone of anteriormost limb" EXACT [OBOL:automatic] +synonym: "long bone of fore limb" EXACT [OBOL:automatic] +synonym: "long bone of forelimb" EXACT [OBOL:automatic] +synonym: "long bone of superior member" EXACT [OBOL:automatic] +synonym: "long bone of upper extremity" EXACT [OBOL:automatic] +synonym: "superior member long bone" EXACT [OBOL:automatic] +synonym: "upper extremity long bone" EXACT [OBOL:automatic] +synonym: "wing long bone" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +xref: EMAPA:35350 +xref: MA:0000299 +is_a: UBERON:0003606 ! limb long bone +is_a: UBERON:0008962 ! forelimb bone + +[Term] +id: UBERON:0003608 +name: hindlimb long bone +def: "A long bone that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] +synonym: "hind limb long bone" EXACT [OBOL:automatic] +synonym: "inferior member long bone" EXACT [OBOL:automatic] +synonym: "long bone of hind limb" EXACT [OBOL:automatic] +synonym: "long bone of hindlimb" EXACT [OBOL:automatic] +synonym: "long bone of inferior member" EXACT [OBOL:automatic] +synonym: "long bone of lower extremity" EXACT [OBOL:automatic] +synonym: "lower extremity long bone" EXACT [OBOL:automatic] +xref: EMAPA:35403 +xref: MA:0000300 +is_a: UBERON:0003464 ! hindlimb bone +is_a: UBERON:0003606 ! limb long bone + +[Term] +id: UBERON:0003657 +name: limb joint +def: "Any joint that is part of a (free) limb." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +synonym: "joint of limb" EXACT [] +synonym: "joint of limb skeletal system" EXACT [OBOL:automatic] +synonym: "skeletal limb joint" EXACT [GO:0036023] +xref: EMAPA:36501 +xref: FMA:321558 +xref: galen:LimbJoint +xref: MA:0000691 +xref: SCTID:312683002 +is_a: UBERON:0000982 ! skeletal joint +relationship: BFO:0000050 UBERON:0002101 ! part of limb + +[Term] +id: UBERON:0003661 +name: limb muscle +def: "Any muscle organ that is part of a limb [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "limb muscle organ" EXACT [OBOL:accepted] +synonym: "limb skeletal muscle" EXACT [OBOL:exploratory] +synonym: "muscle organ of limb" EXACT [OBOL:accepted] +xref: EMAPA:32700 +xref: MA:0000692 +is_a: UBERON:0014892 ! skeletal muscle organ +relationship: BFO:0000050 UBERON:0004480 ! part of musculature of limb + +[Term] +id: UBERON:0003662 +name: forelimb muscle +def: "Any muscle organ that is part of a forelimb." [OBOL:automatic] +synonym: "arm muscle system" RELATED [EHDAA2:0000141] +synonym: "fore limb muscle organ" EXACT [OBOL:automatic] +synonym: "forelimb muscle organ" EXACT [OBOL:automatic] +synonym: "free upper limb muscle" EXACT [FMA:37348] +synonym: "muscle of free upper limb" EXACT [FMA:37348] +synonym: "muscle of upper limb" EXACT [FMA:9621] +synonym: "musculature of arm" RELATED [] +synonym: "musculature of the arm" RELATED [] +synonym: "upper limb skeletal muscle" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "wing muscle" NARROW SENSU [Geisha:syn, NCBITaxon:8782, OBOL:automatic] +xref: AAO:0000204 +xref: BTO:0000479 +xref: EMAPA:36049 +xref: FMA:37348 +is_a: UBERON:0003661 ! limb muscle +is_a: UBERON:0014794 ! pectoral appendage muscle +relationship: BFO:0000050 UBERON:0004481 ! part of musculature of upper limb + +[Term] +id: UBERON:0003663 +name: hindlimb muscle +def: "Any muscle organ that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] +subset: efo_slim +synonym: "free lower limb muscle" EXACT [FMA:37368] +synonym: "hind limb muscle organ" EXACT [OBOL:automatic] +synonym: "hindlimb muscle organ" EXACT [OBOL:automatic] +synonym: "inferior member muscle organ" EXACT [OBOL:automatic] +synonym: "lower extremity muscle organ" EXACT [OBOL:automatic] +synonym: "lower limb skeletal muscle" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "muscle of free lower limb" EXACT [FMA:37368] +synonym: "muscle of posterior limb" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "muscle organ of hind limb" EXACT [OBOL:automatic] +synonym: "muscle organ of hindlimb" EXACT [OBOL:automatic] +synonym: "muscle organ of inferior member" EXACT [OBOL:automatic] +synonym: "muscle organ of lower extremity" EXACT [OBOL:automatic] +xref: AAO:0000222 +xref: EFO:0001928 +xref: FMA:37368 +is_a: UBERON:0003661 ! limb muscle +is_a: UBERON:0014795 ! pelvic appendage muscle +relationship: BFO:0000050 UBERON:0004482 ! part of musculature of lower limb + +[Term] +id: UBERON:0003714 +name: neural tissue +def: "Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature." [FMA:9642] +synonym: "nerve tissue" EXACT [FMA:9642] +synonym: "nervous tissue" EXACT [FMA:9642] +synonym: "portion of neural tissue" EXACT [FMA:9642] +xref: AAO:0000325 +xref: AEO:0000123 +xref: EHDAA2:0003123 +xref: FMA:9642 +xref: GAID:609 +xref: MESH:D009417 +xref: NCIT:C13052 +xref: OpenCyc:Mx4rVmfYCsQ_QdeM_bFAeS8NRQ +xref: SCTID:91728009 +xref: UMLS:C0027757 +is_a: UBERON:0000479 ! tissue +relationship: BFO:0000050 UBERON:0001016 ! part of nervous system + +[Term] +id: UBERON:0003822 +name: forelimb stylopod +def: "The part of the forelimb between pectoral region and the elbow, corresponding to the humerus." [http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "arm" RELATED INCONSISTENT [FMA:24890] +synonym: "brachial region" EXACT [] +synonym: "brachium" EXACT [VSAO:0005057] +synonym: "fore propodium" EXACT [AAO:0000199] +synonym: "forelimb propodium" EXACT [] +synonym: "forelimb stylopodial element" EXACT [MA:th] +synonym: "forelimb stylopodium" EXACT [OBOL:automatic] +synonym: "proximal segment of free upper limb" EXACT [] +synonym: "regio brachialis" EXACT [FMA:24890, FMA:TA] +synonym: "stylopod of arm" EXACT [] +synonym: "stylopod of forelimb" EXACT [] +synonym: "upper arm" EXACT HUMAN_PREFERRED [MA:0000035] +synonym: "wing stylopod" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +xref: AAO:0000199 +xref: EHDAA2:0002112 +xref: EHDAA:4186 +xref: EHDAA:6234 +xref: EMAPA:17424 +xref: FMA:24890 +xref: galen:Arm +xref: MA:0000035 +xref: MESH:D001132 +xref: NCIT:C32141 +xref: OpenCyc:Mx4rvVj0Z5wpEbGdrcN5Y29ycA +xref: SCTID:302538001 +xref: UMLS:C0446516 +xref: VHOG:0000343 +xref: VSAO:0005057 +is_a: UBERON:0002472 ! stylopod +is_a: UBERON:0008785 ! upper limb segment +relationship: BFO:0000050 UBERON:0001460 ! part of arm + +[Term] +id: UBERON:0003823 +name: hindlimb zeugopod +def: "The middle limb segment of the pelvic free limb, between the autopod and stylopod segments. Includes as parts the hindlimb zeugopodial skeleton, which includes as parts the tibia and fibula, or their cartilage precursors, or evolutionary variants." [PHENOSCAPE:curators] +subset: efo_slim +subset: pheno_slim +synonym: "calf" NARROW [] +synonym: "calf of leg" EXACT [FMA:24984] +synonym: "crus" EXACT [VSAO:0005060] +synonym: "crus of hindlimb" EXACT [] +synonym: "hind epipodium" RELATED INCONSISTENT [] +synonym: "hind limb middle limb segment" EXACT [OBOL:automatic] +synonym: "hind limb zeudopodium" EXACT [VHOG:0000348] +synonym: "hind limb zeugopod" EXACT [OBOL:automatic] +synonym: "hindlimb epipodium" EXACT [] +synonym: "hindlimb middle limb segment" EXACT [OBOL:automatic] +synonym: "hindlimb zeudopodium" EXACT [VHOG:0000348] +synonym: "hindlimb zeugopod" EXACT [OBOL:automatic] +synonym: "hindlimb zeugopodium" EXACT [OBOL:automatic] +synonym: "intermediate segment of free lower limb" EXACT [FMA:24979] +synonym: "leg" RELATED INCONSISTENT [FMA:24979, MESH:A01.378.610.500] +synonym: "lower extremity middle limb segment" EXACT [OBOL:automatic] +synonym: "lower extremity zeugopod" EXACT [OBOL:automatic] +synonym: "lower leg" EXACT HUMAN_PREFERRED [MA:0000051] +synonym: "middle limb segment of hind limb" EXACT [OBOL:automatic] +synonym: "middle limb segment of hindlimb" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "posterior curral region" EXACT [FMA:24984] +synonym: "posterior leg region" EXACT [FMA:24984] +synonym: "posterior part of leg" EXACT [FMA:24984] +synonym: "posterior region of leg" EXACT [FMA:24984] +synonym: "regio cruris posterior" EXACT [FMA:24984, FMA:TA] +synonym: "regio surae" EXACT [FMA:24984, FMA:TA] +synonym: "shank" EXACT [VSAO:0005060] +synonym: "sura" EXACT [FMA:24984, FMA:TA] +synonym: "sural region" EXACT [FMA:24984] +synonym: "zeugopod of hind limb" EXACT [OBOL:automatic] +synonym: "zeugopod of hindlimb" EXACT [OBOL:automatic] +xref: EFO:0003051 +xref: EHDAA2:0001030 +xref: EHDAA:5165 +xref: EHDAA:6190 +xref: EMAPA:17496 +xref: FMA:24979 +xref: FMA:24984 +xref: galen:Leg +xref: MA:0000051 +xref: MESH:D007866 +xref: NCIT:C32974 +xref: OpenCyc:Mx4rvczZBpwpEbGdrcN5Y29ycA +xref: SCTID:244015008 +xref: UMLS:C1140621 +xref: VHOG:0000348 +xref: VSAO:0005060 +xref: Wikipedia:Forearm +is_a: UBERON:0002471 ! zeugopod +is_a: UBERON:0008784 ! lower limb segment +relationship: BFO:0000050 UBERON:0000978 ! part of leg + +[Term] +id: UBERON:0003826 +name: upper leg bone +def: "A bone that is part of a hindlimb stylopod [Automatically generated definition]." [https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376, OBOL:automatic] +synonym: "femur" RELATED [https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376] +xref: EMAPA:35893 +xref: MA:0000682 +is_a: UBERON:0005893 ! leg bone +relationship: BFO:0000050 UBERON:0000376 ! part of hindlimb stylopod + +[Term] +id: UBERON:0003835 +name: abdominal segment blood vessel +def: "A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition]." [OBOL:automatic] +synonym: "abdominal segment of trunk blood vessel" EXACT [OBOL:automatic] +synonym: "blood vessel of abdominal segment of trunk" EXACT [OBOL:automatic] +xref: EMAPA:37057 +xref: MA:0000524 +is_a: UBERON:0003513 ! trunk blood vessel +relationship: BFO:0000050 UBERON:0002417 ! part of abdominal segment of trunk + +[Term] +id: UBERON:0003839 +name: forelimb joint +def: "A limb joint that is part of a forelimb [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "anteriormost limb joint of limb" EXACT [OBOL:automatic] +synonym: "anteriormost limb limb joint" EXACT [OBOL:automatic] +synonym: "fore limb joint of limb" EXACT [OBOL:automatic] +synonym: "fore limb limb joint" EXACT [OBOL:automatic] +synonym: "forelimb joint of limb" EXACT [OBOL:automatic] +synonym: "forelimb limb joint" EXACT [OBOL:automatic] +synonym: "joint of free upper limb" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "joint of limb of anteriormost limb" EXACT [OBOL:automatic] +synonym: "joint of limb of fore limb" EXACT [OBOL:automatic] +synonym: "joint of limb of forelimb" EXACT [OBOL:automatic] +synonym: "joint of limb of superior member" EXACT [OBOL:automatic] +synonym: "joint of limb of upper extremity" EXACT [OBOL:automatic] +synonym: "limb joint of anteriormost limb" EXACT [OBOL:automatic] +synonym: "limb joint of fore limb" EXACT [OBOL:automatic] +synonym: "limb joint of forelimb" EXACT [OBOL:automatic] +synonym: "limb joint of superior member" EXACT [OBOL:automatic] +synonym: "limb joint of upper extremity" EXACT [OBOL:automatic] +synonym: "superior member joint of limb" EXACT [OBOL:automatic] +synonym: "superior member limb joint" EXACT [OBOL:automatic] +synonym: "upper extremity joint of limb" EXACT [OBOL:automatic] +synonym: "upper extremity limb joint" EXACT [OBOL:automatic] +synonym: "wing joint" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +xref: EMAPA:19204 +xref: MA:0000614 +is_a: UBERON:0003657 ! limb joint +relationship: BFO:0000050 UBERON:0002102 ! part of forelimb + +[Term] +id: UBERON:0003840 +name: hindlimb joint +def: "A limb joint that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "hind limb joint of limb" EXACT [OBOL:automatic] +synonym: "hind limb limb joint" EXACT [OBOL:automatic] +synonym: "hindlimb joint of limb" EXACT [OBOL:automatic] +synonym: "hindlimb limb joint" EXACT [OBOL:automatic] +synonym: "inferior member joint of limb" EXACT [OBOL:automatic] +synonym: "inferior member limb joint" EXACT [OBOL:automatic] +synonym: "joint of free lower limb" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "joint of limb of hind limb" EXACT [OBOL:automatic] +synonym: "joint of limb of hindlimb" EXACT [OBOL:automatic] +synonym: "joint of limb of inferior member" EXACT [OBOL:automatic] +synonym: "joint of limb of lower extremity" EXACT [OBOL:automatic] +synonym: "joint of lower limb" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "limb joint of hind limb" EXACT [OBOL:automatic] +synonym: "limb joint of hindlimb" EXACT [OBOL:automatic] +synonym: "limb joint of inferior member" EXACT [OBOL:automatic] +synonym: "limb joint of lower extremity" EXACT [OBOL:automatic] +synonym: "lower extremity joint of limb" EXACT [OBOL:automatic] +synonym: "lower extremity limb joint" EXACT [OBOL:automatic] +xref: EMAPA:32635 +xref: MA:0000662 +xref: SCTID:304573000 +is_a: UBERON:0003657 ! limb joint +relationship: BFO:0000050 UBERON:0002103 ! part of hindlimb + +[Term] +id: UBERON:0003842 +name: neural tube lumen +def: "An anatomical space that surrounded_by a neural tube." [OBOL:automatic] +synonym: "cavity of neural tube" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "central lumen" RELATED [] +synonym: "lumen of neural tube" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "neural lumen" RELATED [EHDAA:2889] +synonym: "neural tube neural lumen" EXACT [EHDAA2:0001269] +synonym: "neurocoel" RELATED [VHOG:0001119] +synonym: "prosencoel" NARROW [] +xref: AAO:0011073 +xref: EHDAA2:0001269 +xref: EHDAA:2889 +xref: EHDAA:914 +xref: EMAPA:16167 +xref: VHOG:0001119 +xref: XAO:0000252 +is_a: UBERON:0000464 ! anatomical space +relationship: BFO:0000050 UBERON:0001049 ! part of neural tube + +[Term] +id: UBERON:0003849 +name: mesencephalic neural crest +def: "A neural crest that has_potential_to_developmentally_contribute_to a midbrain." [OBOL:automatic] +subset: efo_slim +subset: vertebrate_core +synonym: "mesencephalic neural crest" EXACT [ZFA:0000935] +synonym: "neural crest midbrain" EXACT [ZFA:0000935] +xref: EFO:0003591 +xref: EHDAA2:0001101 +xref: EHDAA:360 +xref: TAO:0000935 +xref: VHOG:0000796 +xref: ZFA:0000935 +is_a: UBERON:0002342 ! neural crest +is_a: UBERON:0003099 ! cranial neural crest + +[Term] +id: UBERON:0003850 +name: telencephalon neural crest +def: "A neural crest that has_potential_to_developmentally_contribute_to a telencephalon." [OBOL:automatic] +subset: efo_slim +subset: vertebrate_core +synonym: "neural crest telencephalon" EXACT [ZFA:0000812] +xref: EFO:0003574 +xref: RETIRED_EHDAA2:0001991 +xref: TAO:0000812 +xref: VHOG:0000799 +xref: ZFA:0000812 +is_a: UBERON:0002342 ! neural crest + +[Term] +id: UBERON:0003852 +name: rhombencephalon neural crest +def: "A neural crest that has_potential_to_developmentally_contribute_to a hindbrain." [OBOL:automatic] +subset: vertebrate_core +synonym: "neural crest hindbrain" EXACT [ZFA:0007063] +synonym: "rhombencephalic neural crest" EXACT [ZFA:0007063] +synonym: "rhombomere neural crest" RELATED [EMAPA:35747] +xref: EHDAA2:0001628 +xref: EHDAA:362 +xref: EMAPA:35747 +xref: TAO:0007063 +xref: VHOG:0001210 +xref: ZFA:0007063 +is_a: UBERON:0002342 ! neural crest +is_a: UBERON:0003099 ! cranial neural crest + +[Term] +id: UBERON:0003853 +name: spinal cord neural crest +def: "A neural crest that has_potential_to_developmentally_contribute_to a spinal cord." [OBOL:automatic] +synonym: "neural crest spinal cord" EXACT [VHOG:0001006] +synonym: "spinal neural crest" RELATED [VHOG:0001006] +xref: EHDAA:696 +xref: EMAPA:16163 +xref: EMAPA:16881 +xref: VHOG:0001006 +is_a: UBERON:0002342 ! neural crest + +[Term] +id: UBERON:0003859 +name: forelimb mesenchyme +def: "Mesenchyme that is part of a developing forelimb [Automatically generated definition]." [OBOL:automatic] +synonym: "anteriormost limb mesenchyme" EXACT [OBOL:automatic] +synonym: "fore limb mesenchyme" EXACT [OBOL:automatic] +synonym: "mesenchyme of anteriormost limb" EXACT [OBOL:automatic] +synonym: "mesenchyme of fore limb" EXACT [OBOL:automatic] +synonym: "mesenchyme of forelimb" EXACT [OBOL:automatic] +synonym: "mesenchyme of superior member" EXACT [OBOL:automatic] +synonym: "mesenchyme of upper extremity" EXACT [OBOL:automatic] +synonym: "superior member mesenchyme" EXACT [OBOL:automatic] +synonym: "upper extremity mesenchyme" EXACT [OBOL:automatic] +synonym: "wing mesenchyme" NARROW SENSU [Geisha:syn, NCBITaxon:8782, OBOL:automatic] +xref: EMAPA:32628 +xref: VHOG:0001109 +is_a: UBERON:0009749 ! limb mesenchyme +relationship: BFO:0000050 UBERON:0002102 ! part of forelimb + +[Term] +id: UBERON:0003860 +name: hindlimb mesenchyme +def: "Mesenchyme that is part of a developing hindlimb [Automatically generated definition]." [OBOL:automatic] +synonym: "hind limb mesenchyme" EXACT [OBOL:automatic] +synonym: "inferior member mesenchyme" EXACT [OBOL:automatic] +synonym: "lower extremity mesenchyme" EXACT [OBOL:automatic] +synonym: "mesenchyme of hind limb" EXACT [OBOL:automatic] +synonym: "mesenchyme of hindlimb" EXACT [OBOL:automatic] +synonym: "mesenchyme of inferior member" EXACT [OBOL:automatic] +synonym: "mesenchyme of lower extremity" EXACT [OBOL:automatic] +xref: EMAPA:32637 +xref: VHOG:0001074 +is_a: UBERON:0009749 ! limb mesenchyme +relationship: BFO:0000050 UBERON:0002103 ! part of hindlimb + +[Term] +id: UBERON:0003869 +name: presumptive ganglion +def: "A presumptive structure that has the potential to develop into a ganglion." [OBOL:automatic] +is_a: UBERON:0006598 ! presumptive structure + +[Term] +id: UBERON:0003886 +name: future coelemic cavity lumen +def: "An anatomical cavity that has the potential to develop into a coelemic cavity lumen." [OBOL:automatic] +subset: grouping_class +subset: non_informative +synonym: "body cavity precursor" RELATED [] +is_a: UBERON:0000464 ! anatomical space +relationship: BFO:0000050 UBERON:0000926 ! part of mesoderm + +[Term] +id: UBERON:0003887 +name: intraembryonic coelom +def: "The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom." [MGI:anna, MP:0012187] +subset: pheno_slim +synonym: "somatic coelom" EXACT [Wikipedia:Intraembryonic_coelom] +xref: EHDAA:251 +xref: EMAPA:16088 +xref: NCIT:C34195 +xref: UMLS:C1512940 +xref: VHOG:0000316 +xref: Wikipedia:Intraembryonic_coelom +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0011997 ! part of coelom + +[Term] +id: UBERON:0003893 +name: capsule +def: "A cover or envelope partly or wholly surrounding a structure. Examples: egg shell, articular capsules, renal capsules[WP]." [Wikipedia:Capsule_(anatomy)] +subset: grouping_class +subset: non_informative +xref: EHDAA:4739 +xref: EHDAA:9061 +xref: FMA:85272 +xref: galen:Capsule +xref: Wikipedia:Capsule_(anatomy) +is_a: UBERON:0000158 ! membranous layer + +[Term] +id: UBERON:0003914 +name: epithelial tube +def: "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system." [GO:0060562, PMID:12526790] +synonym: "epithelial or endothelial tube" EXACT [] +xref: AEO:0000114 +xref: EHDAA2:0003114 +xref: FBbt:00007474 +is_a: UBERON:0000025 ! tube +is_a: UBERON:0000483 ! epithelium + +[Term] +id: UBERON:0003918 +name: kidney mesenchyme +def: "Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]." [GO:0072074] +subset: pheno_slim +synonym: "mesenchyme of kidney" EXACT [] +is_a: UBERON:0003104 ! mesenchyme + +[Term] +id: UBERON:0003920 +name: venous blood vessel +def: "A blood vessel that carries blood from the capillaries toward the heart." [http://www.thefreedictionary.com/venous+blood+vessel] +synonym: "segment of venous tree organ" EXACT [FMA:86188] +synonym: "venous tree organ segment" EXACT [FMA:86188] +xref: EMAPA:35932 +xref: FMA:86188 +xref: MA:0000066 +is_a: UBERON:0001981 ! blood vessel +relationship: BFO:0000050 UBERON:0004582 ! part of venous system + +[Term] +id: UBERON:0003929 +name: digestive tract epithelium +def: "An epithelium that lines the lumen of the digestive tract." [http://orcid.org/0000-0002-6601-2165] +synonym: "alimentary tract epithelium" RELATED [OBOL:automatic] +synonym: "digestive tract epithelial tissue" EXACT [OBOL:automatic] +synonym: "epithelial tissue of digestive tract" EXACT [OBOL:automatic] +synonym: "epithelial tissue of gut" EXACT [OBOL:automatic] +synonym: "epithelium of digestive tract" EXACT [OBOL:automatic] +synonym: "epithelium of gut" EXACT [OBOL:automatic] +synonym: "gastrodermis" EXACT SENSU [BGEE:ANN, NCBITaxon:6073] +synonym: "gut epithelial tissue" EXACT [OBOL:automatic] +synonym: "gut epithelium" EXACT [EHDAA2:0004567, MA:0003201, ZFA:0005123] +xref: BTO:0000956 +xref: EHDAA2:0004567 +xref: EMAPA:32928 +xref: MA:0003201 +xref: NCIT:C12963 +xref: TAO:0005123 +xref: UMLS:C0836205 +xref: XAO:0003200 +xref: ZFA:0005123 +is_a: UBERON:0000483 ! epithelium +relationship: BFO:0000050 UBERON:0001555 ! part of digestive tract + +[Term] +id: UBERON:0004016 +name: dermatome +def: "A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells." [AEO:0001017, AEO:JB] +subset: pheno_slim +synonym: "cutis plate" EXACT [Wikipedia:Cutis_plate] +synonym: "dermatomal mesenchyme" EXACT [Wikipedia:Cutis_plate] +synonym: "epimere mesoderm" RELATED [] +synonym: "mesenchyma dermatomiale" RELATED [Wikipedia:Dermatomal_mesenchyme] +xref: AAO:0011028 +xref: AEO:0001017 +xref: EHDAA2_RETIRED:0003428 +xref: EHDAA:1719 +xref: EHDAA:1725 +xref: EHDAA:1731 +xref: EHDAA:1737 +xref: EMAPA:32838 +xref: FMA:295656 +xref: NCIT:C61572 +xref: UMLS:C0180383 +xref: Wikipedia:Dermatome_(embryology) +xref: XAO:0000220 +is_a: UBERON:0017650 ! developing mesenchymal structure + +[Term] +id: UBERON:0004022 +name: germinal neuroepithelium +def: "The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells." [http://www.ncbi.nlm.nih.gov/books/NBK10047, MP:0004261] +subset: pheno_slim +synonym: "germinal neuroepithelial layer" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "germinal neuroepithelium" EXACT [NCBIBook:NBK10047] +synonym: "original neural tube" EXACT [NCBIBook:NBK10047] +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0034706 ! proliferating neuroepithelium +relationship: BFO:0000050 UBERON:0001049 ! part of neural tube + +[Term] +id: UBERON:0004035 +name: cortical subplate +def: "The transient outer neural tube region that contains the first generated post-mitotic neurons that receive synaptic input from thalamic axons and in turn project axons to the developing cortical plate." [https://github.com/obophenotype/mouse-anatomy-ontology/issues/1, MP:0008440, Wikipedia:Subplate] +subset: pheno_slim +synonym: "cerebral cortex subplate" EXACT [EMAPA:32833] +synonym: "SP" BROAD [BRAINSPAN:BRAINSPAN] +synonym: "subplate" EXACT [] +synonym: "subplate zone" EXACT [DHBA:10522] +xref: DHBA:10522 +xref: EMAPA:32703 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=3233 +xref: https://upload.wikimedia.org/wikipedia/commons/thumb/a/ac/Corticogenesis_in_a_wild-type_mouse_with_captions_in_english_copy.png/360px-Corticogenesis_in_a_wild-type_mouse_with_captions_in_english_copy.png +xref: PBA:294021932 +xref: Wikipedia:Subplate +is_a: UBERON:0014950 ! layer of developing cerebral cortex + +[Term] +id: UBERON:0004040 +name: cortical intermediate zone +def: "The region of the developing mammalian cortex that extends between the ventricular zone and the cortical plate (CP); normally, the IZ is a region of tangential migration of cells, and at midgestation, the lower part of the IZ develops into the subventricular zone." [MP:0008457] +subset: pheno_slim +synonym: "cerebral cortex mantle layer" RELATED [EMAPA:17545] +synonym: "cerebral cortex mantle zone" RELATED [] +synonym: "cortical mantle layer" RELATED [] +synonym: "IZ" BROAD [BRAINSPAN:BRAINSPAN] +xref: EMAPA:17545 +xref: EMAPA:32712 +is_a: UBERON:0014950 ! layer of developing cerebral cortex + +[Term] +id: UBERON:0004060 +name: neural tube ventricular layer +def: "The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium." [http://www.ncbi.nlm.nih.gov/books/NBK10047, MP:0009689] +subset: pheno_slim +synonym: "ependymal layer" BROAD [NCBIBook:NBK10047] +synonym: "neural tube ependymal layer" EXACT [NCBIBook:NBK10047] +synonym: "neural tube ependymal zone" NARROW [MP:0009689] +synonym: "neural tube ventricular germinal zone" EXACT [NCBIBook:NBK10047] +synonym: "neural tube ventricular zone" EXACT [MP:0009689] +xref: EMAPA:17152 +xref: EMAPA:35362 +xref: EMAPA_RETIRED:16783 +xref: MA:0003193 +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium +is_a: UBERON:0034706 ! proliferating neuroepithelium +relationship: BFO:0000050 UBERON:0001049 ! part of neural tube + +[Term] +id: UBERON:0004061 +name: neural tube mantle layer +def: "The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer." [http://www.ncbi.nlm.nih.gov/books/NBK10047, MP:0009690] +subset: pheno_slim +synonym: "future brain marginal layer" RELATED [EMAPA:35360] +synonym: "neural tube intermediate zone" EXACT [http://www.ncbi.nlm.nih.gov/books/NBK10047, MP:0009690] +xref: EMAPA:17148 +xref: EMAPA:35360 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1367 +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0034707 ! differentiating neuroepithelium +relationship: BFO:0000050 UBERON:0001049 ! part of neural tube + +[Term] +id: UBERON:0004062 +name: neural tube marginal layer +def: "The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter." [http://www.ncbi.nlm.nih.gov/books/NBK10047, MP:0009691] +subset: pheno_slim +synonym: "brain marginal zone" RELATED [] +synonym: "neural tube marginal zone" EXACT [MP:0009691] +xref: EMAPA:17151 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1368 +is_a: UBERON:0005162 ! multi cell part structure +relationship: BFO:0000050 UBERON:0001049 ! part of neural tube + +[Term] +id: UBERON:0004087 +name: vena cava +def: "Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Venae_cavae] +subset: pheno_slim +synonym: "caval vein" RELATED [] +synonym: "venae cavae" RELATED [Wikipedia:Venae_cavae] +xref: AAO:0010215 +xref: BTO:0001438 +xref: EMAPA:18415 +xref: FMA:321896 +xref: GAID:547 +xref: MA:0000068 +xref: MESH:D014684 +xref: NCIT:C12817 +xref: OpenCyc:Mx4rkJQ4U6gEEdudWQACs5b6Bw +xref: SCTID:244405007 +xref: UMLS:C0042460 +xref: Wikipedia:Venae_cavae +is_a: UBERON:0003479 ! thoracic cavity vein +is_a: UBERON:0013768 ! great vessel of heart + +[Term] +id: UBERON:0004100 +name: renal collecting system +def: "The collecting duct system of the kidney consists of a series of tubules and ducts that connect the nephrons to the ureter. It participates in electrolyte and fluid balance through reabsorption and excretion, processes regulated by the hormones aldosterone and antidiuretic hormone." [HP:0004742, Wikipedia:Collecting_duct_system] +subset: pheno_slim +synonym: "collecting duct system" EXACT [Wikipedia:Collecting_duct_system] +synonym: "kidney collecting duct system" EXACT [Wikipedia:Collecting_duct_system] +synonym: "tubulus renalis colligens" RELATED [Wikipedia:Collecting_duct_system] +xref: FMA:265239 +xref: SCTID:279371005 +xref: Wikipedia:Collecting_duct_system +is_a: UBERON:0000467 ! anatomical system +relationship: BFO:0000050 UBERON:0002113 ! part of kidney + +[Term] +id: UBERON:0004111 +name: anatomical conduit +def: "Any tube, opening or passage that connects two distinct anatomical spaces." [http://orcid.org/0000-0002-6601-2165] +synonym: "foramen" NARROW [EHDAA2:0003080] +synonym: "foramina" NARROW [https://orcid.org/0000-0002-6601-2165] +synonym: "opening" RELATED [] +synonym: "ostia" RELATED [] +synonym: "ostium" RELATED [] +xref: AEO:0000080 +xref: EHDAA2:0003080 +xref: FMA:242873 +xref: SCTID:346902003 +xref: Wikipedia:Foramen +is_a: UBERON:0010000 ! multicellular anatomical structure + +[Term] +id: UBERON:0004119 +name: endoderm-derived structure +def: "An anatomical structure that develops (entirely or partially) from the endoderm." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0004120 +name: mesoderm-derived structure +def: "An anatomical structure that develops (entirely or partially) from the mesoderm." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +synonym: "mesodermal derivative" EXACT [FBbt:00025998] +xref: FBbt:00025998 +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0004121 +name: ectoderm-derived structure +def: "An anatomical structure that develops (entirely or partially) from the ectoderm." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +synonym: "ectodermal deriviative" EXACT [FBbt:00025990] +xref: FBbt:00025990 +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0004122 +name: genitourinary system +def: "Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction." [VHOG:0000286] +subset: efo_slim +subset: pheno_slim +synonym: "genito-urinary system" RELATED [FMA:280610] +synonym: "genitourinary tract" RELATED [] +synonym: "GU tract" RELATED [] +synonym: "UG tract" RELATED [] +synonym: "urogenital system" EXACT [] +synonym: "urogenital tract" RELATED [BTO:0003091] +synonym: "Urogenitalsystem" RELATED [BTO:0003091] +xref: AAO:0000624 +xref: BILA:0000122 +xref: BTO:0003091 +xref: EFO:0003864 +xref: EHDAA:1013 +xref: EMAPA:16367 +xref: EV:0100094 +xref: FMA:280610 +xref: GAID:362 +xref: galen:GenitoUrinarySystem +xref: MESH:D014566 +xref: NCIT:C12810 +xref: OpenCyc:Mx4rQRpVMgAKEdyHxgDggVfs8g +xref: SCTID:278861008 +xref: UMLS:C0042066 +xref: VHOG:0000286 +xref: XAO:0000140 +is_a: UBERON:0000467 ! anatomical system + +[Term] +id: UBERON:0004134 +name: proximal tubule +def: "In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO]." [GO:0072014] +synonym: "kidney proximal tubule" EXACT [MA:0002611] +synonym: "proximal kidney tubule" EXACT [MESH:A05.810.453.736.560.570] +synonym: "renal proximal tubule" EXACT [] +xref: BTO:0001498 +xref: CALOHA:TS-0509 +xref: EMAPA:28281 +xref: MA:0002611 +xref: MESH:D007687 +is_a: UBERON:0006853 ! renal cortex tubule + +[Term] +id: UBERON:0004135 +name: distal tubule +def: "The distal tubule is a nephron tubule that consists of the distal convoluted tubule and distal straight tubule segments." [GO:0072017] +synonym: "kidney distal tubule" EXACT [MA:0002633] +synonym: "renal distal tubule" EXACT [] +xref: BTO:0000482 +xref: CALOHA:TS-0504 +xref: EMAPA:28387 +xref: MA:0002633 +xref: MESH:D007686 +is_a: UBERON:0007685 ! region of nephron tubule + +[Term] +id: UBERON:0004136 +name: intermediate tubule +def: "The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules." [GO:0072018] +synonym: "renal intermediate tubule" EXACT [] +synonym: "tubulus attenuatus" EXACT [FMA:17718] +xref: FMA:17718 +is_a: UBERON:0007685 ! region of nephron tubule +relationship: BFO:0000050 UBERON:0001288 ! part of loop of Henle + +[Term] +id: UBERON:0004139 +name: cardiogenic plate +def: "The first recognizable structure derived from the heart field." [GO:0003142] +subset: pheno_slim +synonym: "cardiac crescent" RELATED [EMAPA:16106] +synonym: "cardiogenic crescent" RELATED [GO:0003142] +synonym: "heart rudiment" RELATED [] +synonym: "myocardial plate" EXACT [EHDAA2:0000215] +xref: EHDAA2:0000215 +xref: EMAPA:16106 +xref: VHOG:0000975 +is_a: UBERON:0002050 ! embryonic structure + +[Term] +id: UBERON:0004140 +name: primary heart field +def: "A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle." [GO:0003138, GOC:mtg_heart, GOC:rl] +synonym: "FHF" RELATED [XAO:0004185] +synonym: "first heart field" EXACT [XAO:0004185] +synonym: "heart field" RELATED [XAO:0004185] +synonym: "PHF" RELATED [XAO:0004185] +synonym: "primary heart field" EXACT [PMID:17276708, XAO:0004185] +xref: XAO:0004185 +is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007688 ! anlage +relationship: BFO:0000050 UBERON:0003081 ! part of lateral plate mesoderm +relationship: BFO:0000050 UBERON:0036146 ! part of cardiopharyngeal field + +[Term] +id: UBERON:0004141 +name: heart tube +def: "An epithelial tube that will give rise to the mature heart." [GO:0003143, GOC:mtg_heart] +subset: efo_slim +subset: pheno_slim +subset: vertebrate_core +synonym: "embryonic heart tube" EXACT [GO:0003143] +synonym: "endocardial heart tube" EXACT [MP:0012700] +synonym: "endocardial tube" EXACT [XAO:0000337] +xref: AAO:0010411 +xref: EFO:0003526 +xref: EMAPA:32685 +xref: NCIT:C34161 +xref: TAO:0000360 +xref: XAO:0000337 +xref: ZFA:0000360 +is_a: UBERON:0003914 ! epithelial tube +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0012275 ! meso-epithelium + +[Term] +id: UBERON:0004151 +name: cardiac chamber +def: "A cardiac chamber surrounds an enclosed cavity within the heart." [GO:0003205] +synonym: "chamber of heart" EXACT [] +synonym: "heart chamber" EXACT [] +xref: FMA:7095 +xref: OpenCyc:Mx4rmexpjPdAEduAAAAOpmP6tw +xref: SCTID:276456008 +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0000948 ! part of heart + +[Term] +id: UBERON:0004176 +name: external genitalia +def: "The external genitalia are the outer sex organs, such as the penis or vulva in mammals." [GO:0035261] +subset: organ_slim +subset: pheno_slim +synonym: "external genitalia" EXACT [] +synonym: "external reproductive organ" RELATED [] +synonym: "external sex organ" RELATED [] +xref: FMA:45643 +xref: SCTID:362207005 +is_a: UBERON:0003133 ! reproductive organ + +[Term] +id: UBERON:0004193 +name: loop of Henle ascending limb thin segment +def: "A sub-portion of the loop of Henle in the nephron of the kidney that is permeable to ions but not to water." [GO:0072021, Wikipedia:Thin_ascending_limb_of_loop_of_Henle] +subset: pheno_slim +synonym: "ascending limb thin segment of loop of Henle" EXACT [] +synonym: "ascending thin limb" EXACT [FMA:17720] +synonym: "pars ascendens (tubulus attenuatus)" EXACT [FMA:17720] +synonym: "thin ascending limb" EXACT [EMAPA:28328] +synonym: "thin ascending limb of loop of Henle" EXACT [] +xref: EMAPA:28328 +xref: EMAPA:28361 +xref: FMA:17720 +xref: MA:0001678 +xref: Wikipedia:Thin_ascending_limb_of_loop_of_Henle +is_a: UBERON:0007685 ! region of nephron tubule +relationship: BFO:0000050 UBERON:0003455 ! part of inner renal medulla loop of Henle +relationship: BFO:0000050 UBERON:0005164 ! part of ascending limb of loop of Henle + +[Term] +id: UBERON:0004198 +name: comma-shaped body +def: "The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron." [GO:0072049] +subset: pheno_slim +synonym: "CSB" EXACT [] +xref: EMAPA:27681 +xref: ZFA:0005588 +is_a: UBERON:0005423 ! developing anatomical structure +relationship: BFO:0000050 UBERON:0010532 ! part of primitive nephron + +[Term] +id: UBERON:0004199 +name: S-shaped body +def: "The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron." [GO:0072050] +subset: pheno_slim +synonym: "SSB" EXACT [] +synonym: "stage II nephron" EXACT [http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html] +xref: EMAPA:27756 +xref: ZFA:0005589 +is_a: UBERON:0005423 ! developing anatomical structure +relationship: BFO:0000050 UBERON:0010532 ! part of primitive nephron + +[Term] +id: UBERON:0004200 +name: kidney pyramid +def: "Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts." [GO:0072056, http://anatomy.uams.edu/anatomyhtml/kidney.html] +subset: pheno_slim +synonym: "Malphigian pyramid" RELATED MISSPELLING [BTO:0003926] +synonym: "Malpighian pyramid" EXACT [Wikipedia:Renal_pyramids] +synonym: "Malpighian pyramid" RELATED [] +synonym: "medullary pyramid" RELATED [] +synonym: "pyramid" BROAD [GO:0072056] +synonym: "pyramid of Malphigi" RELATED MISSPELLING [ncithesaurus:Pyramid_of_Malpighi] +synonym: "pyramid of Malpighi" RELATED [UBERON:cjm] +synonym: "pyramides renales" RELATED [Wikipedia:Renal_pyramids] +synonym: "pyramis renalis" RELATED [BTO:0003926] +synonym: "renal medullary region" RELATED [FMA:258870] +synonym: "renal pyramid" EXACT [Wikipedia:Renal_pyramids] +xref: BTO:0003926 +xref: FMA:258870 +xref: MA:0001654 +xref: NCIT:C12886 +xref: NCIT:C33436 +xref: SCTID:361328001 +xref: UMLS:C0227629 +xref: UMLS:C1514613 +xref: Wikipedia:Renal_pyramids +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0000362 ! part of renal medulla + +[Term] +id: UBERON:0004201 +name: kidney outer medulla inner stripe +def: "The inner stripe is a deep, centrally located portion of the renal outer medulla and is traversed by thick and thin portions of nephron tubules." [GO:0072057] +subset: pheno_slim +synonym: "inner stripe" EXACT [GO:0072057] +synonym: "inner stripe of medulla of kidney" EXACT [FMA:76663] +synonym: "inner stripe of outer medulla" EXACT [EMAPA:29675] +synonym: "inner stripe of renal medulla" EXACT [FMA:76663] +synonym: "outer medulla inner stripe" EXACT [MA:0002626] +synonym: "stria interna medullae renalis" EXACT [FMA:76663, FMA:TA] +xref: EMAPA:29675 +xref: FMA:76663 +xref: MA:0002626 +is_a: UBERON:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 UBERON:0001293 ! part of outer medulla of kidney + +[Term] +id: UBERON:0004202 +name: kidney outer medulla outer stripe +def: "The outer stripe is the region of the kidney that lies distal to the line of termination of the straight renal tubules." [GO:0072058] +subset: pheno_slim +synonym: "outer medulla outer stripe" EXACT [MA:0002629] +synonym: "outer stripe" EXACT [GO:0072058] +synonym: "outer stripe of medulla of kidney" EXACT [FMA:76662] +synonym: "outer stripe of outer medulla" EXACT [EMAPA:29663] +synonym: "outer stripe of renal medulla" EXACT [FMA:76662] +synonym: "stria externa medullae renalis" EXACT [FMA:76662, FMA:TA] +xref: EMAPA:29663 +xref: FMA:76662 +xref: MA:0002629 +is_a: UBERON:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 UBERON:0001293 ! part of outer medulla of kidney + +[Term] +id: UBERON:0004208 +name: nephrogenic mesenchyme +def: "Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron." [GO:0072076] +synonym: "mesenchyme of nephron" EXACT [OBOL:automatic] +synonym: "nephron mesenchyme" EXACT [OBOL:automatic] +is_a: UBERON:0003104 ! mesenchyme + +[Term] +id: UBERON:0004209 +name: renal vesicle +def: "The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells." [GO:0072077] +synonym: "stage I nephron" EXACT [http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html, ZFA:0005586] +is_a: UBERON:0007503 ! epithelial vesicle +relationship: BFO:0000050 UBERON:0010536 ! part of nephron progenitor + +[Term] +id: UBERON:0004211 +name: nephron epithelium +def: "The nephron epithelium is a tissue that covers the surface of a nephron." [GO:0072088] +synonym: "epithelial tissue of nephron" EXACT [OBOL:automatic] +synonym: "epithelium of nephron" EXACT [OBOL:automatic] +synonym: "nephron epithelial tissue" EXACT [OBOL:automatic] +is_a: UBERON:0004819 ! kidney epithelium +relationship: BFO:0000050 UBERON:0001285 ! part of nephron + +[Term] +id: UBERON:0004250 +name: upper arm bone +def: "A bone that is part of a forelimb stylopod [Automatically generated definition]." [https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376, OBOL:automatic] +synonym: "humerus" NARROW [https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376] +xref: EMAPA:35892 +xref: MA:0000604 +is_a: UBERON:0003460 ! arm bone +relationship: BFO:0000050 UBERON:0003822 ! part of forelimb stylopod + +[Term] +id: UBERON:0004251 +name: hindlimb zeugopod bone +def: "A bone that is part of a lower leg [Automatically generated definition]." [OBOL:automatic] +synonym: "bone of hind limb middle limb segment" EXACT [OBOL:automatic] +synonym: "bone of hind limb zeugopod" EXACT [OBOL:automatic] +synonym: "bone of hindlimb middle limb segment" EXACT [OBOL:automatic] +synonym: "bone of hindlimb zeugopod" EXACT [OBOL:automatic] +synonym: "bone of inferior member middle limb segment" EXACT [OBOL:automatic] +synonym: "bone of inferior member zeugopod" EXACT [OBOL:automatic] +synonym: "bone of intermediate segment of free lower limb" EXACT [OBOL:automatic] +synonym: "bone of lower extremity middle limb segment" EXACT [OBOL:automatic] +synonym: "bone of lower extremity zeugopod" EXACT [OBOL:automatic] +synonym: "bone of lower leg" EXACT [OBOL:automatic] +synonym: "bone of middle limb segment of hind limb" EXACT [OBOL:automatic] +synonym: "bone of middle limb segment of hindlimb" EXACT [OBOL:automatic] +synonym: "bone of middle limb segment of inferior member" EXACT [OBOL:automatic] +synonym: "bone of middle limb segment of lower extremity" EXACT [OBOL:automatic] +synonym: "bone of zeugopod of hind limb" EXACT [OBOL:automatic] +synonym: "bone of zeugopod of hindlimb" EXACT [OBOL:automatic] +synonym: "bone of zeugopod of inferior member" EXACT [OBOL:automatic] +synonym: "bone of zeugopod of leg" EXACT [OBOL:automatic] +synonym: "bone of zeugopod of lower extremity" EXACT [OBOL:automatic] +synonym: "bone organ of hind limb middle limb segment" EXACT [OBOL:automatic] +synonym: "bone organ of hind limb zeugopod" EXACT [OBOL:automatic] +synonym: "bone organ of hindlimb middle limb segment" EXACT [OBOL:automatic] +synonym: "bone organ of hindlimb zeugopod" EXACT [OBOL:automatic] +synonym: "bone organ of inferior member middle limb segment" EXACT [OBOL:automatic] +synonym: "bone organ of inferior member zeugopod" EXACT [OBOL:automatic] +synonym: "bone organ of intermediate segment of free lower limb" EXACT [OBOL:automatic] +synonym: "bone organ of lower extremity middle limb segment" EXACT [OBOL:automatic] +synonym: "bone organ of lower extremity zeugopod" EXACT [OBOL:automatic] +synonym: "bone organ of lower leg" EXACT [OBOL:automatic] +synonym: "bone organ of middle limb segment of hind limb" EXACT [OBOL:automatic] +synonym: "bone organ of middle limb segment of hindlimb" EXACT [OBOL:automatic] +synonym: "bone organ of middle limb segment of inferior member" EXACT [OBOL:automatic] +synonym: "bone organ of middle limb segment of lower extremity" EXACT [OBOL:automatic] +synonym: "bone organ of zeugopod of hind limb" EXACT [OBOL:automatic] +synonym: "bone organ of zeugopod of hindlimb" EXACT [OBOL:automatic] +synonym: "bone organ of zeugopod of inferior member" EXACT [OBOL:automatic] +synonym: "bone organ of zeugopod of leg" EXACT [OBOL:automatic] +synonym: "bone organ of zeugopod of lower extremity" EXACT [OBOL:automatic] +synonym: "hind limb middle limb segment bone" EXACT [OBOL:automatic] +synonym: "hind limb middle limb segment bone organ" EXACT [OBOL:automatic] +synonym: "hind limb zeugopod bone" EXACT [OBOL:automatic] +synonym: "hind limb zeugopod bone organ" EXACT [OBOL:automatic] +synonym: "hindlimb middle limb segment bone" EXACT [OBOL:automatic] +synonym: "hindlimb middle limb segment bone organ" EXACT [OBOL:automatic] +synonym: "hindlimb zeugopod bone" EXACT [OBOL:automatic] +synonym: "hindlimb zeugopod bone organ" EXACT [OBOL:automatic] +synonym: "inferior member middle limb segment bone" EXACT [OBOL:automatic] +synonym: "inferior member middle limb segment bone organ" EXACT [OBOL:automatic] +synonym: "inferior member zeugopod bone" EXACT [OBOL:automatic] +synonym: "inferior member zeugopod bone organ" EXACT [OBOL:automatic] +synonym: "intermediate segment of free lower limb bone" EXACT [OBOL:automatic] +synonym: "intermediate segment of free lower limb bone organ" EXACT [OBOL:automatic] +synonym: "lower extremity middle limb segment bone" EXACT [OBOL:automatic] +synonym: "lower extremity middle limb segment bone organ" EXACT [OBOL:automatic] +synonym: "lower extremity zeugopod bone" EXACT [OBOL:automatic] +synonym: "lower extremity zeugopod bone organ" EXACT [OBOL:automatic] +synonym: "lower leg bone" EXACT [MA:0000676] +synonym: "middle limb segment of hind limb bone" EXACT [OBOL:automatic] +synonym: "middle limb segment of hind limb bone organ" EXACT [OBOL:automatic] +synonym: "middle limb segment of hindlimb bone" EXACT [OBOL:automatic] +synonym: "middle limb segment of hindlimb bone organ" EXACT [OBOL:automatic] +synonym: "middle limb segment of inferior member bone" EXACT [OBOL:automatic] +synonym: "middle limb segment of inferior member bone organ" EXACT [OBOL:automatic] +synonym: "middle limb segment of lower extremity bone" EXACT [OBOL:automatic] +synonym: "middle limb segment of lower extremity bone organ" EXACT [OBOL:automatic] +synonym: "zeugopod of hind limb bone" EXACT [OBOL:automatic] +synonym: "zeugopod of hind limb bone organ" EXACT [OBOL:automatic] +synonym: "zeugopod of hindlimb bone" EXACT [OBOL:automatic] +synonym: "zeugopod of hindlimb bone organ" EXACT [OBOL:automatic] +synonym: "zeugopod of inferior member bone" EXACT [OBOL:automatic] +synonym: "zeugopod of inferior member bone organ" EXACT [OBOL:automatic] +synonym: "zeugopod of leg bone" EXACT [OBOL:automatic] +synonym: "zeugopod of leg bone organ" EXACT [OBOL:automatic] +synonym: "zeugopod of lower extremity bone" EXACT [OBOL:automatic] +synonym: "zeugopod of lower extremity bone organ" EXACT [OBOL:automatic] +xref: EMAPA:35519 +xref: MA:0000676 +is_a: UBERON:0005893 ! leg bone +relationship: BFO:0000050 UBERON:0003823 ! part of hindlimb zeugopod + +[Term] +id: UBERON:0004252 +name: hindlimb stylopod muscle +def: "Any muscle organ that is part of a hindlimb stylopod (upper leg)[Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "muscle of thigh" EXACT [FMA:22470] +synonym: "thigh muscle" EXACT [FMA:22470] +synonym: "upper leg muscle" EXACT [MA:0000684] +xref: BTO:0001367 +xref: EMAPA:19144 +xref: FMA:22470 +xref: MA:0000684 +xref: SCTID:245013005 +is_a: UBERON:0001383 ! muscle of leg +relationship: BFO:0000050 UBERON:0004463 ! part of musculature of hindlimb stylopod + +[Term] +id: UBERON:0004254 +name: forelimb zeugopod muscle +def: "Any muscle organ that is part of a forelimb zeugopod (lower arm)[Automatically generated definition]." [OBOL:automatic] +synonym: "forearm muscle" EXACT [FMA:37371] +synonym: "lower arm muscle" EXACT [MA:0000600] +synonym: "muscle of forearm" EXACT [FMA:37371] +synonym: "wing zeugopod muscle" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +xref: EMAPA:32622 +xref: FMA:37371 +xref: MA:0000600 +xref: SCTID:181631004 +is_a: UBERON:0001499 ! muscle of arm +relationship: BFO:0000050 UBERON:0004487 ! part of musculature of forelimb zeugopod + +[Term] +id: UBERON:0004255 +name: forelimb stylopod muscle +def: "Any muscle organ that is part of a forelimb stylopod (upper arm)[Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "muscle of arm" RELATED INCONSISTENT [FMA:37370] +synonym: "muscle of upper arm" EXACT [MA:0000606] +synonym: "skeletal muscle of upper arm" RELATED [EMAPA:19107] +synonym: "upper arm muscle" EXACT [MA:0000606] +synonym: "wing stylopod muscle" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +xref: EMAPA:19107 +xref: FMA:37370 +xref: MA:0000606 +xref: SCTID:244979005 +is_a: UBERON:0001499 ! muscle of arm +relationship: BFO:0000050 UBERON:0014791 ! part of musculature of forelimb stylopod + +[Term] +id: UBERON:0004256 +name: hindlimb zeugopod muscle +def: "Any muscle organ that is part of a hindlimb zeugopod (lower leg) [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "calf muscle" RELATED [OBOL:automatic] +synonym: "lower leg muscle" EXACT [MA:0000678] +synonym: "muscle of leg" RELATED INCONSISTENT [FMA:22471] +xref: EMAPA:19318 +xref: FMA:22471 +xref: MA:0000678 +xref: SCTID:265806001 +is_a: UBERON:0001383 ! muscle of leg +relationship: BFO:0000050 UBERON:0006067 ! part of musculature of hindlimb zeugopod + +[Term] +id: UBERON:0004288 +name: skeleton +def: "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body." [VSAO:0000026] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "set of all bones" EXACT [] +synonym: "set of bones of body" EXACT [] +xref: AEO:0000168 +xref: EHDAA2:0001843 +xref: EHDAA:5047 +xref: EMAPA:17213 +xref: FMA:23875 +xref: GAID:177 +xref: galen:Skeleton +xref: MA:0003006 +xref: MAT:0000032 +xref: MESH:D012863 +xref: MIAA:0000032 +xref: OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA +xref: SCTID:361378004 +xref: VSAO:0000026 +xref: Wikipedia:Skeleton +xref: XAO:0004053 +is_a: UBERON:0034925 ! anatomical collection +relationship: BFO:0000050 UBERON:0001434 ! part of skeletal system + +[Term] +id: UBERON:0004290 +name: dermomyotome +def: "The bilaminar epithelium formed from the myotome and dermatome." [AEO:0000214] +synonym: "dermamyotome" RELATED [VHOG:0000676] +synonym: "dermomyotomes" RELATED [VHOG:0000676] +xref: AAO:0010572 +xref: AEO:0000214 +xref: EHDAA2:0003259 +xref: EMAPA:31109 +xref: FMA:295654 +xref: NCIT:C34140 +xref: TAO:0001513 +xref: UMLS:C1511786 +xref: VHOG:0000676 +xref: ZFA:0001513 +is_a: UBERON:0000486 ! multilaminar epithelium +is_a: UBERON:0016888 ! transitional anatomical structure + +[Term] +id: UBERON:0004291 +name: heart rudiment +def: "A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube." [GO:0003313] +synonym: "heart cone" EXACT [GO:0003313] +synonym: "rudimentary heart" EXACT [ZFA:0000115] +xref: TAO:0000115 +xref: ZFA:0000115 +is_a: UBERON:0012275 ! meso-epithelium + +[Term] +id: UBERON:0004341 +name: primitive streak +def: "The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP]." [MP:0002231, Wikipedia:Primitive_streak] +subset: early_development +subset: pheno_slim +synonym: "primitive streak - blastopore - germ ring" EXACT [VHOG:0001202] +xref: EHDAA2:0001525 +xref: EHDAA:185 +xref: EMAPA:16072 +xref: FMA:293110 +xref: NCIT:C28402 +xref: SCTID:361438007 +xref: UMLS:C0033153 +xref: VHOG:0001202 +xref: Wikipedia:Primitive_streak +is_a: UBERON:0000485 ! simple columnar epithelium +is_a: UBERON:0005291 ! embryonic tissue + +[Term] +id: UBERON:0004347 +name: limb bud +def: "An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP]." [https://orcid.org/0000-0002-6601-2165, ISBN:9780878932504, MP:0005650, Wikipedia:Limb_bud] +subset: pheno_slim +synonym: "gemmae membrorum" RELATED [Wikipedia:Limb_bud] +synonym: "limb buds" EXACT [] +synonym: "limbbud" EXACT [GO:0060174] +xref: AAO:0010375 +xref: BTO:0001640 +xref: EMAPA:35944 +xref: FMA:296780 +xref: GAID:1307 +xref: MESH:A16.254.462 +xref: NCIT:C34203 +xref: UMLS:C0282505 +xref: Wikipedia:Limb_bud +xref: XAO:0003161 +is_a: UBERON:0004357 ! paired limb/fin bud + +[Term] +id: UBERON:0004356 +name: apical ectodermal ridge +def: "Multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP]." [MP:0001676, Wikipedia:Apical_ectodermal_ridge] +subset: pheno_slim +synonym: "AER" RELATED [MP:0001676] +synonym: "apical epidermal ridge" EXACT [XAO:0004121] +synonym: "crista ectodermalis apicalis" RELATED [Wikipedia:Apical_ectodermal_ridge] +xref: AAO:0010760 +xref: EMAPA:32744 +xref: NCIT:C34109 +xref: TAO:0002146 +xref: UMLS:C1516037 +xref: Wikipedia:Apical_ectodermal_ridge +xref: XAO:0004121 +xref: ZFA:0001702 +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0000924 ! part of ectoderm +relationship: BFO:0000050 UBERON:0004357 ! part of paired limb/fin bud + +[Term] +id: UBERON:0004357 +name: paired limb/fin bud +def: "An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]." [https://orcid.org/0000-0002-6601-2165, ISBN:9780878932504, MP:0005650] +subset: homology_grouping +synonym: "limb - fin bud" EXACT [VHOG:0001258] +synonym: "paired appendage bud" EXACT [] +synonym: "paired limb/fin bud" EXACT [VHOG:0001258] +xref: VHOG:0001258 +is_a: UBERON:0003102 ! surface structure +is_a: UBERON:0006598 ! presumptive structure + +[Term] +id: UBERON:0004362 +name: pharyngeal arch 1 +def: "The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries." [http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "1st arch" RELATED [EHDAA2:0000006] +synonym: "1st pharyngeal arch" EXACT [] +synonym: "1st visceral arch" RELATED [VHOG:0000296] +synonym: "arcus pharyngeus primus" RELATED [Wikipedia:First_pharyngeal_arch] +synonym: "branchial arch 1" EXACT SENSU [] +synonym: "first branchial arch" EXACT SENSU [] +synonym: "first pharyngeal arch" EXACT [] +synonym: "first visceral arch" EXACT SENSU [] +synonym: "mandibular arch" EXACT [] +synonym: "visceral arch 1" EXACT SENSU [] +xref: AAO:0010364 +xref: CALOHA:TS-2089 +xref: EHDAA2:0000006 +xref: EHDAA:573 +xref: EMAPA:16118 +xref: FMA:293019 +xref: MFMO:0000095 +xref: NCIT:C34175 +xref: SCTID:308767008 +xref: TAO:0001595 +xref: UMLS:C1517197 +xref: VHOG:0000296 +xref: Wikipedia:First_pharyngeal_arch +xref: XAO:0000097 +xref: ZFA:0001612 +is_a: UBERON:0002539 ! pharyngeal arch + +[Term] +id: UBERON:0004375 +name: bone of free limb or fin +def: "A bone that is part of an appendage [Automatically generated definition]." [OBOL:automatic] +subset: homology_grouping +synonym: "appendage bone" EXACT [] +synonym: "bone of appendage" EXACT [] +synonym: "bone of free segment of appendicular skeleton" EXACT [] +is_a: UBERON:0010740 ! bone of appendage girdle complex +relationship: BFO:0000050 UBERON:0011582 ! part of paired limb/fin skeleton + +[Term] +id: UBERON:0004381 +name: skeleton of limb +def: "The collection of all skeletal elements in an individual limb." [https://orcid.org/0000-0002-6601-2165] +synonym: "free limb skeleton" EXACT [VSAO:0000300] +synonym: "limb skeleton" EXACT [EHDAA2:0002221] +synonym: "set of bones of limb" EXACT [] +xref: EHDAA2:0002221 +xref: EMAPA:32702 +xref: VSAO:0000300 +is_a: UBERON:0010712 ! limb skeleton subdivision +is_a: UBERON:0011582 ! paired limb/fin skeleton + +[Term] +id: UBERON:0004456 +name: entire sense organ system +def: "Sum of all sensory systems in an organism." [http://orcid.org/0000-0002-6601-2165] +subset: uberon_slim +synonym: "sense organ system" EXACT [FMA:78499] +xref: FMA:78499 +is_a: UBERON:0000467 ! anatomical system + +[Term] +id: UBERON:0004463 +name: musculature of hindlimb stylopod +def: "Any collection of muscles that is part of a hindlimb stylopod (upper leg / thigh)[Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "muscle group of thigh" EXACT [FMA:50208] +synonym: "musculature of thigh" EXACT [FMA:50208] +synonym: "set of muscles of thigh" EXACT [FMA:50208] +synonym: "thigh musculature" EXACT [FMA:50208] +xref: FMA:50208 +is_a: UBERON:0004466 ! musculature of leg +relationship: BFO:0000050 UBERON:0000376 ! part of hindlimb stylopod + +[Term] +id: UBERON:0004466 +name: musculature of leg +def: "Any collection of muscles that is part of a lower leg or upper leg [Automatically generated definition]." [OBOL:automatic] +synonym: "leg muscle system" EXACT [EHDAA2:0000973] +xref: EHDAA2:0000973 +is_a: UBERON:0004482 ! musculature of lower limb +relationship: BFO:0000050 UBERON:0000978 ! part of leg + +[Term] +id: UBERON:0004474 +name: musculature of arm +def: "Any collection of muscles that is part of an arm [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "arm muscle system" EXACT [EHDAA2:0000141] +synonym: "arm musculature" EXACT [FMA:50202] +synonym: "muscle group of arm" EXACT [FMA:50202] +synonym: "set of muscles of arm" EXACT [FMA:50202] +xref: EHDAA2:0000141 +is_a: UBERON:0004481 ! musculature of upper limb +relationship: BFO:0000050 UBERON:0001460 ! part of arm + +[Term] +id: UBERON:0004480 +name: musculature of limb +def: "Any collection of muscles that is part of a limb [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "limb muscle system" EXACT [EHDAA2:0000995] +synonym: "limb musculature" EXACT [FMA:50188] +synonym: "muscle group of limb" EXACT [FMA:50188] +synonym: "set of muscles of limb" EXACT [FMA:50188] +xref: EHDAA2:0000995 +xref: EMAPA:32700 +xref: FMA:50188 +is_a: UBERON:0007271 ! appendage musculature +relationship: BFO:0000050 UBERON:0002101 ! part of limb + +[Term] +id: UBERON:0004481 +name: musculature of upper limb +def: "Any collection of muscles that is part of a forelimb [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "free upper limb musculature" EXACT [FMA:50396] +synonym: "muscle group of free upper limb" EXACT [FMA:50396] +synonym: "musculature of free upper limb" EXACT [FMA:50396] +synonym: "set of muscles of free upper limb" EXACT [FMA:50396] +xref: FMA:50396 +is_a: UBERON:0004480 ! musculature of limb +is_a: UBERON:0007269 ! pectoral appendage musculature +relationship: BFO:0000050 UBERON:0002102 ! part of forelimb + +[Term] +id: UBERON:0004482 +name: musculature of lower limb +def: "Any collection of muscles that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "free lower limb musculature" EXACT [FMA:50399] +synonym: "muscle group of free lower limb" EXACT [FMA:50399] +synonym: "musculature of free lower limb" EXACT [FMA:50399] +synonym: "set of muscles of free lower limb" EXACT [FMA:50399] +xref: FMA:50399 +is_a: UBERON:0004480 ! musculature of limb +is_a: UBERON:0007270 ! pelvic appendage musculature +relationship: BFO:0000050 UBERON:0002103 ! part of hindlimb + +[Term] +id: UBERON:0004487 +name: musculature of forelimb zeugopod +def: "Any collection of muscles that is part of a lower arm [Automatically generated definition]." [OBOL:automatic] +synonym: "muscle group of forearm" EXACT [FMA:39089] +synonym: "musculature of forearm" EXACT [FMA:39089] +synonym: "set of muscles of forearm" EXACT [FMA:39089] +xref: FMA:39089 +is_a: UBERON:0004474 ! musculature of arm +relationship: BFO:0000050 UBERON:0002386 ! part of forelimb zeugopod + +[Term] +id: UBERON:0004529 +name: anatomical projection +def: "A projection or outgrowth of tissue from a larger body or organ." [https://github.com/obophenotype/uberon/issues/39, Wikipedia:Process_(anatomy)] +subset: upper_level +synonym: "anatomical process" BROAD [] +synonym: "anatomical protrusion" RELATED [] +synonym: "flange" NARROW [VSAO:0000180] +synonym: "flanges" NARROW [VSAO:0000180] +synonym: "lamella" NARROW [VSAO:0000180] +synonym: "lamellae" NARROW [VSAO:0000180] +synonym: "lamina" NARROW [VSAO:0000180] +synonym: "laminae" NARROW [VSAO:0000180] +synonym: "organ process" NARROW [] +synonym: "papilla" NARROW [] +synonym: "process" BROAD [VSAO:0000180] +synonym: "process of organ" NARROW [] +synonym: "processes" NARROW [VSAO:0000180] +synonym: "processus" EXACT [FMA:67601, FMA:TA] +synonym: "projection" EXACT [] +synonym: "projection" NARROW [VSAO:0000180] +synonym: "projections" NARROW [VSAO:0000180] +synonym: "protrusion" RELATED [] +synonym: "ridge" NARROW [VSAO:0000180] +synonym: "ridges" NARROW [VSAO:0000180] +synonym: "shelf" NARROW [VSAO:0000180] +synonym: "shelves" NARROW [VSAO:0000180] +synonym: "spine" RELATED [] +xref: AAO:0010278 +xref: FMA:67601 +xref: galen:Ridge +xref: HAO:0000822 +xref: NCIT:C61549 +xref: TAO:0001834 +xref: VSAO:0000180 +xref: Wikipedia:Process_(anatomy) +xref: XAO:0004020 +is_a: UBERON:0034768 ! morphological feature +relationship: BFO:0000050 UBERON:0000062 ! part of organ + +[Term] +id: UBERON:0004535 +name: cardiovascular system +def: "Anatomical system that has as its parts the heart and blood vessels." [BTO:0000088] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "CV system" RELATED [BTO:0000088] +synonym: "Herz und Gefaesssystem" RELATED [BTO:0000088] +xref: AAO:0011001 +xref: BILA:0000016 +xref: BTO:0000088 +xref: CALOHA:TS-1297 +xref: EFO:0000791 +xref: EHDAA2:0000216 +xref: EHDAA:394 +xref: EMAPA:16104 +xref: EMAPA:16370 +xref: EV:0100017 +xref: FMA:7161 +xref: GAID:467 +xref: MA:0000010 +xref: MAT:0000016 +xref: MESH:D002319 +xref: MIAA:0000016 +xref: NCIT:C12686 +xref: OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA +xref: SCTID:278198007 +xref: TAO:0000010 +xref: UMLS:C0007226 +xref: VHOG:0000302 +xref: WikipediaCategory:Cardiovascular_system +xref: XAO:0000100 +xref: XAO:0001010 +xref: ZFA:0000010 +is_a: UBERON:0000467 ! anatomical system +relationship: BFO:0000050 UBERON:0001009 ! part of circulatory system + +[Term] +id: UBERON:0004536 +name: lymph vasculature +def: "A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep." [ZFA:0005105] +subset: vertebrate_core +synonym: "lymph vessels" RELATED [ZFA:0005105] +synonym: "lymphatic trunks and ducts" EXACT [FMA:63815] +synonym: "lymphatic vasculature" EXACT [] +synonym: "lymphatic vessel network" EXACT [] +synonym: "lymphatic vessels set" EXACT [FMA:63815] +synonym: "set of lymphatic vessels" EXACT [] +synonym: "trunci et ductus lymphatici" EXACT [FMA:63815, FMA:TA] +xref: FMA:63815 +xref: TAO:0005105 +xref: ZFA:0005105 +is_a: UBERON:0002049 ! vasculature +relationship: BFO:0000050 UBERON:0006558 ! part of lymphatic part of lymphoid system + +[Term] +id: UBERON:0004537 +name: blood vasculature +def: "A vascular network consisting of blood vessels." [https://orcid.org/0000-0002-6601-2165] +synonym: "blood system" RELATED [] +synonym: "blood vascular network" EXACT [] +synonym: "blood vessel system" RELATED [] +synonym: "blood vessels" RELATED [TAO:0001079] +synonym: "set of blood vessels" EXACT [] +xref: TAO:0001079 +xref: ZFA:0001079 +is_a: UBERON:0002049 ! vasculature + +[Term] +id: UBERON:0004552 +name: digital artery +def: "An artery that is part of a digit [Automatically generated definition]." [OBOL:automatic] +xref: EMAPA:37076 +xref: MA:0001941 +xref: SCTID:181335004 +is_a: UBERON:0001637 ! artery +is_a: UBERON:0003514 ! limb blood vessel +relationship: BFO:0000050 UBERON:0002544 ! part of digit + +[Term] +id: UBERON:0004553 +name: forelimb digital artery +def: "A digital artery that is part of a forelimb [Automatically generated definition]." [OBOL:automatic] +synonym: "digital artery of manus" EXACT [] +synonym: "forelimb digital arteries" EXACT [MA:0001953] +synonym: "wing digital artery" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +xref: EMAPA:37210 +xref: MA:0001953 +xref: SCTID:265791006 +is_a: UBERON:0003522 ! manual digit blood vessel +is_a: UBERON:0004552 ! digital artery + +[Term] +id: UBERON:0004554 +name: hindlimb digital artery +def: "A digital artery that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] +synonym: "digital artery of foot" EXACT [FMA:69713] +synonym: "hindlimb digital arteries" EXACT [MA:0001964] +xref: EMAPA:37214 +xref: FMA:69713 +xref: MA:0001964 +is_a: UBERON:0003516 ! hindlimb blood vessel +is_a: UBERON:0004552 ! digital artery + +[Term] +id: UBERON:0004572 +name: arterial system +def: "The part of the cardiovascular system consisting of all arteries." [https://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +xref: BTO:0004690 +xref: EHDAA2:0000143 +xref: EHDAA:396 +xref: EMAPA:16201 +xref: EMAPA:16371 +xref: MA:0002719 +xref: SCTID:362030008 +xref: VHOG:0000273 +is_a: UBERON:0007798 ! vascular system + +[Term] +id: UBERON:0004582 +name: venous system +def: "The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions." [https://orcid.org/0000-0002-6601-2165] +synonym: "vein system" EXACT [] +xref: BTO:0004692 +xref: EHDAA2:0002171 +xref: EHDAA:486 +xref: EMAPA:16240 +xref: MA:0002720 +xref: NCIT:C33858 +xref: SCTID:362060003 +xref: UMLS:C1267406 +xref: VHOG:0000277 +is_a: UBERON:0007798 ! vascular system + +[Term] +id: UBERON:0004637 +name: otic capsule +def: "The capsule surrounding the inner ear mechanism." [http://www.biology-online.org/dictionary/Otic_capsule] +synonym: "auditory capsule" RELATED [VHOG:0000854] +synonym: "otic capsule" EXACT [ZFA:0001500] +synonym: "otic capsule element" EXACT [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +synonym: "otic capsule endochondral element" EXACT [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +synonym: "otic capsule skeletal element" BROAD [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +synonym: "otic region" RELATED [] +synonym: "periotic" RELATED [] +synonym: "periotic capsule" RELATED [VHOG:0000854] +xref: AAO:0010143 +xref: SCTID:361515007 +xref: VHOG:0000854 +is_a: UBERON:0010363 ! endochondral element +relationship: BFO:0000050 UBERON:0001846 ! part of internal ear +relationship: BFO:0000050 UBERON:0003110 ! part of otic region + +[Term] +id: UBERON:0004638 +name: blood vessel endothelium +def: "An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart." [https://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +subset: vertebrate_core +xref: BTO:0000766 +xref: CALOHA:TS-2155 +xref: EMAPA:35176 +xref: MA:0000709 +xref: NCIT:C53395 +xref: TAO:0005257 +xref: UMLS:C1706972 +xref: ZFA:0005257 +is_a: UBERON:0004852 ! cardiovascular system endothelium +relationship: BFO:0000050 UBERON:0001981 ! part of blood vessel + +[Term] +id: UBERON:0004681 +name: vestibular system +def: "The sensory system for the sense of balance." [NLXANAT:090819] +subset: pheno_slim +synonym: "equilibrioception system" NARROW [] +synonym: "vestibular organ system" EXACT [FMA:7193] +synonym: "vestibular system" EXACT [NLXANAT:090819] +synonym: "vestibulomotor system" NARROW [] +xref: BTO:0003381 +xref: EMAPA:37986 +xref: FMA:7193 +xref: NLXANAT:090819 +xref: SCTID:361533001 +xref: Wikipedia:Vestibular_system +is_a: UBERON:0001032 ! sensory system +relationship: BFO:0000050 UBERON:0002105 ! part of vestibulo-auditory system + +[Term] +id: UBERON:0004704 +name: bone fossa +def: "A depression or hollow in a bone[WP]." [Wikipedia:Fossa#Anatomy] +subset: vertebrate_core +synonym: "concavities" RELATED [TAO:0001743] +synonym: "concavity" RELATED [TAO:0001743] +synonym: "depression" RELATED [TAO:0001743] +synonym: "depressions" RELATED [TAO:0001743] +synonym: "fossa" BROAD [] +synonym: "fossae" RELATED [TAO:0001743] +synonym: "groove" RELATED [TAO:0001743] +xref: AAO:0010439 +xref: FMA:45791 +xref: TAO:0001743 +xref: UMLS:C0836913 +xref: VSAO:0005069 +xref: Wikipedia:Fossa#Anatomy +xref: ZFA:0005388 +is_a: UBERON:0002553 ! anatomical cavity +relationship: BFO:0000050 UBERON:0001474 ! part of bone element + +[Term] +id: UBERON:0004708 +name: paired limb/fin +def: "An appendage that is part of an appendage girdle complex." [https://github.com/geneontology/go-ontology/issues/9029, UBERON:cjm] +subset: homology_grouping +synonym: "girdle-associated appendage" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "jointed paired lateral appendage" NARROW [https://orcid.org/0000-0002-6601-2165] +synonym: "limb or fin" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "limb/fin" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "paired appendage" NARROW [VSAO:0000067] +synonym: "pectoral or pelvic appendage" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "pelvic/pectoral appendage" EXACT [https://orcid.org/0000-0002-6601-2165] +xref: VSAO:0000067 +is_a: UBERON:0000026 ! appendage +relationship: BFO:0000050 UBERON:0010707 ! part of appendage girdle complex + +[Term] +id: UBERON:0004709 +name: pelvic appendage +def: "Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues." [VSAO:0000150] +subset: homology_grouping +synonym: "hindlimb/pelvic fin" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "pelvic appendage" EXACT [VSAO:0000126] +synonym: "pelvic limb/fin" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "posterior appendage" BROAD [] +synonym: "posterior limb/fin" EXACT [] +synonym: "posterior paired appendage" EXACT [VSAO:0000126] +xref: VSAO:0000126 +is_a: UBERON:0004708 ! paired limb/fin +relationship: BFO:0000050 UBERON:0010709 ! part of pelvic complex + +[Term] +id: UBERON:0004710 +name: pectoral appendage +def: "Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues." [VSAO:0000150-modified] +subset: homology_grouping +synonym: "anterior appendage" BROAD [] +synonym: "anterior limb/fin" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "anterior paired appendage" EXACT [VSAO:0000148] +synonym: "forelimb - pectoral fin" EXACT [VHOG:0001753] +synonym: "forelimb or pectoral fin" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "forelimb/pectoral fin" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "pectoral limb/fin" EXACT [https://orcid.org/0000-0002-6601-2165] +xref: VHOG:0001753 +xref: VSAO:0000125 +is_a: UBERON:0004708 ! paired limb/fin +relationship: BFO:0000050 UBERON:0010708 ! part of pectoral complex + +[Term] +id: UBERON:0004716 +name: conceptus +def: "The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]." [BTO:0003834, Wikipedia:Conceptus] +synonym: "embryo plus adnexa" EXACT [] +xref: AEO:0000194 +xref: BTO:0003834 +xref: EHDAA2:0000001 +xref: EHDAA2:0003235 +xref: EMAPA:36040 +xref: NCIT:C34131 +xref: UMLS:C1516779 +xref: Wikipedia:Conceptus +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0004726 +name: vasa recta +def: "In the blood supply of the kidney, the vasa recta renis (or straight arteries of kidney, or straight arterioles of kidney) form a series of straight capillaries in the medulla. They lie parallel to the loop of Henle. These vessels branch off the efferent arterioles of juxtamedullary nephrons (those nephrons closest to the medulla), enter the medulla, and surround the loop of Henle." [Wikipedia:Vasa_recta] +subset: pheno_slim +synonym: "arteria recta" RELATED [Wikipedia:Vasa_recta] +synonym: "arteriae rectae" RELATED [Wikipedia:Vasa_recta] +synonym: "arteriolae rectae renis" EXACT [FMA:72006, FMA:TA] +synonym: "arteriolae rectae renis" RELATED [Wikipedia:Vasa_recta] +synonym: "arteriolae recti" RELATED [Wikipedia:Vasa_recta] +synonym: "kidney vasa recta" EXACT [MP:0011324] +synonym: "renal medullary capillary" EXACT [EMAPA:30043] +synonym: "set of straight arterioles of kidney" EXACT [FMA:72006] +synonym: "straight arterioles of kidney" EXACT [FMA:72006] +synonym: "vasa recta of kidney" EXACT [FMA:72006] +synonym: "vasa recta renis" EXACT [FMA:72006, FMA:TA] +synonym: "vasa rectae" RELATED [Wikipedia:Vasa_recta] +xref: EMAPA:30043 +xref: FMA:72006 +xref: galen:ArteriaeRectae +xref: MA:0002595 +xref: Wikipedia:Vasa_recta +is_a: UBERON:0001140 ! renal vein + +[Term] +id: UBERON:0004732 +name: segmental subdivision of nervous system +def: "Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres." [FBbt:00005140, http://orcid.org/0000-0002-6601-2165] +subset: non_informative +synonym: "neuromere" RELATED [FBbt:00005140] +xref: FBbt:00005140 +is_a: UBERON:0000063 ! organ subunit +relationship: BFO:0000050 UBERON:0001016 ! part of nervous system + +[Term] +id: UBERON:0004733 +name: segmental subdivision of hindbrain +def: "An organ subunit that is part of a hindbrain [Automatically generated definition]." [OBOL:automatic] +subset: non_informative +synonym: "hindbrain segment" EXACT [FMA:61998] +synonym: "segment of hindbrain" EXACT [FMA:61998] +xref: FMA:61998 +is_a: UBERON:0004732 ! segmental subdivision of nervous system +relationship: BFO:0000050 UBERON:0002028 ! part of hindbrain + +[Term] +id: UBERON:0004734 +name: gastrula +def: "Organism at the gastrula stage." [Wikipedia:Gastrula, Wikipedia:Trilaminar_blastocyst] +subset: pheno_slim +synonym: "blastocystis trilaminaris" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "gastrula embryo" EXACT [BILA:0000060] +synonym: "tri-laminar disc" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "tri-laminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar blastocyst" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar blastoderm" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar disc" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] +xref: BILA:0000060 +xref: BTO:0001403 +xref: FBbt:00005317 +xref: FMA:293108 +xref: GAID:1302 +xref: MESH:A16.254.412 +xref: MIAA:0000179 +xref: NCIT:C34057 +xref: NCIT:C34058 +xref: UMLS:C0017199 +xref: UMLS:C1284022 +xref: Wikipedia:Gastrula +xref: Wikipedia:Trilaminar_blastocyst +is_a: UBERON:0000922 ! embryo + +[Term] +id: UBERON:0004753 +name: scapulocoracoid +def: "Skeletal element that consists of the scapula and the coracoid[VSAO, modified]." [https://github.com/obophenotype/uberon/issues/125, https://github.com/obophenotype/uberon/issues/66, VSAO:0005002, Wikipedia:Scapulocoracoid] +synonym: "coraco-scapular cartilage" NARROW [ZFA:0001455] +synonym: "scapulo-coracoid cartilage" NARROW [TAO:0001455] +synonym: "scapulocoracoid cartilage" NARROW [TAO:0001455] +synonym: "scapulocoracoideum" EXACT [VSAO:0005002] +xref: AAO:0000781 +xref: TAO:0001455 +xref: VSAO:0005002 +xref: Wikipedia:Scapulocoracoid +xref: ZFA:0001455 +is_a: UBERON:0004765 ! skeletal element +relationship: BFO:0000050 UBERON:0007831 ! part of pectoral girdle skeleton + +[Term] +id: UBERON:0004755 +name: skeletal tissue +def: "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, https://github.com/obophenotype/uberon/issues/134, PSPUB:0000170, VSAO:0000015] +xref: EMAPA:37744 +xref: MA:0003047 +xref: SCTID:309311006 +xref: VSAO:0000015 +xref: XAO:0004038 +xref: ZFA:0005619 +is_a: UBERON:0002384 ! connective tissue +relationship: BFO:0000050 UBERON:0004765 ! part of skeletal element + +[Term] +id: UBERON:0004761 +name: cartilaginous neurocranium +def: "The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]." [Wikipedia:Chondrocranium] +synonym: "cartilaginous chondocranium" EXACT [] +synonym: "cartilaginous skull" RELATED [] +synonym: "cartiligionous skeletal structure of skull" EXACT [] +synonym: "chondocranium" RELATED [Wikipedia:Chondrocranium] +synonym: "embryonic chondocranium" RELATED [] +synonym: "neurocranium" RELATED SENSU [] +xref: AAO:0000094 +xref: AAO:0010153 +xref: EHDAA:6031 +xref: FMA:76621 +xref: NCIT:C34121 +xref: SCTID:155540009 +xref: UMLS:C1516496 +xref: Wikipedia:Chondrocranium +xref: XAO:0003059 +is_a: UBERON:0000075 ! subdivision of skeletal system + +[Term] +id: UBERON:0004765 +name: skeletal element +def: "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles." [https://orcid.org/0000-0002-6601-2165] +subset: organ_slim +subset: uberon_slim +xref: AAO:0011129 +xref: galen:SkeletalStructure +xref: TAO:0001890 +xref: VSAO:0000128 +xref: XAO:0004012 +xref: ZFA:0005494 +is_a: UBERON:0000062 ! organ +relationship: BFO:0000050 UBERON:0001434 ! part of skeletal system + +[Term] +id: UBERON:0004770 +name: articular system +def: "Anatomical system that consists of all the joints of the body." [VSAO:0000181] +synonym: "joint system" EXACT [FMA:23878] +synonym: "set of all joints" RELATED [] +synonym: "set of all joints of body" EXACT [FMA:23878] +synonym: "set of joints of body" RELATED [FMA:23878] +xref: EMAPA:35150 +xref: FMA:23878 +xref: MA:0003007 +xref: SCTID:361827000 +xref: VSAO:0000181 +is_a: UBERON:0034925 ! anatomical collection +relationship: BFO:0000050 UBERON:0001434 ! part of skeletal system + +[Term] +id: UBERON:0004775 +name: outer renal medulla vasa recta +def: "A vasa recta that is part of a outer medulla of kidney [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "kidney outer medulla vasa recta" EXACT [MP:0011330] +synonym: "kidney outer renal medulla vasa recta" EXACT [MP:0011330] +synonym: "outer medulla of kidney vasa recta" EXACT [OBOL:automatic] +synonym: "outer zone of medulla of kidney vasa recta" EXACT [OBOL:automatic] +synonym: "outer zone of renal medulla vasa recta" EXACT [OBOL:automatic] +synonym: "vasa recta of outer medulla of kidney" EXACT [OBOL:automatic] +synonym: "vasa recta of outer renal medulla" EXACT [OBOL:automatic] +synonym: "vasa recta of outer zone of medulla of kidney" EXACT [OBOL:automatic] +synonym: "vasa recta of outer zone of renal medulla" EXACT [OBOL:automatic] +xref: EMAPA:36560 +xref: MA:0002597 +is_a: UBERON:0004726 ! vasa recta +is_a: UBERON:0013126 ! vein of abdomen +is_a: UBERON:0014401 ! renal venous blood vessel +relationship: BFO:0000050 UBERON:0001293 ! part of outer medulla of kidney + +[Term] +id: UBERON:0004776 +name: inner renal medulla vasa recta +def: "A vasa recta that is part of a inner medulla of kidney [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "inner medulla of kidney vasa recta" EXACT [OBOL:automatic] +synonym: "inner zone of medulla of kidney vasa recta" EXACT [OBOL:automatic] +synonym: "inner zone of renal medulla vasa recta" EXACT [OBOL:automatic] +synonym: "set of inner region of renal pyramids vasa recta" EXACT [OBOL:automatic] +synonym: "vasa recta of inner medulla of kidney" EXACT [OBOL:automatic] +synonym: "vasa recta of inner renal medulla" EXACT [OBOL:automatic] +synonym: "vasa recta of inner zone of medulla of kidney" EXACT [OBOL:automatic] +synonym: "vasa recta of inner zone of renal medulla" EXACT [OBOL:automatic] +synonym: "vasa recta of set of inner region of renal pyramids" EXACT [OBOL:automatic] +xref: EMAPA:36559 +xref: MA:0002596 +is_a: UBERON:0004726 ! vasa recta +is_a: UBERON:0013126 ! vein of abdomen +is_a: UBERON:0014401 ! renal venous blood vessel +relationship: BFO:0000050 UBERON:0001294 ! part of inner medulla of kidney + +[Term] +id: UBERON:0004810 +name: nephron tubule epithelium +def: "The cellular avascular layer of the renal tubule luminar surfaces." [MGI:csmith, MP:0009640] +subset: pheno_slim +synonym: "kidney tubule epithelium" EXACT [MA:0001681] +xref: BTO:0005239 +xref: EMAPA:36524 +xref: MA:0001681 +xref: NCIT:C49276 +xref: UMLS:C1709902 +is_a: UBERON:0004211 ! nephron epithelium +relationship: BFO:0000050 UBERON:0001231 ! part of nephron tubule + +[Term] +id: UBERON:0004819 +name: kidney epithelium +def: "The cellular avascular layer of the kidney luminar surfaces." [MGI:csmith, MP:0004967] +subset: pheno_slim +synonym: "epithelial tissue of kidney" EXACT [OBOL:automatic] +synonym: "epithelium of kidney" EXACT [OBOL:automatic] +synonym: "kidney epithelial tissue" EXACT [OBOL:automatic] +synonym: "renal epithelium" RELATED [EMAPA:35457] +xref: BTO:0000059 +xref: CALOHA:TS-0505 +xref: EMAPA:35457 +xref: MA:0002846 +is_a: UBERON:0000483 ! epithelium +relationship: BFO:0000050 UBERON:0002113 ! part of kidney + +[Term] +id: UBERON:0004852 +name: cardiovascular system endothelium +def: "An endothelium that is part of the cardiovascular system." [https://orcid.org/0000-0002-6601-2165] +subset: vertebrate_core +synonym: "endothelia" RELATED [ZFA:0001639] +synonym: "vascular endothelia" RELATED [XAO:0000356] +xref: BTO:0001853 +xref: EMAPA:35201 +xref: GAID:519 +xref: MA:0000717 +xref: MESH:D004730 +xref: NCIT:C13053 +xref: TAO:0002171 +xref: UMLS:C0014261 +xref: VHOG:0001217 +xref: XAO:0000356 +xref: ZFA:0001639 +is_a: UBERON:0001986 ! endothelium +relationship: BFO:0000050 UBERON:0004535 ! part of cardiovascular system + +[Term] +id: UBERON:0004872 +name: splanchnic layer of lateral plate mesoderm +def: "Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]." [Wikipedia:Lateral_plate_mesoderm#Division_into_layers] +subset: pheno_slim +synonym: "inner layer of lateral plate mesoderm" EXACT [] +synonym: "splanchnic mesoderm" RELATED [ISBN:9780878932504] +synonym: "visceral mesoderm" BROAD [BILA:0000044, http://www.drugs.com/dict/visceral-mesoderm.html, http://www.stedmans.com/] +xref: AAO:0011102 +xref: BILA:0000044 +xref: FMA:295568 +xref: Wikipedia:Lateral_plate_mesoderm#Division_into_layers +xref: XAO:0000276 +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0003081 ! part of lateral plate mesoderm + +[Term] +id: UBERON:0004874 +name: somatopleure +def: "A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]." [Wikipedia:Somatopleure] +xref: EHDAA2:0001847 +xref: EHDAA:381 +xref: EMAPA:16180 +xref: FMA:295566 +xref: NCIT:C34301 +xref: UMLS:C1519423 +xref: VHOG:0000557 +xref: Wikipedia:Somatopleure +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0003081 ! part of lateral plate mesoderm + +[Term] +id: UBERON:0004875 +name: nephrogenic cord +def: "A portion of the urogenital ridge which is the source of much of the urinary system[WP]." [Wikipedia:Nephrogenic_cord] +synonym: "chorda nephrogenica" RELATED [Wikipedia:Nephrogenic_cord] +xref: FMA:72168 +xref: NCIT:C34219 +xref: SCTID:361405003 +xref: UMLS:C1283944 +xref: Wikipedia:Nephrogenic_cord +is_a: UBERON:0002050 ! embryonic structure + +[Term] +id: UBERON:0004876 +name: urogenital fold +def: "One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP]." [MP:0011835, MP:anna, Wikipedia:Urogenital_folds] +subset: pheno_slim +synonym: "urethral fold" EXACT [EMAPA:30888] +synonym: "urogenital fold" EXACT [EHDAA2:0004022, MP:0011835] +synonym: "urogenital ridge" RELATED INCONSISTENT [MP:0011835] +xref: EHDAA2:0004022 +xref: EMAPA:30888 +xref: FMA:321919 +xref: Wikipedia:Urogenital_folds +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0009196 ! part of indifferent external genitalia + +[Term] +id: UBERON:0004880 +name: chordamesoderm +def: "The central region of trunk mesoderm. This tissue forms the notochord." [https://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: pheno_slim +synonym: "axial chorda mesoderm" EXACT [ZFA:0000091] +synonym: "chorda mesoderm" EXACT [] +synonym: "dorsal mesoderm" EXACT [https://github.com/obophenotype/uberon/wiki/The-neural-crest] +synonym: "presumptive notochord" EXACT [ZFA:0000091] +xref: AAO:0000478 +xref: EFO:0003426 +xref: TAO:0000091 +xref: ZFA:0000091 +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0003068 ! part of axial mesoderm + +[Term] +id: UBERON:0004905 +name: articulation +def: "Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] +subset: grouping_class +synonym: "joint" NARROW [] +xref: FBbt:00005811 +is_a: UBERON:0034921 ! multi organ part structure +relationship: BFO:0000050 UBERON:0004770 ! part of articular system + +[Term] +id: UBERON:0004921 +name: subdivision of digestive tract +def: "A proximal-distal subdivision of the digestive tract." [http://orcid.org/0000-0002-6601-2165] +subset: non_informative +synonym: "alimentary system subdivision" RELATED [FMA:71131] +synonym: "intestinal tract" RELATED [] +synonym: "segment of intestinal tract" RELATED [] +synonym: "subdivision of alimentary system" RELATED [FMA:71131] +xref: FBbt:00100315 +xref: FMA:71131 +is_a: UBERON:0013522 ! subdivision of tube +relationship: BFO:0000050 UBERON:0001555 ! part of digestive tract + +[Term] +id: UBERON:0004923 +name: organ component layer +def: "A part of a wall of an organ that forms a layer." [http://orcid.org/0000-0002-6601-2165] +subset: upper_level +xref: FMA:82485 +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0000060 ! part of anatomical wall + +[Term] +id: UBERON:0005057 +name: immune organ +def: "An organ that is part of a immune system [Automatically generated definition]." [OBOL:automatic] +subset: organ_slim +subset: pheno_slim +synonym: "immune system organ" EXACT [] +is_a: UBERON:0000062 ! organ +relationship: BFO:0000050 UBERON:0002405 ! part of immune system + +[Term] +id: UBERON:0005061 +name: neural groove +def: "The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds." [GO:0001842, http://orcid.org/0000-0002-6601-2165, Wikipedia:Neural_groove] +xref: AAO:0011071 +xref: EMAPA:35594 +xref: FMA:295624 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1363 +xref: NCIT:C34224 +xref: SCTID:361463007 +xref: UMLS:C0814992 +xref: Wikipedia:Neural_groove +xref: XAO:0000248 +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0003075 ! part of neural plate + +[Term] +id: UBERON:0005062 +name: neural fold +def: "One of the two elevated edges of the neural groove[GO,MP]." [GO:0001842, MP:0011256, Wikipedia:Neural_fold] +subset: pheno_slim +synonym: "medullary fold" EXACT [MP:0011256] +xref: EHDAA2:0001249 +xref: FMA:295618 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1364 +xref: NCIT:C34223 +xref: SCTID:361461009 +xref: UMLS:C0814993 +xref: Wikipedia:Neural_fold +xref: XAO:0004087 +is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0005157 ! epithelial fold +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0015212 ! lateral structure +relationship: BFO:0000050 UBERON:0005061 ! part of neural groove + +[Term] +id: UBERON:0005068 +name: neural rod +def: "A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]." [GO:0014024, ZFA:0000133] +subset: efo_slim +synonym: "neural tube rod" RELATED [GO:0014027] +xref: EFO:0003498 +xref: TAO:0000133 +xref: ZFA:0000133 +is_a: UBERON:0016879 ! future central nervous system + +[Term] +id: UBERON:0005080 +name: metanephric ureteric bud +def: "The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]." [GO:0035502] +is_a: UBERON:0000084 ! ureteric bud + +[Term] +id: UBERON:0005081 +name: ureter ureteric bud +def: "The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO]." [GO:0035503] +is_a: UBERON:0000084 ! ureteric bud + +[Term] +id: UBERON:0005085 +name: ectodermal placode +def: "An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]." [GO:0060788] +synonym: "epithelial placode" RELATED [AEO:0000112] +xref: AEO:0000218 +is_a: UBERON:0001048 ! primordium +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0000924 ! part of ectoderm + +[Term] +id: UBERON:0005086 +name: hair follicle placode +def: "A bud-like thickening in the epidermis consisting of elongated keratinocytes, which at the distal end are in touch with numerous aggregated specialized dermal fibroblasts, the dermal condensate." [DOI:10.1016/j.cub.2008.12.005] +synonym: "hair gem" RELATED [ISBN:9780878932504] +synonym: "hair germ" RELATED [DOI:10.1016/j.cub.2008.12.005] +synonym: "hair peg" RELATED [ISBN:9780878932504] +synonym: "hair placode" EXACT [DOI:10.1016/j.cub.2008.12.005] +synonym: "vibrissa placode" NARROW [] +xref: EMAPA:36479 +is_a: UBERON:0011817 ! skin appendage placode + +[Term] +id: UBERON:0005088 +name: sebaceous gland placode +def: "A sebaceous gland placode is a thickening of the ectoderm that will give rise to the sebaceous gland bud[GO]." [GO:0060791] +is_a: UBERON:0006598 ! presumptive structure +is_a: UBERON:0011814 ! non-neurogenic ectodermal placode + +[Term] +id: UBERON:0005090 +name: muscle structure +def: "Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]." [GO:0061061] +synonym: "muscle" RELATED [] +synonym: "muscle element" RELATED [] +synonym: "musculus" EXACT [FMA:30316] +xref: EMAPA:32715 +xref: FBbt:00005073 +xref: FMA:30316 +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0005095 +name: kidney rudiment +def: "." [GO:0072003] +synonym: "kidney anlage" RELATED [GOC:mtg_kidney_jan10] +is_a: UBERON:0002050 ! embryonic structure + +[Term] +id: UBERON:0005096 +name: descending thin limb +def: "The descending thin limb is a part of the loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the loop of Henle[GO]." [GO:0072022, Wikipedia:Descending_limb_of_loop_of_Henle] +subset: uberon_slim +synonym: "descending limb of Henle's loop" RELATED [Wikipedia:Descending_limb_of_loop_of_Henle] +synonym: "descending limb of loop of Henle" RELATED [Wikipedia:Descending_limb_of_loop_of_Henle] +synonym: "descending thin limb of loop of Henle" EXACT [] +synonym: "loop of Henle descending thin limb" EXACT [] +synonym: "loop of Henle thin descending limb" EXACT [MA:0002625] +synonym: "pars descendens (tubulus attenuatus)" EXACT [FMA:17719] +synonym: "thin descending limb" EXACT [] +synonym: "thin descending limb of loop of Henle" RELATED [Wikipedia:Descending_limb_of_loop_of_Henle] +synonym: "thin descending limb of the loop of Henle" RELATED [Wikipedia:Descending_limb_of_loop_of_Henle] +synonym: "thin descending loop of Henle" RELATED [Wikipedia:Descending_limb_of_loop_of_Henle] +xref: EMAPA:35514 +xref: FMA:17719 +xref: MA:0002625 +xref: Wikipedia:Descending_limb_of_loop_of_Henle +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0004136 ! part of intermediate tubule + +[Term] +id: UBERON:0005103 +name: mesonephric epithelium +def: "An epithelium that is part of a mesonephros [Automatically generated definition]." [OBOL:automatic] +is_a: UBERON:0004819 ! kidney epithelium +relationship: BFO:0000050 UBERON:0000080 ! part of mesonephros + +[Term] +id: UBERON:0005106 +name: metanephric tubule +def: "A metanephric tubule is an epithelial tube that is part of the metanephros[GO]." [GO:0072173] +xref: VHOG:0001526 +is_a: UBERON:0003914 ! epithelial tube +is_a: UBERON:0005108 ! metanephric epithelium +is_a: UBERON:0006555 ! excretory tube + +[Term] +id: UBERON:0005108 +name: metanephric epithelium +def: "An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO]." [GO:0072207] +is_a: UBERON:0004819 ! kidney epithelium +relationship: BFO:0000050 UBERON:0000081 ! part of metanephros + +[Term] +id: UBERON:0005110 +name: metanephric nephron +def: "A metanephric nephron is the functional unit of the metanephros[GO]." [GO:0072273] +xref: VHOG:0000719 +is_a: UBERON:0001285 ! nephron +is_a: UBERON:0004120 ! mesoderm-derived structure +relationship: BFO:0000050 UBERON:0000081 ! part of metanephros + +[Term] +id: UBERON:0005113 +name: metanephric cortex mesenchyme +xref: EHDAA2:0001140 +is_a: UBERON:0003104 ! mesenchyme +is_a: UBERON:0004120 ! mesoderm-derived structure + +[Term] +id: UBERON:0005114 +name: metanephric ascending thin limb +def: "The metanephric ascending thin limb is a segment of a nephron tubule in the metanephros lying in the inner medulla that is permeable to ions but not to water and has a simple epithelium; active transepithelial solute transport is absent[GO]." [GO:0072218] +is_a: UBERON:0004193 ! loop of Henle ascending limb thin segment +is_a: UBERON:0005146 ! metanephric nephron tubule +relationship: BFO:0000050 UBERON:0005129 ! part of metanephric distal tubule + +[Term] +id: UBERON:0005116 +name: metanephric descending thin limb +def: "It extends to the tip of the metanephric loop of Henle[GO]." [GO:0072220] +is_a: UBERON:0005096 ! descending thin limb +relationship: BFO:0000050 UBERON:0005130 ! part of metanephric loop of Henle + +[Term] +id: UBERON:0005127 +name: metanephric thick ascending limb +def: "At the macula densa, the thick ascending limb connects to the distal convoluted tubule[GO]." [GO:0072233] +is_a: UBERON:0001291 ! thick ascending limb of loop of Henle +is_a: UBERON:0005146 ! metanephric nephron tubule + +[Term] +id: UBERON:0005129 +name: metanephric distal tubule +def: "The metanephric distal tubule is a metanephric nephron tubule that begins at the metanephric macula densa and extends to the metanephric connecting tubule[GO]." [GO:0072235] +is_a: UBERON:0004135 ! distal tubule +is_a: UBERON:0005146 ! metanephric nephron tubule + +[Term] +id: UBERON:0005130 +name: metanephric loop of Henle +def: "The metanephric loop of Henle is a metanephric nephron tubule that connects the proximal convoluted tubule to the distal convoluted tubule in the metanephros[GO]." [GO:0072236] +is_a: UBERON:0001288 ! loop of Henle +is_a: UBERON:0005146 ! metanephric nephron tubule +relationship: BFO:0000050 UBERON:0004136 ! part of intermediate tubule + +[Term] +id: UBERON:0005134 +name: metanephric nephron epithelium +def: "The metanephric nephron epithelium is a tissue that covers the surface of a nephron in the metanephros[GO]." [GO:0072243] +is_a: UBERON:0004211 ! nephron epithelium +is_a: UBERON:0005108 ! metanephric epithelium +relationship: BFO:0000050 UBERON:0005110 ! part of metanephric nephron + +[Term] +id: UBERON:0005146 +name: metanephric nephron tubule +def: "A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros[GO]." [GO:0072282] +is_a: UBERON:0001231 ! nephron tubule +is_a: UBERON:0005106 ! metanephric tubule +is_a: UBERON:0005134 ! metanephric nephron epithelium +is_a: UBERON:0012275 ! meso-epithelium + +[Term] +id: UBERON:0005156 +name: reproductive structure +def: "Any anatomical structure that is part of the reproductive system." [http://orcid.org/0000-0002-6601-2165] +subset: grouping_class +synonym: "reproductive system element" EXACT [] +synonym: "reproductive system structure" EXACT [] +is_a: UBERON:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 UBERON:0000990 ! part of reproductive system + +[Term] +id: UBERON:0005157 +name: epithelial fold +def: "An epithelial sheet bent on a linear axis." [GO:0060571] +is_a: UBERON:0000483 ! epithelium + +[Term] +id: UBERON:0005162 +name: multi cell part structure +def: "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part." [CARO:0001000] +subset: upper_level +synonym: "cell part cluster" RELATED [FMA:83115] +synonym: "multi-cell-component structure" EXACT [CARO:0001000] +synonym: "multi-cell-part structure" EXACT [CARO:0001000] +xref: AAO:0011000 +xref: CARO:0001000 +xref: FBbt:00007060 +xref: FMA:83115 +is_a: UBERON:0000477 ! anatomical cluster + +[Term] +id: UBERON:0005164 +name: ascending limb of loop of Henle +def: "The distal part of the loop of Henle that is impermeable to water and actively pumps sodium out of the filtrate to generate the hypertonic interstitium that drives countercurrent exchange; it consists of an initial very thin segment lined by simple squamous epithelium followed by a distal thick segment lined by simple cuboidal epithelium[MP]." [MP:0011342, Wikipedia:Ascending_limb_of_loop_of_Henle] +subset: pheno_slim +subset: uberon_slim +synonym: "ascending limb" BROAD [] +synonym: "ascending limb of Henle's loop" EXACT [] +synonym: "distal straight tubule" RELATED [] +synonym: "loop of Henle ascending limb" EXACT [MP:0011342] +xref: EMAPA:35510 +xref: FMA:17717 +xref: MA:0001676 +xref: NCIT:C32154 +xref: SCTID:245434005 +xref: UMLS:C0227658 +xref: Wikipedia:Ascending_limb_of_loop_of_Henle +is_a: UBERON:0004135 ! distal tubule +relationship: BFO:0000050 UBERON:0001288 ! part of loop of Henle + +[Term] +id: UBERON:0005172 +name: abdomen element +def: "An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland." [http://orcid.org/0000-0002-6601-2165] +subset: non_informative +synonym: "abdomen organ" EXACT [MA:0000522] +xref: MA:0000522 +xref: SCTID:272631008 +is_a: UBERON:0005173 ! abdominal segment element +relationship: BFO:0000050 UBERON:0000916 ! part of abdomen + +[Term] +id: UBERON:0005173 +name: abdominal segment element +def: "An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region." [http://orcid.org/0000-0002-6601-2165] +subset: non_informative +synonym: "abdominal segment organ" EXACT [MA:0000529] +xref: EMAPA:37062 +xref: MA:0000529 +is_a: UBERON:0005177 ! trunk region element +relationship: BFO:0000050 UBERON:0002417 ! part of abdominal segment of trunk + +[Term] +id: UBERON:0005174 +name: dorsal region element +def: "An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back." [http://orcid.org/0000-0002-6601-2165] +subset: non_informative +synonym: "back organ" EXACT [MA:0001901] +synonym: "dorsal region organ" EXACT [] +xref: EMAPA:37274 +xref: MA:0001901 +is_a: UBERON:0000062 ! organ +relationship: BFO:0000050 UBERON:0001137 ! part of dorsum + +[Term] +id: UBERON:0005177 +name: trunk region element +def: "An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions." [http://orcid.org/0000-0002-6601-2165] +subset: non_informative +subset: organ_slim +synonym: "trunk organ" EXACT [MA:0000516] +xref: EMAPA:37270 +xref: MA:0000516 +is_a: UBERON:0000062 ! organ +relationship: BFO:0000050 UBERON:0002100 ! part of trunk + +[Term] +id: UBERON:0005178 +name: thoracic cavity element +def: "An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli." [http://orcid.org/0000-0002-6601-2165] +subset: non_informative +subset: pheno_slim +synonym: "thoracic cavity organ" EXACT [MA:0000557] +xref: EMAPA:37273 +xref: MA:0000557 +is_a: UBERON:0002075 ! viscus +is_a: UBERON:0005181 ! thoracic segment organ + +[Term] +id: UBERON:0005179 +name: pelvic region element +def: "An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis." [http://orcid.org/0000-0002-6601-2165] +subset: non_informative +subset: organ_slim +subset: pheno_slim +synonym: "pelvic element" EXACT [] +synonym: "pelvis organ" EXACT [MA:0000543] +synonym: "pelvis region organ" EXACT [] +xref: EMAPA:37275 +xref: MA:0000543 +is_a: UBERON:0005173 ! abdominal segment element +relationship: BFO:0000050 UBERON:0002355 ! part of pelvic region of trunk + +[Term] +id: UBERON:0005181 +name: thoracic segment organ +def: "An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions." [http://orcid.org/0000-0002-6601-2165] +subset: non_informative +synonym: "upper body organ" RELATED [MA:0000563] +xref: EMAPA:37271 +xref: MA:0000563 +is_a: UBERON:0005177 ! trunk region element +relationship: BFO:0000050 UBERON:0000915 ! part of thoracic segment of trunk + +[Term] +id: UBERON:0005253 +name: head mesenchyme +def: "Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells." [ISBN:0683400088, MP:0011260] +subset: efo_slim +subset: pheno_slim +subset: vertebrate_core +synonym: "cephalic mesenchyme" EXACT [MP:0011260] +synonym: "cranial mesenchyme" RELATED [MGI:anna] +synonym: "desmocranium" RELATED PENDING_REVIEW [FMA:76622] +xref: EFO:0003492 +xref: EHDAA2:0000732 +xref: EHDAA:179 +xref: EMAPA:16098 +xref: EMAPA_RETIRED:16269 +xref: FMA:76622 +xref: TAO:0000113 +xref: VHOG:0000332 +xref: ZFA:0000113 +is_a: UBERON:0003104 ! mesenchyme +is_a: UBERON:0005291 ! embryonic tissue +relationship: BFO:0000050 UBERON:0000033 ! part of head +relationship: BFO:0000050 UBERON:0009142 ! part of entire embryonic mesenchyme + +[Term] +id: UBERON:0005254 +name: upper leg mesenchyme +def: "Mesenchyme that is part of a developing hindlimb stylopod [Automatically generated definition]." [OBOL:automatic] +xref: EHDAA2:0002132 +xref: EMAPA:17501 +xref: VHOG:0000506 +is_a: UBERON:0003860 ! hindlimb mesenchyme +relationship: BFO:0000050 UBERON:0000376 ! part of hindlimb stylopod + +[Term] +id: UBERON:0005256 +name: trunk mesenchyme +def: "Mesenchyme that is part of a developing trunk." [OBOL:automatic] +subset: efo_slim +subset: vertebrate_core +synonym: "trunk and cervical mesenchyme" RELATED [EHDAA2:0002092] +xref: EFO:0003485 +xref: EHDAA2:0002092 +xref: EHDAA:377 +xref: EMAPA:16177 +xref: TAO:0000081 +xref: VHOG:0000281 +xref: ZFA:0000081 +is_a: UBERON:0003104 ! mesenchyme +is_a: UBERON:0005291 ! embryonic tissue +relationship: BFO:0000050 UBERON:0002100 ! part of trunk +relationship: BFO:0000050 UBERON:0009142 ! part of entire embryonic mesenchyme + +[Term] +id: UBERON:0005258 +name: upper arm mesenchyme +def: "Mesenchyme that is part of a developing forelimb stylopod [Automatically generated definition]." [OBOL:automatic] +xref: EHDAA2:0002114 +xref: EMAPA:17426 +xref: VHOG:0000505 +is_a: UBERON:0003859 ! forelimb mesenchyme +relationship: BFO:0000050 UBERON:0003822 ! part of forelimb stylopod + +[Term] +id: UBERON:0005290 +name: myelencephalon +def: "The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]." [BTO:0000758, Wikipedia:Myelencephalon] +subset: uberon_slim +synonym: "myelencephalon (medulla oblongata)" RELATED [DHBA:10662] +xref: BTO:0000758 +xref: CALOHA:TS-0607 +xref: CALOHA:TS-2365 +xref: DHBA:10662 +xref: EHDAA2:0001207 +xref: EHDAA:5526 +xref: EMAPA:17082 +xref: HBA:9512 +xref: MA:0000205 +xref: VHOG:0000456 +xref: Wikipedia:Myelencephalon +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0004733 ! segmental subdivision of hindbrain +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest + +[Term] +id: UBERON:0005291 +name: embryonic tissue +def: "A portion of tissue that is part of an embryo." [OBOL:automatic] +subset: pheno_slim +subset: upper_level +synonym: "developing tissue" RELATED [] +synonym: "portion of embryonic tissue" EXACT [OBOL:automatic] +xref: CALOHA:TS-2100 +is_a: UBERON:0000479 ! tissue +relationship: BFO:0000050 UBERON:0002050 ! part of embryonic structure + +[Term] +id: UBERON:0005343 +name: cortical plate +def: "The outer neural tube region in which post-mitotic neuroblasts migrate along radial glia to form the adult cortical layers[MP]." [http://www.ncbi.nlm.nih.gov/books/NBK10047, MP:0008439] +subset: pheno_slim +synonym: "cerebral cortex cortical plate" EXACT [] +synonym: "CP" BROAD [BRAINSPAN:BRAINSPAN] +synonym: "CxP" BROAD [PMID:23375746] +synonym: "future cortical layers II-VI" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "future neocortex" RELATED [http://orcid.org/0000-0002-6601-2165] +synonym: "neocortex cortical plate" EXACT [] +xref: BAMS:CTXpl +xref: DHBA:10515 +xref: EMAPA:32711 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2702 +xref: MBA:695 +xref: PBA:294021914 +is_a: UBERON:0014950 ! layer of developing cerebral cortex + +[Term] +id: UBERON:0005401 +name: cerebral hemisphere gray matter +def: "A gray matter that is part of a cerebral hemisphere." [OBOL:automatic] +synonym: "cerebral gray matter" EXACT [BTO:0000823] +synonym: "cerebral grey matter" EXACT [MA:0000944] +synonym: "cerebral hemisphere grey matter" EXACT [] +xref: BTO:0000823 +xref: CALOHA:TS-2361 +xref: EMAPA:37477 +xref: FMA:61821 +xref: MA:0000944 +is_a: UBERON:0011300 ! gray matter of telencephalon +relationship: BFO:0000050 UBERON:0001869 ! part of cerebral hemisphere + +[Term] +id: UBERON:0005417 +name: forelimb bud +def: "A limb bud that develops into a forelimb." [http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "anterior limb bud" EXACT [] +synonym: "arm bud" RELATED [] +synonym: "limb bud - forelimb" EXACT [MIAA:0000065] +synonym: "upper limb bud" EXACT [RETIRED_EHDAA2:0003198] +synonym: "wing bud" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +xref: AAO:0010381 +xref: BTO:0001645 +xref: EHDAA:1699 +xref: EMAPA:16406 +xref: FMA:296782 +xref: MIAA:0000065 +xref: RETIRED_EHDAA2:0003198 +xref: SCTID:346062002 +xref: XAO:0003065 +is_a: UBERON:0004347 ! limb bud +is_a: UBERON:0005419 ! pectoral appendage bud + +[Term] +id: UBERON:0005418 +name: hindlimb bud +def: "A limb bud that develops into a hindlimb." [http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "hind limb bud" EXACT [XAO:0003066] +synonym: "leg bud" RELATED [] +synonym: "limb bud - hindlimb" RELATED [] +synonym: "posterior limb bud" EXACT [] +xref: AAO:0010382 +xref: EHDAA:2358 +xref: EMAPA:16779 +xref: MIAA:0000256 +xref: RETIRED_EHDAA2:0003197 +xref: SCTID:346164003 +xref: XAO:0003066 +is_a: UBERON:0004347 ! limb bud +is_a: UBERON:0005420 ! pelvic appendage bud + +[Term] +id: UBERON:0005419 +name: pectoral appendage bud +def: "A limb bud that develops into a forelimb or pectoral fin." [OBOL:automatic] +subset: efo_slim +synonym: "forelimb - pectoral fin bud" EXACT [VHOG:0001754] +synonym: "pectoral fin bud" RELATED [TAO:0000141] +synonym: "pectoral fin buds" RELATED [TAO:0000141] +xref: EFO:0003430 +xref: TAO:0000141 +xref: VHOG:0001754 +xref: VHOG_RETIRED:0001259 +xref: ZFA:0000141 +is_a: UBERON:0004357 ! paired limb/fin bud +relationship: BFO:0000050 UBERON:0000153 ! part of anterior region of body + +[Term] +id: UBERON:0005420 +name: pelvic appendage bud +def: "A limb bud that develops into a hindlimb or pelvic fin." [OBOL:automatic] +subset: efo_slim +synonym: "hindlimb/pelvic fin bud" EXACT [VHOG:0001260] +synonym: "pelvic fin bud" RELATED [TAO:0001384] +synonym: "pelvic fin buds" RELATED [ZFA:0001384] +xref: EFO:0003469 +xref: TAO:0001384 +xref: VHOG:0001260 +xref: ZFA:0001384 +is_a: UBERON:0004357 ! paired limb/fin bud +relationship: BFO:0000050 UBERON:0000154 ! part of posterior region of body + +[Term] +id: UBERON:0005423 +name: developing anatomical structure +synonym: "developing structure" RELATED [] +synonym: "developmental structure" RELATED [] +synonym: "developmental tissue" RELATED [MIAA:0000019] +xref: AEO:0000125 +xref: CALOHA:TS-2122 +xref: EHDAA2:0003125 +xref: FBbt:00007006 +xref: FMA:292313 +xref: MIAA:0000019 +is_a: UBERON:0000465 ! material anatomical entity + +[Term] +id: UBERON:0005451 +name: segment of manus +def: "A segment of autopod that is part of a manus." [OBOL:automatic] +subset: pheno_slim +synonym: "hand region" BROAD [FMA:24945] +synonym: "hand subdivision" EXACT [FMA:24945] +synonym: "regio manus" EXACT [] +synonym: "segment of hand" EXACT [FMA:24945] +synonym: "subdivision of hand" EXACT [FMA:24945] +xref: FMA:24945 +xref: SCTID:127950000 +is_a: UBERON:0008785 ! upper limb segment +is_a: UBERON:0012139 ! segment of autopod +relationship: BFO:0000050 UBERON:0002398 ! part of manus + +[Term] +id: UBERON:0005497 +name: non-neural ectoderm +subset: efo_slim +subset: vertebrate_core +synonym: "epidermal ectoderm" NARROW [https://github.com/obophenotype/uberon/wiki/The-neural-crest] +synonym: "epithelial ectoderm" NARROW [https://github.com/obophenotype/uberon/wiki/The-neural-crest] +synonym: "non neural ectoderm" EXACT [ZFA:0001178] +synonym: "surface ectoderm" RELATED [https://github.com/obophenotype/uberon/wiki/The-neural-crest] +synonym: "ventral ectoderm" RELATED [ZFA:0001178] +xref: EFO:0003643 +xref: EHDAA:257 +xref: EMAPA:16074 +xref: RETIRED_EHDAA2:0001273 +xref: TAO:0001178 +xref: VHOG:0001372 +xref: XAO:0004091 +xref: ZFA:0001178 +is_a: UBERON:0000479 ! tissue +is_a: UBERON:0004121 ! ectoderm-derived structure + +[Term] +id: UBERON:0005498 +name: primitive heart tube +def: "Multi-tissue structure that arises from the heart rudiment and will become the heart tube." [ZFA:0000149] +subset: vertebrate_core +synonym: "early primitive heart tube" NARROW [EMAPA:16208] +synonym: "primitive heart tube" EXACT [EMAPA:16215] +xref: EHDAA2:0001512 +xref: EHDAA:424 +xref: EHDAA:436 +xref: EMAPA:16215 +xref: FMA:321916 +xref: SCTID:361522004 +xref: TAO:0000149 +xref: Wikipedia:Primitive_heart_tube +xref: ZFA:0000149 +is_a: UBERON:0000481 ! multi-tissue structure +is_a: UBERON:0004120 ! mesoderm-derived structure +relationship: BFO:0000050 UBERON:0000922 ! part of embryo + +[Term] +id: UBERON:0005564 +name: gonad primordium +def: "Portion of tissue that gives rise to the immature gonad." [ZFA:0001262] +subset: efo_slim +subset: grouping_class +subset: vertebrate_core +synonym: "future gonad" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "gonadal primordium" EXACT [ZFA:0001262] +synonym: "immature gonad" RELATED [http://orcid.org/0000-0002-6601-2165] +synonym: "primitive gonad" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "undifferentiated gonad" EXACT [ZFA:0001262] +xref: EFO:0003651 +xref: EHDAA:5927 +xref: EMAPA:17204 +xref: RETIRED_EHDAA2:0002148 +xref: TAO:0001262 +xref: WBbt:0008366 +xref: ZFA:0001262 +is_a: UBERON:0001048 ! primordium +relationship: BFO:0000050 UBERON:0000990 ! part of reproductive system + +[Term] +id: UBERON:0005721 +name: pronephric mesoderm +def: "A mesoderm that has the potential to develop into a pronephros." [OBOL:automatic] +subset: efo_slim +synonym: "pronephric anlage" RELATED [XAO:0000264] +synonym: "pronephric bulge" RELATED [XAO:0000264] +synonym: "pronephric mesenchyme" RELATED [XAO:0000264] +synonym: "pronephric primordium" RELATED [XAO:0000264] +xref: AAO:0011090 +xref: EFO:0003479 +xref: TAO:0000067 +xref: VHOG:0001239 +xref: XAO:0000264 +xref: ZFA:0000067 +is_a: UBERON:0000926 ! mesoderm +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0003064 ! part of intermediate mesoderm + +[Term] +id: UBERON:0005729 +name: pectoral appendage field +def: "A limb/fin field that has the potential to develop into a pectoral appendage bud mesenchyme." [OBOL:automatic] +synonym: "pectoral appendage field of lateral plate mesoderm" EXACT [] +synonym: "pectoral fin field" NARROW SENSU [ZFA:0001453] +xref: TAO:0001453 +xref: ZFA:0001453 +is_a: UBERON:0005732 ! paired limb/fin field +is_a: UBERON:0006598 ! presumptive structure + +[Term] +id: UBERON:0005730 +name: pelvic appendage field +def: "A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme." [OBOL:automatic] +synonym: "pelvic appendage field of lateral plate mesoderm" EXACT [] +synonym: "pelvic fin field" NARROW SENSU [ZFA:0001454] +xref: TAO:0001454 +xref: ZFA:0001454 +is_a: UBERON:0005732 ! paired limb/fin field +is_a: UBERON:0006598 ! presumptive structure + +[Term] +id: UBERON:0005732 +name: paired limb/fin field +def: "A ring of cells capable of forming a limb or paired fin[Gilbert,modified]." [ISBN:9780878932504] +subset: homology_grouping +synonym: "limb/fin field of lateral plate mesoderm" EXACT [] +synonym: "paired limb/fin field" EXACT [] +is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007688 ! anlage +relationship: BFO:0000050 UBERON:0003081 ! part of lateral plate mesoderm + +[Term] +id: UBERON:0005733 +name: limb field +def: "A ring of cells capable of forming a limb." [ISBN:9780878932504] +synonym: "limb field of lateral plate mesoderm" EXACT [] +is_a: UBERON:0005732 ! paired limb/fin field + +[Term] +id: UBERON:0005749 +name: glomerular tuft +def: "The capillary loops of the kidney that normally function as a filtration unit[MP]." [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron, MP:0005325, Wikipedia:Glomerulus] +subset: pheno_slim +synonym: "glomerular capillary tuft" RELATED [] +synonym: "glomerulus" RELATED INCONSISTENT [EMAPA:28239] +xref: EMAPA:28239 +xref: SCTID:362217000 +xref: Wikipedia:Glomerulus +is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure +relationship: BFO:0000050 UBERON:0001230 ! part of glomerular capsule + +[Term] +id: UBERON:0005753 +name: caudal part of nephrogenic cord +def: "The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm." [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] +synonym: "caudal portion of nephrogenic cord" EXACT [OBOL:automatic] +synonym: "caudal region of nephrogenic cord" EXACT [OBOL:automatic] +synonym: "rear part of nephrogenic cord" EXACT [OBOL:automatic] +synonym: "rear portion of nephrogenic cord" EXACT [Wikipedia:Metanephros#Metanephros] +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0004875 ! part of nephrogenic cord + +[Term] +id: UBERON:0005754 +name: rostral part of nephrogenic cord +def: "The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros." [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0004875 ! part of nephrogenic cord + +[Term] +id: UBERON:0005764 +name: acellular membrane +def: "An acellular anatomical structure that is the bounding layer of a anatomical structure." [OBOL:automatic] +xref: FMA:63871 +is_a: UBERON:0000476 ! acellular anatomical structure + +[Term] +id: UBERON:0005769 +name: basement membrane of epithelium +def: "An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Basement_membrane] +synonym: "basement membrane" RELATED [FMA:63872] +synonym: "basement membrane of connective tissue" EXACT [FMA:63872] +synonym: "membrana basalis" EXACT [Wikipedia:Basement_membrane] +xref: AAO:0010596 +xref: FMA:63872 +xref: GAID:915 +xref: NCIT:C13191 +xref: SCTID:68989006 +xref: UMLS:C0004799 +xref: Wikipedia:Basement_membrane +is_a: UBERON:0005764 ! acellular membrane +relationship: BFO:0000050 UBERON:0000483 ! part of epithelium + +[Term] +id: UBERON:0005792 +name: nephric ridge +def: "Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions." [http://cwx.prenhall.com/bookbind/pubbooks/martini10/chapter27/custom2/deluxe-content.html] +synonym: "nephric cord" RELATED [VHOG:0001240] +xref: EHDAA2:0001242 +xref: EHDAA:1015 +xref: EMAPA:16368 +xref: VHOG:0001240 +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0001008 ! part of renal system +relationship: BFO:0000050 UBERON:0004122 ! part of genitourinary system + +[Term] +id: UBERON:0005856 +name: developing mesenchymal condensation +def: "A delimited region of dense mesenchyme within looser mesenchyme." [AEO:0000148] +synonym: "mesenchyme condensation" EXACT [EMAPA:25351] +xref: AEO:0000148 +xref: EHDAA2_RETIRED:0003148 +xref: EHDAA:8979 +is_a: UBERON:0007524 ! dense mesenchyme tissue +is_a: UBERON:0011585 ! cell condensation + +[Term] +id: UBERON:0005863 +name: cartilaginous condensation +def: "Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes." [GO:curator] +synonym: "cartilage condensation" EXACT [EMAPA:25353] +synonym: "cartilagenous condensation" EXACT [EHDAA2:0003147] +synonym: "chondrogenic condensation" EXACT [VSAO:0000092] +xref: AEO:0000147 +xref: EHDAA2_RETIRED:0003147 +xref: EMAPA:32731 +xref: VSAO:0000092 +xref: XAO:0004022 +is_a: UBERON:0005856 ! developing mesenchymal condensation +relationship: BFO:0000050 UBERON:0004288 ! part of skeleton + +[Term] +id: UBERON:0005866 +name: pre-cartilage condensation +def: "A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts." [AEO:0000150, AEO:JB] +synonym: "pre-chondrogenic condensation" EXACT [] +synonym: "precartilage condensation" EXACT [] +synonym: "precartilagenous condensation" EXACT [] +synonym: "prechondrogenic condensation" EXACT [] +xref: AEO:0000150 +xref: EHDAA2:0003150 +xref: EMAPA:32736 +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0005856 ! developing mesenchymal condensation +relationship: BFO:0000050 UBERON:0004288 ! part of skeleton + +[Term] +id: UBERON:0005867 +name: mandibular prominence +def: "The paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip." [ISBN:0-683-40008-8, MP:0010939] +subset: pheno_slim +synonym: "mandibular process" RELATED [Wikipedia:Mandibular_prominence] +synonym: "mandibular swelling" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "prominentia mandibularis" RELATED [Wikipedia:Mandibular_prominence] +xref: EHDAA2:0001061 +xref: EHDAA:5871 +xref: EMAPA:17355 +xref: FMA:293051 +xref: NCIT:C34204 +xref: UMLS:C1512982 +xref: Wikipedia:Mandibular_prominence +is_a: UBERON:0012314 ! embryonic facial prominence +relationship: BFO:0000050 UBERON:0000166 ! part of oral opening + +[Term] +id: UBERON:0005881 +name: autopodial extension +def: "A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis." [http://orcid.org/0000-0002-6601-2165] +synonym: "digit or predigit" RELATED [] +synonym: "limb outgrowth" RELATED [] +is_a: UBERON:0000475 ! organism subdivision +relationship: BFO:0000050 UBERON:0002470 ! part of autopod region + +[Term] +id: UBERON:0005893 +name: leg bone +def: "A bone that is part of the region of the hindlimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia. Counter-examples: any pes phalanx." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +xref: EMAPA:37304 +xref: MA:0000670 +xref: MESH:A02.835.232.500 +is_a: UBERON:0003464 ! hindlimb bone +relationship: BFO:0000050 UBERON:0000978 ! part of leg + +[Term] +id: UBERON:0005911 +name: endo-epithelium +def: "Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]." [FMA:69065] +synonym: "endoderm-derived epithelium" EXACT [] +synonym: "endoepithelium" EXACT [] +xref: FMA:69065 +is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0004119 ! endoderm-derived structure + +[Term] +id: UBERON:0005913 +name: zone of bone organ +synonym: "bone organ zone" EXACT [FMA:10483] +xref: FMA:10483 +is_a: UBERON:0034944 ! zone of organ +relationship: BFO:0000050 UBERON:0001474 ! part of bone element + +[Term] +id: UBERON:0005944 +name: axial skeleton plus cranial skeleton +def: "Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]." [FMA:71221, https://github.com/obophenotype/uberon/issues/44, https://github.com/obophenotype/uberon/wiki/The-axial-skeleton, VSAO:0000056, Wikipedia:Axial_skeleton] +subset: pheno_slim +subset: uberon_slim +synonym: "skeleton axiale" RELATED [Wikipedia:Axial_skeleton] +xref: AAO:0000963 +xref: EMAPA:17214 +xref: EMAPA:18043 +xref: MA:0000308 +xref: NCIT:C32172 +xref: SCTID:361725000 +xref: UMLS:C0222645 +xref: VSAO:0000056 +xref: Wikipedia:Axial_skeleton +xref: XAO:0004011 +is_a: UBERON:0010912 ! subdivision of skeleton +relationship: BFO:0000050 UBERON:0011137 ! part of axial skeletal system + +[Term] +id: UBERON:0006003 +name: integumentary adnexa +def: "Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers." [http://code.google.com/p/caro2/issues/detail?id=5, http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "adnexae cutis" RELATED [Wikipedia:Skin_appendage] +synonym: "body hair or bristle" NARROW [GO:GO] +synonym: "skin adnexa" RELATED [Wikipedia:Skin_appendage] +synonym: "skin adnexal structure" RELATED [] +synonym: "skin appendage" RELATED [Wikipedia:Skin_appendage] +xref: EMAPA:37883 +xref: Wikipedia:Skin_appendage +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0002416 ! part of integumental system + +[Term] +id: UBERON:0006058 +name: multi-limb segment region +def: "A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions)." [https://orcid.org/0000-0002-6601-2165] +subset: non_informative +is_a: UBERON:0010758 ! subdivision of organism along appendicular axis + +[Term] +id: UBERON:0006067 +name: musculature of hindlimb zeugopod +def: "Any collection of muscles that is part of a hindlimb zeugopod." [OBOL:automatic] +subset: pheno_slim +synonym: "leg musculature" EXACT [FMA:50211] +synonym: "muscle group of leg" EXACT [FMA:50211] +synonym: "set of muscles of leg" EXACT [FMA:50211] +xref: FMA:50211 +is_a: UBERON:0004466 ! musculature of leg +relationship: BFO:0000050 UBERON:0003823 ! part of hindlimb zeugopod + +[Term] +id: UBERON:0006134 +name: nerve fiber +def: "A threadlike extension of a nerve cell and consists of an axon and myelin sheath (if it is myelinated) in the nervous system. There are nerve fibers in the central nervous system and peripheral nervous system. A nerve fiber may be myelinated and/or unmyelinated. In the central nervous system (CNS), myelin by oligodendroglia cells is formed. Schwann cells form myelin in the peripheral nervous system (PNS). Schwann cells also make a thin covering in an axon without myelin (in the PNS). A peripheral nerve fiber contains an axon, myelin sheath, schwann cells and its endoneurium. There are no endoneurium and schwann cells in the central nervous system." [Wikipedia:Nervous_system_fiber] +synonym: "nerve fibers" RELATED [BAMS:nfi] +synonym: "nerve fibre" EXACT [FMA:5914] +synonym: "neurofibra" EXACT [FMA:5914, FMA:TA] +synonym: "neurofibra" RELATED [Wikipedia:Nerve_fiber] +synonym: "neurofibrum" EXACT [FMA:5914] +xref: BAMS:nfi +xref: FMA:5914 +xref: MESH:A08.663.542 +xref: SCTID:88545005 +xref: Wikipedia:Nervous_system_fiber +is_a: UBERON:0005162 ! multi cell part structure +relationship: BFO:0000050 UBERON:0001019 ! part of nerve fasciculus + +[Term] +id: UBERON:0006135 +name: myelinated nerve fiber +def: "Axons of neurons encased in a lipoproteinaceous material called myelin. (MeSH)." [ncithesaurus:Myelinated_Nerve_Fiber] +subset: pheno_slim +xref: FMA:5915 +xref: GAID:745 +xref: MESH:A08.663.542.512 +xref: NCIT:C12627 +xref: SCTID:362296008 +xref: UMLS:C0027750 +is_a: UBERON:0006134 ! nerve fiber + +[Term] +id: UBERON:0006210 +name: body-wall mesenchyme +subset: emapa_ehdaa2 +xref: EHDAA2:0000179 +xref: EHDAA:3217 +xref: EMAPA:16893 +is_a: UBERON:0003104 ! mesenchyme +relationship: BFO:0000050 UBERON:0000309 ! part of body wall + +[Term] +id: UBERON:0006217 +name: cloacal membrane +def: "The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings." [MP:0011837, MP:anna, Wikipedia:Cloacal_membrane] +subset: emapa_ehdaa2 +subset: pheno_slim +synonym: "embryonic cloacal membrane" EXACT [] +synonym: "membrana cloacalis" RELATED [Wikipedia:Cloacal_membrane] +xref: EHDAA2:0000257 +xref: EHDAA:214 +xref: EHDAA:2933 +xref: EMAPA:16832 +xref: FMA:295525 +xref: NCIT:C34128 +xref: SCTID:308826008 +xref: UMLS:C0231056 +xref: VHOG:0001198 +xref: Wikipedia:Cloacal_membrane +is_a: UBERON:0000158 ! membranous layer +relationship: BFO:0000050 UBERON:0000163 ! part of embryonic cloaca + +[Term] +id: UBERON:0006234 +name: femur pre-cartilage condensation +def: "A femur endochondral element that is composed primarily of a pre-cartilage condensation." [OBOL:automatic] +subset: emapa_ehdaa2 +synonym: "femoral pre-cartilage condensation" RELATED [EMAPA:17502] +xref: EHDAA2:0000508 +xref: EMAPA:17502 +xref: VHOG:0000951 +is_a: UBERON:0005254 ! upper leg mesenchyme +is_a: UBERON:0005866 ! pre-cartilage condensation +is_a: UBERON:0010886 ! hindlimb pre-cartilage condensation +is_a: UBERON:0015052 ! femur endochondral element + +[Term] +id: UBERON:0006238 +name: future brain +def: "The embryonic precursor of the brain." [NLX:94995] +subset: cumbo +subset: efo_slim +subset: emapa_ehdaa2 +subset: vertebrate_core +synonym: "brain rudiment" EXACT [TAO:0000146] +synonym: "embryonic brain" RELATED [BTO:0004726] +synonym: "encephalon" NARROW [NLX:94995] +synonym: "presumptive brain" EXACT [ZFA:0000146] +xref: BAMS:Enc +xref: BTO:0004726 +xref: EFO:0003431 +xref: EHDAA:300 +xref: EHDAA:830 +xref: EMAPA:16089 +xref: FMA:312967 +xref: RETIRED_EHDAA2:0000591 +xref: TAO:0000146 +xref: ZFA:0000146 +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0002346 ! part of neurectoderm + +[Term] +id: UBERON:0006240 +name: future forebrain +def: "A presumptive structure that has the potential to develop into a forebrain." [OBOL:automatic] +subset: efo_slim +subset: emapa_ehdaa2 +subset: vertebrate_core +synonym: "future prosencephalon" EXACT [] +synonym: "presumptive forebrain" EXACT [ZFA:0000062] +synonym: "presumptive prosencephalon" EXACT [TAO:0000062] +synonym: "prosencephalon" RELATED [EHDAA2:0000661] +xref: BAMS:Pros +xref: EFO:0003423 +xref: EHDAA2:0000661 +xref: EHDAA:2643 +xref: EMAPA:16640 +xref: TAO:0000062 +xref: Wikipedia:Prosencephalon +xref: ZFA:0000062 +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0006238 ! part of future brain + +[Term] +id: UBERON:0006241 +name: future spinal cord +subset: efo_slim +subset: vertebrate_core +synonym: "presumptive spinal cord" EXACT [ZFA:0000417] +synonym: "presumptive spinal cord neural keel" EXACT [TAO:0000417] +synonym: "presumptive spinal cord neural plate" EXACT [TAO:0000417] +synonym: "presumptive spinal cord neural rod" EXACT [TAO:0000417] +xref: EFO:0003438 +xref: EHDAA2:0000674 +xref: EHDAA:898 +xref: EMAPA:16092 +xref: EMAPA:16755 +xref: TAO:0000417 +xref: ZFA:0000417 +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0001017 ! part of central nervous system + +[Term] +id: UBERON:0006245 +name: humerus cartilage element +def: "A humerus endochondral element that is composed primarily of cartilage tissue." [OBOL:automatic] +subset: emapa_ehdaa2 +synonym: "humeral cartilage condensation" RELATED [EMAPA:17713] +xref: EHDAA2:0000787 +xref: EHDAA:6240 +xref: EMAPA:17713 +xref: VHOG:0001120 +is_a: UBERON:0005258 ! upper arm mesenchyme +is_a: UBERON:0005863 ! cartilaginous condensation +is_a: UBERON:0010883 ! forelimb cartilage element +is_a: UBERON:0015053 ! humerus endochondral element +relationship: BFO:0000050 UBERON:0005258 ! part of upper arm mesenchyme + +[Term] +id: UBERON:0006246 +name: humerus pre-cartilage condensation +def: "A humerus endochondral element that is composed primarily of a pre-cartilage condensation." [OBOL:automatic] +subset: emapa_ehdaa2 +synonym: "humeral pre-cartilage condensation" RELATED [EMAPA:17427] +xref: EHDAA2:0000788 +xref: EHDAA:4192 +xref: EMAPA:17427 +xref: VHOG:0000950 +is_a: UBERON:0005258 ! upper arm mesenchyme +is_a: UBERON:0005866 ! pre-cartilage condensation +is_a: UBERON:0010884 ! forelimb bone pre-cartilage condensation +is_a: UBERON:0015053 ! humerus endochondral element +relationship: BFO:0000050 UBERON:0005258 ! part of upper arm mesenchyme + +[Term] +id: UBERON:0006267 +name: notochordal plate +def: "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord." [VHOG:0001212] +subset: emapa_ehdaa2 +xref: EHDAA2:0001278 +xref: EHDAA:264 +xref: EMAPA:16101 +xref: NCIT:C34231 +xref: UMLS:C1518429 +xref: VHOG:0001212 +is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium + +[Term] +id: UBERON:0006268 +name: notochordal process +def: "A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot." [http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/05embryonicperiod.htm] +subset: emapa_ehdaa2 +synonym: "chordamesoderm" RELATED [] +synonym: "presumptive notochord" RELATED [] +xref: EHDAA2:0001279 +xref: EHDAA:224 +xref: EMAPA:16102 +xref: FMA:293135 +xref: NCIT:C34232 +xref: UMLS:C1518430 +xref: VHOG:0001213 +is_a: UBERON:0005423 ! developing anatomical structure + +[Term] +id: UBERON:0006273 +name: otic pit +def: "The pair of depressions of thickened otic placode epithelium, that further develops into the otic vesicles." [ISBN:0-683-40008-8, MP:0011172] +subset: emapa_ehdaa2 +subset: pheno_slim +synonym: "otic cup" EXACT [NCBIBook:NBK53175] +xref: EHDAA2:0001336 +xref: EHDAA:929 +xref: EMAPA:16536 +xref: FMA:302911 +xref: NCIT:C34238 +xref: VHOG:0001147 +xref: Wikipedia:Otic_pit +is_a: UBERON:0016566 ! pit +relationship: BFO:0000050 UBERON:0003069 ! part of otic placode + +[Term] +id: UBERON:0006290 +name: scapula cartilage element +def: "A scapula endochondral element that is composed primarily of cartilage tissue." [OBOL:automatic] +subset: emapa_ehdaa2 +xref: EHDAA2:0001777 +xref: EHDAA:8368 +xref: EMAPA:18343 +xref: VHOG:0001125 +is_a: UBERON:0007844 ! cartilage element +is_a: UBERON:0015057 ! scapula endochondral element +relationship: BFO:0000050 UBERON:0000922 ! part of embryo + +[Term] +id: UBERON:0006291 +name: scapula pre-cartilage condensation +def: "A scapula endochondral element that is composed primarily of a pre-cartilage condensation." [OBOL:automatic] +subset: emapa_ehdaa2 +xref: EHDAA2:0001778 +xref: EHDAA:6041 +xref: EMAPA:18027 +xref: VHOG:0000960 +is_a: UBERON:0015057 ! scapula endochondral element + +[Term] +id: UBERON:0006292 +name: shoulder joint primordium +subset: emapa_ehdaa2 +xref: EHDAA2:0001836 +xref: EHDAA:8493 +xref: EMAPA:17712 +is_a: UBERON:0003322 ! mesenchyme of shoulder +is_a: UBERON:0005856 ! developing mesenchymal condensation +relationship: BFO:0000050 UBERON:0003322 ! part of mesenchyme of shoulder + +[Term] +id: UBERON:0006314 +name: bodily fluid +def: "Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not." [MESH:A12.207, Wikipedia:Body_fluid] +subset: pheno_slim +synonym: "body fluid" EXACT [GAID:266] +synonym: "fluid" BROAD [] +xref: BIRNLEX:20 +xref: EMAPA:37441 +xref: FMA:280556 +xref: GAID:266 +xref: galen:BodyFluid +xref: MESH:D001826 +xref: Wikipedia:Body_fluid +is_a: UBERON:0000463 ! organism substance + +[Term] +id: UBERON:0006376 +name: premacula segment of distal straight tubule +def: "." [https://sourceforge.net/tracker/?func=detail&aid=3123600&group_id=76834&atid=1205376, PMID:14595018] +synonym: "distal straight tubule premacula segment" EXACT [MA:0002628] +synonym: "kidney medulla loop of Henle ascending limb thick segment" EXACT [MA:th] +synonym: "medullary thick ascending limb of Henle's loop" EXACT [MA:th] +synonym: "renal medulla loop of Henle ascending limb thick segment" EXACT [MA:th] +synonym: "renal medulla thick ascending limb" EXACT [MA:th] +xref: EMAPA:29671 +xref: MA:0002628 +is_a: UBERON:0007685 ! region of nephron tubule +relationship: BFO:0000050 UBERON:0001291 ! part of thick ascending limb of loop of Henle +relationship: BFO:0000050 UBERON:0006541 ! part of outer medulla inner stripe loop of Henle +relationship: BFO:0000050 UBERON:0006542 ! part of outer medulla outer stripe loop of Henle + +[Term] +id: UBERON:0006534 +name: renal convoluted tubule +def: "Any region of a nephron tubule that is convoluted. Examples: distal convoluted tubule, proximal convoluted tuble." [http://orcid.org/0000-0002-6601-2165] +subset: grouping_class +synonym: "convoluted tubule" EXACT [] +synonym: "kidney convoluted tubule" EXACT [MA:0001665] +xref: EMAPA:35725 +xref: MA:0001665 +xref: NCIT:C49479 +xref: SCTID:361333002 +xref: UMLS:C1707510 +xref: Wikipedia:Convoluted_tubule +is_a: UBERON:0007685 ! region of nephron tubule + +[Term] +id: UBERON:0006541 +name: outer medulla inner stripe loop of Henle +def: "A loop of Henle that is part of a kidney outer medulla inner stripe." [OBOL:automatic] +xref: EMAPA:29679 +xref: MA:0002627 +is_a: UBERON:0034996 ! outer renal medulla loop of Henle +relationship: BFO:0000050 UBERON:0004201 ! part of kidney outer medulla inner stripe + +[Term] +id: UBERON:0006542 +name: outer medulla outer stripe loop of Henle +def: "A loop of Henle that is part of a kidney outer medulla outer stripe." [OBOL:automatic] +xref: EMAPA:29665 +xref: MA:0002630 +is_a: UBERON:0034996 ! outer renal medulla loop of Henle +relationship: BFO:0000050 UBERON:0004202 ! part of kidney outer medulla outer stripe + +[Term] +id: UBERON:0006544 +name: kidney vasculature +def: "A vasculature that is part of a kidney." [OBOL:automatic] +subset: vertebrate_core +xref: EMAPA:28457 +xref: TAO:0005305 +xref: ZFA:0005305 +is_a: UBERON:0002201 ! vasculature of trunk +is_a: UBERON:0006876 ! vasculature of organ +relationship: BFO:0000050 UBERON:0002113 ! part of kidney + +[Term] +id: UBERON:0006553 +name: renal duct +def: "A tube in the kidney that collect and transport urine." [ZFIN:ZDB-PUB-071029-9] +xref: TAO:0005289 +xref: ZFA:0005289 +is_a: UBERON:0000058 ! duct +relationship: BFO:0000050 UBERON:0002113 ! part of kidney + +[Term] +id: UBERON:0006555 +name: excretory tube +def: "A tube that is part of a excretory system." [OBOL:automatic] +is_a: UBERON:0000025 ! tube +relationship: BFO:0000050 UBERON:0001008 ! part of renal system + +[Term] +id: UBERON:0006558 +name: lymphatic part of lymphoid system +def: "An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: pheno_slim +synonym: "lymphatic system" EXACT [FMA:7162, MA:0002435] +synonym: "lymphatic tree system" EXACT [FMA:7162] +synonym: "lymporeticular system" RELATED [VHOG:0001761] +xref: AAO:0010522 +xref: CALOHA:TS-2024 +xref: EFO:0000870 +xref: EMAPA:18248 +xref: FMA:7162 +xref: MA:0002961 +xref: MESH:D008208 +xref: SCTID:362597000 +xref: VHOG:0001761 +xref: Wikipedia:Lymphatic_system +is_a: UBERON:0011216 ! organ system subdivision +relationship: BFO:0000050 UBERON:0001009 ! part of circulatory system +relationship: BFO:0000050 UBERON:0002465 ! part of lymphoid system + +[Term] +id: UBERON:0006562 +name: pharynx +def: "The pharynx is the part of the digestive system immediately posterior to the mouth[GO]." [GO:0060465] +subset: grouping_class +subset: uberon_slim +synonym: "anterior part of foregut" RELATED [] +synonym: "pharyngeal tube" RELATED [] +xref: FBbt:00005380 +xref: MAT:0000049 +xref: MIAA:0000049 +is_a: UBERON:0004921 ! subdivision of digestive tract + +[Term] +id: UBERON:0006595 +name: presumptive endoderm +def: "Presumptive structure of the blastula that will develop into endoderm." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +xref: AAO:0000471 +xref: EFO:0003437 +xref: TAO:0000416 +xref: ZFA:0000416 +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0000307 ! part of blastula + +[Term] +id: UBERON:0006596 +name: presumptive blood +subset: efo_slim +synonym: "future blood" EXACT [] +xref: AAO:0000468 +xref: EFO:0003439 +xref: TAO:0000568 +xref: ZFA:0000568 +is_a: UBERON:0006598 ! presumptive structure + +[Term] +id: UBERON:0006598 +name: presumptive structure +def: "Portion of embryonic tissue determined by fate mapping to become a structure." [GOC:CVS, GOC:YMB, ZFA:0001116] +synonym: "future structure" EXACT [] +synonym: "presumptive structures" EXACT [ZFA:0001116] +xref: AAO:0000479 +xref: TAO:0001116 +xref: ZFA:0001116 +is_a: UBERON:0002050 ! embryonic structure + +[Term] +id: UBERON:0006601 +name: presumptive ectoderm +def: "Presumptive structure of the blastula that will develop into ectoderm." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +synonym: "presumptive epidermis" RELATED [ZFA:0001376] +xref: AAO:0000470 +xref: EFO:0003466 +xref: TAO:0001376 +xref: XAO:0004132 +xref: ZFA:0001376 +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0000307 ! part of blastula + +[Term] +id: UBERON:0006603 +name: presumptive mesoderm +def: "Presumptive structure of the blastula that will develop into mesoderm." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +xref: AAO:0000476 +xref: EFO:0003467 +xref: TAO:0001377 +xref: ZFA:0001377 +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0000307 ! part of blastula + +[Term] +id: UBERON:0006657 +name: glenoid fossa +def: "Anatomical cavity for the proximal articular surface of the proximal limb or fin element with the scapulocoracoid or equivalent structure." [PHENOSCAPE:ad] +subset: pheno_slim +synonym: "cavitas glenoidalis" RELATED [Wikipedia:Glenoid_cavity] +synonym: "cavitas glenoidalis scapulae" EXACT [FMA:23275, FMA:TA] +synonym: "cavitus glenoidalis" EXACT [FMA:23275] +synonym: "glenoid cavity" EXACT [FMA:23275] +synonym: "glenoid cavity" RELATED [AAO:0000749] +synonym: "glenoid cavity of scapula" EXACT [FMA:23275] +synonym: "glenoid facet" EXACT [] +xref: AAO:0000749 +xref: EMAPA:25122 +xref: FMA:23275 +xref: NCIT:C32682 +xref: SCTID:181914008 +xref: UMLS:C1261046 +xref: Wikipedia:Glenoid_cavity +is_a: UBERON:0004704 ! bone fossa +relationship: BFO:0000050 UBERON:0004753 ! part of scapulocoracoid + +[Term] +id: UBERON:0006716 +name: mesopodium region +def: "The third segment of the limb, including either the wrist segment (carpus) or the ankle segment (tarsus)." [https://orcid.org/0000-0002-6601-2165, MA:th, Wikipedia:Carpus_and_tarsus_of_land_vertebrates] +synonym: "carpus/tarsus" EXACT [] +synonym: "mesopod" RELATED [] +synonym: "mesopodial limb segment" EXACT [MA:th] +synonym: "mesopodial segment" EXACT [] +xref: Wikipedia:Carpus_and_tarsus_of_land_vertebrates +is_a: UBERON:0002529 ! limb segment +relationship: BFO:0000050 UBERON:0002470 ! part of autopod region + +[Term] +id: UBERON:0006717 +name: autopodial skeleton +def: "The collection of all skeletal elements in an autopodium region." [https://orcid.org/0000-0002-6601-2165] +synonym: "autopod skeleton" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "autopodial skeleton" EXACT [VSAO:0005019] +synonym: "autopodium" RELATED [VSAO:0005019, VSAO:NI] +synonym: "skeletal parts of autopod" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "skeleton of autopod" EXACT [https://orcid.org/0000-0002-6601-2165] +xref: VSAO:0005019 +is_a: UBERON:0010712 ! limb skeleton subdivision +relationship: BFO:0000050 UBERON:0002470 ! part of autopod region +relationship: BFO:0000050 UBERON:0004381 ! part of skeleton of limb + +[Term] +id: UBERON:0006849 +name: scapula +def: "Endochondral bone that is dorsoventrally compressed and provides attachment site for muscles of the pectoral appendage." [https://github.com/obophenotype/uberon/issues/204, https://github.com/obophenotype/uberon/issues/339, VSAO:0000157] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "scapula bone" RELATED [BTO:0001218] +synonym: "scapulae" EXACT [ZFA:0000583] +synonym: "scapulas" RELATED [TAO:0000583] +synonym: "shoulder blade" NARROW [] +xref: AAO:0000751 +xref: BTO:0001218 +xref: CALOHA:TS-0897 +xref: EFO:0001400 +xref: EMAPA:18722 +xref: FMA:13394 +xref: GAID:186 +xref: galen:Scapula +xref: MA:0001330 +xref: MESH:D012540 +xref: NCIT:C12783 +xref: OpenCyc:Mx4rvVji0JwpEbGdrcN5Y29ycA +xref: SCTID:302517007 +xref: TAO:0000583 +xref: UMLS:C0036277 +xref: VHOG:0001398 +xref: VSAO:0000157 +xref: Wikipedia:Scapula +xref: ZFA:0000583 +is_a: UBERON:0002513 ! endochondral bone +is_a: UBERON:0007829 ! pectoral girdle bone +is_a: UBERON:0015057 ! scapula endochondral element + +[Term] +id: UBERON:0006853 +name: renal cortex tubule +def: "A region of nephron tubule that is part of a cortex of kidney." [OBOL:automatic] +synonym: "cortical tubule" RELATED [MA:0002609] +synonym: "kidney cortex tubule" EXACT [MA:0002609] +xref: EMAPA:18976 +xref: MA:0002609 +is_a: UBERON:0007685 ! region of nephron tubule +relationship: BFO:0000050 UBERON:0001225 ! part of cortex of kidney + +[Term] +id: UBERON:0006854 +name: distal straight tubule postmacula segment +def: "." [https://sourceforge.net/tracker/?func=detail&aid=3123598&group_id=76834&atid=1205376] +synonym: "cortical thick ascending limb of Henle's loop" EXACT [MA:th] +synonym: "kidney cortex loop of Henle ascending limb thick segment" EXACT [MA:th] +synonym: "renal cortex loop of Henle ascending limb thick segment" EXACT [MA:th] +synonym: "renal cortex thick ascending limb" EXACT [MA:th] +xref: EMAPA:28402 +xref: MA:0002615 +is_a: UBERON:0006853 ! renal cortex tubule +relationship: BFO:0000050 UBERON:0001291 ! part of thick ascending limb of loop of Henle +relationship: BFO:0000050 UBERON:0006853 ! part of renal cortex tubule + +[Term] +id: UBERON:0006866 +name: terminal part of digestive tract +def: "The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus." [http://orcid.org/0000-0002-6601-2165] +synonym: "rectal part of digestive tract" RELATED [] +synonym: "rectum" NARROW [FBbt:00005756] +synonym: "terminal section of digestive tract" RELATED [] +xref: FBbt:00005756 +xref: WBbt:0005773 +is_a: UBERON:0004921 ! subdivision of digestive tract + +[Term] +id: UBERON:0006871 +name: embryonic footplate +def: "The distal elements of the developing limb of vertebrates that will give rise to the pes (foot)." [https://github.com/obophenotype/mammalian-phenotype-ontology/issues/2218, MGI:csmith, MP:0004576, UBERON:cjm] +subset: pheno_slim +synonym: "distal part of hindlimb bud" RELATED [EMAPA:17249] +synonym: "foot disk" RELATED [] +synonym: "foot plate" BROAD [] +synonym: "footplate" BROAD [] +xref: EHDAA:5143 +xref: EHDAA:6096 +xref: EMAPA:17249 +xref: FMA:296800 +xref: NCIT:C34177 +xref: UMLS:C1517291 +is_a: UBERON:0010130 ! embryonic autopod plate + +[Term] +id: UBERON:0006875 +name: embryonic handplate +def: "The distal elements of the developing limb of vertebrates that will give rise to the manus (hand)." [MGI:csmith, MP:0004576, UBERON:cjm] +synonym: "distal part of forelimb bud" RELATED [EMAPA:17245] +synonym: "hand plate" EXACT [] +synonym: "handplate" EXACT [] +xref: EHDAA:4194 +xref: EHDAA:6242 +xref: EMAPA:17245 +xref: FMA:296794 +xref: NCIT:C34185 +xref: UMLS:C1512334 +is_a: UBERON:0010130 ! embryonic autopod plate + +[Term] +id: UBERON:0006876 +name: vasculature of organ +def: "A vasculature that is part of a organ." [OBOL:automatic] +subset: non_informative +synonym: "organ vasculature" EXACT [FMA:74612] +synonym: "set of blood vessels of organ" EXACT [FMA:74612] +xref: FMA:74612 +is_a: UBERON:0002049 ! vasculature +relationship: BFO:0000050 UBERON:0000062 ! part of organ + +[Term] +id: UBERON:0006914 +name: squamous epithelium +def: "An epithelium characterised by its most superficial layer consisting of squamous epithelial cells." [Wikipedia:Squamous_epithelium] +xref: BTO:0002072 +xref: NCIT:C12848 +xref: SCTID:40118003 +xref: UMLS:C0221909 +xref: Wikipedia:Squamous_epithelium +is_a: UBERON:0000483 ! epithelium + +[Term] +id: UBERON:0006965 +name: vascular cord +def: "The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]." [GO:0072360, ZFA:0005077] +subset: efo_slim +xref: EFO:0003709 +xref: TAO:0005077 +xref: ZFA:0005077 +is_a: UBERON:0005423 ! developing anatomical structure +relationship: BFO:0000050 UBERON:0014903 ! part of primordial vasculature + +[Term] +id: UBERON:0006984 +name: anatomical surface +def: "A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n." [CARO:0001002] +subset: upper_level +xref: BILA:0000010 +xref: CARO:0001002 +xref: EHDAA2_RETIRED:0003192 +xref: FMA:24137 +xref: NCIT:C34022 +xref: UMLS:C1515977 +is_a: UBERON:0010199 ! bona-fide anatomical boundary + +[Term] +id: UBERON:0007005 +name: cardiogenic splanchnic mesoderm +def: "The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]." [http://www.drugs.com/dict/cardiogenic-mesoderm.html, https://github.com/obophenotype/insect_neuroanatomy_ontology/issues/7, XAO:0000235] +subset: efo_slim +subset: pheno_slim +synonym: "cardiac mesoderm" RELATED [XAO:0000235] +synonym: "cardiogenic mesoderm" RELATED [http://www.drugs.com/dict/cardiogenic-mesoderm.html] +synonym: "cardiogenic region" RELATED [http://orcid.org/0000-0002-6601-2165] +synonym: "cardiogenic splanchnopleure" EXACT [EHDAA2:0000214] +synonym: "heart primordia" RELATED [XAO:0000235] +xref: AAO:0011021 +xref: BILA:0000051 +xref: EFO:0000315 +xref: EHDAA2:0000214 +xref: EHDAA:385 +xref: FMA:293143 +xref: SCTID:360387000 +xref: VHOG:0001641 +xref: XAO:0000235 +is_a: UBERON:0005291 ! embryonic tissue +relationship: BFO:0000050 UBERON:0004140 ! part of primary heart field +relationship: BFO:0000050 UBERON:0009881 ! part of anterior lateral plate mesoderm + +[Term] +id: UBERON:0007010 +name: cleaving embryo +def: "Organism at the cleavage stage." [OBOL:automatic] +xref: BILA:0000058 +is_a: UBERON:0000922 ! embryo + +[Term] +id: UBERON:0007026 +name: presumptive gut +synonym: "embryonic digestive tube" RELATED [] +synonym: "future digestive tract" EXACT [] +synonym: "future digestive tube" EXACT [] +synonym: "future gut" EXACT [] +synonym: "primitive gut" EXACT [] +synonym: "primordial digestive tube" RELATED [] +synonym: "primordial gut" RELATED [] +xref: BILA:0000084 +xref: NCIT:C34268 +xref: SCTID:360394002 +xref: UMLS:C1514442 +is_a: UBERON:0006598 ! presumptive structure + +[Term] +id: UBERON:0007100 +name: primary circulatory organ +def: "A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]." [GO:0007507] +subset: grouping_class +synonym: "adult heart" RELATED [FBbt:00003154] +synonym: "dorsal tube" NARROW [Wikipedia:Heart] +synonym: "heart" NARROW [GO:0007507] +xref: FBbt:00003154 +xref: http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg +xref: SPD:0000130 +xref: TADS:0000147 +is_a: UBERON:0015228 ! circulatory organ + +[Term] +id: UBERON:0007135 +name: neural keel +def: "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section." [ZFIN:ZDB-PUB-961014-576] +subset: efo_slim +synonym: "presumptive central nervous system" RELATED [ZFA:0000131] +xref: EFO:0003497 +xref: TAO:0000131 +xref: ZFA:0000131 +is_a: UBERON:0016879 ! future central nervous system + +[Term] +id: UBERON:0007237 +name: 1st arch mandibular component +synonym: "ventral mandibular arch" RELATED [VHOG:0000510] +synonym: "ventral pharyngeal arch 1" EXACT [VHOG:0000510] +synonym: "ventral visceral arch 1" RELATED [VHOG:0000510] +xref: EHDAA2:0000031 +xref: EHDAA:583 +xref: EMAPA:16382 +xref: VHOG:0000510 +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0004362 ! part of pharyngeal arch 1 + +[Term] +id: UBERON:0007269 +name: pectoral appendage musculature +def: "Any collection of muscles that is part of a pectoral appendage." [OBOL:automatic] +subset: efo_slim +synonym: "pectoral fin muscle" NARROW [ZFA:0000563] +synonym: "pectoral fin musculature" NARROW SENSU [ZFA:0000563] +xref: EFO:0003540 +xref: TAO:0000563 +xref: ZFA:0000563 +is_a: UBERON:0007271 ! appendage musculature +is_a: UBERON:0014793 ! musculature of pectoral complex +relationship: BFO:0000050 UBERON:0004710 ! part of pectoral appendage + +[Term] +id: UBERON:0007270 +name: pelvic appendage musculature +def: "Any collection of muscles that is part of a pelvic appendage." [OBOL:automatic] +synonym: "pelvic fin musculature" NARROW SENSU [ZFA:0000258] +xref: TAO:0000258 +xref: ZFA:0000258 +is_a: UBERON:0007271 ! appendage musculature +is_a: UBERON:0014792 ! musculature of pelvic complex +relationship: BFO:0000050 UBERON:0004709 ! part of pelvic appendage + +[Term] +id: UBERON:0007271 +name: appendage musculature +def: "Any collection of muscles that is part of an appendage." [OBOL:automatic] +synonym: "fin musculature" NARROW SENSU [ZFA:0000207] +xref: TAO:0000207 +xref: ZFA:0000207 +is_a: UBERON:0001015 ! musculature +relationship: BFO:0000050 UBERON:0000026 ! part of appendage + +[Term] +id: UBERON:0007272 +name: pectoral appendage skeleton +def: "Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle." [VSAO:0005000, VSAO:NI] +synonym: "cheiropterygium" RELATED [VSAO:0005000, VSAO:NI] +xref: VSAO:0005000 +is_a: UBERON:0011582 ! paired limb/fin skeleton +relationship: BFO:0000050 UBERON:0004710 ! part of pectoral appendage + +[Term] +id: UBERON:0007273 +name: pelvic appendage skeleton +def: "The collection of all skeletal elements in a pelvic appendage region." [https://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0011582 ! paired limb/fin skeleton +relationship: BFO:0000050 UBERON:0004709 ! part of pelvic appendage + +[Term] +id: UBERON:0007277 +name: presumptive hindbrain +def: "The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure." [Wikipedia:Rhombencephalon] +subset: efo_slim +synonym: "embryonic rhombencephalon" RELATED [CALOHA:TS-2118] +synonym: "future hindbrain" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "presumptive rhombencephalon" EXACT [ZFA:0000569] +synonym: "rhombencephalon" RELATED [EHDAA2:0001630] +xref: BAMS:HB +xref: CALOHA:TS-2118 +xref: EFO:0003440 +xref: EHDAA2:0001630 +xref: FMA:295640 +xref: TAO:0000569 +xref: Wikipedia:Rhombencephalon +xref: ZFA:0000569 +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0006238 ! part of future brain + +[Term] +id: UBERON:0007281 +name: presumptive midbrain hindbrain boundary +def: "Embryonic structure that gives rise to the midbrain hindbrain boundary." [ZFA:0001187] +subset: efo_slim +synonym: "presumptive MHB" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "presumptive midbrain-hindbrain boundary" EXACT [ZFA:0001187] +xref: EFO:0003446 +xref: TAO:0001187 +xref: XAO:0004086 +xref: ZFA:0001187 +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0006238 ! part of future brain + +[Term] +id: UBERON:0007282 +name: presumptive segmental plate +def: "A presumptive structure that has the potential to develop into a presomitic mesoderm." [OBOL:automatic] +subset: efo_slim +synonym: "presumptive segmental plates" RELATED [ZFA:0000053] +xref: EFO:0003421 +xref: TAO:0000053 +xref: ZFA:0000053 +is_a: UBERON:0006598 ! presumptive structure + +[Term] +id: UBERON:0007284 +name: presumptive neural plate +def: "A presumptive structure that has the potential to develop into a neural plate." [OBOL:automatic] +subset: efo_slim +synonym: "prospective neuroectoderm" EXACT [ZFA:0000063] +synonym: "prospective vegetal ectoderm" EXACT [ZFA:0000063] +xref: EFO:0003424 +xref: TAO:0000063 +xref: ZFA:0000063 +is_a: UBERON:0016879 ! future central nervous system +relationship: BFO:0000050 UBERON:0004734 ! part of gastrula + +[Term] +id: UBERON:0007285 +name: presumptive paraxial mesoderm +def: "The part of the blastula that has the potential to develop into a paraxial mesoderm." [https://github.com/obophenotype/uberon/issues/1277, UBERON:cjm] +subset: efo_slim +synonym: "future paraxial mesenchyme" EXACT [UBERON:cjm] +synonym: "future paraxial mesoderm" EXACT [] +xref: EFO:0003443 +xref: TAO:0000591 +xref: XAO:0004134 +xref: ZFA:0000591 +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0000307 ! part of blastula + +[Term] +id: UBERON:0007297 +name: presumptive pronephric mesoderm +def: "A presumptive structure that has the potential to develop into a pronephric mesoderm." [OBOL:automatic] +subset: efo_slim +synonym: "nephron primordium" EXACT [ZFA:0001070] +xref: EFO:0003619 +xref: TAO:0001070 +xref: ZFA:0001070 +is_a: UBERON:0006598 ! presumptive structure + +[Term] +id: UBERON:0007300 +name: pectoral appendage blood vessel +def: "A blood vessel that is part of a pectoral appendage." [OBOL:automatic] +synonym: "pectoral fin blood vessel" NARROW SENSU [ZFA:0005301] +xref: TAO:0005301 +xref: ZFA:0005301 +is_a: UBERON:0007301 ! appendage blood vessel +relationship: BFO:0000050 UBERON:0004710 ! part of pectoral appendage + +[Term] +id: UBERON:0007301 +name: appendage blood vessel +def: "A blood vessel that is part of a limb/fin." [OBOL:automatic] +synonym: "fin blood vessel" NARROW SENSU [ZFA:0005299] +synonym: "limb blood vessel" NARROW SENSU [] +xref: TAO:0005299 +xref: ZFA:0005299 +is_a: UBERON:0001981 ! blood vessel +relationship: BFO:0000050 UBERON:0007304 ! part of appendage vasculature + +[Term] +id: UBERON:0007304 +name: appendage vasculature +def: "A vasculature that is part of a limb/fin." [OBOL:automatic] +synonym: "fin vasculature" NARROW SENSU [ZFA:0005095] +xref: TAO:0005095 +xref: ZFA:0005095 +is_a: UBERON:0002049 ! vasculature +relationship: BFO:0000050 UBERON:0000026 ! part of appendage + +[Term] +id: UBERON:0007376 +name: outer epithelium +def: "The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]." [GO:0008544] +subset: grouping_class +synonym: "epidermis" EXACT [GO:0008544] +synonym: "epidermis (sensu Metazoa)" EXACT [] +synonym: "hypoderm" RELATED INCONSISTENT [BTO:0000313] +synonym: "hypodermis" RELATED INCONSISTENT [GO:0008544, WBbt:0005733] +synonym: "outer epidermal layer" EXACT [] +synonym: "outer epithelial layer" EXACT [] +xref: BSA:0000073 +xref: BTO:0000313 +xref: FBbt:00004993 +xref: HAO:0000298 +xref: TADS:0000109 +xref: WBbt:0005733 +xref: Wikipedia:Epidermis_(zoology) +is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0003102 ! surface structure + +[Term] +id: UBERON:0007383 +name: enveloping layer of ectoderm +def: "Outermost layer of cells surrounding the embryo." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +synonym: "enveloping layer" EXACT [ZFIN:ZDB-PUB-961014-576] +synonym: "EVL" EXACT [ZFA:0000086] +xref: EFO:0003425 +xref: TAO:0000086 +xref: ZFA:0000086 +is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0005291 ! embryonic tissue + +[Term] +id: UBERON:0007389 +name: paired limb/fin cartilage +def: "A cartilage tissue that is part of a paired limb or fin." [http://orcid.org/0000-0002-6601-2165] +subset: homology_grouping +xref: TAO:0001543 +xref: ZFA:0001543 +is_a: UBERON:0002418 ! cartilage tissue +relationship: BFO:0000050 UBERON:0002091 ! part of appendicular skeleton +relationship: BFO:0000050 UBERON:0004708 ! part of paired limb/fin + +[Term] +id: UBERON:0007499 +name: epithelial sac +def: "An epithelial tube that is open at one end only." [AEO:JB, UBERONREF:0000001] +xref: AEO:0000115 +xref: EHDAA2:0003115 +is_a: UBERON:0003914 ! epithelial tube +is_a: UBERON:0009856 ! sac + +[Term] +id: UBERON:0007500 +name: epithelial tube open at both ends +def: "An epithelial tube open at both ends that allows fluid flow." [AEO:JB, UBERONREF:0000001] +xref: AEO_RETIRED:0000116 +xref: RETIRED_EHDAA2:0003116 +is_a: UBERON:0003914 ! epithelial tube + +[Term] +id: UBERON:0007503 +name: epithelial vesicle +def: "A closed epithelium with a lumen." [AEO:JB] +xref: AEO:0000119 +xref: EHDAA2:0003119 +is_a: UBERON:0000483 ! epithelium + +[Term] +id: UBERON:0007524 +name: dense mesenchyme tissue +def: "Mesenchyme with little extracellular matrix." [AEO:JB] +xref: AEO:0000146 +xref: EHDAA2:0003146 +is_a: UBERON:0003104 ! mesenchyme + +[Term] +id: UBERON:0007530 +name: migrating mesenchyme population +def: "Mesenchymal cells that are migrating." [AEO:JB] +xref: AEO:0000152 +xref: EHDAA2:0003152 +is_a: UBERON:0003104 ! mesenchyme + +[Term] +id: UBERON:0007567 +name: regenerating anatomical structure +def: "An anatomical structure that is undergoing regeneration." [http://orcid.org/0000-0002-6601-2165] +synonym: "regenerating tissue" RELATED [ZFA:0005147] +synonym: "regenerating tissues" RELATED [ZFA:0005147] +synonym: "regenerative tissue" RELATED [] +xref: AEO:0000200 +xref: EHDAA2:0003233 +xref: TAO:0005147 +xref: XAO:0004059 +xref: ZFA:0005147 +is_a: UBERON:0000061 ! anatomical structure +relationship: BFO:0000050 UBERON:0000468 ! part of multicellular organism + +[Term] +id: UBERON:0007616 +name: layer of synovial tissue +def: "A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]." [BTO:0001338, http://www.britannica.com/EBchecked/topic/578563/synovial-tissue] +synonym: "stratum synoviale" NARROW [FMA:TA] +synonym: "synovial layer" NARROW [FMA:66762] +synonym: "synovial membrane" NARROW [FMA:66762] +synonym: "synovial tissue" RELATED [BTO:0001338] +synonym: "synovium" EXACT [CALOHA:TS-0998] +xref: BTO:0001338 +xref: CALOHA:TS-0998 +xref: FMA:66762 +is_a: UBERON:0000042 ! serous membrane + +[Term] +id: UBERON:0007617 +name: synovial cavity of joint +def: "An anatomical cavity that surrounded_by a synovial joint." [OBOL:automatic] +synonym: "articular cavity (synovial joint)" EXACT [FMA:11356] +synonym: "cavitas articularis (junctura synovialis)" EXACT [FMA:11356] +synonym: "cavity of synovial joint" EXACT [FMA:11356] +synonym: "joint cavity" RELATED [FMA:11356] +synonym: "synovial cavity" RELATED [FMA:11356] +xref: FMA:11356 +is_a: UBERON:0002553 ! anatomical cavity + +[Term] +id: UBERON:0007651 +name: anatomical junction +def: "An anatomical structure that connects two structures." [http://code.google.com/p/caro2/issues/detail?id=15] +subset: upper_level +synonym: "anatomical junction" EXACT [] +synonym: "junction" BROAD [] +xref: FMA:5898 +xref: SCTID:91833003 +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0007684 +name: uriniferous tubule +def: "Functional unit of the kidney that forms urine, consisting of two parts, the nephron and the collecting tubule." [ISBN:0073040584] +xref: FMA:17691 +is_a: UBERON:0003914 ! epithelial tube +is_a: UBERON:0004819 ! kidney epithelium +is_a: UBERON:0006555 ! excretory tube + +[Term] +id: UBERON:0007685 +name: region of nephron tubule +synonym: "region of renal tubule" RELATED [FMA:17692] +synonym: "renal tubule region" EXACT [FMA:17692] +xref: FMA:17692 +is_a: UBERON:0001231 ! nephron tubule +relationship: BFO:0000050 UBERON:0001231 ! part of nephron tubule + +[Term] +id: UBERON:0007687 +name: kidney field +def: "Region of the embryo into the area in which the kidney rudiment will develop." [DOI:10.1371/journal.pone.0099864, GO:0072004, GOC:mtg_kidney_jan10] +synonym: "kidney anlage" RELATED [GOC:mtg_kidney_jan10] +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0006598 ! presumptive structure +is_a: UBERON:0007688 ! anlage + +[Term] +id: UBERON:0007688 +name: anlage +def: "Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue." [FBbt:00005426, http://flybase.org/reports/FBrf0178740.html, JB:DEF] +subset: efo_slim +synonym: "developmental field" EXACT [] +synonym: "field" BROAD [] +synonym: "future organ" RELATED [] +synonym: "organ field" RELATED [] +xref: AEO:0000170 +xref: EFO:0001649 +xref: EHDAA2:0003170 +xref: FBbt:00005426 +xref: Wikipedia:Anlage_(biology) +is_a: UBERON:0000479 ! tissue +is_a: UBERON:0005423 ! developing anatomical structure + +[Term] +id: UBERON:0007690 +name: early pharyngeal endoderm +def: "." [http://dev.biologists.org/content/128/22/4573.full] +subset: efo_slim +synonym: "early pharyngeal arch endoderm" EXACT [EHDAA2:0001457] +synonym: "pharyngeal arch endoderm" RELATED [] +synonym: "pharyngeal endoderm" RELATED [ZFA:0001104] +synonym: "pharyngeal region endoderm" RELATED [EHDAA2:0001456] +xref: EFO:0003626 +xref: EHDAA2:0001457 +xref: EHDAA:962 +xref: EMAPA:32754 +xref: FMA:293087 +xref: TAO:0001104 +xref: ZFA:0001104 +is_a: UBERON:0003258 ! endoderm of foregut +is_a: UBERON:0005291 ! embryonic tissue +relationship: BFO:0000050 UBERON:0009722 ! part of entire pharyngeal arch endoderm + +[Term] +id: UBERON:0007771 +name: epidermis gland +def: "A gland that is part of a epidermis." [OBOL:automatic] +subset: grouping_class +synonym: "epidermal gland" EXACT [] +synonym: "gland of epidermis" EXACT [FMA:59153] +xref: FMA:59153 +is_a: UBERON:0002419 ! skin gland +relationship: BFO:0000050 UBERON:0001003 ! part of skin epidermis + +[Term] +id: UBERON:0007779 +name: transudate +def: "Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces." [http://medical-dictionary.thefreedictionary.com/transudate] +synonym: "plasma ultrafiltrate" RELATED [] +xref: FMA:12276 +xref: GAID:1195 +xref: MESH:D005122 +xref: ncithesaurus:Transudate +is_a: UBERON:0006314 ! bodily fluid + +[Term] +id: UBERON:0007794 +name: secretion of serous gland +def: "Any fluid produced by a serous gland." [UBERON:cjm] +synonym: "serosal fluid" EXACT [Wikipedia:Serous_fluid] +synonym: "serous fluid" BROAD [] +synonym: "serous gland fluid" EXACT [] +xref: Wikipedia:Serous_fluid +is_a: UBERON:0000456 ! secretion of exocrine gland +is_a: UBERON:0006314 ! bodily fluid + +[Term] +id: UBERON:0007798 +name: vascular system +def: "Anatomical system that consists of all blood and lymph vessels." [http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +xref: BTO:0001085 +xref: CALOHA:TS-2053 +xref: EHDAA2:0004520 +xref: EMAPA:35905 +xref: MA:0002718 +xref: NCIT:C33854 +xref: UMLS:C0489903 +is_a: UBERON:0000467 ! anatomical system +relationship: BFO:0000050 UBERON:0004535 ! part of cardiovascular system + +[Term] +id: UBERON:0007811 +name: craniocervical region +def: "The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae." [https://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "cephalic area" RELATED [https://github.com/obophenotype/uberon/issues/379] +synonym: "cephalic part of animal" RELATED [Wikipedia:Head] +synonym: "cephalic region" RELATED [https://github.com/obophenotype/uberon/issues/379] +synonym: "head and neck" RELATED [FMA:280881] +synonym: "head or neck" RELATED [] +xref: CALOHA:TS-2356 +xref: EV:0100009 +xref: FMA:280881 +xref: galen:HeadAndNeck +xref: MA:0000006 +xref: NCIT:C12418 +xref: SCTID:361355005 +xref: UMLS:C0460004 +xref: WikipediaCategory:Head_and_neck +is_a: UBERON:0000475 ! organism subdivision +relationship: BFO:0000050 UBERON:0000153 ! part of anterior region of body +relationship: BFO:0000050 UBERON:0013702 ! part of body proper + +[Term] +id: UBERON:0007823 +name: appendage girdle region +def: "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc)." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] +synonym: "fin girdle" RELATED SENSU [] +synonym: "fin girdle region" RELATED SENSU [] +synonym: "girdle" BROAD [] +synonym: "girdle region" BROAD [] +synonym: "limb girdle" RELATED SENSU [] +synonym: "limb girdle region" RELATED SENSU [] +xref: EMAPA:37854 +xref: FMA:24874 +xref: VSAO:0000303 +is_a: UBERON:0000475 ! organism subdivision +relationship: BFO:0000050 UBERON:0010707 ! part of appendage girdle complex + +[Term] +id: UBERON:0007828 +name: girdle bone/zone +def: "A bone that is part of a appendage girdle region." [OBOL:automatic] +synonym: "girdle bone" EXACT [MA:0000291] +xref: EMAPA:35379 +xref: MA:0000291 +is_a: UBERON:0010740 ! bone of appendage girdle complex +relationship: BFO:0000050 UBERON:0010719 ! part of girdle skeleton + +[Term] +id: UBERON:0007829 +name: pectoral girdle bone +def: "A bone that is part of a pectoral girdle region." [OBOL:automatic] +subset: vertebrate_core +synonym: "bone of pectoral girdle" EXACT [] +xref: EMAPA:35669 +xref: MA:0000292 +is_a: UBERON:0007828 ! girdle bone/zone +is_a: UBERON:0010741 ! bone of pectoral complex +relationship: BFO:0000050 UBERON:0007831 ! part of pectoral girdle skeleton + +[Term] +id: UBERON:0007831 +name: pectoral girdle skeleton +def: "A subdivision of a limb or fin skeleton consisting of bones which connects the upper limb or fin to the axial skeleton on each side. It consists of the clavicle and scapula in humans and, in those species with three bones in the pectoral girdle, the coracoid. Some mammalian species (e.g. the dog and the horse) have only the scapula. In humans, the only joints between the shoulder girdle and axial skeleton are the sternoclavicular joints on each side. No joint exists between each scapula and the rib cage; instead the muscular connection between the two permits relatively great mobility of the shoulder girdle in relation to the pelvic girdle. In those species having only the scapula, no joint exists between the forelimb and the thorax, the only attachment being muscular[WP]. Examples: There are only two instances, right and left pectoral girdle skeletons." [Wikipedia:Pectoral_girdle] +subset: efo_slim +subset: vertebrate_core +synonym: "cingulum pectorale" RELATED [Wikipedia:Pectoral_girdle] +synonym: "pectoral girdle" RELATED INCONSISTENT [VSAO:0000156] +synonym: "scapular girdle" RELATED [TAO:0000407] +synonym: "skeletal parts of pectoral girdle" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "skeleton of pectoral girdle" EXACT [https://orcid.org/0000-0002-6601-2165] +xref: AAO:0000422 +xref: AAO:0000754 +xref: EFO:0000946 +xref: EHDAA2:0001420 +xref: FMA:24141 +xref: MAT:0000181 +xref: MIAA:0000181 +xref: NCIT:C33547 +xref: TAO:0000407 +xref: UMLS:C0427245 +xref: VHOG:0001156 +xref: VSAO:0000156 +xref: Wikipedia:Pectoral_girdle +xref: XAO:0003063 +xref: ZFA:0000407 +is_a: UBERON:0010719 ! girdle skeleton +relationship: BFO:0000050 UBERON:0001421 ! part of pectoral girdle region +relationship: BFO:0000050 UBERON:0012475 ! part of skeleton of pectoral complex + +[Term] +id: UBERON:0007832 +name: pelvic girdle skeleton +def: "Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature." [VSAO:0000155, Wikipedia:Pelvis] +subset: efo_slim +subset: vertebrate_core +synonym: "pelvic girdle" RELATED INCONSISTENT [VSAO:0000155] +synonym: "pelvic girdle skeleton" EXACT [VSAO:0000155] +synonym: "skeletal parts of pelvic girdle" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "skeleton of pelvic girdle" EXACT [https://orcid.org/0000-0002-6601-2165] +xref: AAO:0000426 +xref: AAO:0000768 +xref: EFO:0000947 +xref: EHDAA2:0001426 +xref: EHDAA:7149 +xref: EHDAA:8324 +xref: EMAPA:18028 +xref: FMA:87592 +xref: galen:PelvicGirdle +xref: http://people.eku.edu/ritchisong/pectoralgirdles.gif +xref: MAT:0000182 +xref: MIAA:0000182 +xref: TAO:0000565 +xref: VHOG:0000305 +xref: VSAO:0000155 +xref: Wikipedia:Pelvis +xref: XAO:0003064 +xref: ZFA:0000565 +is_a: UBERON:0010719 ! girdle skeleton +relationship: BFO:0000050 UBERON:0001271 ! part of pelvic girdle region +relationship: BFO:0000050 UBERON:0012476 ! part of skeleton of pelvic complex + +[Term] +id: UBERON:0007844 +name: cartilage element +def: "Skeletal element that is composed of cartilage tissue and may be permanent or transient." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000000] +subset: organ_slim +subset: pheno_slim +synonym: "cartilage" RELATED [VSAO:0000000] +synonym: "cartilage organ" EXACT [FMA:55107] +synonym: "cartilaginous element" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "chondrogenic element" EXACT [VSAO:0000000] +xref: AAO:0011130 +xref: CALOHA:TS-0118 +xref: EMAPA:32730 +xref: FMA:55107 +xref: VSAO:0000000 +xref: XAO:0004013 +xref: ZFA:0001501 +is_a: UBERON:0004765 ! skeletal element + +[Term] +id: UBERON:0007845 +name: regular connective tissue +def: "Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue." [FMA:20103] +xref: FMA:20103 +is_a: UBERON:0002384 ! connective tissue + +[Term] +id: UBERON:0007846 +name: dense regular connective tissue +def: "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts)." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000050] +synonym: "dense fibrous connective tissue" EXACT [FMA:64781] +synonym: "dense regular collagenous connective tissue" EXACT [FMA:64781] +synonym: "dense regular collagenous tissue" EXACT [FMA:64781] +synonym: "regular dense connective tissue" EXACT [] +synonym: "typus regularis (textus connectivus collagenosus compactus)" EXACT [FMA:64781] +xref: FMA:64781 +xref: NCIT:C33453 +xref: SCTID:22560007 +xref: UMLS:C0225333 +xref: VSAO:0000050 +xref: Wikipedia:Dense_regular_connective_tissue +xref: XAO:0004030 +is_a: UBERON:0007845 ! regular connective tissue +is_a: UBERON:0011823 ! dense connective tissue + +[Term] +id: UBERON:0008114 +name: joint of girdle +def: "A skeletal joint that is part of a appendage girdle region." [OBOL:automatic] +subset: grouping_class +synonym: "girdle joint" EXACT [OBOL:automatic] +xref: MA:0001505 +is_a: UBERON:0000982 ! skeletal joint +relationship: BFO:0000050 UBERON:0007823 ! part of appendage girdle region + +[Term] +id: UBERON:0008193 +name: pneumatized bone +def: "A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]." [http://www.medilexicon.com/medicaldictionary.php?t=11303] +synonym: "hollow bone" RELATED [] +synonym: "os pneumaticum" EXACT [FMA:7478] +synonym: "pneumatic bone" EXACT [FMA:7478] +xref: FMA:7478 +xref: galen:PneumaticBone +xref: SCTID:333008005 +xref: Wikipedia:Skeletal_pneumaticity +is_a: UBERON:0001474 ! bone element + +[Term] +id: UBERON:0008202 +name: bone of hip region +subset: grouping_class +subset: non_informative +subset: pheno_slim +xref: EMAPA:37308 +xref: FMA:42854 +xref: MA:0000655 +xref: SCTID:304907005 +is_a: UBERON:0001474 ! bone element + +[Term] +id: UBERON:0008784 +name: lower limb segment +def: "A limb segment that is part of a hindlimb." [OBOL:automatic] +synonym: "free lower limb segment" EXACT [FMA:24877] +synonym: "free lower limb subdivision" EXACT [FMA:24877] +synonym: "segment of free lower limb" EXACT [FMA:24877] +synonym: "subdivision of free lower limb" EXACT [FMA:24877] +xref: FMA:24877 +is_a: UBERON:0002529 ! limb segment +relationship: BFO:0000050 UBERON:0002103 ! part of hindlimb + +[Term] +id: UBERON:0008785 +name: upper limb segment +def: "A limb segment that is part of a forelimb." [OBOL:automatic] +synonym: "free upper limb segment" EXACT [FMA:24876] +synonym: "free upper limb subdivision" EXACT [FMA:24876] +synonym: "segment of free upper limb" EXACT [FMA:24876] +synonym: "subdivision of free upper limb" EXACT [FMA:24876] +xref: FMA:24876 +is_a: UBERON:0002529 ! limb segment +relationship: BFO:0000050 UBERON:0002102 ! part of forelimb + +[Term] +id: UBERON:0008814 +name: pharyngeal arch system +def: "A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]." [GO:0060037, GOC:dph] +synonym: "embryonic pharyngeal complex" EXACT [] +synonym: "pharyngeal apparatus" EXACT [] +synonym: "pharyngeal arch complex" RELATED [] +synonym: "pharyngeal arch region" RELATED [EHDAA2:0000187] +synonym: "pharyngeal arches and clefts" RELATED [] +synonym: "pharyngeal complex" RELATED [] +synonym: "pharyngeal system" EXACT [GO:0060037] +xref: EHDAA2:0000187 +xref: FMA:293041 +xref: NCIT:C34248 +xref: UMLS:C1519038 +is_a: UBERON:0000477 ! anatomical cluster +relationship: BFO:0000050 UBERON:0000922 ! part of embryo +relationship: BFO:0000050 UBERON:0009145 ! part of pharyngeal region of foregut + +[Term] +id: UBERON:0008816 +name: embryonic head +def: "A head that is part of a embryo." [OBOL:automatic] +subset: non_informative +xref: CALOHA:TS-0246 +xref: FBbt:00000155 +xref: FMA:293011 +is_a: UBERON:0000033 ! head +relationship: BFO:0000050 UBERON:0000922 ! part of embryo + +[Term] +id: UBERON:0008895 +name: splanchnocranium +def: "Subdivision of endoskeleton derived from pharyngeal arches." [https://orcid.org/0000-0002-6601-2165, ISBN:0073040584, Wikipedia:Facial_skeleton] +synonym: "branchial arch skeleton" RELATED [] +synonym: "gill arch skeleton" RELATED [] +synonym: "pharyngeal arch" RELATED INCONSISTENT [VSAO:0000149] +synonym: "pharyngeal arch skeleton" RELATED [ZFA:0001216] +synonym: "pharyngeal endoskeleton" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "pharyngeal skeleton" RELATED [ZFA:0001216] +synonym: "visceral cranium" RELATED [http://orcid.org/0000-0002-6601-2165] +synonym: "visceral skeletal system" RELATED [http://orcid.org/0000-0002-6601-2165] +synonym: "visceral skeleton" RELATED [UBERONREF:0000007] +synonym: "viscerocranium" EXACT INCONSISTENT [VHOG:0000315, Wikipedia:Viscerocranium, ZFA:0001216] +xref: AAO:0010157 +xref: TAO:0001216 +xref: VHOG:0000315 +xref: VSAO:0000149 +xref: Wikipedia:Facial_skeleton +xref: XAO:0003176 +xref: ZFA:0001216 +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: UBERON:0011159 ! primary subdivision of cranial skeletal system + +[Term] +id: UBERON:0008962 +name: forelimb bone +def: "A bone that is part of a forelimb region. Examples: humerus, any of the phalanges. Counter-example: scapula (a bone of the pectoral girdle). Note that we consider the forelimb to end at the shoulder." [https://orcid.org/0000-0002-6601-2165] +synonym: "free forelimb bone" EXACT [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] +synonym: "wing bone" NARROW SENSU [Geisha:syn, NCBITaxon:8782, OBOL:automatic] +xref: GAID:178 +xref: MESH:D001133 +xref: NCIT:C12983 +xref: SCTID:368532003 +xref: UMLS:C0003793 +is_a: UBERON:0002428 ! limb bone +is_a: UBERON:0010741 ! bone of pectoral complex +is_a: UBERON:0015021 ! forelimb endochondral element + +[Term] +id: UBERON:0008987 +name: renal parenchyma +def: "The functional tissue of the kidney, consisting of the nephrons." [BTO:0003604] +synonym: "kidney parenchyma" RELATED [BTO:0003604] +synonym: "parenchyma of kidney" EXACT [FMA:15574] +xref: BTO:0003604 +xref: FMA:15574 +xref: SCTID:29704000 +is_a: UBERON:0000353 ! parenchyma +relationship: BFO:0000050 UBERON:0002113 ! part of kidney + +[Term] +id: UBERON:0009035 +name: renal straight tubule +def: "Any region of a nephron tubule that is straight. Examples: distal convoluted tubule, proximal convoluted tuble." [http://orcid.org/0000-0002-6601-2165] +synonym: "kidney straight tubule" EXACT [MA:0002634] +synonym: "straight tubule" EXACT [] +xref: EMAPA:37489 +xref: MA:0002634 +xref: SCTID:245151008 +xref: Wikipedia:Tubuli_seminiferi_recti +is_a: UBERON:0007685 ! region of nephron tubule + +[Term] +id: UBERON:0009089 +name: inner medulla vasa recta descending limb +xref: KUPO:0001003 +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0004776 ! part of inner renal medulla vasa recta + +[Term] +id: UBERON:0009090 +name: outer medulla vasa recta descending limb +xref: KUPO:0001004 +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0004775 ! part of outer renal medulla vasa recta + +[Term] +id: UBERON:0009091 +name: vasa recta ascending limb +xref: KUPO:0001005 +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0004726 ! part of vasa recta + +[Term] +id: UBERON:0009092 +name: inner medulla vasa recta ascending limb +xref: KUPO:0001006 +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0004776 ! part of inner renal medulla vasa recta + +[Term] +id: UBERON:0009093 +name: outer medulla vasa recta ascending limb +xref: KUPO:0001007 +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0004775 ! part of outer renal medulla vasa recta + +[Term] +id: UBERON:0009142 +name: entire embryonic mesenchyme +def: "Sum total of mesenchyme in the embryo." [https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7] +xref: EHDAA2:0001113 +xref: EHDAA:177 +xref: EMAPA:16097 +is_a: UBERON:0000477 ! anatomical cluster +relationship: BFO:0000050 UBERON:0000922 ! part of embryo + +[Term] +id: UBERON:0009145 +name: pharyngeal region of foregut +synonym: "pharyngeal region" EXACT [EMAPA:16549] +xref: EMAPA:16549 +xref: RETIRED_EHDAA2:0001454 +is_a: UBERON:0005423 ! developing anatomical structure +relationship: BFO:0000050 UBERON:0001041 ! part of foregut + +[Term] +id: UBERON:0009196 +name: indifferent external genitalia +subset: organ_slim +xref: EHDAA2:0004021 +is_a: UBERON:0004176 ! external genitalia +relationship: BFO:0000050 UBERON:0000922 ! part of embryo + +[Term] +id: UBERON:0009200 +name: limb epidermis +def: "The limb epidermis is the outer epithelial layer of the limb, it is a complex stratified squamous epithelium." [GOC:dph, GOC:sdb_2009, GOC:tb] +xref: EMAPA:32728 +is_a: UBERON:0001003 ! skin epidermis +is_a: UBERON:3000981 ! limb external integument structure + +[Term] +id: UBERON:0009201 +name: nephric duct +def: "A nephric duct is a tube that drains a primitive kidney[GO]." [GO:0072176] +xref: EMAPA:16577 +xref: Wikipedia:Wolffian_duct +is_a: UBERON:0003914 ! epithelial tube +is_a: UBERON:0004819 ! kidney epithelium +is_a: UBERON:0006553 ! renal duct +is_a: UBERON:0006555 ! excretory tube + +[Term] +id: UBERON:0009202 +name: vasa recta descending limb +xref: KUPO:0001002 +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0004726 ! part of vasa recta + +[Term] +id: UBERON:0009569 +name: subdivision of trunk +subset: non_informative +synonym: "region of trunk" EXACT [FMA:25054] +synonym: "trunk subdivision" EXACT [FMA:25054] +xref: FMA:25054 +xref: SCTID:22943007 +is_a: UBERON:0000475 ! organism subdivision +relationship: BFO:0000050 UBERON:0002100 ! part of trunk + +[Term] +id: UBERON:0009581 +name: midbrain mantle layer +synonym: "mantle layer lateral wall mesencephalon" RELATED [VHOG:0000910] +synonym: "mantle layer lateral wall midbrain" EXACT [VHOG:0000910] +synonym: "midbrain lateral wall mantle layer" EXACT [] +xref: EHDAA2:0001172 +xref: EMAPA:16977 +xref: VHOG:0000910 +is_a: UBERON:0004061 ! neural tube mantle layer +relationship: BFO:0000050 UBERON:0009616 ! part of presumptive midbrain + +[Term] +id: UBERON:0009615 +name: midbrain hindbrain boundary neural plate +synonym: "MHB neural plate" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "midbrain-hindbrain boundary neural plate" EXACT [ZFA:0007044] +xref: TAO:0007044 +xref: ZFA:0007044 +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0003075 ! part of neural plate + +[Term] +id: UBERON:0009616 +name: presumptive midbrain +def: "A presumptive structure that has the potential to develop into a midbrain." [OBOL:automatic] +subset: efo_slim +synonym: "early midbrain" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "future midbrain" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "mesencephalon" RELATED [EHDAA2:0000615] +synonym: "presumptive mesencephalon" EXACT [ZFA:0000148] +xref: BAMS:MES +xref: EFO:0003432 +xref: EHDAA2:0000615 +xref: EMAPA:16140 +xref: TAO:0000148 +xref: Wikipedia:Mesencephalon +xref: ZFA:0000148 +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0006238 ! part of future brain + +[Term] +id: UBERON:0009617 +name: head paraxial mesoderm +def: "Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles." [PMID:21610022] +synonym: "cephalic paraxial mesenchyme" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "cephalic paraxial mesoderm" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "cranial paraxial mesenchyme" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "cranial paraxial mesoderm" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "head paraxial mesenchyme" EXACT [EHDAA2:0000736, https://github.com/obophenotype/uberon/issues/30] +synonym: "somitomere" RELATED [] +synonym: "somitomeric mesoderm" RELATED [] +xref: EHDAA2:0000736 +xref: EHDAA:364 +xref: EMAPA:16171 +is_a: UBERON:0005253 ! head mesenchyme +relationship: BFO:0000050 UBERON:0003077 ! part of paraxial mesoderm +relationship: BFO:0000050 UBERON:0005253 ! part of head mesenchyme + +[Term] +id: UBERON:0009618 +name: trunk paraxial mesoderm +synonym: "trunk and cervical paraxial mesenchyme" EXACT [EHDAA2:0002094] +synonym: "trunk paraxial mesenchyme" RELATED [https://github.com/obophenotype/uberon/issues/30] +xref: EHDAA2:0002094 +is_a: UBERON:0005256 ! trunk mesenchyme +relationship: BFO:0000050 UBERON:0003077 ! part of paraxial mesoderm +relationship: BFO:0000050 UBERON:0005256 ! part of trunk mesenchyme + +[Term] +id: UBERON:0009722 +name: entire pharyngeal arch endoderm +synonym: "pharyngeal arch endoderm" RELATED [EHDAA2:0004621] +xref: EHDAA2:0004621 +xref: EMAPA:32754 +xref: FMA:293087 +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0005911 ! endo-epithelium +is_a: UBERON:0015833 ! foregut epithelium +relationship: BFO:0000050 UBERON:0003929 ! part of digestive tract epithelium +relationship: BFO:0000050 UBERON:0008814 ! part of pharyngeal arch system + +[Term] +id: UBERON:0009744 +name: lymph node medullary sinus +def: "The channels in the lymph node medulla that separate the medullary cords and are crossed by a reticulum of cells and fibers and bounded by littoral cells; lymph flows through the medullary sinus from the cortical sinuses and into the efferent lymphatic vessels." [MP:0011222] +subset: pheno_slim +synonym: "lymph node medullary sinusoid" RELATED [] +synonym: "medullary sinus" BROAD [] +xref: EMAPA:37898 +xref: FMA:312359 +is_a: UBERON:0004111 ! anatomical conduit +relationship: BFO:0000050 UBERON:0002007 ! part of medulla of lymph node + +[Term] +id: UBERON:0009745 +name: lymph node medullary cord +def: "The dense rope-like structures of lymphatic tissue located between the medullary sinuses in the medulla of a lymph node." [MP:0011224] +subset: pheno_slim +synonym: "medullary cord" BROAD [] +xref: EMAPA:37897 +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0002007 ! part of medulla of lymph node + +[Term] +id: UBERON:0009749 +name: limb mesenchyme +def: "The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells." [MP:0011261] +subset: pheno_slim +synonym: "limb mesoderm" RELATED [Geisha:syn, NCBITaxon:8782] +xref: EMAPA:32705 +is_a: UBERON:0003104 ! mesenchyme +relationship: BFO:0000050 UBERON:0002101 ! part of limb + +[Term] +id: UBERON:0009773 +name: renal tubule +def: "A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis." [DOI:10.1371/journal.pone.0099864, GO:0061333, GOC:dph, GOC:mtg_kidney_jan10] +subset: grouping_class +subset: pheno_slim +synonym: "renal tubule (generic)" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "tubule of excretory system" EXACT [https://orcid.org/0000-0002-6601-2165, OBOL:automatic] +is_a: UBERON:0003914 ! epithelial tube +is_a: UBERON:0006555 ! excretory tube + +[Term] +id: UBERON:0009842 +name: glandular acinus +def: "The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form." [Wikipedia:Acinus] +synonym: "acini" RELATED [Wikipedia:Acinus] +synonym: "acinus" BROAD [FMA:55588] +xref: FMA:55588 +xref: Wikipedia:Acinus +is_a: UBERON:0034922 ! cell cluster +relationship: BFO:0000050 UBERON:0002530 ! part of gland + +[Term] +id: UBERON:0009856 +name: sac +synonym: "diverticulum" RELATED [] +synonym: "pouch" EXACT [] +xref: galen:Diverticulum +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0009871 +name: nephrogenic zone +def: "Outer portion of the renal cortex. Site of formation of medullary and cortical elements." [http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "cortical nephrogenic niche" EXACT [PMID:29449449] +synonym: "cortical nephrogenic zone" EXACT [PMID:29449449] +synonym: "nephrogenic tissue" RELATED [] +xref: EMAPA:27721 +xref: http://www.gudmap.org/Images/Organ_Summaries/Metanephros/NZ.png +xref: MA:0002996 +is_a: UBERON:0005423 ! developing anatomical structure +relationship: BFO:0000050 UBERON:0001225 ! part of cortex of kidney + +[Term] +id: UBERON:0009877 +name: metapodium region +def: "Intermediate segment of the autopod, between the mesopodial region and and acropodial region. Examples: metacarpal region, metatarsal region." [https://orcid.org/0000-0002-6601-2165, MA:th] +synonym: "cannon region" NARROW [http://orcid.org/0000-0002-6601-2165, NCBITaxon:9788] +synonym: "equine cannon region" NARROW [http://orcid.org/0000-0002-6601-2165, NCBITaxon:9788] +synonym: "metacarpal or metatarsal part of limb" EXACT [] +synonym: "metacarpus/metatarsus" RELATED [] +synonym: "metacarpus/metatarsus region" EXACT [] +synonym: "metapodial segment" EXACT [] +synonym: "metapodium" RELATED [] +xref: SCTID:370640001 +is_a: UBERON:0002529 ! limb segment +relationship: BFO:0000050 UBERON:0012140 ! part of digitopodium region + +[Term] +id: UBERON:0009878 +name: mesopodial skeleton +def: "The collection of all skeletal elements in a mesopodium. Examples: the tarsal skeleton, the carpal skeleton." [https://orcid.org/0000-0002-6601-2165] +synonym: "basipodium" RELATED [VSAO:0005022, VSAO:NI] +synonym: "basipodium skeleton" EXACT [VSAO:0005022, VSAO:NI] +synonym: "carpal/tarsal skeleton" EXACT [] +synonym: "mesopodial skeleton" EXACT [VSAO:0005022] +synonym: "mesopodium" RELATED [VSAO:0005022, VSAO:NI] +synonym: "mesopodium skeleton" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "skeletal parts of mesopodium" EXACT [https://orcid.org/0000-0002-6601-2165] +xref: VSAO:0005022 +is_a: UBERON:0010712 ! limb skeleton subdivision +relationship: BFO:0000050 UBERON:0006716 ! part of mesopodium region +relationship: BFO:0000050 UBERON:0006717 ! part of autopodial skeleton + +[Term] +id: UBERON:0009881 +name: anterior lateral plate mesoderm +subset: efo_slim +synonym: "ALPM" EXACT [ZFA:0005041] +xref: EFO:0003704 +xref: TAO:0005041 +xref: ZFA:0005041 +is_a: UBERON:0005291 ! embryonic tissue +relationship: BFO:0000050 UBERON:0003081 ! part of lateral plate mesoderm + +[Term] +id: UBERON:0009955 +name: neurogenic placode +def: "Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia." [http://orcid.org/0000-0002-6601-2165, PMID:11523831] +subset: efo_slim +synonym: "neurogenic placodes" EXACT [ZFA:0001309] +synonym: "placodae neurogenicae" RELATED [Wikipedia:Neurogenic_placodes] +xref: EFO:0003460 +xref: TAO:0001309 +xref: Wikipedia:Neurogenic_placodes +xref: XAO:0004620 +xref: ZFA:0001309 +is_a: UBERON:0002546 ! cranial placode + +[Term] +id: UBERON:0010000 +name: multicellular anatomical structure +def: "An anatomical structure that has more than one cell as a part." [CARO:0010000] +subset: upper_level +synonym: "multicellular structure" EXACT [FBbt:00100313] +xref: CARO:0010000 +xref: FBbt:00100313 +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0010001 +name: cell cluster organ +def: "A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function." [CARO:0010001] +subset: upper_level +xref: CARO:0010001 +xref: FBbt:00007229 +is_a: UBERON:0000062 ! organ +is_a: UBERON:0034922 ! cell cluster + +[Term] +id: UBERON:0010083 +name: future dermis +def: "Mesenchyme that has the potential to develop into a dermis." [OBOL:automatic] +xref: EHDAA2:0000598 +is_a: UBERON:0003104 ! mesenchyme +relationship: BFO:0000050 UBERON:0002199 ! part of integument + +[Term] +id: UBERON:0010096 +name: future myelencephalon +def: "A developing anatomical structure that has the potential to develop into a myelencephalon." [OBOL:automatic] +xref: EHDAA2:0000640 +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0002028 ! part of hindbrain + +[Term] +id: UBERON:0010129 +name: femur cartilage element +def: "A femur endochondral element that is composed primarily of cartilage tissue." [OBOL:automatic] +synonym: "femoral cartilage condensation" EXACT [EMAPA:17742] +xref: EMAPA:17742 +is_a: UBERON:0005254 ! upper leg mesenchyme +is_a: UBERON:0005863 ! cartilaginous condensation +is_a: UBERON:0010885 ! hindlimb cartilage element +is_a: UBERON:0015052 ! femur endochondral element +relationship: BFO:0000050 UBERON:0005254 ! part of upper leg mesenchyme + +[Term] +id: UBERON:0010130 +name: embryonic autopod plate +def: "The distal elements of the developing limb of vertebrates that will give rise to the autopod (e.g. manus, pes, paw)." [https://github.com/obophenotype/mammalian-phenotype-ontology/issues/1151, MP:0004576, UBERON:cjm] +synonym: "autopod plate" EXACT [] +synonym: "limb plate" EXACT [] +is_a: UBERON:0006598 ! presumptive structure + +[Term] +id: UBERON:0010188 +name: protuberance +def: "A roughly circular bulge in a surface." [EHDAA2:0003250] +xref: AEO:0000205 +xref: EHDAA2:0003250 +xref: FMA:82506 +is_a: UBERON:0034944 ! zone of organ + +[Term] +id: UBERON:0010199 +name: bona-fide anatomical boundary +def: "An anatomical boundary that corresponds to some physical discontinuity." [CARO:0001004] +subset: upper_level +xref: CARO:0001004 +is_a: UBERON:0000466 ! immaterial anatomical entity + +[Term] +id: UBERON:0010285 +name: midbrain basal plate +def: "Portion of tissue that is dorsolateral to the floor plate and part of the midbrain." [ZFA:0000761] +subset: efo_slim +synonym: "basal plate midbrain" EXACT [TAO:0000761] +synonym: "basal plate midbrain region" EXACT [ZFA:0000761] +xref: DHBA:12322 +xref: EFO:0003567 +xref: EHDAA2:0004375 +xref: TAO:0000761 +xref: ZFA:0000761 +is_a: UBERON:0002020 ! gray matter +relationship: BFO:0000050 UBERON:0009581 ! part of midbrain mantle layer +relationship: BFO:0000050 UBERON:0010286 ! part of midbrain neural tube + +[Term] +id: UBERON:0010286 +name: midbrain neural tube +def: "Portion of neural tube that gives rise to the midbrain." [ZFA:0007039] +xref: TAO:0007039 +xref: ZFA:0007039 +is_a: UBERON:0005291 ! embryonic tissue +relationship: BFO:0000050 UBERON:0003080 ! part of anterior neural tube + +[Term] +id: UBERON:0010313 +name: neural crest-derived structure +def: "An anatomical structure that develops from the neural crest." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest + +[Term] +id: UBERON:0010314 +name: structure with developmental contribution from neural crest +def: "An anatomical structure that has some part that develops from the neural crest." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0010316 +name: germ layer / neural crest +is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0005291 ! embryonic tissue + +[Term] +id: UBERON:0010323 +name: cranial skeletal system +def: "Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000049] +synonym: "cranial skeleton" NARROW [] +synonym: "cranium" RELATED INCONSISTENT [ZFA:0000737] +synonym: "osteocranium" NARROW [] +xref: AAO:0000109 +xref: AAO:0000971 +xref: AAO:0010185 +xref: TAO:0000737 +xref: VSAO:0000049 +xref: XAO:0003075 +xref: ZFA:0000737 +is_a: UBERON:0000075 ! subdivision of skeletal system +relationship: BFO:0000050 UBERON:0011137 ! part of axial skeletal system + +[Term] +id: UBERON:0010328 +name: limb bud mesenchyme +def: "Mesenchyme that is part of a limb bud." [OBOL:automatic] +is_a: UBERON:0010329 ! paired limb/fin bud mesenchyme +relationship: BFO:0000050 UBERON:0004347 ! part of limb bud + +[Term] +id: UBERON:0010329 +name: paired limb/fin bud mesenchyme +def: "Mesenchyme that is part of a limb/fin bud." [OBOL:automatic] +is_a: UBERON:0010377 ! mesenchyme from somatopleure +relationship: BFO:0000050 UBERON:0004357 ! part of paired limb/fin bud + +[Term] +id: UBERON:0010363 +name: endochondral element +def: "A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000139] +synonym: "endochondral replacement element" EXACT [VSAO:0000139] +xref: VSAO:0000139 +xref: XAO:0004017 +xref: ZFA:0005620 +is_a: UBERON:0004765 ! skeletal element + +[Term] +id: UBERON:0010364 +name: dermal skeleton +def: "Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000035] +synonym: "dermal skeletal system" RELATED [VSAO:curator] +synonym: "dermoskeleton" RELATED [VSAO:curator] +synonym: "desmoskeleton" RELATED [VSAO:curator] +synonym: "exoskeleton" BROAD INCONSISTENT [VSAO:curator] +xref: VSAO:0000035 +xref: XAO:0004025 +is_a: UBERON:0010912 ! subdivision of skeleton + +[Term] +id: UBERON:0010371 +name: ecto-epithelium +def: "Epithelium composed of cells that develops from the ectoderm[FMA,modified]." [FMA:69064] +synonym: "ectoderm-derived epithelium" EXACT [] +xref: FMA:69064 +is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0004121 ! ectoderm-derived structure + +[Term] +id: UBERON:0010377 +name: mesenchyme from somatopleure +def: "Mesenchyme that develops_from a somatopleure." [OBOL:automatic] +xref: EHDAA2:0001120 +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007524 ! dense mesenchyme tissue +relationship: BFO:0000050 UBERON:0009142 ! part of entire embryonic mesenchyme + +[Term] +id: UBERON:0010523 +name: microcirculatory vessel +def: "A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses." [http://orcid.org/0000-0002-6601-2165, MESH:A07.231.432, ZFA:0005251] +synonym: "microcirculatory vessels" RELATED [TAO:0005251] +xref: MESH:A07.231.432 +xref: TAO:0005251 +xref: ZFA:0005251 +is_a: UBERON:0000055 ! vessel +relationship: BFO:0000050 UBERON:0002049 ! part of vasculature + +[Term] +id: UBERON:0010527 +name: cavity of bone organ +def: "An organ cavity that surrounded_by a bone." [OBOL:automatic] +synonym: "bone organ cavity" EXACT [FMA:24021] +xref: FMA:24021 +is_a: UBERON:0002558 ! organ cavity +relationship: BFO:0000050 UBERON:0001474 ! part of bone element + +[Term] +id: UBERON:0010528 +name: pneumatic cavity of bone +synonym: "air space of bone" EXACT [FMA:24028] +xref: FMA:24028 +is_a: UBERON:0010527 ! cavity of bone organ +relationship: BFO:0000050 UBERON:0008193 ! part of pneumatized bone + +[Term] +id: UBERON:0010531 +name: metanephros induced blastemal cells +def: "." [http://www.embryology.ch/anglais/turinary/urinhaute03.html] +synonym: "cap mesenchyme of metanephros of urinary system" RELATED [EMAPA:17645] +synonym: "induced blastemal cells" EXACT [VHOG:0001241] +synonym: "nephrogenic interstitium" RELATED [] +synonym: "nephrogenic interstitium of nephrogenic zone" EXACT [EMAPA:17953] +synonym: "peripheral blastema" RELATED [EMAPA:17953] +xref: EHDAA2:0001143 +xref: EHDAA:7007 +xref: EHDAA:8105 +xref: EMAPA:17953 +xref: EMAPA:27621 +xref: MA:0002998 +xref: VHOG:0001241 +is_a: UBERON:0005423 ! developing anatomical structure +relationship: BFO:0000050 UBERON:0009871 ! part of nephrogenic zone + +[Term] +id: UBERON:0010532 +name: primitive nephron +def: "An epithelial tube that is fated to become a nephron." [http://orcid.org/0000-0002-6601-2165] +synonym: "developing nephron" BROAD [] +synonym: "future nephron" EXACT [] +synonym: "presumptive nephron" EXACT [] +synonym: "primitive nephron" BROAD [] +is_a: UBERON:0003914 ! epithelial tube +is_a: UBERON:0004819 ! kidney epithelium +is_a: UBERON:0006555 ! excretory tube + +[Term] +id: UBERON:0010535 +name: primitive metanephric nephron +def: "A primitive nephron that is part of a metanephros." [OBOL:automatic] +synonym: "developing metanephric nephron" EXACT [] +synonym: "primitive metanephric nephron" EXACT [] +synonym: "primitive nephron" BROAD [EHDAA2:0001516] +xref: EHDAA2:0001516 +is_a: UBERON:0005106 ! metanephric tubule +is_a: UBERON:0010532 ! primitive nephron +relationship: BFO:0000050 UBERON:0005113 ! part of metanephric cortex mesenchyme + +[Term] +id: UBERON:0010536 +name: nephron progenitor +is_a: UBERON:0000479 ! tissue +relationship: BFO:0000050 UBERON:0003918 ! part of kidney mesenchyme + +[Term] +id: UBERON:0010538 +name: paired limb/fin segment +def: "An appendage segment that is part of a limb/fin." [OBOL:automatic] +subset: homology_grouping +synonym: "limb/fin segment" EXACT [] +is_a: UBERON:0010758 ! subdivision of organism along appendicular axis +relationship: BFO:0000050 UBERON:0004708 ! part of paired limb/fin + +[Term] +id: UBERON:0010543 +name: acropodial skeleton +def: "The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the autopodium - i.e. the bones of the digits or their cartilaginous precursors[VSAO,modified]." [https://orcid.org/0000-0002-6601-2165, VSAO:0005028, VSAO:NI] +synonym: "acropodial skeleton" EXACT [] +synonym: "acropodium" RELATED [VSAO:0005028, VSAO:NI] +synonym: "acropodium skeleton" EXACT [] +synonym: "digital skeleton" RELATED [] +synonym: "digits skeleton" RELATED [] +synonym: "phalangeal skeleton" RELATED [] +synonym: "set of phalanges" EXACT [FMA:231315] +synonym: "skeletal parts of acropodial region" EXACT [] +synonym: "skeletal parts of acropodium" RELATED [] +synonym: "skeleton of digits" RELATED [] +xref: FMA:231315 +xref: VSAO:0005028 +is_a: UBERON:0010712 ! limb skeleton subdivision +relationship: BFO:0000050 UBERON:0012150 ! part of skeleton of digitopodium +relationship: BFO:0000050 UBERON:0012354 ! part of acropodium region + +[Term] +id: UBERON:0010546 +name: metapodial skeleton +def: "Subdivision of skeleton that corresponds to metapodium region, between acropodial skeleton and mesopdoial skeleton." [https://orcid.org/0000-0002-6601-2165] +synonym: "metacarpal/metatarsal skeleton" EXACT [] +synonym: "metapodial skeleton" EXACT [VSAO:0005025] +synonym: "metapodium" RELATED [VSAO:0005025, VSAO:NI] +synonym: "metapodium skeleton" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "skeletal parts of metapodium" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "skeleton of metapodium" EXACT [] +xref: VSAO:0005025 +is_a: UBERON:0010712 ! limb skeleton subdivision +relationship: BFO:0000050 UBERON:0009877 ! part of metapodium region +relationship: BFO:0000050 UBERON:0012150 ! part of skeleton of digitopodium + +[Term] +id: UBERON:0010703 +name: forelimb zeugopod skeleton +def: "The collection of all skeletal elements in an forelimb zeugopod region." [https://orcid.org/0000-0002-6601-2165] +synonym: "antebrachial skeleton" EXACT [] +synonym: "antebrachium skeleton" EXACT [PHENOSCAPE:ni] +synonym: "anterior zeugopodium" RELATED [VSAO:0005011, VSAO:NI] +synonym: "anterior zeugopodium skeleton" EXACT [VSAO:0005011, VSAO:NI] +synonym: "fore epipodium" RELATED [AAO:0000200] +synonym: "fore epipodium skeleton" EXACT [] +synonym: "forearm skeleton" EXACT [FMA:71199] +synonym: "forelimb epipodium" RELATED [VSAO:0005011, VSAO:NI] +synonym: "forelimb epipodium skeleton" RELATED [] +synonym: "mesomere 2 of pectoral appendage" RELATED HOMOLOGY [ISBN:0226313409] +synonym: "radius and ulna" RELATED [] +synonym: "skeleton of forearm" EXACT HUMAN_PREFERRED [FMA:71199] +synonym: "wing zeugopod skeleton" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +xref: AAO:0000200 +xref: FMA:71199 +xref: VSAO:0005011 +is_a: UBERON:0011584 ! zeugopodial skeleton +relationship: BFO:0000050 UBERON:0001440 ! part of forelimb skeleton +relationship: BFO:0000050 UBERON:0002386 ! part of forelimb zeugopod + +[Term] +id: UBERON:0010707 +name: appendage girdle complex +def: "An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc)." [https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton, https://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "appendage complex" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "appendage-girdle complex" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "appendage/girdle complex" EXACT [VSAO:0000214] +synonym: "girdle plus limb or fin" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "limb" RELATED INCONSISTENT [FMA:7182] +xref: EMAPA:37858 +xref: FMA:7182 +xref: VSAO:0000214 +is_a: UBERON:0000475 ! organism subdivision +is_a: UBERON:0015212 ! lateral structure + +[Term] +id: UBERON:0010708 +name: pectoral complex +def: "Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle." [VSAO:0000213] +subset: pheno_slim +synonym: "pectoral appendage/girdle complex" EXACT [VSAO:0000213] +synonym: "pectoral girdle plus anterior limb or fin" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "pectoral girdle plus pectoral limb or fin" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "upper limb" RELATED INCONSISTENT [FMA:7183] +synonym: "upper limb and pectoral girdle" RELATED HUMAN_PREFERRED [https://orcid.org/0000-0002-6601-2165] +synonym: "upper limb and shoulder" RELATED [https://orcid.org/0000-0002-6601-2165] +xref: EMAPA:37860 +xref: FMA:7183 +xref: SCTID:110716002 +xref: VSAO:0000213 +is_a: UBERON:0010707 ! appendage girdle complex + +[Term] +id: UBERON:0010709 +name: pelvic complex +def: "Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle." [VSAO:0000215] +subset: pheno_slim +synonym: "lower limb" RELATED INCONSISTENT [FMA:7184] +synonym: "lower limb and pelvic girdle" RELATED HUMAN_PREFERRED [https://orcid.org/0000-0002-6601-2165] +synonym: "lower limb and pelvis" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "pelvic appendage/girdle complex" EXACT [VSAO:0000215] +synonym: "pelvic girdle plus pelvic limb or fin" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "pelvic girdle plus posterior limb or fin" EXACT [https://orcid.org/0000-0002-6601-2165] +xref: EMAPA:37863 +xref: FMA:7184 +xref: SCTID:416631005 +xref: VSAO:0000215 +is_a: UBERON:0010707 ! appendage girdle complex + +[Term] +id: UBERON:0010712 +name: limb skeleton subdivision +def: "Skeletal subdivision that is a segment of the limb skeleton." [VSAO:0005018, VSAO:NI] +xref: VSAO:0005018 +is_a: UBERON:0010912 ! subdivision of skeleton +relationship: BFO:0000050 UBERON:0002091 ! part of appendicular skeleton +relationship: BFO:0000050 UBERON:0002101 ! part of limb + +[Term] +id: UBERON:0010719 +name: girdle skeleton +def: "The subdivision of the skeleton of either the pectoral or pelvic girdle." [https://orcid.org/0000-0002-6601-2165] +synonym: "skeleton of girdle" EXACT [] +xref: AAO:0010686 +xref: VSAO:0000302 +is_a: UBERON:0010912 ! subdivision of skeleton +relationship: BFO:0000050 UBERON:0002091 ! part of appendicular skeleton +relationship: BFO:0000050 UBERON:0007823 ! part of appendage girdle region + +[Term] +id: UBERON:0010720 +name: hindlimb zeugopod skeleton +def: "Subdivision of skeleton consisting of all skeletal elements in an hindlimb zeugopod region. Typically consists of the tibia and the fibula." [https://orcid.org/0000-0002-6601-2165] +synonym: "crural skeleton" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "crus skeleton" EXACT [PHENOSCAPE:ni] +synonym: "hind epipodium" RELATED [AAO:0000216] +synonym: "hindlimb epipodium" RELATED [VSAO:0005014, VSAO:NI] +synonym: "hindlimb zygopod skeleton" EXACT [] +synonym: "mesomere 2 of pelvic appendage" RELATED HOMOLOGY [ISBN:0226313409] +synonym: "posterior zeugopodium" RELATED INCONSISTENT [VSAO:0005014] +synonym: "posterior zeugopodium skeleton" EXACT [] +synonym: "skeleton cruris" EXACT [NominaAnatomicaVeterinaria:2005] +xref: AAO:0000216 +xref: VSAO:0005014 +is_a: UBERON:0011584 ! zeugopodial skeleton +relationship: BFO:0000050 UBERON:0003823 ! part of hindlimb zeugopod + +[Term] +id: UBERON:0010740 +name: bone of appendage girdle complex +def: "A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle)." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] +subset: pheno_slim +synonym: "bone of extended limb/fin region" RELATED [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] +synonym: "limb bone" RELATED [MA:0000688, UBERONREF:0000003] +xref: EMAPA:35494 +xref: MA:0000688 +is_a: UBERON:0001474 ! bone element +relationship: BFO:0000050 UBERON:0002091 ! part of appendicular skeleton +relationship: BFO:0000050 UBERON:0010707 ! part of appendage girdle complex + +[Term] +id: UBERON:0010741 +name: bone of pectoral complex +def: "A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] +subset: pheno_slim +synonym: "bone of forelimb or pectoral fin or pectoral girdle" RELATED [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] +synonym: "forelimb bone" RELATED [MA:0000612, UBERONREF:0000003] +synonym: "wing bone" NARROW SENSU [UBERONREF:0000003] +xref: EMAPA:32623 +xref: EMAPA:35933 +xref: MA:0000612 +is_a: UBERON:0010740 ! bone of appendage girdle complex +relationship: BFO:0000050 UBERON:0010708 ! part of pectoral complex + +[Term] +id: UBERON:0010742 +name: bone of pelvic complex +def: "A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] +subset: pheno_slim +synonym: "hindlimb bone" RELATED [MA:0000660, UBERONREF:0000003] +xref: EMAPA:32633 +xref: EMAPA:35934 +xref: MA:0000660 +is_a: UBERON:0010740 ! bone of appendage girdle complex +relationship: BFO:0000050 UBERON:0010709 ! part of pelvic complex + +[Term] +id: UBERON:0010758 +name: subdivision of organism along appendicular axis +def: "A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg." [https://orcid.org/0000-0002-6601-2165] +subset: upper_level +synonym: "appendage segment" EXACT [FBbt:00007018] +synonym: "appendicular segment" EXACT [] +xref: FBbt:00007018 +is_a: UBERON:0000475 ! organism subdivision +relationship: BFO:0000050 UBERON:0000026 ! part of appendage + +[Term] +id: UBERON:0010881 +name: limb cartilage element +def: "A skeletal element that is part of a limb and composed of cartilage tissue." [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0007844 ! cartilage element +is_a: UBERON:0015061 ! limb endochondral element + +[Term] +id: UBERON:0010882 +name: limb bone pre-cartilage condensation +def: "A skeletal element that is part of a limb and composed of pre-cartilage tissue." [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0015061 ! limb endochondral element + +[Term] +id: UBERON:0010883 +name: forelimb cartilage element +def: "A cartilaginous condensation that has the potential to develop into a forelimb bone." [OBOL:automatic] +subset: grouping_class +synonym: "forelimb wing cartilaginous condensation" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +synonym: "wing cartilaginous condensation" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +xref: EMAPA:32626 +is_a: UBERON:0010881 ! limb cartilage element +is_a: UBERON:0015021 ! forelimb endochondral element + +[Term] +id: UBERON:0010884 +name: forelimb bone pre-cartilage condensation +def: "A pre-cartilage condensation that has the potential to develop into a forelimb bone." [OBOL:automatic] +subset: grouping_class +synonym: "wing bone pre-cartilage condensation" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] +xref: EMAPA:32625 +is_a: UBERON:0010882 ! limb bone pre-cartilage condensation +is_a: UBERON:0015021 ! forelimb endochondral element + +[Term] +id: UBERON:0010885 +name: hindlimb cartilage element +def: "A cartilaginous condensation that has the potential to develop into a hindlimb bone." [OBOL:automatic] +synonym: "hindlimb cartilage condensation" EXACT [EMAPA:32632] +xref: EMAPA:32632 +is_a: UBERON:0010881 ! limb cartilage element +is_a: UBERON:0015022 ! hindlimb endochondral element + +[Term] +id: UBERON:0010886 +name: hindlimb pre-cartilage condensation +def: "A pre-cartilage condensation that has the potential to develop into a hindlimb bone." [OBOL:automatic] +synonym: "hindlimb pre-cartilage condensation" EXACT [EMAPA:32638] +xref: EMAPA:32638 +is_a: UBERON:0010882 ! limb bone pre-cartilage condensation +is_a: UBERON:0015022 ! hindlimb endochondral element + +[Term] +id: UBERON:0010890 +name: pelvic complex muscle +def: "Muscles of the pelvic girdle, hindlimb or pelvic fin." [https://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "lower limb muscle" RELATED INCONSISTENT [FMA:9622] +synonym: "muscle of lower limb" RELATED INCONSISTENT [FMA:9622] +synonym: "muscle of pelvic girdle and leg" RELATED [] +synonym: "pelvic girdle and hind limb muscles" EXACT [AAO:0000218] +synonym: "pelvic girdle or hind limb muscle" NARROW [https://orcid.org/0000-0002-6601-2165] +synonym: "pelvic girdle or posterior limb muscle" NARROW [https://orcid.org/0000-0002-6601-2165] +xref: AAO:0000218 +xref: EMAPA:32634 +xref: FMA:9622 +xref: MA:0000663 +is_a: UBERON:0014892 ! skeletal muscle organ +relationship: BFO:0000050 UBERON:0014792 ! part of musculature of pelvic complex + +[Term] +id: UBERON:0010891 +name: pectoral complex muscle +def: "A muscle of a pectoral girdle, pectoral fin or anterior limb." [https://orcid.org/0000-0002-6601-2165] +synonym: "muscle of pectoral girdle and limb" RELATED [] +synonym: "muscle of pectoral girdle and wing" NARROW SENSU [NCBITaxon:8782] +synonym: "muscle of upper limb" NARROW INCONSISTENT [FMA:9621] +synonym: "pectoral girdle and fore limb muscles" EXACT [AAO:0010687] +synonym: "upper limb muscle" NARROW INCONSISTENT [FMA:9621] +xref: AAO:0010687 +xref: EMAPA:32624 +xref: FMA:9621 +xref: MA:0000615 +is_a: UBERON:0014892 ! skeletal muscle organ +relationship: BFO:0000050 UBERON:0014793 ! part of musculature of pectoral complex + +[Term] +id: UBERON:0010912 +name: subdivision of skeleton +def: "Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] +subset: non_informative +synonym: "skeletal subdivision" EXACT [VSAO:0000042] +synonym: "subdivision of skeleton (in vivo)" RELATED [FMA:23879] +xref: FMA:23879 +xref: SCTID:129140006 +xref: VSAO:0000042 +is_a: UBERON:0011216 ! organ system subdivision +relationship: BFO:0000050 UBERON:0000075 ! part of subdivision of skeletal system +relationship: BFO:0000050 UBERON:0004288 ! part of skeleton + +[Term] +id: UBERON:0011108 +name: synovial joint of pectoral girdle +def: "A synovial joint that is part of a pectoral girdle region." [OBOL:automatic] +synonym: "joint of shoulder girdle" EXACT [] +synonym: "pectoral girdle joint" EXACT [FMA:35243] +xref: FMA:35243 +xref: SCTID:303080001 +is_a: UBERON:0002217 ! synovial joint +is_a: UBERON:0008114 ! joint of girdle +relationship: BFO:0000050 UBERON:0001421 ! part of pectoral girdle region + +[Term] +id: UBERON:0011137 +name: axial skeletal system +def: "Subdivision of the skeletal system which consists of the axial skeleton plus associated joints." [https://orcid.org/0000-0002-6601-2165] +xref: FMA:7483 +is_a: UBERON:0000075 ! subdivision of skeletal system + +[Term] +id: UBERON:0011138 +name: postcranial axial skeletal system +def: "Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints." [https://github.com/obophenotype/uberon/issues/44, https://orcid.org/0000-0002-6601-2165] +synonym: "axial skeletal system" BROAD [https://github.com/obophenotype/uberon/wiki/The-axial-skeleton] +synonym: "post-cranial axial skeletal system" EXACT [] +xref: FMA:302077 +is_a: UBERON:0000075 ! subdivision of skeletal system + +[Term] +id: UBERON:0011139 +name: synovial limb joint +def: "Any synovial joint that is part of a (free) limb." [https://orcid.org/0000-0002-6601-2165] +synonym: "synovial joint of free limb segment" EXACT [FMA:258776] +xref: FMA:258776 +is_a: UBERON:0002217 ! synovial joint +is_a: UBERON:0003657 ! limb joint + +[Term] +id: UBERON:0011143 +name: upper urinary tract +def: "Subdivision of urinary system which consists of the kidney and the ureters." [FMA:45658] +subset: pheno_slim +xref: FMA:45658 +xref: galen:UpperUrinaryTract +xref: NCIT:C61107 +xref: SCTID:181413006 +is_a: UBERON:0000477 ! anatomical cluster +relationship: BFO:0000050 UBERON:0001008 ! part of renal system + +[Term] +id: UBERON:0011156 +name: facial skeleton +def: "Subdivision of skull that consists of the facial bones." [http://www.bartleby.com/107/37.html, https://orcid.org/0000-0002-6601-2165, MP:0005274, Wikipedia:Facial_skeleton] +subset: pheno_slim +synonym: "facial bone" RELATED [MA:0000318] +synonym: "facial skeleton" EXACT [FMA:53673] +synonym: "ossa facialia" RELATED [Wikipedia:Facial_skeleton] +synonym: "ossa faciei" RELATED [Wikipedia:Facial_skeleton] +synonym: "viscerocranium" RELATED INCONSISTENT [MA:0000318] +xref: EHDAA2:0002206 +xref: EHDAA:8361 +xref: EMAPA:18022 +xref: FMA:53673 +xref: MA:0000318 +xref: Wikipedia:Facial_skeleton +is_a: UBERON:0010313 ! neural crest-derived structure +is_a: UBERON:0011158 ! primary subdivision of skull +relationship: BFO:0000050 UBERON:0001456 ! part of face + +[Term] +id: UBERON:0011158 +name: primary subdivision of skull +def: "The skull can be divided into two: the neurocranium and the facial skeleton." [http://orcid.org/0000-0002-6601-2165] +subset: non_informative +synonym: "skull subdivision" EXACT [FMA:54964] +synonym: "subdivision of skull" EXACT [FMA:54964] +xref: FMA:54964 +is_a: UBERON:0000075 ! subdivision of skeletal system +relationship: BFO:0000050 UBERON:0003129 ! part of skull + +[Term] +id: UBERON:0011159 +name: primary subdivision of cranial skeletal system +subset: non_informative +is_a: UBERON:0000075 ! subdivision of skeletal system +relationship: BFO:0000050 UBERON:0010323 ! part of cranial skeletal system + +[Term] +id: UBERON:0011215 +name: central nervous system cell part cluster +def: "A multi cell part structure that is part of a central nervous system." [OBOL:automatic] +subset: upper_level +synonym: "cell part cluster of neuraxis" EXACT [FMA:83143] +synonym: "neuraxis layer" EXACT [FMA:83143] +xref: FMA:83143 +is_a: UBERON:0005162 ! multi cell part structure +relationship: BFO:0000050 UBERON:0001017 ! part of central nervous system + +[Term] +id: UBERON:0011216 +name: organ system subdivision +def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2165] +subset: upper_level +xref: FBbt:00007330 +xref: FMA:67509 +xref: SCTID:91690000 +is_a: UBERON:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 UBERON:0000467 ! part of anatomical system + +[Term] +id: UBERON:0011249 +name: appendicular skeletal system +def: "Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints." [https://orcid.org/0000-0002-6601-2165] +xref: FMA:7484 +xref: VHOG:0001666 +xref: VSAO:0000306 +is_a: UBERON:0000075 ! subdivision of skeletal system + +[Term] +id: UBERON:0011272 +name: embryonic skin basal layer +synonym: "basal cell layer of skin" RELATED [] +synonym: "outer epithelium of body" RELATED [Wikipathways:WP2062] +xref: EHDAA2:0001845 +is_a: UBERON:0000490 ! unilaminar epithelium +relationship: BFO:0000050 UBERON:0002199 ! part of integument + +[Term] +id: UBERON:0011299 +name: white matter of telencephalon +def: "A partion of white matter that is part of a telencephalon. This can be further subdivided in some species, for example, into hemisphere white matter and the corpus callosum." [https://orcid.org/0000-0002-6601-2165] +synonym: "predominantly white regional part of telencephalon" EXACT [BIRNLEX:1075] +synonym: "telencephalic tract/commissure" EXACT [ZFA:0000597] +synonym: "telencephalic tracts" NARROW [TAO:0000597] +synonym: "telencephalic white matter" EXACT [HBA:TELWM] +xref: BIRNLEX:1075 +xref: FMA:83930 +xref: HBA:9219 +xref: HBA:9230 +xref: TAO:0000597 +xref: ZFA:0000597 +is_a: UBERON:0019261 ! white matter of forebrain +relationship: BFO:0000050 UBERON:0001893 ! part of telencephalon + +[Term] +id: UBERON:0011300 +name: gray matter of telencephalon +def: "A portion of gray matter that is part of a telencephalon." [OBOL:automatic] +synonym: "predominantly gray regional part of telencephalon" EXACT [BIRNLEX:1067] +xref: BIRNLEX:1067 +xref: FMA:83911 +is_a: UBERON:0019264 ! gray matter of forebrain +relationship: BFO:0000050 UBERON:0001893 ! part of telencephalon + +[Term] +id: UBERON:0011582 +name: paired limb/fin skeleton +def: "The collection of all skeletal elements in an individual limb or fin." [https://orcid.org/0000-0002-6601-2165] +subset: homology_grouping +synonym: "limb/fin skeleton" EXACT [VSAO:0000301] +synonym: "skeletal parts of limb/fin" EXACT [] +synonym: "skeleton of limb/fin" EXACT [] +xref: VSAO:0000301 +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0010912 ! subdivision of skeleton +relationship: BFO:0000050 UBERON:0002091 ! part of appendicular skeleton +relationship: BFO:0000050 UBERON:0004708 ! part of paired limb/fin + +[Term] +id: UBERON:0011583 +name: stylopodial skeleton +def: "Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified]." [VSAO:0005007] +synonym: "mesomere 1" RELATED HOMOLOGY [ISBN:0226313409] +synonym: "propodial skeleton" RELATED [] +synonym: "propodium" RELATED [VSAO:0005007] +synonym: "proximal metapterygial mesomere" RELATED HOMOLOGY [ISBN:0226313409] +synonym: "stylopod" RELATED [VSAO:0005007] +synonym: "stylopodium" RELATED [] +synonym: "stylopodium skeleton" EXACT [] +xref: VSAO:0005007 +is_a: UBERON:0010712 ! limb skeleton subdivision +relationship: BFO:0000050 UBERON:0002472 ! part of stylopod +relationship: BFO:0000050 UBERON:0004381 ! part of skeleton of limb + +[Term] +id: UBERON:0011584 +name: zeugopodial skeleton +def: "Section of the forelimb skeleton located between the stylopodium and the autopodium." [VSAO:0005010] +synonym: "epipodial skeleton" EXACT [] +synonym: "epipodium" RELATED [VSAO:0005010] +synonym: "mesomere 2" RELATED HOMOLOGY [ISBN:0226313409] +synonym: "mesomere 2 skeleton" RELATED HOMOLOGY [ISBN:0226313409] +synonym: "skeleton of zeugopod" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "zeugopod skeleton" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "zygopodium" RELATED [VSAO:0005010] +xref: VSAO:0005010 +is_a: UBERON:0010712 ! limb skeleton subdivision +relationship: BFO:0000050 UBERON:0002471 ! part of zeugopod +relationship: BFO:0000050 UBERON:0004381 ! part of skeleton of limb + +[Term] +id: UBERON:0011585 +name: cell condensation +def: "Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995)." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000006] +xref: VSAO:0000006 +xref: XAO:0004021 +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0011595 +name: jaw region +def: "A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions." [http://orcid.org/0000-0002-6601-2165] +xref: EMAPA:32905 +xref: NCIT:C114916 +is_a: UBERON:0000475 ! organism subdivision +relationship: BFO:0000050 UBERON:0000165 ! part of mouth + +[Term] +id: UBERON:0011676 +name: subdivision of organism along main body axis +def: "A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column." [https://orcid.org/0000-0002-6601-2165] +subset: upper_level +synonym: "axial subdivision of organism" EXACT [] +synonym: "body segment" RELATED [] +synonym: "main body segment" RELATED [] +is_a: UBERON:0000475 ! organism subdivision +relationship: BFO:0000050 UBERON:0013701 ! part of main body axis + +[Term] +id: UBERON:0011695 +name: embryonic cardiovascular system +def: "A cardiovascular system that is part of a conceptus." [OBOL:automatic] +synonym: "conceptus cardiovascular system" EXACT [] +synonym: "embryonic circulatory system" RELATED [] +synonym: "fetal circulatory system" RELATED [] +xref: EHDAA2:0000216 +xref: FMA:305965 +xref: NCIT:C34148 +is_a: UBERON:0004535 ! cardiovascular system +relationship: BFO:0000050 UBERON:0004716 ! part of conceptus + +[Term] +id: UBERON:0011779 +name: nerve of head region +def: "A nerve that is part of a head." [OBOL:automatic] +subset: grouping_class +synonym: "cephalic nerve" RELATED [] +synonym: "head nerve" RELATED [] +is_a: UBERON:0001021 ! nerve +relationship: BFO:0000050 UBERON:0000033 ! part of head + +[Term] +id: UBERON:0011814 +name: non-neurogenic ectodermal placode +def: "Ectodermal placode that does not develop into a component of the nervous system." [http://orcid.org/0000-0002-6601-2165, PMID:11523831] +is_a: UBERON:0005085 ! ectodermal placode + +[Term] +id: UBERON:0011817 +name: skin appendage placode +def: "An ectodermal placode that gives rise to any of the cutaneous appendages that protrude from the skin epidermis (heair, feathers, epidermal scales)." [https://github.com/obophenotype/uberon/issues/1266] +synonym: "cutaneous appendage follicle placode" EXACT [] +synonym: "skin follicle placode" EXACT [] +is_a: UBERON:0006598 ! presumptive structure +is_a: UBERON:0011814 ! non-neurogenic ectodermal placode + +[Term] +id: UBERON:0011821 +name: irregular connective tissue +def: "Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium." [FMA:20107] +xref: FMA:20107 +is_a: UBERON:0002384 ! connective tissue + +[Term] +id: UBERON:0011822 +name: dense irregular connective tissue +def: "Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium." [FMA:20109, Wikipedia:Dense_irregular_connective_tissue] +synonym: "irregular dense connective tissue" EXACT [] +synonym: "typus irregularis (textus connectivus collagenosus compactus)" EXACT [FMA:20109] +xref: FMA:20109 +xref: NCIT:C32882 +xref: UMLS:C0738366 +xref: Wikipedia:Dense_irregular_connective_tissue +is_a: UBERON:0011821 ! irregular connective tissue +is_a: UBERON:0011823 ! dense connective tissue + +[Term] +id: UBERON:0011823 +name: dense connective tissue +def: "Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets." [Wikipedia:Dense_connective_tissue] +xref: AAO:0000121 +xref: NCIT:C32450 +xref: UMLS:C1511770 +xref: Wikipedia:Dense_connective_tissue +is_a: UBERON:0002384 ! connective tissue + +[Term] +id: UBERON:0011825 +name: loose connective tissue +def: "Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue." [FMA:19783] +synonym: "textus connectivus collagenosus laxus" EXACT [FMA:19783, FMA:TA] +synonym: "textus connectivus laxus" EXACT [FMA:19783, FMA:TA] +xref: FMA:19783 +xref: NCIT:C33007 +xref: UMLS:C1253917 +xref: Wikipedia:Loose_connective_tissue +is_a: UBERON:0011821 ! irregular connective tissue + +[Term] +id: UBERON:0011858 +name: acinus of exocrine gland +def: "An acinus that is part of a exocrine gland." [OBOL:automatic] +synonym: "exocrine gland acinus" EXACT [] +is_a: UBERON:0009842 ! glandular acinus +relationship: BFO:0000050 UBERON:0002365 ! part of exocrine gland + +[Term] +id: UBERON:0011860 +name: collection of collagen fibrils +xref: FMA:63212 +xref: MESH:D024022 +xref: NCIT:C32339 +xref: NIF_Subcellular:sao7547390221 +is_a: UBERON:0000476 ! acellular anatomical structure + +[Term] +id: UBERON:0011899 +name: epimysium +def: "Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous." [Wikipedia:Epimysium] +synonym: "epimysia" RELATED [Wikipedia:Epimysium] +synonym: "fascia of muscle organ" EXACT [FMA:9726] +xref: FMA:9726 +xref: NCIT:C32527 +xref: UMLS:C0504096 +xref: Wikipedia:Epimysium +is_a: UBERON:0011822 ! dense irregular connective tissue +relationship: BFO:0000050 UBERON:0001134 ! part of skeletal muscle tissue + +[Term] +id: UBERON:0011932 +name: pilosebaceous unit +def: "An epidermal invagination that has as parts a hair follicle, a sebaceous gland, and arrector pili muscle." [ISBN:0123813611, PMCID:PMC3130146, Wikipedia:Pilosebaceous_unit] +subset: pheno_slim +synonym: "fabrica pilosebacea" EXACT [Wikipedia:Pilosebaceous_unit] +synonym: "pilo-sebaceous apparatus" EXACT [FMA:70661] +synonym: "pilo-sebaceous unit" EXACT [] +synonym: "pilosebaceous apparatus" EXACT [] +synonym: "pilosebaceous gland" RELATED [FMA:70661] +xref: EMAPA:36582 +xref: FMA:70661 +xref: Wikipedia:Pilosebaceous_unit +is_a: UBERON:0000063 ! organ subunit +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: BFO:0000050 UBERON:0006003 ! part of integumentary adnexa + +[Term] +id: UBERON:0011997 +name: coelom +def: "The aggregate of the coelemic cavity lumen plus the membranes that line the lumen." [UBERON:cjm, Wikipedia:Body_cavity, Wikipedia:Coelom] +synonym: "coelem" RELATED [] +synonym: "coelomic cavity" RELATED [EHDAA2:0004731] +synonym: "enterocoelom" NARROW [NCBITaxon:33511] +synonym: "haemocoelom" NARROW [] +synonym: "schizocoelom" NARROW [] +xref: EHDAA2:0004731 +xref: Wikipedia:Coelom +is_a: UBERON:0000481 ! multi-tissue structure + +[Term] +id: UBERON:0012139 +name: segment of autopod +is_a: UBERON:0002529 ! limb segment +relationship: BFO:0000050 UBERON:0002470 ! part of autopod region + +[Term] +id: UBERON:0012140 +name: digitopodium region +def: "A segment of the autopod consisting of both acropodial region and metapodial region, but excluding the mesopodial/basopodial region." [https://github.com/obophenotype/uberon/issues/131, PHENOSCAPE:ni] +synonym: "acropodium (Wagner)" RELATED [] +is_a: UBERON:0012139 ! segment of autopod + +[Term] +id: UBERON:0012141 +name: manual digitopodium region +def: "A digitopodium region that is part of a manus[Obol]. This includes the fingers and metacarpal region, but excludes the carpal region." [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0005451 ! segment of manus +is_a: UBERON:0012140 ! digitopodium region + +[Term] +id: UBERON:0012150 +name: skeleton of digitopodium +def: "A subdivision of the autopod skeleton consisting of both acropodial skeleon and metapodial skeleton, but excluding the mesopodial/basopodial skeleton." [PHENOSCAPE:ni] +synonym: "digitopodium" RELATED [PHENOSCAPE:ni] +synonym: "skeleton of digits" RELATED COMPARATIVE_PREFERRED [] +is_a: UBERON:0010712 ! limb skeleton subdivision +relationship: BFO:0000050 UBERON:0006717 ! part of autopodial skeleton +relationship: BFO:0000050 UBERON:0012140 ! part of digitopodium region + +[Term] +id: UBERON:0012151 +name: skeleton of manual digitopodium +def: "A subdivision of the manus skeleton consisting of both manual acropodial skeleton and metacarpal skeleton, but excluding the carpal skeleton." [https://orcid.org/0000-0002-6601-2165, PHENOSCAPE:ni] +synonym: "manual digitopodium" RELATED [] +is_a: UBERON:0012150 ! skeleton of digitopodium +relationship: BFO:0000050 UBERON:0001442 ! part of skeleton of manus +relationship: BFO:0000050 UBERON:0012141 ! part of manual digitopodium region + +[Term] +id: UBERON:0012274 +name: columnar epithelium +def: "An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified]." [Wikipedia:Columnar_epithelium] +xref: Wikipedia:Columnar_epithelium +is_a: UBERON:0000483 ! epithelium + +[Term] +id: UBERON:0012275 +name: meso-epithelium +def: "Epithelium that derives from the mesoderm. [Automatically generated definition]." [OBOL:automatic] +synonym: "mesoderm-derived epithelium" EXACT [] +synonym: "mesoepithelium" EXACT [] +xref: FMA:86452 +is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0004120 ! mesoderm-derived structure + +[Term] +id: UBERON:0012292 +name: embryonic cloacal fold +def: "One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly." [MP:0011836, MP:anna] +synonym: "cloacal fold" BROAD [EHDAA2:0004009] +xref: EHDAA2:0004009 +is_a: UBERON:0000481 ! multi-tissue structure +relationship: BFO:0000050 UBERON:0000922 ! part of embryo +relationship: BFO:0000050 UBERON:0012469 ! part of external anal region + +[Term] +id: UBERON:0012314 +name: embryonic facial prominence +def: "One of five swellings formed during the development of the face." [http://www.indiana.edu/~anat550/hnanim/face/face.html] +synonym: "embryonic facial process" RELATED [] +synonym: "facial primordium" RELATED [] +synonym: "primordium of face" RELATED [] +xref: FMA:293103 +xref: SCTID:89066004 +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0000033 ! part of head + +[Term] +id: UBERON:0012344 +name: holocrine gland +def: "Any exocrine gland whose secretion consists of its own disintegrated secretory cells along with its secretory product; holocrine secretions are produced in the cytoplasm of the cell and released by the rupture of the plasma membrane, which destroys the cell and results in the secretion of the product into the lumen." [MP:0013543] +subset: pheno_slim +xref: BTO:0002325 +xref: MA:0003042 +xref: Wikipedia:Holocrine +is_a: UBERON:0002365 ! exocrine gland + +[Term] +id: UBERON:0012354 +name: acropodium region +def: "The segment of the autopod that is distal to the metapodial region and consists of the digits." [https://orcid.org/0000-0002-6601-2165] +synonym: "acropodial limb segment" EXACT [] +synonym: "acropodial region" EXACT [] +synonym: "acropodial segment of autopod" EXACT [] +synonym: "set of digits" EXACT [] +is_a: UBERON:0012139 ! segment of autopod +relationship: BFO:0000050 UBERON:0012140 ! part of digitopodium region + +[Term] +id: UBERON:0012361 +name: internal anal region +xref: EHDAA2:0004588 +is_a: UBERON:0000481 ! multi-tissue structure +relationship: BFO:0000050 UBERON:0001353 ! part of anal region + +[Term] +id: UBERON:0012429 +name: hematopoietic tissue +def: "Blood-forming tissue, consisting of reticular fibers and cells." [http://encyclopedia2.thefreedictionary.com/hematopoietic+tissue] +synonym: "bone marrow tissue" NARROW [NCBITaxon:9606] +synonym: "haemopoietic tissue" EXACT [FMA:14073] +synonym: "hematopoietic tissue" EXACT [FMA:14073] +synonym: "hemopoietic tissue" EXACT [FMA:14073] +synonym: "textus haemopoieticus" EXACT [FMA:14073] +xref: CALOHA:TS-2142 +xref: FMA:14073 +xref: NCIT:C13051 +xref: UMLS:C0229619 +is_a: UBERON:0034769 ! lymphomyeloid tissue +relationship: BFO:0000050 UBERON:0002390 ! part of hematopoietic system + +[Term] +id: UBERON:0012469 +name: external anal region +xref: EHDAA2:0004589 +is_a: UBERON:0000481 ! multi-tissue structure +relationship: BFO:0000050 UBERON:0001353 ! part of anal region + +[Term] +id: UBERON:0012475 +name: skeleton of pectoral complex +def: "The collection of all skeletal elements in a pectoral complex - i.e. the combination of free limb or fin plus pectoral girdle." [https://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "bones of upper limb" RELATED [FMA:24139] +synonym: "ossa membri superioris" RELATED [FMA:TA] +synonym: "pectoral complex skeleton" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "set of bones of upper limb" RELATED [FMA:24139] +synonym: "skeleton of anterior limb/fin and girdle" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "upper limb skeleton" RELATED [FMA:24139] +xref: FMA:24139 +is_a: UBERON:0010912 ! subdivision of skeleton +relationship: BFO:0000050 UBERON:0002091 ! part of appendicular skeleton +relationship: BFO:0000050 UBERON:0010708 ! part of pectoral complex + +[Term] +id: UBERON:0012476 +name: skeleton of pelvic complex +def: "The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle." [https://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "bones of lower limb" RELATED [FMA:24140] +synonym: "lower limb skeleton" RELATED [FMA:24140] +synonym: "ossa membri inferioris" RELATED [FMA:TA] +synonym: "pelvic complex skeleton" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "set of bones of lower limb" RELATED [FMA:24140] +synonym: "skeleton of posterior limb/fin and girdle" RELATED [https://orcid.org/0000-0002-6601-2165] +xref: FMA:24140 +is_a: UBERON:0010912 ! subdivision of skeleton +relationship: BFO:0000050 UBERON:0002091 ! part of appendicular skeleton +relationship: BFO:0000050 UBERON:0010709 ! part of pelvic complex + +[Term] +id: UBERON:0013126 +name: vein of abdomen +def: "A vein that is part of a abdomen." [OBOL:automatic] +subset: grouping_class +synonym: "abdominal vein" EXACT [] +xref: SCTID:281473003 +is_a: UBERON:0001638 ! vein +is_a: UBERON:0003497 ! abdomen blood vessel + +[Term] +id: UBERON:0013232 +name: serous acinus +def: "The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells." [http://orcid.org/0000-0002-6601-2165, http://www.siumed.edu/~dking2/intro/glands.htm] +synonym: "acinus of serous gland" EXACT [] +xref: FMA:86279 +is_a: UBERON:0011858 ! acinus of exocrine gland +relationship: BFO:0000050 UBERON:0000409 ! part of serous gland + +[Term] +id: UBERON:0013241 +name: embryonic urethral groove +def: "The precursor of the urethra." [http://orcid.org/0000-0002-6601-2165] +synonym: "sulcus urethralis primarius" EXACT [Wikipedia:Urethral_groove] +synonym: "urethral groove" EXACT [] +synonym: "urethral sulcus" EXACT [] +xref: SCTID:361531004 +xref: Wikipedia:Urethral_groove +is_a: UBERON:0002050 ! embryonic structure + +[Term] +id: UBERON:0013514 +name: space surrounding organism +def: "The space that surrounds an organism." [https://orcid.org/0000-0002-6601-2165] +synonym: "external to organism" EXACT [] +synonym: "outside of body" EXACT [] +is_a: UBERON:0000464 ! anatomical space + +[Term] +id: UBERON:0013522 +name: subdivision of tube +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0000025 ! part of tube + +[Term] +id: UBERON:0013686 +name: anatomical conduit space +def: "An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]." [FMA:9338, http://orcid.org/0000-0002-6601-2165] +synonym: "foramen space" NARROW [] +xref: FMA:9338 +is_a: UBERON:0000464 ! anatomical space + +[Term] +id: UBERON:0013701 +name: main body axis +def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] +subset: non_informative +is_a: UBERON:0000475 ! organism subdivision + +[Term] +id: UBERON:0013702 +name: body proper +def: "The region of the organism associated with the visceral organs." [AEO:0000103] +subset: non_informative +synonym: "body" RELATED [AEO:0000103] +synonym: "whole body" RELATED [BTO:0001489] +xref: AEO:0000103 +xref: BTO:0001489 +xref: EMAPA:36031 +xref: FMA:231424 +is_a: UBERON:0000475 ! organism subdivision +relationship: BFO:0000050 UBERON:0013701 ! part of main body axis + +[Term] +id: UBERON:0013703 +name: integumentary projection +def: "Anatomical projection that is part of the integumentl system." [http://orcid.org/0000-0002-6601-2165] +synonym: "skin projection" NARROW [] +is_a: UBERON:0004529 ! anatomical projection +is_a: UBERON:0006003 ! integumentary adnexa + +[Term] +id: UBERON:0013754 +name: integumentary system layer +def: "An organ component layer that is part of a integumental system." [OBOL:automatic] +subset: non_informative +synonym: "layer of skin" NARROW [] +synonym: "skin layer" NARROW [] +xref: SCTID:314820002 +is_a: UBERON:0004923 ! organ component layer +relationship: BFO:0000050 UBERON:0002416 ! part of integumental system + +[Term] +id: UBERON:0013756 +name: venous blood +def: "A blood that is part of a vein." [OBOL:automatic] +synonym: "blood in vein" EXACT [FMA:83067] +synonym: "portion of venous blood" EXACT [FMA:83067] +synonym: "venous blood" EXACT [FMA:83067] +xref: FMA:83067 +is_a: UBERON:0000178 ! blood +relationship: BFO:0000050 UBERON:0001638 ! part of vein + +[Term] +id: UBERON:0013768 +name: great vessel of heart +def: "Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart." [Wikipedia:Great_vessels] +subset: grouping_class +synonym: "great vessel" BROAD [] +synonym: "great vessel of thorax" EXACT [] +xref: EMAPA:36460 +xref: SCTID:304066000 +xref: Wikipedia:Great_vessels +is_a: UBERON:0001981 ! blood vessel + +[Term] +id: UBERON:0014371 +name: future telencephalon +def: "Embryonic structure that gives rise to the telencephalon." [ZFA:0000571, ZFA:curator] +synonym: "presumptive telencephalon" EXACT [ZFA:0000571] +xref: EHDAA2:0004424 +xref: EMAPA:36024 +xref: TAO:0000571 +xref: ZFA:0000571 +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0006240 ! part of future forebrain + +[Term] +id: UBERON:0014401 +name: renal venous blood vessel +def: "Any member of the network of tubes that return blood from the renal tissues to the systemic circulation." [MGI:csmith] +subset: pheno_slim +synonym: "kidney venous blood vessel" EXACT [MA:0002591] +synonym: "kidney venous system" RELATED [EMAPA:31450] +synonym: "venous blood vessel of kidney" EXACT [] +xref: EMAPA:31450 +xref: MA:0002591 +is_a: UBERON:0003517 ! kidney blood vessel +is_a: UBERON:0003920 ! venous blood vessel + +[Term] +id: UBERON:0014477 +name: thoracic skeleton +def: "Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum." [https://orcid.org/0000-0002-6601-2165, Wikipedia:Rib_cage] +subset: pheno_slim +synonym: "skeleton of thorax" EXACT [] +synonym: "thoracic part of axial skeleton" EXACT [] +synonym: "thoracic skeleton" EXACT [EHDAA2:0002013] +xref: EHDAA2:0002013 +xref: FMA:77169 +xref: Wikipedia:Thoracic_skeleton +is_a: UBERON:0010912 ! subdivision of skeleton +relationship: BFO:0000050 UBERON:0000915 ! part of thoracic segment of trunk +relationship: BFO:0000050 UBERON:0002090 ! part of postcranial axial skeleton + +[Term] +id: UBERON:0014791 +name: musculature of forelimb stylopod +def: "Any collection of muscles that is part of the forelimb stylopod region [Automatically generated definition]." [OBOL:automatic] +synonym: "arm musculature" RELATED INCONSISTENT [FMA:50202] +synonym: "muscle group of arm" RELATED INCONSISTENT [FMA:50202] +synonym: "musculature of arm" RELATED INCONSISTENT [FMA:50202] +synonym: "set of muscles of arm" RELATED INCONSISTENT [FMA:50202] +xref: FMA:50202 +is_a: UBERON:0004474 ! musculature of arm +relationship: BFO:0000050 UBERON:0003822 ! part of forelimb stylopod + +[Term] +id: UBERON:0014792 +name: musculature of pelvic complex +def: "Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin." [OBOL:automatic] +synonym: "muscles of lower limb" NARROW [FMA:71297] +synonym: "musculature of lower limb" NARROW [FMA:71297] +synonym: "musculi membri inferioris" NARROW [FMA:TA] +xref: EMAPA:37864 +xref: FMA:71297 +is_a: UBERON:0001015 ! musculature +relationship: BFO:0000050 UBERON:0010709 ! part of pelvic complex + +[Term] +id: UBERON:0014793 +name: musculature of pectoral complex +def: "Any collection of muscles that is part of a pectoral complex. The pectoral complex comprises the pectoral girdle and the associated limb or fin." [OBOL:automatic] +synonym: "muscles of upper limb" NARROW [FMA:71296] +synonym: "musculature of upper limb" NARROW [FMA:71296] +synonym: "musculi membri superioris" NARROW [FMA:TA] +synonym: "set of muscles of upper limb" NARROW [FMA:71296] +synonym: "upper limb musculature" NARROW [FMA:71296] +xref: EMAPA:37861 +xref: FMA:71296 +is_a: UBERON:0001015 ! musculature +relationship: BFO:0000050 UBERON:0010708 ! part of pectoral complex + +[Term] +id: UBERON:0014794 +name: pectoral appendage muscle +def: "Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin)." [OBOL:automatic] +is_a: UBERON:0010891 ! pectoral complex muscle +relationship: BFO:0000050 UBERON:0007269 ! part of pectoral appendage musculature + +[Term] +id: UBERON:0014795 +name: pelvic appendage muscle +def: "Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin)." [OBOL:automatic] +is_a: UBERON:0010890 ! pelvic complex muscle +relationship: BFO:0000050 UBERON:0007270 ! part of pelvic appendage musculature + +[Term] +id: UBERON:0014892 +name: skeletal muscle organ +def: "A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles)." [GOC:dos] +synonym: "skeletal muscle" BROAD [] +xref: AAO:0011099 +xref: BTO:0001103 +xref: CALOHA:TS-0933 +xref: EFO:0000888 +xref: EHDAA:5035 +xref: EHDAA:5043 +xref: EHDAA:5978 +xref: EHDAA:5984 +xref: EMAPA:35988 +xref: EV:0100377 +xref: GAID:141 +xref: MA:0003148 +xref: MAT:0000302 +xref: MESH:D018482 +xref: MIAA:0000302 +xref: OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA +xref: TAO:0005277 +xref: VHOG:0000319 +xref: XAO:0000174 +xref: ZFA:0005277 +is_a: UBERON:0001630 ! muscle organ +relationship: BFO:0000050 UBERON:0018254 ! part of skeletal musculature + +[Term] +id: UBERON:0014903 +name: primordial vasculature +def: "A portion of tissue that will develop into vasculature." [ZFA:0005076, ZFA:curator] +xref: EFO:0003708 +xref: TAO:0005076 +xref: ZFA:0005076 +is_a: UBERON:0001048 ! primordium +relationship: BFO:0000050 UBERON:0011695 ! part of embryonic cardiovascular system + +[Term] +id: UBERON:0014950 +name: layer of developing cerebral cortex +is_a: UBERON:0005423 ! developing anatomical structure +relationship: BFO:0000050 UBERON:0000956 ! part of cerebral cortex + +[Term] +id: UBERON:0015021 +name: forelimb endochondral element +def: "A forelimb bone or its cartilage or pre-cartilage precursor." [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +synonym: "forelimb skeletal element" BROAD [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +is_a: UBERON:0015061 ! limb endochondral element +relationship: BFO:0000050 UBERON:0001440 ! part of forelimb skeleton + +[Term] +id: UBERON:0015022 +name: hindlimb endochondral element +def: "A hindlimb bone or its cartilage or pre-cartilage precursor." [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +synonym: "hindlimb bone skeletal element" BROAD [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +is_a: UBERON:0015061 ! limb endochondral element +relationship: BFO:0000050 UBERON:0001441 ! part of hindlimb skeleton + +[Term] +id: UBERON:0015023 +name: phalanx endochondral element +def: "A phalanx bone or its cartilage or pre-cartilage precursor." [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +synonym: "phalanx element" EXACT [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +synonym: "phalanx skeletal element" BROAD [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +is_a: UBERON:0015063 ! autopod endochondral element +relationship: BFO:0000050 UBERON:0002544 ! part of digit +relationship: BFO:0000050 UBERON:0012150 ! part of skeleton of digitopodium + +[Term] +id: UBERON:0015052 +name: femur endochondral element +def: "A femur bone or its cartilage or pre-cartilage precursor." [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +synonym: "femur element" EXACT [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +synonym: "femur skeletal element" BROAD [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +is_a: UBERON:0015022 ! hindlimb endochondral element +relationship: BFO:0000050 UBERON:0000376 ! part of hindlimb stylopod + +[Term] +id: UBERON:0015053 +name: humerus endochondral element +def: "A humerus bone or its cartilage or pre-cartilage precursor." [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +synonym: "humerus element" EXACT [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +synonym: "humerus skeletal element" BROAD [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +is_a: UBERON:0015021 ! forelimb endochondral element +relationship: BFO:0000050 UBERON:0003822 ! part of forelimb stylopod + +[Term] +id: UBERON:0015057 +name: scapula endochondral element +def: "A scapula bone or its cartilage or pre-cartilage precursor." [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +synonym: "scapula element" EXACT [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +synonym: "scapula skeletal element" BROAD [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +is_a: UBERON:0010363 ! endochondral element +relationship: BFO:0000050 UBERON:0007831 ! part of pectoral girdle skeleton + +[Term] +id: UBERON:0015061 +name: limb endochondral element +def: "A limb bone or its cartilage or pre-cartilage precursor." [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +synonym: "limb bone endochondral element" EXACT [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +synonym: "limb bone skeletal element" BROAD [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +is_a: UBERON:0010363 ! endochondral element +relationship: BFO:0000050 UBERON:0004381 ! part of skeleton of limb + +[Term] +id: UBERON:0015063 +name: autopod endochondral element +def: "An endochondral element that is part of a autopod region." [OBOL:automatic] +is_a: UBERON:0015061 ! limb endochondral element +relationship: BFO:0000050 UBERON:0006717 ! part of autopodial skeleton + +[Term] +id: UBERON:0015212 +name: lateral structure +def: "Any structure that is placed on one side of the left-right axis of a bilaterian." [http://orcid.org/0000-0002-6601-2165] +subset: grouping_class +subset: non_informative +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0015228 +name: circulatory organ +def: "A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile." [http://orcid.org/0000-0002-6601-2165] +subset: grouping_class +synonym: "cardiac pump" EXACT [] +synonym: "cardiac structure" RELATED [] +synonym: "circulatory vessel" NARROW [] +synonym: "heart" BROAD [] +synonym: "heart or heart like organ" EXACT [] +xref: SPD:0000130 +is_a: UBERON:0003103 ! compound organ +relationship: BFO:0000050 UBERON:0001009 ! part of circulatory system + +[Term] +id: UBERON:0015410 +name: heart plus pericardium +synonym: "heart/pericardium" EXACT [MA:0002449] +xref: EMAPA:37597 +xref: MA:0002449 +is_a: UBERON:0005178 ! thoracic cavity element +relationship: BFO:0000050 UBERON:0004535 ! part of cardiovascular system + +[Term] +id: UBERON:0015757 +name: heterogeneous tissue +synonym: "portion of heterogeneous tissue" EXACT [FMA:62798] +xref: FMA:62798 +is_a: UBERON:0000479 ! tissue + +[Term] +id: UBERON:0015833 +name: foregut epithelium +def: "An epithelium that is part of a foregut." [OBOL:automatic] +xref: EMAPA:32922 +xref: MA:0003204 +is_a: UBERON:0003929 ! digestive tract epithelium +relationship: BFO:0000050 UBERON:0001041 ! part of foregut + +[Term] +id: UBERON:0016398 +name: lymph node of lower limb +def: "A lymph node that is part of a hindlimb." [OBOL:automatic] +xref: FMA:44310 +xref: SCTID:361109000 +is_a: UBERON:0000029 ! lymph node +relationship: BFO:0000050 UBERON:0002103 ! part of hindlimb + +[Term] +id: UBERON:0016399 +name: lymph node of upper limb +def: "A lymph node that is part of a forelimb." [OBOL:automatic] +xref: FMA:44311 +xref: SCTID:276155004 +is_a: UBERON:0000029 ! lymph node +relationship: BFO:0000050 UBERON:0002102 ! part of forelimb + +[Term] +id: UBERON:0016526 +name: lobe of cerebral hemisphere +def: "Subdivision of telencephalon which is one of a number of subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries[FMA,modified]." [FMA:61823] +synonym: "cerebral cortical segment" RELATED [FMA:68603] +synonym: "cerebral hemisphere lobe" EXACT [FMA:61823] +synonym: "cerebral lobe" EXACT [BTO:0000445] +synonym: "lobe of cerebral cortex" EXACT [BIRNLEX:922] +synonym: "lobe parts of cerebral cortex" EXACT [BIRNLEX:922] +synonym: "lobes of the brain" RELATED [BIRNLEX:922] +synonym: "lobi cerebri" EXACT [FMA:77800, FMA:TA] +synonym: "regional organ part of cerebral cortex" RELATED [FMA:68603] +synonym: "segment of cerebral cortex" RELATED [BIRNLEX:922] +xref: BIRNLEX:922 +xref: BTO:0000445 +xref: FMA:61823 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1210 +xref: SCTID:272632001 +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0001869 ! part of cerebral hemisphere + +[Term] +id: UBERON:0016527 +name: white matter of cerebral lobe +xref: FMA:256176 +is_a: UBERON:0002437 ! cerebral hemisphere white matter +relationship: BFO:0000050 UBERON:0016526 ! part of lobe of cerebral hemisphere + +[Term] +id: UBERON:0016529 +name: cortex of cerebral lobe +def: "Grey matter neocortex region of a lobe of the cerebral hemisphere." [http://orcid.org/0000-0002-6601-2165] +synonym: "cortex of cerebral hemisphere lobe" EXACT [FMA:242197] +synonym: "cortex of lobe of cerebral hemisphere" EXACT [FMA:242197] +synonym: "gray matter of lobe of cerebral hemisphere" RELATED [FMA:242197] +synonym: "neocortical part of cerebral hemisphere" RELATED [] +xref: FMA:242197 +is_a: UBERON:0005401 ! cerebral hemisphere gray matter +relationship: BFO:0000050 UBERON:0001950 ! part of neocortex +relationship: BFO:0000050 UBERON:0016526 ! part of lobe of cerebral hemisphere + +[Term] +id: UBERON:0016536 +name: white matter of limbic lobe +def: "A white matter of cerebral lobe that is part of a limbic lobe." [OBOL:automatic] +xref: FMA:261091 +is_a: UBERON:0016527 ! white matter of cerebral lobe +relationship: BFO:0000050 UBERON:0002600 ! part of limbic lobe + +[Term] +id: UBERON:0016542 +name: limbic cortex +synonym: "cortex of limbic lobe" EXACT [FMA:242234] +synonym: "gray matter of limbic lobe" RELATED [FMA:242234] +synonym: "limbic lobe cortex" EXACT [FMA:242234] +xref: FMA:242234 +is_a: UBERON:0016529 ! cortex of cerebral lobe +relationship: BFO:0000050 UBERON:0002600 ! part of limbic lobe + +[Term] +id: UBERON:0016548 +name: central nervous system gray matter layer +def: "A layer of of the central nervous system that is part of gray matter." [http://orcid.org/0000-0002-6601-2165] +synonym: "CNS gray matter layer" EXACT [] +synonym: "CNS grey matter layer" EXACT [] +synonym: "gray matter layer of neuraxis" EXACT [FMA:83142] +synonym: "grey matter layer" BROAD [] +synonym: "grey matter layer of neuraxis" EXACT [] +xref: FMA:83142 +is_a: UBERON:0022303 ! nervous system cell part layer + +[Term] +id: UBERON:0016566 +name: pit +def: "An roughly circular indentation in a surface." [AEO:0000204, AEO:JB] +subset: upper_level +xref: AEO:0000204 +is_a: UBERON:0036215 ! anatomical surface region + +[Term] +id: UBERON:0016879 +name: future central nervous system +def: "Primordium that develops into the central nervous system." [http://orcid.org/0000-0002-6601-2165] +synonym: "future CNS" EXACT [] +synonym: "presumptive central nervous system" EXACT [] +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0016880 ! part of future nervous system + +[Term] +id: UBERON:0016880 +name: future nervous system +def: "Primordium that develops into the nervous system." [http://orcid.org/0000-0002-6601-2165] +synonym: "presumptive nervous system" EXACT [AAO:0000477] +xref: AAO:0000477 +is_a: UBERON:0006598 ! presumptive structure + +[Term] +id: UBERON:0016884 +name: shoulder joint +def: "The joint that is formed by the union of the humerus, the scapula (or shoulder blade), and the clavicle (or collarbone). Commonly thought of as a single joint, the shoulder is actually made up of two separate joints - the glenohumeral and acromioclavicular joints." [http://www.innerbody.com/image/skel17.html] +synonym: "joint of shoulder region" EXACT [] +xref: SCTID:361835002 +is_a: UBERON:0000982 ! skeletal joint +relationship: BFO:0000050 UBERON:0001467 ! part of shoulder + +[Term] +id: UBERON:0016887 +name: entire extraembryonic component +def: "The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism." [AEO:0000195, AEO:JB] +synonym: "extra-embryonic component" EXACT [] +synonym: "extraembryonic component" EXACT [AEO:0000195] +xref: AEO:0000195 +xref: EHDAA2:0000003 +xref: EMAPA:16042 +is_a: UBERON:0000481 ! multi-tissue structure +relationship: BFO:0000050 UBERON:0004716 ! part of conceptus + +[Term] +id: UBERON:0016888 +name: transitional anatomical structure +def: "An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development." [AEO:0000132, AEO:JB] +xref: AEO:0000132 +is_a: UBERON:0005423 ! developing anatomical structure + +[Term] +id: UBERON:0017650 +name: developing mesenchymal structure +def: "A mesenchyme-derived anatomical entity undergoing a transtion to become another structure." [AEO:0001016, AEO:JB] +xref: AEO:0001016 +is_a: UBERON:0005423 ! developing anatomical structure + +[Term] +id: UBERON:0018254 +name: skeletal musculature +subset: grouping_class +xref: EHDAA2:0001842 +xref: EMAPA:35578 +xref: MA:0000165 +is_a: UBERON:0000061 ! anatomical structure +relationship: BFO:0000050 UBERON:0000383 ! part of musculature of body + +[Term] +id: UBERON:0018707 +name: bladder organ +def: "A membranous sac in animals that serves as the receptacle of a liquid or contains gas." [BTO:0000123] +synonym: "bladder" NARROW [BTO:0000123] +xref: BTO:0000123 +is_a: UBERON:0000489 ! cavitated compound organ +is_a: UBERON:0009856 ! sac + +[Term] +id: UBERON:0019261 +name: white matter of forebrain +def: "A white matter that is part of the forebrain." [OBOL:automatic] +xref: DHBA:10557 +xref: FMA:268634 +is_a: UBERON:0003544 ! brain white matter +relationship: BFO:0000050 UBERON:0001890 ! part of forebrain + +[Term] +id: UBERON:0019264 +name: gray matter of forebrain +xref: DHBA:10157 +xref: FMA:268608 +is_a: UBERON:0003528 ! brain gray matter +relationship: BFO:0000050 UBERON:0001890 ! part of forebrain + +[Term] +id: UBERON:0019319 +name: exocrine gland of integumental system +def: "An exocrine gland that is part of a integumental system." [GOC:dos, http://orcid.org/0000-0002-6601-2165] +synonym: "integumental exocrine gland" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "integumental system exocrine gland" EXACT [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0002365 ! exocrine gland +is_a: UBERON:0003297 ! gland of integumental system + +[Term] +id: UBERON:0022303 +name: nervous system cell part layer +def: "Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO]." [NLX:149357] +subset: cumbo +synonym: "lamina" BROAD [CUMBO:CUMBO] +synonym: "layer" BROAD [CUMBO:CUMBO] +xref: NLX:149357 +is_a: UBERON:0005162 ! multi cell part structure +relationship: BFO:0000050 UBERON:0001016 ! part of nervous system + +[Term] +id: UBERON:0034705 +name: developing neuroepithelium +def: "An embryonic or larval epithelium that is committed to form part of the nervous system." [AEO:0001008, AEO:JB] +synonym: "embryonic neuroepithelium" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "neurepithelium" BROAD [BTO:0000314] +synonym: "neuroepithelium" EXACT [AEO:0001008] +xref: AEO:0001008 +xref: BTO:0000314 +xref: EHDAA2_RETIRED:0004654 +xref: FMA:64807 +is_a: UBERON:0000483 ! epithelium +relationship: BFO:0000050 UBERON:0001016 ! part of nervous system + +[Term] +id: UBERON:0034706 +name: proliferating neuroepithelium +def: "An epithelium that is undergoing proliferation to provide large numbers of neuronal cells." [AEO:0001009] +xref: AEO:0001009 +is_a: UBERON:0034705 ! developing neuroepithelium + +[Term] +id: UBERON:0034707 +name: differentiating neuroepithelium +def: "A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells." [AEO:0001010] +xref: AEO:0001010 +is_a: UBERON:0034705 ! developing neuroepithelium + +[Term] +id: UBERON:0034711 +name: cortical preplate +def: "The layer of the developing cerebral cortex that is formed from the first cohort of neurons to migrate out of the cortical ventricular zone; split by the second wave into marginal zone and subplate." [PMID:12626695] +xref: EMAPA:35261 +is_a: UBERON:0014950 ! layer of developing cerebral cortex + +[Term] +id: UBERON:0034713 +name: cranial neuron projection bundle +def: "Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain." [http://orcid.org/0000-0002-6601-2165, ISBN:0471888893] +synonym: "cranial nerve fiber bundle" RELATED [http://orcid.org/0000-0002-6601-2165] +synonym: "cranial nerve fiber tract" RELATED [http://orcid.org/0000-0002-6601-2165] +synonym: "cranial nerve or tract" RELATED [http://orcid.org/0000-0002-6601-2165] +synonym: "neuron projection bundle from brain" RELATED [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0000122 ! neuron projection bundle + +[Term] +id: UBERON:0034768 +name: morphological feature +def: "A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology." [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0000061 ! anatomical structure +relationship: BFO:0000050 UBERON:0000468 ! part of multicellular organism + +[Term] +id: UBERON:0034769 +name: lymphomyeloid tissue +xref: FMA:79770 +xref: NCIT:C41168 +is_a: UBERON:0015757 ! heterogeneous tissue + +[Term] +id: UBERON:0034921 +name: multi organ part structure +def: "An multicellular anatomical structure that has subparts of multiple organs as a part." [CARO:0020001] +synonym: "anatomical cluster" RELATED [CARO:0020001] +xref: CARO:0020001 +is_a: UBERON:0010000 ! multicellular anatomical structure + +[Term] +id: UBERON:0034922 +name: cell cluster +def: "A cluster of cells, largely surrounded by a morphological boundary." [CARO:0020002] +xref: CARO:0020002 +xref: FMA:62807 +is_a: UBERON:0010000 ! multicellular anatomical structure + +[Term] +id: UBERON:0034925 +name: anatomical collection +def: "A collection of anatomical structures that are alike in terms of their morphology or developmental origin." [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0000465 ! material anatomical entity + +[Term] +id: UBERON:0034944 +name: zone of organ +synonym: "organ region with floating fiat boundary" RELATED [FMA:55268] +synonym: "organ sector" EXACT [FMA:55268] +synonym: "organ zonal region" EXACT [] +synonym: "organ zone" EXACT [FMA:55268] +xref: FMA:55268 +is_a: UBERON:0000064 ! organ part + +[Term] +id: UBERON:0034953 +name: embryonic lymph sac +def: "A population of lymphatic endothelial cell precursors that will form the lymph vessels." [DOI:10.1152/japplphysiol.00201.2013, https://github.com/obophenotype/uberon/issues/1383] +synonym: "primary lymph sac" RELATED [] +xref: NCIT:C34262 +xref: UMLS:C1514424 +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007499 ! epithelial sac +relationship: BFO:0000050 UBERON:0006558 ! part of lymphatic part of lymphoid system + +[Term] +id: UBERON:0034969 +name: epithelial layer of duct +synonym: "duct epithelium" RELATED [] +synonym: "ductal epithelium" RELATED [] +xref: NCIT:C25787 +xref: UMLS:C1512086 +is_a: UBERON:0003914 ! epithelial tube +relationship: BFO:0000050 UBERON:0000058 ! part of duct + +[Term] +id: UBERON:0034996 +name: outer renal medulla loop of Henle +synonym: "loop of Henle, outer medullary portion" EXACT [EMAPA:28322] +xref: EMAPA:28322 +is_a: UBERON:0034997 ! renal medulla loop of Henle +relationship: BFO:0000050 UBERON:0001293 ! part of outer medulla of kidney + +[Term] +id: UBERON:0034997 +name: renal medulla loop of Henle +synonym: "loop of Henle of renal medulla" EXACT [EMAPA:35460] +synonym: "loop of Henle, medullary portion" EXACT [] +xref: EMAPA:35460 +is_a: UBERON:0001288 ! loop of Henle +relationship: BFO:0000050 UBERON:0000362 ! part of renal medulla + +[Term] +id: UBERON:0035804 +name: future mouth +def: "The primordial mouth region of the developing head." [MP:0003119] +synonym: "primitive mouth" EXACT [FMA:293105] +synonym: "primordial mouth" EXACT [] +xref: FMA:293105 +is_a: UBERON:0013522 ! subdivision of tube +relationship: BFO:0000050 UBERON:0007026 ! part of presumptive gut + +[Term] +id: UBERON:0036146 +name: cardiopharyngeal field +def: "An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles." [BGEE:ann, http://www.nature.com/nature/journal/v520/n7548/full/nature14435.html#bx1] +is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007688 ! anlage + +[Term] +id: UBERON:0036150 +name: skin appendage follicle +def: "An organ subunit in the skin that gives rise to cutaneous appendage." [https://github.com/obophenotype/uberon/issues/1266, UBERON:cjm] +synonym: "cutaneous appendage follicle" EXACT [] +synonym: "follicle" BROAD [] +synonym: "skin follicle" EXACT [] +is_a: UBERON:0000063 ! organ subunit +relationship: BFO:0000050 UBERON:0000014 ! part of zone of skin + +[Term] +id: UBERON:0036215 +name: anatomical surface region +def: "Material anatomical entity that forms the outermost boundary of an anatomical structure." [https://github.com/obophenotype/uberon/issues/1324] +xref: AAO:0010270 +xref: AEO:0000154 +xref: ZFA:0005594 +is_a: UBERON:0000465 ! material anatomical entity + +[Term] +id: UBERON:0036295 +name: renal pelvis/ureter +def: "The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra." [NCIT:C54419] +synonym: "renal pelvis and ureter" EXACT [] +synonym: "renal pelvis plus ureter" EXACT [] +xref: NCIT:C54419 +is_a: UBERON:0000477 ! anatomical cluster +relationship: BFO:0000050 UBERON:0011143 ! part of upper urinary tract + +[Term] +id: UBERON:0037459 +name: hair of limb +synonym: "limb hair" EXACT [FMA:54243] +xref: FMA:54243 +is_a: UBERON:0001037 ! strand of hair +relationship: BFO:0000050 UBERON:0002101 ! part of limb + +[Term] +id: UBERON:2001269 +name: regenerating fin/limb +def: "Fin or limb undergoing the process of regeneration." [https://orcid.org/0000-0002-6601-2165] +subset: efo_slim +synonym: "regenerating fins" NARROW [ZFA:0001269] +xref: EFO:0003657 +xref: TAO:0001269 +xref: ZFA:0001269 +is_a: UBERON:0004708 ! paired limb/fin +is_a: UBERON:0007567 ! regenerating anatomical structure + +[Term] +id: UBERON:2001389 +name: regeneration epithelium of fin/limb +def: "An epithelium that is part of a regenerating fin/limb." [OBOL:automatic] +subset: efo_slim +synonym: "epidermal cap" BROAD [ZFA:0001389] +synonym: "epidermal cap of fin" EXACT [] +synonym: "wound epidermis" BROAD [ZFA:0001389] +synonym: "wound epidermis of fin" EXACT [] +synonym: "wound epithelium" BROAD [ZFA:0001389] +synonym: "wound epithelium of fin" EXACT [] +xref: EFO:0003682 +xref: TAO:0001389 +xref: ZFA:0001389 +is_a: UBERON:0000483 ! epithelium +relationship: BFO:0000050 UBERON:2001269 ! part of regenerating fin/limb + +[Term] +id: UBERON:2007013 +name: preplacodal ectoderm +def: "Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes." [ZFIN:curator] +xref: ZFA:0007013 +is_a: UBERON:0005497 ! non-neural ectoderm + +[Term] +id: UBERON:3000961 +name: external integument structure +def: "Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument." [AAO:EJS] +is_a: UBERON:0003102 ! surface structure +relationship: BFO:0000050 UBERON:0002199 ! part of integument + +[Term] +id: UBERON:3000981 +name: limb external integument structure +def: "Dermal, epidermal, glandular and pigment structures of the limb integument." [AAO:EJS] +is_a: UBERON:3000961 ! external integument structure +relationship: BFO:0000050 UBERON:0002101 ! part of limb + +[Term] +id: UBERON:4300226 +name: forelimb bud mesenchyme +def: "Mesenchyme that is part of a forelimb bud." [PHENOSCAPE] +is_a: UBERON:0003413 ! pectoral appendage bud mesenchyme +is_a: UBERON:0010328 ! limb bud mesenchyme +relationship: BFO:0000050 UBERON:0005417 ! part of forelimb bud + +[Term] +id: UBERON:4300227 +name: hindlimb bud mesenchyme +def: "Mesenchyme that is part of a hindlimb bud." [PHENOSCAPE] +is_a: UBERON:0003412 ! pelvic appendage bud mesenchyme +is_a: UBERON:0010328 ! limb bud mesenchyme +relationship: BFO:0000050 UBERON:0005418 ! part of hindlimb bud + +[Term] +id: UBERON:5002389 +name: manual digit plus metapodial segment +def: "A subdivision of the autopod consisting of manual digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis." [http://orcid.org/0000-0002-6601-2165] +synonym: "manual digit" BROAD [http://orcid.org/0000-0002-6601-2165] +synonym: "manual digit ( phalanges plus metapodial) plus soft tissue" BROAD COMPARATIVE_PREFERRED [http://orcid.org/0000-0002-6601-2165] +synonym: "manual digit digitopodial subdivision" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "manual digit ray" EXACT [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:5002544 ! digit plus metapodial segment +relationship: BFO:0000050 UBERON:0002102 ! part of forelimb + +[Term] +id: UBERON:5002544 +name: digit plus metapodial segment +def: "A subdivision of the autopod consisting of digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis." [http://orcid.org/0000-0002-6601-2165] +synonym: "digit" BROAD [http://orcid.org/0000-0002-6601-2165] +synonym: "digit ( phalanges plus metapodial) plus soft tissue" BROAD COMPARATIVE_PREFERRED [http://orcid.org/0000-0002-6601-2165] +synonym: "digit digitopodial subdivision" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "digit ray" EXACT [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0000475 ! organism subdivision +relationship: BFO:0000050 UBERON:0012140 ! part of digitopodium region + +[Term] +id: UBERON:5102389 +name: manual digit digitopodial skeleton +def: "A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit plus the associated metapodial element." [http://orcid.org/0000-0002-6601-2165] +synonym: "manual digit" RELATED COMPARATIVE_PREFERRED [http://orcid.org/0000-0002-6601-2165] +synonym: "manual digit skeleton" RELATED [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:5102544 ! individual digit of digitopodial skeleton +relationship: BFO:0000050 UBERON:5002389 ! part of manual digit plus metapodial segment + +[Term] +id: UBERON:5102544 +name: individual digit of digitopodial skeleton +def: "A subdivision of the skeleton of the autopod consisting of the phalanges of a single digit plus the associated metapodial element." [http://orcid.org/0000-0002-6601-2165] +synonym: "digit" RELATED COMPARATIVE_PREFERRED [http://orcid.org/0000-0002-6601-2165] +synonym: "digit skeleton" RELATED [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0010712 ! limb skeleton subdivision +relationship: BFO:0000050 UBERON:0012150 ! part of skeleton of digitopodium +relationship: BFO:0000050 UBERON:5002544 ! part of digit plus metapodial segment + +[Term] +id: UBERON:8300001 +name: right forelimb +def: "A forelimb that is on the right side of a pectoral complex." [UBERONREF:0000003] +xref: FMA:7185 +is_a: UBERON:0002102 ! forelimb +is_a: UBERON:0015212 ! lateral structure + +[Term] +id: UBERON:8300002 +name: left forelimb +def: "A forelimb that is on the left side of a pectoral complex." [UBERONREF:0000003] +xref: FMA:7186 +is_a: UBERON:0002102 ! forelimb +is_a: UBERON:0015212 ! lateral structure + +[Term] +id: UBERON:8300003 +name: right hindlimb +def: "A hindlimb that is on the right side of a pelvic complex." [UBERONREF:0000003] +xref: FMA:7187 +is_a: UBERON:0002103 ! hindlimb +is_a: UBERON:0015212 ! lateral structure + +[Term] +id: UBERON:8300004 +name: left hindlimb +def: "A hindlimb that is on the left side of a pelvic complex." [UBERONREF:0000003] +xref: FMA:7188 +is_a: UBERON:0002103 ! hindlimb +is_a: UBERON:0015212 ! lateral structure + +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: BFO:0000050 +is_transitive: true diff --git a/tests/test_cli.py b/tests/test_cli.py index 7161b8466..fa3a7ee99 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -12,6 +12,7 @@ TEST_OUT = OUTPUT_DIR / 'go-nucleus.saved.owl' NUCLEUS = 'GO:0005634' ATOM = 'CHEBI:33250' +INTERNEURON = 'CL:0000099' class TestCommandLineInterface(unittest.TestCase): diff --git a/tests/test_implementations/test_aggregator.py b/tests/test_implementations/test_aggregator.py new file mode 100644 index 000000000..9bd3117b0 --- /dev/null +++ b/tests/test_implementations/test_aggregator.py @@ -0,0 +1,91 @@ +import logging +import unittest + +import yaml +from oaklib.implementations.aggregator.aggregator_implementation import AggregatorImplementation +from oaklib.implementations.pronto.pronto_implementation import ProntoImplementation +from oaklib.resource import OntologyResource +from oaklib.utilities.obograph_utils import graph_as_dict +from oaklib.datamodels.vocabulary import IS_A, PART_OF, HAS_PART + +from tests import OUTPUT_DIR, INPUT_DIR, VACUOLE, CYTOPLASM, CELLULAR_COMPONENT +from tests.test_cli import NUCLEUS, INTERNEURON + +TEST_ONT = INPUT_DIR / 'go-nucleus.obo' +TEST_ONT2 = INPUT_DIR / 'interneuron.obo' + + +class TestAggregator(unittest.TestCase): + """ + Tests the ability to wrap multiple implementations as if it were a single source + """ + + def setUp(self) -> None: + resource1 = OntologyResource(slug='go-nucleus.obo', directory=INPUT_DIR, local=True) + resource2 = OntologyResource(slug='interneuron.obo', directory=INPUT_DIR, local=True) + oi1 = ProntoImplementation(resource1) + oi2 = ProntoImplementation(resource2) + self.oi = AggregatorImplementation(implementations=[oi1, oi2]) + + def test_all_terms(self): + curies = list(self.oi.all_entity_curies()) + self.assertIn(NUCLEUS, curies) + self.assertIn(INTERNEURON, curies) + + def test_relations(self): + oi = self.oi + label = oi.get_label_by_curie(PART_OF) + assert label.startswith('part') + t = self.oi.node(PART_OF) + assert t.id == PART_OF + assert t.label.startswith('part') + + @unittest.skip('TODO') + def test_metadata(self): + for curie in self.oi.all_entity_curies(): + m = self.oi.metadata_map_by_curie(curie) + print(f'{curie} {m}') + m = self.oi.metadata_map_by_curie('GO:0005622') + assert 'term_tracker_item' in m.keys() + assert 'https://github.com/geneontology/go-ontology/issues/17776' in m['term_tracker_item'] + + def test_labels(self): + """ + Tests labels can be retrieved, and no label is retrieved when a term does not exist + :return: + """ + oi = self.oi + label = oi.get_label_by_curie(VACUOLE) + self.assertEqual(str, type(label)) + self.assertEqual(label, 'vacuole') + label = oi.get_label_by_curie('FOOBAR:123') + self.assertIsNone(label) + # TODO: test strict mode + label = oi.get_label_by_curie(IS_A) + self.assertIsNotNone(label) + self.assertEqual('interneuron', oi.get_label_by_curie(INTERNEURON)) + + def test_synonyms(self): + syns = self.oi.aliases_by_curie(CELLULAR_COMPONENT) + self.assertCountEqual(syns, ['cellular_component', + 'cellular component', + 'cell or subcellular entity', + 'subcellular entity']) + syns = self.oi.aliases_by_curie('CL:0000100') + self.assertCountEqual(syns, ['motoneuron', 'motor neuron']) + + def test_subsets(self): + oi = self.oi + subsets = list(oi.all_subset_curies()) + self.assertIn('goslim_aspergillus', subsets) + self.assertIn('GO:0003674', oi.curies_by_subset('goslim_generic')) + self.assertNotIn('GO:0003674', oi.curies_by_subset('gocheck_do_not_manually_annotate')) + + + + + + + + + diff --git a/tests/test_selector.py b/tests/test_selector.py new file mode 100644 index 000000000..a6319baac --- /dev/null +++ b/tests/test_selector.py @@ -0,0 +1,37 @@ +import logging +import unittest + +from oaklib.implementations.bioportal.bioportal_implementation import BioportalImplementation +from oaklib.implementations.ols.ols_implementation import OlsImplementation +from oaklib.implementations.ontobee.ontobee_implementation import OntobeeImplementation +from oaklib.implementations.pronto.pronto_implementation import ProntoImplementation +from oaklib.implementations.sqldb.sql_implementation import SqlImplementation +from oaklib.implementations.ubergraph import UbergraphImplementation +from oaklib.selector import get_resource_from_shorthand + + + +class TestResource(unittest.TestCase): + + + def test_from_descriptor(self): + # no scheme + resource = get_resource_from_shorthand('foo.obo') + assert resource.implementation_class == ProntoImplementation + self.assertEqual('foo.obo', resource.slug) + resource = get_resource_from_shorthand('foo.owl') + # this may change: + assert resource.implementation_class == ProntoImplementation + resource = get_resource_from_shorthand('foo.db') + assert resource.implementation_class == SqlImplementation + assert resource.slug.startswith('sqlite') + # with scheme + resource = get_resource_from_shorthand('pronto:foo.obo') + assert resource.implementation_class == ProntoImplementation + self.assertEqual('foo.obo', resource.slug) + resource = get_resource_from_shorthand('ubergraph:') + assert resource.implementation_class == UbergraphImplementation + self.assertIsNone(resource.slug) + resource = get_resource_from_shorthand('ontobee:') + assert resource.implementation_class == OntobeeImplementation + self.assertIsNone(resource.slug) diff --git a/tests/test_utilities/test_roll_up_to_subset.py b/tests/test_utilities/test_roll_up_to_subset.py new file mode 100644 index 000000000..5db5f524b --- /dev/null +++ b/tests/test_utilities/test_roll_up_to_subset.py @@ -0,0 +1,47 @@ +import logging +import unittest + +from oaklib.implementations.pronto.pronto_implementation import ProntoImplementation +from oaklib.implementations.sqldb.sql_implementation import SqlImplementation +from oaklib.resource import OntologyResource +from oaklib.datamodels.vocabulary import IS_A, PART_OF +from oaklib.utilities.subsets.slimmer_utils import roll_up_to_named_subset +from oaklib.utilities.subsets.subset_analysis import all_subsets_overlap, compare_all_subsets, terms_by_subsets + +from tests import OUTPUT_DIR, INPUT_DIR + +DB = INPUT_DIR / 'go-nucleus.db' +TEST_ONT = INPUT_DIR / 'go-nucleus.obo' +TEST_OUT = OUTPUT_DIR / 'go-nucleus.saved.owl' + +BIOLOGICAL_PROCESS = 'GO:0008150' +NEGEG_PHOSPH = 'GO:0042326' +NUCLEUS = 'GO:0005634' +DICTYOSTELIUM = 'NCBITaxon:5782' +NUCLEAR_MEMBRANE = 'GO:0031965' + + +PREDS = [IS_A, PART_OF] + +class TestSubsetUtils(unittest.TestCase): + + def setUp(self) -> None: + oi = SqlImplementation(OntologyResource(slug=f'sqlite:///{str(DB)}')) + self.oi = oi + + def test_roll_up(self): + oi = self.oi + term_curies = [t for t in oi.all_entity_curies() if t.startswith('GO:')] + for subset in oi.all_subset_curies(): + #print(f'SUBSET: {subset}') + m = roll_up_to_named_subset(self.oi, subset, term_curies, predicates=[IS_A, PART_OF]) + n = 0 + for term, mapped_to in m.items(): + #print(f'm[{term}] == {mapped_to}') + n += len(mapped_to) + if subset.startswith('chebi'): + assert n == 0 + if subset == 'goslim_yeast': + self.assertCountEqual(m['GO:0004857'], ['GO:0003674', 'GO:0008150']) + if subset == 'goslim_generic': + self.assertCountEqual(m['GO:0009893'], ['GO:0008150']) diff --git a/tests/test_utilities/test_subset_utils.py b/tests/test_utilities/test_subset_analysis.py similarity index 100% rename from tests/test_utilities/test_subset_utils.py rename to tests/test_utilities/test_subset_analysis.py