From 7a3364795f44adeffa6c9395341b5305b545169e Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Fri, 3 May 2024 11:13:16 -0500 Subject: [PATCH] Release Candidate 2024-05-03 --- obi.owl | 4058 ++++++--------------------------------- views/NIAID-GSC-BRC.owl | 652 +------ views/obi-base.owl | 2747 ++++++++++++++++++++++++-- views/obi.obo | 1084 +---------- views/obi_core.owl | 456 +---- 5 files changed, 3459 insertions(+), 5538 deletions(-) diff --git a/obi.owl b/obi.owl index aceacdcc..af77fdaf 100755 --- a/obi.owl +++ b/obi.owl @@ -13,7 +13,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -80,7 +80,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2024-01-09 + 2024-05-03 @@ -213,7 +213,7 @@ We don't have definitions of 'meaning' or 'expression' Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> @@ -256,12 +256,15 @@ We also have the outstanding issue of how to aim different definitions to differ - alternative term + alternative label - An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. + OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). + alternative label alternative term @@ -411,6 +414,7 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property + @@ -549,18 +553,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - retired from use as of - relates a class of CRID to the date after which further instances should not be made, according to the central authority - In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp - Alan Ruttenberg - retired from use as of - - - - @@ -687,10 +679,229 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. + OBO Operations call + + logical characteristic of object property + + + + + + + + 'part disjoint with' 'defined by construct' """ + PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX : <http://example.org/ + CONSTRUCT { + [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?a ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?b + ] + ] + } + WHERE { + ?a :part_disjoint_with ?b . + } + Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + + + + defined by construct + + + + + + + + CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) + A synonym type for describing abbreviations or initalisms + + + 2023-03-03 + abbreviation + + + + + + + + + A synonym type for describing ambiguous synonyms + + + 2023-03-03 + ambiguous synonym + + + + + + + + + A synonym type for describing dubious synonyms + + + 2023-03-03 + dubious synonym + + + + + + + + + EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) + A synonym type for describing layperson or colloquial synonyms + + + 2023-03-03 + layperson synonym + + + + + + + + + CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) + A synonym type for describing pluralization synonyms + + + 2023-03-03 + plural form + + + + + + + + + CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) + A synonym type for describing UK spelling variants + + + 2023-03-03 + UK spelling synonym + + + + + + + + + A synonym type for common misspellings + + + 2023-03-03 + misspelling + + + + + + + + + A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway + + + 2023-03-03 + misnomer + + + + + + + + + MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. + A synonym type for names that have been used as primary labels in the past. + + + 2023-07-25 + previous name + + + + + + + + + The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College + A synonym type for the legal entity name + + + 2023-07-27 + legal name + + + + + + + + + CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label + The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese. + + + 2023-09-30 + INN + International Nonproprietary Name + + + + + + + + + nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis + A synonym type for describing Latin term synonyms. + + + 2023-10-12 + latin term + + + + + + + + + NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced. + A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. + + + 2023-11-01 + acronym + + + + + - An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation https://oborel.github.io/obo-relations/temporal-semantics/ @@ -952,6 +1163,18 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + + + + + + + + + @@ -967,6 +1190,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + + + @@ -979,6 +1208,58 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + An alternative label for a class or property which has a more general meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + has broad synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + + + + + + + + + An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + has exact synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + + + + + + + + + An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + has narrow synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + + + + + + + + + An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + has related synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + + + + + @@ -1020,12 +1301,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1134,6 +1409,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part + has part @@ -1250,199 +1526,54 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + has measurement unit label + has measurement unit label - - - - - The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. - -Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. - -c = pattern in the ink -b = paper + ink -r = friend - - c specifically denotes r =def -r is a portion of reality -& c is a particular quality -& c depends specifically on some independent continuant b -& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. - -Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. - -Case 1 -Memory trace as mark created when reading some description of some friend. The trace can denote. - -Case 2 -Pattern of ink arrayed on paper as mark when writing down a friend's name - -Case 3 -Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file. - 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense - see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote - Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - - obsolete_specifically denotes - true - - - - - - This document is about information artifacts and their representations - + is about A (currently) primitive relation that relates an information artifact to an entity. - 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. - -We will try to build it back up by elaborating the various subproperties that are more precisely defined. - -Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. - person:Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy + is about - - - - - - An information artifact IA mentions an entity E exactly when it has a component/part that denotes E - 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity) - 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition - PERSON: Jonathan Rees - Person: Alan Ruttenberg - mentions - - - - - - - - A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. + denotes A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically - 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. -g denotes r =def -r is a portion of reality -there is some c that is a concretization of g -every c that is a concretization of g specifically denotes r - person:Alan Ruttenberg - Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan - + denotes - - - - - see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote - - obsolete_materially denotes - true - - - - - - - + is quality measurement of m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q - 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later - From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] - -This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. --- -From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] - -unit of measure is a quality, e.g. the length of a ruler. - -[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] - -[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] - -a represents b means either a denotes b or a describes - -describe: -a describes b means a is about b and a allows an inference of at least one quality of b - -We have had a long discussion about denotes versus describes. - From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. - -a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. - From the second meeting on IAO: - -An attempt at defining assay using Barry's "reliability" wording - -assay: -process and has_input some material entity -and has_output some information content entity -and which is such that instances of this process type reliably generate -outputs that describes the input. - This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. - Alan Ruttenberg + is quality measurement of - - - - - - obsolete_describes - true - - - - - - - - - - obsolete_represents - true - - - - - - + denoted by inverse of the relation 'denotes' - Person: Jie Zheng, Chris Stoeckert, Mike Conlon - + denoted by @@ -1453,9 +1584,8 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point + has coordinate unit label + has coordinate unit label @@ -1465,93 +1595,14 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - + is duration of relates a process to a time-measurement-datum that represents the duration of the process - Person:Alan Ruttenberg + is duration of - - - - - inverse of the relation of is quality measurement of - 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship - Person:Alan Ruttenberg - is quality measured as - - - - - - - - - - - A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality. - Person:Alan Ruttenberg - Person:Bjoern Peters - is quality specification of - - - - - - - - - inverse of the relation of is quality specification of - 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship - Person:Alan Ruttenberg - Person:Bjoern Peters - quality is specified as - - - - - - - - - - - - - relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken - Alan Ruttenberg - has time stamp - - - - - - - - - - - - - - - - - - - - - relates a time stamped measurement datum to the measurement datum that was measured - Alan Ruttenberg - has measurement datum - - - - @@ -1586,16 +1637,10 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - - has_specified_input - has_specified_input see is_input_of example_of_usage The inverse property of is_specified_input_of @@ -1604,7 +1649,6 @@ Werner suggests a solution based on "Magnitudes" a proposal for which PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot - has_specified_input @@ -1682,23 +1726,16 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - - - - - has_specified_output - has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot - has_specified_output @@ -1860,12 +1897,10 @@ instance level relation [GOC:cjm] is_specified_output_of - is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters - is_specified_output_of @@ -2440,7 +2475,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence @@ -2480,28 +2514,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - - - - - - - - - disposition of - - - - @@ -2557,28 +2569,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - - - - - - - - - - - - - - - - - located in my brain is located in my head this rat is located in this cage @@ -2590,18 +2580,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ http://www.obofoundry.org/ro/#OBO_REL:located_in located in - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - @@ -2790,46 +2768,13 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + has measurement value + has measurement value - - - - - - - has x coordinate value - - - - - - - - - - - has z coordinate value - - - - - - - - - - - has y coordinate value - - - - @@ -2903,180 +2848,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - - - - - - - - - - - - - - - - - - A planned process that has specified output a software product and that involves the creation of source code. - Mathias Brochhausen - William R. Hogan - http://en.wikipedia.org/wiki/Software_development - A planned process resulting in a software product involving the creation of source code. - software development - - - - - - - - - - - - - - - - - - - - A measurement datum that is the output of counting. - Mathias Brochhausen - A measurement datum that is the output of counting. - count - - - - - - - - - - - - - - - - - - - - The planned process of finding the number of elements in a finite set of objects. - Mathias Brochhausen - http://en.wikipedia.org/wiki/Counting - The planned process of finding the number of elements in a finite set of objects. - counting - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - software source code version control repository - A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc. - William R. Hogan - Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based - source code repository - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - process of compiling software - A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions. - William R. Hogan - It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.). - Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code. - compiling software - - - - - - - - - - - - - - - - - - - - creating a data set - A planned process that has a data set as its specified output. - William R. Hogan - data set creation - dataset creation - dataset creating - - - - @@ -3084,12 +2855,14 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ entity Entity + entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity @@ -3116,19 +2889,13 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - continuant Continuant continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) @@ -3201,12 +2968,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. @@ -3272,8 +3033,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - ic IndependentContinuant a chair @@ -3335,23 +3094,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. - obsolete dependent continuant - true - - - - - - s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. @@ -3363,18 +3109,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ spatial region - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - @@ -3394,6 +3128,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) + + + + (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] + + + + + + (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] + + @@ -3401,9 +3147,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional @@ -3466,7 +3209,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. @@ -3709,7 +3451,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) @@ -3745,7 +3486,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ the mass of this piece of gold. the shape of your nose the shape of your nostril - + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] @@ -3784,7 +3525,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - sdc SpecificallyDependentContinuant specifically dependent continuant @@ -3803,7 +3543,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - + (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] @@ -3883,7 +3623,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ fiat-object - fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. @@ -3897,7 +3636,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object - fiat object part @@ -3918,7 +3656,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. @@ -3969,6 +3706,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ object aggregate + + + + b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) + + + + + + (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] + + @@ -3987,18 +3736,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - @@ -4364,8 +4101,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator @@ -4445,7 +4180,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ RelationalQuality John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. a marriage bond, an instance of love, an obligation between one person and another. - a marriage bond, an instance of requited love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] @@ -6092,7 +5826,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + cell line cell cell line cell 细胞系细胞 @@ -6107,14 +5841,14 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ cell line cell 细胞系细胞 - + - + 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. @@ -9028,11 +8762,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ conditional specification - A directive information entity that specifies what should happen if the trigger condition is fulfilled. - PlanAndPlannedProcess Branch - OBI branch derived - OBI_0000349 + conditional specification @@ -9043,17 +8774,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ measurement unit label - Examples of measurement unit labels are liters, inches, weight per volume. - A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. - 2009-03-16: provenance: a term measurement unit was -proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and -Cristian Cocos, and subsequently moved to IAO where the objective for -which the original term was defined was satisfied with the definition -of this, different, term. - 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot + measurement unit label @@ -9064,19 +8786,8 @@ of this, different, term. objective specification - In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. - A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." - 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. - Answers the question, why did you do this experiment? - PERSON: Alan Ruttenberg - PERSON: Barry Smith - PERSON: Bjoern Peters - PERSON: Jennifer Fostel - goal specification - OBI Plan and Planned Process/Roles Branch - OBI_0000217 + objective specification @@ -9087,14 +8798,8 @@ of this, different, term. narrative object - Examples of narrative objects are reports, journal articles, and patents submission. - A narrative object is an information content entity that is a set of propositions. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion - agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions - person:Chris Stoeckert - OBI_0000013 - group:OBI + narrative object @@ -9104,38 +8809,21 @@ of this, different, term. - Pour the contents of flask 1 into flask 2 - + action specification A directive information entity that describes an action the bearer will take. - Alan Ruttenberg - OBI Plan and Planned Process branch + action specification - - - - - - obsolete_artifact - true - - - - datum label - A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label - http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n - GROUP: IAO - 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. - + datum label @@ -9146,184 +8834,33 @@ of this, different, term. software - Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. - see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert - PERSON: Melanie Courtot - GROUP: OBI + software - - - - - obsolete_digital entity - A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 - -Superclass was 'digitial quality' - person:Chris Stoeckert - OBI_0000261 - group:OBI - - obsolete2_digital entity - true - - - - - - - - - journal article - Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. - - A report that is published in a journal. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000159 - group:OBI - journal article - - - - - - - - - - - - - - - information carrier - In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. - A quality of an information bearer that imparts the information content - 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. - 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. - PERSON: Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy + information carrier - - - - - model number - - A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers - Person: Alan Ruttenberg - model number - - - - - - - - - - obsolete_material_entity - true - - - - - - - - - binary digital entity - MS Word document, ZIP file, DICOM file, JPEG file - A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -Superclass was 'digital entity' - digital_entity - person:Chris Stoeckert - OBI_0000244 - group:OBI - - obsolete2_binary digital entity - true - - - - - - - - - The length of a ruler. - a unit of measure is the quality of some material entity compared to which another quality is some multiple of. - Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - - obsolete_unit of measure - true - - - - - - - - - programming language - R, Perl, Java - - A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000058 - group:OBI - programming language - - - - data item - Data items include counts of things, analyte concentrations, and statistical summaries. - An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. - 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. - 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. - 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ - JAR: datum -- well, this will be very tricky to define, but maybe some -information-like stuff that might be put into a computer and that is -meant, by someone, to denote and/or to be interpreted by some -process... I would include lists, tables, sentences... I think I might -defer to Barry, or to Brian Cantwell Smith - -JAR: A data item is an approximately justified approximately true approximate belief - PERSON: Alan Ruttenberg - PERSON: Chris Stoeckert - PERSON: Jonathan Rees - data + data item @@ -9335,73 +8872,26 @@ JAR: A data item is an approximately justified approximately true approximate be symbol - a serial number such as "12324X" - a stop sign - a written proper name such as "OBI" - An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - 20091104, MC: this needs work and will most probably change - 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). - PERSON: James A. Overton - PERSON: Jonathan Rees - based on Oxford English Dictionary + symbol - - - - - numeral - - A symbol that denotes a number. - PERSON: Jonathan Rees - numeral - - - - - - - - - - information content entity - Examples of information content entites include journal articles, data, graphical layouts, and graphs. - A generically dependent continuant that is about some thing. - 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). - information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). - -Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. - PERSON: Chris Stoeckert - OBI_0000142 + information content entity - - - - - integer numeral - - A numeral that denotes an integer - PERSON: Jonathan Rees - integer numeral - - - - @@ -9412,26 +8902,9 @@ Previous. An information content entity is a non-realizable information entity t - - - - 1 - - - - - - 1 - - - 10 feet. 3 ml. - + scalar measurement datum A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. - 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in -this case we explicitly refer to the singular form - Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot + scalar measurement datum @@ -9441,72 +8914,21 @@ this case we explicitly refer to the singular form - - - - - - - + directive information entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. - 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. - 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO - Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters + directive information entity - - - - - time trigger - - PlanAndPlannedProcess Branch - time trigger - - - - - - - - - obsolete_study interpretation - - A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses - 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application." - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead. - Lawrence Hunter - PERSON: Alan Ruttenberg - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - conclusion - OBI_0000005 - - obsolete_study interpretation - true - - - - dot plot - Dot plot of SSC-H and FSC-H. - A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000123 - group:OBI + dot plot @@ -9517,127 +8939,37 @@ this case we explicitly refer to the singular form graph - A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. - PERSON: Lawrence Hunter - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000240 - group:OBI + graph - - - - - text based digital entity - XML file, C++ source code file - A text based digital entity is a digital entity that is encoded so that it only contains text characters. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digital document' - digital_entity - person:Chris Stoeckert - OBI_0000132 - group:OBI - - obsolete2_text based digital entity - true - - - - rule - example to be added - A rule is an executable which guides, defines, restricts actions. - MSI - PRS - OBI_0500021 - PRS + rule - - - - - contour plot - Contour plot of SSC-H, FSC-H, and FL1-H. - - generically_dependent_continuants - person:Allyson Lister - person:Chris Stoeckert - OBI_0000246 - group:Flow Cytometry community - contour plot - - - - - - - - - report figure - - A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements - I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report - Replaced by defined version of figure - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000027 - group:OBI - - obsolete2_report figure - true - - - - algorithm - PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. - A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. - Philippe Rocca-Serra - PlanAndPlannedProcess Branch - OBI_0000270 - adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) + algorithm - - - - - software interpreter - R program, Perl interpreter, Java virtual machine - - A software interpreter is a software application that executes some specified input software. - Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000199 - group:OBI - software interpreter - - - - @@ -9664,6 +8996,7 @@ superclass was 'digital document' PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 + curation status specification @@ -9674,13 +9007,8 @@ superclass was 'digital document' density plot - Density plot of SSC-H and FSC-H. - A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000179 - group:Flow Cytometry community + density plot @@ -9691,123 +9019,21 @@ superclass was 'digital document' report - Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. - A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). - 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on -something that has completed." Should it be restricted to those things -that are completed? For example, a progress report is (usually) about -something that definitely has *not* been completed, or may include -(only) projections. I think the definition would not suffer if the -whole sentence is deleted. - 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion - disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - PERSON:Chris Stoeckert - GROUP: OBI - OBI_0000099 + report - - - - - report element - - A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page). - 2009-03-16: needs some more work (clarify relations). - 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements. - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion - Replaced by textual entity and figure - There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text - PERSON: Alan Ruttenberg - PERSON: Allyson Lister - PERSON: Melanie Courtot - GROUP:OBI - OBI_0000001 - - obsolete_report element - true - - - - - - - - - binary executable - Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007) - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digital entity' - person:Jennifer Fostel - OBI_0000222 - group:OBI - - obsolete2_binary executable - true - - - - - - - - - source code module - The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. - - A source code module is a directive information entity that specifies, using a programming language, some algorithm. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000039 - group:OBI - source code module - - - - - - - - - report table - - A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000265 - group:OBI - - obsolete_report table - true - - - - data format specification - A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file - 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes -information. Example: The ISO document specifying what encompasses an -XML document; The instructions in a XSD file" - PERSON: Alan Ruttenberg - PlanAndPlannedProcess Branch - OBI branch derived - OBI_0000187 + data format specification @@ -9818,15 +9044,8 @@ XML document; The instructions in a XSD file" data set - Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). - A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. - 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type - 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000042 - group:OBI + data set @@ -9837,13 +9056,8 @@ XML document; The instructions in a XSD file" image - An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. - person:Alan Ruttenberg - person:Allyson - person:Chris Stoeckert - OBI_0000030 - group:OBI + image @@ -9856,6 +9070,7 @@ XML document; The instructions in a XSD file" data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg + data about an ontology part @@ -9865,58 +9080,14 @@ XML document; The instructions in a XSD file" - - - - - - - - - - - - plan specification - PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. - - A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2014-03-31: A plan specification can have other parts, such as conditional specifications. - Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved - Alan Ruttenberg - OBI Plan and Planned Process branch - OBI_0000344 - 2/3/2009 Comment from OBI review. - -Action specification not well enough specified. -Conditional specification not well enough specified. -Question whether all plan specifications have objective specifications. - -Request that IAO either clarify these or change definitions not to use them + A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. + plan specification - - - - - digital document - A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digial entity' - person:Jennifer Fostel - OBI_0000195 - group:OBI - - obsolete2_digital document - true - - - - @@ -9928,106 +9099,13 @@ superclass was 'digial entity' measurement datum - Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. - A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. - 2/2/2009 is_specified_output of some assay? - person:Chris Stoeckert - OBI_0000305 - group:OBI + measurement datum - - - - - - _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - -Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final. - - obsolete_identifier - true - - - - - - - - - version number - - A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. - Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version - GROUP: IAO - version number - - - - - - - - - serial number - - A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-) - GROUP: IAO - serial number - - - - - - - - - lot number - - A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. - GROUP: IAO - batch number - lot number - - - - - - - - - - A settings datum is a datum that denotes some configuration of an instrument. - 2/3/2009 Feedback from OBI - -This should be a "setting specification". There is a question of whether it is information about a realizable or not. - -Pro other specification are about realizables. -Cons sometimes specifies a quality which is not a realizable. - Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. - setting datum - - - - - - - - - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 - Need to rework digital entity. Digital quality was suggested by Barry. - - obsolete_digital quality - true - - - - @@ -10046,12 +9124,8 @@ Cons sometimes specifies a quality which is not a realizable. conclusion textual entity - that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 - A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - 2009/10/23 Alan Ruttenberg: We need to work on the definition still - Person:Alan Ruttenberg + conclusion textual entity @@ -10060,30 +9134,10 @@ Cons sometimes specifies a quality which is not a realizable. - - - - - - - - - - - - - - - - material information bearer - A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. - a brain - a hard drive - A material entity in which a concretization of an information content entity inheres. - GROUP: IAO + material information bearer @@ -10094,13 +9148,9 @@ Cons sometimes specifies a quality which is not a realizable. histogram - A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI + histogram @@ -10111,69 +9161,24 @@ distribution in terms of occurrence frequencies of different event classes. heatmap - A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI + heatmap - - - - - Venn diagram - - A Venn diagram is a report graph showing all hypothetically possible -logical relations between a finite collection of sets. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Venn_diagram - Venn diagram - - - - - - - - - obsolete_survival curve - - A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://www.graphpad.com/www/book/survive.htm - - obsolete_survival curve - true - - - - dendrogram - Dendrograms are often used in computational biology to -illustrate the clustering of genes. - A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Dendrogram + dendrogram @@ -10184,64 +9189,13 @@ clustering algorithm. scatter plot - Comparison of gene expression values in two samples can be displayed in a scatter plot - A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - scattergraph - WEB: http://en.wikipedia.org/wiki/Scatterplot + scatter plot - - - - - - A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc. - PERSON:Alan Ruttenberg - PERSON:Joanne Luciano - PERSON:Melanie Courtot - WEB: http://en.wiktionary.org/wiki/photograph - photograph - - - - - - - - - - - - - - - - - - - - - - - - - photographic print - - A photographic print is a material entity upon which a photograph generically depends. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - photographic print - - - - @@ -10253,6 +9207,7 @@ clustering algorithm. + @@ -10273,142 +9228,32 @@ clustering algorithm. textual entity - Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities - A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. - AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. - MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. - PERSON: Lawrence Hunter - text + textual entity - - - - - - - - - - - citation - Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183. - - A textual entity intended to identify a particular publication. - PERSON: Lawrence Hunter - citation - - - - - - - - - author identification - L. Hunter - - A textual entity intended to identify a particular author - PERSON: Lawrence Hunter - author identification - - - - - - - - - institutional identification - University of Colorado Denver School of Medicine - - A textual entity intended to identify a particular institution - PERSON: Lawrence Hunter - institutional identification - - - - - - - - - - - - - - - caption - Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool. - - A textual entity that describes a figure - PERSON: Lawrence Hunter - caption - - - - - - - - - document title - Textual characteristics of traditional and Open Access scientific journals are similar - - A textual entity that names a document - PERSON: Lawrence Hunter - document title - - - - table - | T F ---+----- -T | T F -F | F F - A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions - PERSON: Lawrence Hunter + table - - - - - table of abbreviations - IAO information artifact ontology -OBI ontology of biomedical investiations -GO gene ontology - - A table where the constituent texts are abbreviations and their expansions - PERSON: Lawrence Hunter - table of abbreviations - - - - figure - Any picture, diagram or table - An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. - PERSON: Lawrence Hunter + figure @@ -10419,10 +9264,8 @@ GO gene ontology diagram - A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. - A figure that expresses one or more propositions - PERSON: Lawrence Hunter + diagram @@ -10433,10 +9276,8 @@ GO gene ontology document - A journal article, patent application, laboratory notebook, or a book - A collection of information content entities intended to be understood together as a whole - PERSON: Lawrence Hunter + document @@ -10447,10 +9288,8 @@ GO gene ontology publication - A journal article or book - - A document that has been accepted by a publisher - PERSON: Lawrence Hunter + A document that is the output of a publishing process. + publication @@ -10460,366 +9299,22 @@ GO gene ontology - - - - - - publication about an investigation - Most scientific journal articles - A publication that is about an investigation - PERSON: Lawrence Hunter - scientific publication + publication about an investigation - - - - - patent - US Patent 6,449,603 - - A document that has been accepted by a patent authority - PERSON: Lawrence Hunter - patent - - - - - - - - - - - - - - - document part - An abstract, introduction, method or results section. - - An information content entity that is part of a document. - PERSON: Lawrence Hunter - document part - - - - - - - - - - - - - - - abstract - The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. - - A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes. - PERSON: Lawrence Hunter - abstract - - - - - - - - - - - - - - - introduction to a publication about an investigation - Section labelled 'introduction' of a typical scientific journal article - - A part of a publication about an investigation that is about the objective specification (why the investigation is being done) - PERSON: Lawrence Hunter - background - introduction - introduction to a publication about an investigation - - - - - - - - - - - - - - - methods section - The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article. - - A part of a publication about an investigation that is about the study design of the investigation - PERSON: Lawrence Hunter - experimental - experimental procedures - experimental section - methods - methods section - - - - - - - - - - - - - - - results section - The section labelled 'results' in a typical scientific journal article - - A part of a publication about an investigation that is about a study design execution - PERSON: Lawrence Hunter - results - results section - - - - - - - - - discussion section of a publication about an investigation - - A part of a publication about an investigation that is about the study interpretation of the investigation - PERSON: Lawrence Hunter - discussion - discussion section - discussion section of a publication about an investigation - - - - - - - - - - - - - - - references section - The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography" - - A part of a document that has citations as parts - PERSON: Lawrence Hunter - references section - - - - - - - - - - - - - - - author list - Lawrence Hunter and Kevin Brettonel Cohen - - A part of a document that enumerates the authors of the document - PERSON: Lawrence Hunter - author list - - - - - - - - - - - - - - - institution list - The University of Colorado Denver School of Medicine and the University of Colorado Boulder. - - A part of a document that has parts that are institution identifications associated with the authors of the document - PERSON: Lawrence Hunter - institution list - - - - - - - - - author contributions section - LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript. - - A part of a publication that is about the specific contributions of each author - PERSON: Lawrence Hunter - author contributions - contributions by the authors - author contributions section - - - - - - - - - acknowledgements section - The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript - - Part of a publication that is about the contributions of people or institutions other than the authors. - PERSON: Lawrence Hunter - acknowledgements - acknowledgments - acknowledgements section - - - - - - - - - - - - - - - footnote - The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text. - - A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document. - PERSON: Lawrence Hunter - endnote - footnote - - - - - - - - - supplementary material to a document - - A part of a document that is segregated from the rest of the document due to its size - PERSON: Lawrence Hunter - additional information - appendix - supplemental information - supplementary material - supporting information - supplementary material to a document - - - - - - - - - table of contents - - A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred). - PERSON: Lawrence Hunter - table of contents - - - - - - - - - table of figures - - A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred). - PERSON: Lawrence Hunter - table of figures - - - - - - - - - running title - - A shorter version of a document title - PERSON: Lawrence Hunter - running title - - - - - - - - - copyright section - This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License. - - A document part that describes legal restrictions on making or distributing copies of the document - PERSON: Lawrence Hunter - copyright section - - - - - - - - - - - - - - 1 - - - + cartesian spatial coordinate datum A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude - 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 - Alan Ruttenberg - AR notes: We need to discuss whether it should include site. + cartesian spatial coordinate datum - http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 @@ -10828,141 +9323,21 @@ GO gene ontology - - - - - - - - - - - - - - - - - - - - 1 - - - + one dimensional cartesian spatial coordinate datum A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region - Alan Ruttenberg + one dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - 1 - - - - A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region - Alan Ruttenberg - two dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region - Alan Ruttenberg - three dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - + length measurement datum A scalar measurement datum that is the result of measurement of length quality - Alan Ruttenberg + length measurement datum @@ -10995,66 +9370,21 @@ GO gene ontology - - - - - - - - - - - - - - - + mass measurement datum A scalar measurement datum that is the result of measurement of mass quality - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg + mass measurement datum - - - - - hypothesis textual entity - that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 - - A textual entity that expresses an assertion that is intended to be tested. - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg - hypothesis textual entity - - - - - - - - - - - - - - - - - - - + time measurement datum A scalar measurement datum that is the result of measuring a temporal interval - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg + time measurement datum @@ -11064,15 +9394,9 @@ GO gene ontology - - - - - - - + postal address A textual entity that is used as directive to deliver something to a person, or organization - 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59 + postal address @@ -11083,75 +9407,19 @@ GO gene ontology email address - - Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583 - Person:Alan Ruttenberg - Person:Chris Stoeckart + email address - - - - - author role - - A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - author role - - - - - - - - - - - - - - - - - - - - - - A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing - Person:Alan Ruttenberg - data item extraction from journal article - - - - - - - - - - - - - - - - - Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. - + documenting A planned process in which a document is created or added to by including the specified input in it. - 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape - Bjoern Peters - wikipedia http://en.wikipedia.org/wiki/Documenting + documenting @@ -11162,14 +9430,9 @@ GO gene ontology line graph - A line graph is a type of graph created by connecting a series of data points together with a line. - PERSON:Chris Stoeckert - PERSON:Melanie Courtot - line chart - GROUP:OBI - WEB: http://en.wikipedia.org/wiki/Line_chart + line graph @@ -11179,1218 +9442,58 @@ points together with a line. - - - - - - - - - - - - - A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned. - + assigning a centrally registered identifier A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity - 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry. - Person:Alan Ruttenberg - Person:Bjoern Peters - Person:Melanie Courtot - assigning a CRID + assigning a centrally registered identifier - - - - - - - - - - - - - - - - - - - - - - - Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. - - A planned process in which a CRID registry associates an information content entity with a CRID symbol - PERSON:Alan Ruttenberg - associating information with a CRID in the CRID registry - associating information with a centrally registered identifier in its registry - - - - - - - - - a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID. - MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now. - - obsolete_establishing a CRID registry - true - - - - - - - - - - - The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. - + centrally registered identifier symbol A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID symbol - Original proposal from Bjoern, discussions at IAO calls + centrally registered identifier symbol - - - - - - - - - - - - - - - - - - - - - - The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. - - An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. - 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). - Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. - - Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier - - - - - - PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. - - A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID registry - Original proposal from Bjoern, discussions at IAO calls + + centrally registered identifier registry + A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. + centrally registered identifier registry - - - - - - - - - - - - - - - - - - - - - - - Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. - - A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - looking up a CRID - looking up a centrally registered identifier - - - - - - - - - - - - - - - - - - - - - - - - time stamped measurement datum - - - - - - - - - - - - - - - pmid:20604925 - time-lapse live cell microscopy - - A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. - Alan Ruttenberg - experimental time series - time sampled measurement data set - - - - - - - - - written name - "Bill Clinton" - "The Eiffel Tower" - "United States of America" - - A textual entity that denotes a particular in reality. - PERSON: Bill Hogan - https://github.com/information-artifact-ontology/IAO/issues/114 - The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. - written name - - - - - - - - - - A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software method - - - - - - - - - - A software module is software composed of a collection of software methods. - PERSON: Melanei Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software module - - - - - - - - - - A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software library - - - - - + software application A software application is software that can be directly executed by some processing unit. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 + software application - - - - - - A software script is software whose instructions can be executed using a software interpreter. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software script - - - - - - - - - abbreviation textual entity - From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): - -BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect. - A textual entity listing abbreviations and their expansions that are used in a document. - PERSON: Bill Baumgartner - - abbreviation textual entity - - - - - - - - - - - - - - - abbreviations section - The section labelled 'abbreviations' in a typical scientific journal article. - A part of a document where abbreviations and their long-forms used within the document are listed. - PERSON: Bill Baumgartner - abbreviations - abbreviations list - abbreviations used - list of abbreviations - list of abbreviations used - - abbreviations section - - - - - - - - - - - - - - - author information section - The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/) - A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. - PERSON: Bill Baumgartner - author information - authors’ information - - author information section - - - - - - - - - author information textual entity - From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): - -IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD. - A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. - PERSON: Bill Baumgartner - - author information textual entity - - - - - - - - - - - - - - - author summary section - The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/) - A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers. - PERSON: Bill Baumgartner - author summary - summary - synopsis - Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines) - - author summary section - - - - - + - - - author summary textual entity - From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): - - -The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX. - A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). - PERSON: Bill Baumgartner - Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). - - author summary textual entity - - - - - - - - - - - - - - - availability section - The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). - A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained. - PERSON: Bill Baumgartner - availability - - availability section - - - - - - - - - availability textual entity - From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): - -Project home page:http://krux.googlecode.com - A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained. - PERSON: Bill Baumgartner - - availability textual entity - - - - - - - - - - - - - - - case report section - The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/) - A part of a document about the medical history of a specific patient as it relates to the topic of the document. - PERSON: Bill Baumgartner - case presentation - case report - - case report section - - - - - - - - - case report textual entity - Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): - -The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension. - A textual entity that expresses a detailed account of a portion of the medical history for a specific patient. - PERSON: Bill Baumgartner - - case report textual entity - - - - - - - - - - - - - - - conclusion section - The section labelled 'conclusion' in a typical scientific journal article. - A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document. - PERSON: Bill Baumgartner - concluding remarks - conclusion - conclusions - findings - summary - - conclusion section - - - - - - - - - - - - - - - conflict of interest section - The section labelled 'conflict of interest statement' in a typical scientific journal article. - A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document. - PERSON: Bill Baumgartner - competing interests - conflict of interest - conflict of interest statement - declaration of competing interests - disclosure of potential conflicts of interest - - conflict of interest section - - - - - - - - - conflict of interest statement - SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] - A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document. - PERSON: Bill Baumgartner - - conflict of interest textual entity - - - - - - - - - - - - - - - consent section - The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/) - A part of a document about the consent process that was used to enroll patients in a study. - PERSON: Bill Baumgartner - consent - - consent section - - - - - - - - - consent textual entity - From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): - -Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal. - A textual entity that documents the consenting process used to enroll patients in a study. - PERSON: Bill Baumgartner - - consent textual entity - - - - - - - - - - - - - - - ethical approval section - The section labelled 'ethical approval' in a typical scientific journal article. - A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis. - PERSON: Bill Baumgartner - ethical approval - - ethical approval section - - - - - - - - - - - - - - - ethical approval textual entity - From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): - -The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review. - A textual entity that documents the ethical approval of some study design. - PERSON: Bill Baumgartner - - ethical approval textual entity - - - - - - - - - - - - - - - figures section - The section labelled 'figures' in a typical scientific journal article. - A part of a document that contains one or more figures. - PERSON: Bill Baumgartner - figures - - figures section - - - - - - - - - - - - - - - funding source declaration section - The section labelled 'funding' in a typical scientific journal article. - A part of a document used to detail information regarding the source of funding used in support of the generation of the document content. - PERSON: Bill Baumgartner - funding - funding information - funding sources - funding statement - funding/support - source of funding - sources of funding - - funding source declaration section - - - - - - - - - funding souce declaration textual entity - From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): - -This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication. - A textual entity documenting the source of funding that supported some study. - PERSON: Bill Baumgartner - - funding source declaration textual entity - - - - - - - - - - - - - - - future directions section - The section labelled 'future directions' in a typical scientific journal article. - A part of a document detailing extensions of the described work that may be implemented at some future point in time. - PERSON: Bill Baumgartner - future challenges - future considerations - future developments - future directions - future outlook - future perspectives - future plans - future prospects - future research - future research directions - future studies - future work - - future directions section - - - - - - - - - future directions textual entity - Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): - -In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members. - A textual entity expressing ideas regarding future work relevant to work described in a document that could be done. - PERSON: Bill Baumgartner - - future directions textual entity - - - - - - - - - - - - - - - genome announcement section - The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/) - A document part announcing the publication of a novel draft genome sequence. - PERSON: Bill Baumgartner - genome announcement - - genome announcement section - - - - - - - - - genome announcement textual entity - Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): - -Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB). - A textual entity that describes the generation and public release of a novel, draft genome sequence. - PERSON: Bill Baumgartner - - genome announcement textual entity - - - - - - - - - keyword textual entity - From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): - -Exon orthology; alternative splicing; exon duplication; intron-exon structure. - A textual entity listing keywords indicating the major theme(s) of a document. - PERSON: Bill Baumgartner - - keyword textual entity - - - - - - - - - - - - - - - keywords section - The section labelled 'keywords' in a typical scientific journal article. - A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed. - PERSON: Bill Baumgartner - keywords - - keywords section - - - - - - - - - - - - - - - - - - - - - study limitations section - The section labelled 'limitations' in a typical scientific journal article. - A part of a document about biases or short comings related to the study design and execution. - PERSON: Bill Baumgartner - limitations - study limitations - Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) - - study limitations section - - - - - - - - - study limitations textual entity - Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). - -Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out. - A textual entity addressing a shortcoming or bias of a study design or execution. - PERSON: Bill Baumgartner - Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) - - study limitations textual entity - - - - - - - - - materials section - The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/) - A part of a document about the materials required to reproduce the content of the document. - PERSON: Bill Baumgartner - materials - - materials section - - - - - - - - - notes section - The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): - A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc. - PERSON: Bill Baumgartner - footnotes - notes - - notes section - - - - - - - - - - - - - - - patients section - The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/) - A part of a document about the patients that participated in a study. - PERSON: Bill Baumgartner - - patients section - - - - - - - - - patients textual entity - Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): - -Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred. - A textual entity expressing information regarding the patients used in a study. - PERSON: Bill Baumgartner - - patients textual entity - - - - - - - - - - - - - - - pre-publication history section - The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/) - A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors. - PERSON: Bill Baumgartner - notice of republication - pre-publication history - - pre-publication history section - - - - - - - - - pre-publication history textual entity - From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): - -The pre-publication history for this paper can be accessed here: -http://www.biomedcentral.com/1471-2253/13/33/prepub - A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information. - PERSON: Bill Baumgartner - - pre-publication history textual entity - - - - - - - - - - - - - - - related work section - The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/) - A part of a document about work in other publications that is relevant to the content of the document. - PERSON: Bill Baumgartner - related literature - related work - - related work section - - - - - - - - - related work textual entity - Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): - -Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015). - - - A textual entity that discusses work from other publications and expresses their relevancy to the content of a document. - PERSON: Bill Baumgartner - - related work textual entity - - - - - - - - - - - - - - - requirements section - The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). - A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource. - PERSON: Bill Baumgartner - requirements - - requirements section - - - - - - - - - requirements textual entity - From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): - -• Operating systems: Platform independent - -• Programming language: Matlab, R, Python - -• Other requirements: None - -• License: GNU GPL v3 - -• Any restrictions to use by non-academics: None - A textual entity that expresses the requirements necessary to use a resource, e.g. software. - PERSON: Bill Baumgartner - - requirements textual entity - - - - - - - - - statistical analysis textual entity - From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): - -Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant. - A textual entity documenting statistical analysis tools and techniques employed. - PERSON: Bill Baumgartner - - statistical analysis textual entity - - - - - - - - - - - - - - - statistical analysis section - The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/) - A part of the document used to describe the statistical methodologies employed in the work presented in the document. - PERSON: Bill Baumgartner - statistical analysis - - statistical analysis section - - - - - - - - - - - - - - - tables section - The section labelled 'tables' in a typical scientific journal article. - A part of a document that contains one or more tables. - PERSON: Bill Baumgartner - tables - - tables section - - - - - - - - - An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail. - Mathias Brochhausen - postal code - - - - - - - - - A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region. - Mathias Brochhausen - Postal delivery route - - - - - - - - - A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes. - Mathias Brochhausen - ZIP code - zone improvement plan code - - - - - - - - - - - - - - - - - - - - - database extract, transform, and load process - A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second. - Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second - Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output. - PERSON:Alan Ruttenberg - ETL - WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load - - - database extract, transform, and load process - - - - - - - - + - identifier - An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. - - identifier + code set + An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things. + + code set @@ -13933,7 +11036,6 @@ No imports planned process - planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. @@ -13944,7 +11046,6 @@ objectives is a planned process. branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - planned process @@ -14677,7 +11778,6 @@ objectives is a planned process. Could add specific objective specification Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS - study investigation @@ -19670,7 +16770,6 @@ that has_part some material entity is a material entity. If we add as equivalent removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. branch derived 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. - study design execution @@ -24154,7 +21253,6 @@ http://sourceforge.net/p/obi/obi-terms/716/ - @@ -24989,7 +22087,6 @@ the role 'adjuvant role' inheres in some 'material entity' a - @@ -30504,7 +27601,7 @@ In the examples above, a reagent is an operational component of a device, but th - + @@ -78799,7 +75896,6 @@ https://www.doi.org/ - @@ -85597,7 +82693,8 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A specimen that is collected with a suctioning tube from the nasal cavity. Asiyah Yu Lin ORCID:0000-0003-2620-0345 - nasal wash specimen|nasopharyngeal aspirate + nasal wash specimen + nasopharyngeal aspirate Asiyah Yu Lin ORCID:0000-0003-2620-0345 nasal aspirate specimen @@ -97355,7 +94452,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - raw magnetic resonance image data set reconstruction A Fourier transform of raw "k-space" data produced into an image data set that represents the anatomical structure of the tissue examined. @@ -105830,6 +102926,125 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + + + albumin-free serum + + A blood serum specimen that contains no albumin. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/493 + Philippe Rocca-Serra + albumin-free serum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + fasting + Pre-test fasting is required or recommended for several blood tests, including glucose and C-peptide tests. 8–12 hours is typical for fasting duration. + + A planned process in which an organism drinks only water and does not eat for a specified period of time. + Sebastian Duesing + A.M. Simundic et al., Standardization of collection requirements for fasting samples: For the Working Group on Preanalytical Phase (WG-PA) of the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM), Clinica Chimica Acta, Volume 432, 2014, Pages 33-37, ISSN 0009-8981, https://doi.org/10.1016/j.cca.2013.11.008. + https://github.com/obi-ontology/obi/issues/494 + Philippe Rocca-Serra + fasting + + + + + + + + + overnight fasting + Overnight fasting commonly occurs prior to a blood draw scheduled in the morning. + + A fasting with a duration of 8–12 hours, typically occurring overnight. + Sebastian Duesing + A.M. Simundic et al., Standardization of collection requirements for fasting samples: For the Working Group on Preanalytical Phase (WG-PA) of the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM), Clinica Chimica Acta, Volume 432, 2014, Pages 33-37, ISSN 0009-8981, https://doi.org/10.1016/j.cca.2013.11.008. + https://github.com/obi-ontology/obi/issues/494 + Philippe Rocca-Serra + overnight fasting + + + + + + + + + + + + + + + fasted + + An organismal quality that inheres in an organism that has completed a fasting process, and which ceases to inhere in that organism once that organism drinks a liquid other than water or eats. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/494 + Philippe Rocca-Serra + fasted + + + + + + + + + minimum resolved unit of measurement + + An information content entity that indicates the smallest increment that can be resolved on the scale of a measurement instrument. + Sebastian Duesing + least count + https://en.wikipedia.org/wiki/Least_count + https://github.com/obi-ontology/obi/issues/506 + Philippe Rocca-Serra + minimum resolved unit of measurement + + + + @@ -106277,30 +103492,26 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - + + + + 0 + + + primary cultured cell population Spleen cells put directly into culture; Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934 cells that have been isolated from some organismal source, expanded in culture, but not undergone a complete passaging (ie are still in culture, or have been lifted from culture and frozen in aliquots for future use) A cultured cell population comprised of cells expanded directly from living tissue prior to being passaged. 2013-6-5 MHB: This OBI class was formerly called 'primary cell culture', but label changed and definition updated following CLO alignment work. Previous definition: 'a primary cell culture is a cell culture where the cells derive from a fresh tissue source.' + consider if we really want to be so strict here . . . ie maybe we we say that they have not been output from an 'establishing cell line' process, but in some cases a passage or two may be allowed for a primary culture. the establishing of a line requires some procedss that attains a degree of homogeneity in the culture. PERSON:Matthew Brush primary cell culture primary cell culture sample PERSON:Matthew Brush primary cultured cell population - - - 0 - - - - - - - consider if we really want to be so strict here . . . ie maybe we we say that they have not been output from an 'establishing cell line' process, but in some cases a passage or two may be allowed for a primary culture. the establishing of a line requires some procedss that attains a degree of homogeneity in the culture. - @@ -106547,7 +103758,6 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ data analysis data processing Branch editors - data transformation @@ -106556,7 +103766,6 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ - @@ -106681,7 +103890,6 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ - @@ -107109,7 +104317,6 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ - @@ -107368,7 +104575,6 @@ specified input and output of dt which were missing - @@ -107406,7 +104612,6 @@ specified input and output of dt which were missing - @@ -107519,7 +104724,6 @@ specified input and output of dt which were missing - @@ -107937,7 +105141,6 @@ TO BE DEALT WITH STILL BY RICHARD. JAMES - @@ -108074,7 +105277,6 @@ allows correct classification of FWER dt - @@ -108423,7 +105625,6 @@ variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variabl - @@ -108482,7 +105683,6 @@ variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variabl - @@ -108549,7 +105749,6 @@ where \beta_0 = 0 is the intercept ("constant" term), the \beta_i s - @@ -108648,7 +105847,6 @@ In this equation b0 is the regression coefficient for the intercept and the bi v - @@ -108768,7 +105966,6 @@ information_encoding - @@ -108846,7 +106043,6 @@ information_encoding - @@ -108905,7 +106101,6 @@ information_encoding - @@ -109028,7 +106223,6 @@ information_encoding - @@ -109599,7 +106793,6 @@ information_encoding - @@ -109656,7 +106849,6 @@ information_encoding - @@ -109688,7 +106880,6 @@ allows correct classification of FDR dt - @@ -109718,7 +106909,6 @@ allows correct classification of FDR dt - @@ -114377,7 +111567,6 @@ Manual editing of automatically recorded data in an anesthesia information manag PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. - study design @@ -148790,7 +145979,7 @@ realizes some 'host of immune response role' - + length A 1-D extent quality which is equal to the distance between two points. @@ -149027,18 +146216,6 @@ realizes some 'host of immune response role' - - - - - electromagnetic (EM) radiation quality - A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. - - electromagnetic (EM) radiation quality - - - - @@ -149054,7 +146231,7 @@ realizes some 'host of immune response role' - + optical quality An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. @@ -149294,7 +146471,7 @@ realizes some 'host of immune response role' - + cellular quality A monadic quality of continuant that exists at the cellular level of organisation. @@ -149388,26 +146565,26 @@ realizes some 'host of immune response role' - + - + - 3-D extent - A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. + 1-D extent + A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. - 3-D extent + 1-D extent - + - - - radiation quality - A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. + + + 3-D extent + A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. - radiation quality + 3-D extent @@ -149415,7 +146592,7 @@ realizes some 'host of immune response role' - + activity (of a radionuclide) A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate. @@ -149628,6 +146805,30 @@ realizes some 'host of immune response role' + + + + + anatomical structure quality + A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components. + + anatomical structure quality + + + + + + + + + quality of interaction of a substance with electromagnetic radiation + A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength. + + quality of interaction of a substance with electromagnetic radiation + + + + @@ -151793,7 +148994,6 @@ realizes some 'host of immune response role' length unit - A unit which is a standard measure of the distance between two points. length unit @@ -151805,7 +149005,6 @@ realizes some 'host of immune response role' mass unit - A unit which is a standard measure of the amount of matter/energy of a physical object. mass unit @@ -151817,7 +149016,6 @@ realizes some 'host of immune response role' time unit - A unit which is a standard measure of the dimension in which events occur in sequence. time unit @@ -151980,14 +149178,13 @@ realizes some 'host of immune response role' - - + failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term - + @@ -152079,12 +149276,11 @@ realizes some 'host of immune response role' - - + placeholder removed placeholder removed - + @@ -152121,17 +149317,6 @@ realizes some 'host of immune response role' - - - - This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. - We expect to be able to mine these new reasons and add instances as required. - obsolete_other - true - - - - @@ -155535,6 +152720,34 @@ realizes some 'host of immune response role' + + + + + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. + This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/77 + https://orcid.org/0000-0001-5208-3432 + out of scope + + + + + + + + + The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality. + This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). + + https://github.com/information-artifact-ontology/ontology-metadata/issues/136 + https://orcid.org/0000-0002-4142-7153 + domain entity does not exist + + + + @@ -156272,18 +153485,12 @@ binary, and takes no temporal argument. microgram per liter - - - - - - - - - - - - + + + + + + @@ -156315,6 +153522,7 @@ binary, and takes no temporal argument. + geographic location A reference to a place on the Earth, by its name or by its geographical location. geographic location diff --git a/views/NIAID-GSC-BRC.owl b/views/NIAID-GSC-BRC.owl index 98ba5558..882d16eb 100644 --- a/views/NIAID-GSC-BRC.owl +++ b/views/NIAID-GSC-BRC.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> - + en Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Alan Ruttenberg @@ -77,7 +77,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2024-01-09 + 2024-05-03 @@ -196,7 +196,7 @@ We don't have definitions of 'meaning' or 'expression' Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> @@ -239,12 +239,15 @@ We also have the outstanding issue of how to aim different definitions to differ - alternative term + alternative label - An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. + OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). + alternative label alternative term @@ -347,7 +350,6 @@ We also have the outstanding issue of how to aim different definitions to differ - An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation https://oborel.github.io/obo-relations/temporal-semantics/ @@ -480,6 +482,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part + has part @@ -528,7 +531,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + has measurement unit label + has measurement unit label @@ -537,17 +541,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - This document is about information artifacts and their representations - + is about A (currently) primitive relation that relates an information artifact to an entity. - 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. - -We will try to build it back up by elaborating the various subproperties that are more precisely defined. - -Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. - person:Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy + is about @@ -557,19 +553,9 @@ Some currently missing phenomena that should be considered "about" are - - - - A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. + denotes A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically - 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. -g denotes r =def -r is a portion of reality -there is some c that is a concretization of g -every c that is a concretization of g specifically denotes r - person:Alan Ruttenberg - Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan - + denotes @@ -579,90 +565,14 @@ every c that is a concretization of g specifically denotes r - - - + is quality measurement of m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q - 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later - From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] - -This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. --- -From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] - -unit of measure is a quality, e.g. the length of a ruler. - -[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] - -[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] - -a represents b means either a denotes b or a describes - -describe: -a describes b means a is about b and a allows an inference of at least one quality of b - -We have had a long discussion about denotes versus describes. - From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. - -a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. - From the second meeting on IAO: - -An attempt at defining assay using Barry's "reliability" wording - -assay: -process and has_input some material entity -and has_output some information content entity -and which is such that instances of this process type reliably generate -outputs that describes the input. - This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. - Alan Ruttenberg + is quality measurement of - - - - - - inverse of the relation 'denotes' - Person: Jie Zheng, Chris Stoeckert, Mike Conlon - denoted by - - - - - - - - - - - - relates a process to a time-measurement-datum that represents the duration of the process - Person:Alan Ruttenberg - is duration of - - - - - - - - - inverse of the relation of is quality measurement of - 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship - Person:Alan Ruttenberg - is quality measured as - - - - @@ -697,16 +607,10 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - - has_specified_input - has_specified_input see is_input_of example_of_usage The inverse property of is_specified_input_of @@ -715,7 +619,6 @@ Werner suggests a solution based on "Magnitudes" a proposal for which PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot - has_specified_input @@ -740,23 +643,16 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - - has_specified_output - has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot - has_specified_output @@ -768,12 +664,10 @@ Werner suggests a solution based on "Magnitudes" a proposal for which is_specified_output_of - is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters - is_specified_output_of @@ -1063,7 +957,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence @@ -1189,17 +1082,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - - has measurement value - - - - @@ -1242,64 +1124,16 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - - - - - - - - - - - creating a data set - A planned process that has a data set as its specified output. - William R. Hogan - data set creation - dataset creation - dataset creating - - - - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - - entity - - - - - - - - - - - continuant Continuant continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - + continuant @@ -1309,13 +1143,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - - occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. @@ -1331,8 +1158,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - ic IndependentContinuant a chair @@ -1356,9 +1181,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - t-region TemporalRegion @@ -1454,7 +1276,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ the mass of this piece of gold. the shape of your nose the shape of your nostril - + quality @@ -1465,7 +1287,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - sdc SpecificallyDependentContinuant specifically dependent continuant @@ -1481,7 +1302,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - + specifically dependent continuant @@ -1883,17 +1704,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ measurement unit label - Examples of measurement unit labels are liters, inches, weight per volume. - A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. - 2009-03-16: provenance: a term measurement unit was -proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and -Cristian Cocos, and subsequently moved to IAO where the objective for -which the original term was defined was satisfied with the definition -of this, different, term. - 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot + measurement unit label @@ -1904,105 +1716,32 @@ of this, different, term. objective specification - In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. - A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." - 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. - Answers the question, why did you do this experiment? - PERSON: Alan Ruttenberg - PERSON: Barry Smith - PERSON: Bjoern Peters - PERSON: Jennifer Fostel - goal specification - OBI Plan and Planned Process/Roles Branch - OBI_0000217 + objective specification - - - - - Pour the contents of flask 1 into flask 2 - - A directive information entity that describes an action the bearer will take. - Alan Ruttenberg - OBI Plan and Planned Process branch - action specification - - - - datum label - A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label - http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n - GROUP: IAO - 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. - + datum label - - - - - - - - - - - - - - - - information carrier - In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. - - A quality of an information bearer that imparts the information content - 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. - 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. - PERSON: Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - information carrier - - - - data item - Data items include counts of things, analyte concentrations, and statistical summaries. - An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. - 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. - 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. - 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ - JAR: datum -- well, this will be very tricky to define, but maybe some -information-like stuff that might be put into a computer and that is -meant, by someone, to denote and/or to be interpreted by some -process... I would include lists, tables, sentences... I think I might -defer to Barry, or to Brian Cantwell Smith - -JAR: A data item is an approximately justified approximately true approximate belief - PERSON: Alan Ruttenberg - PERSON: Chris Stoeckert - PERSON: Jonathan Rees - data + data item @@ -2014,16 +1753,8 @@ JAR: A data item is an approximately justified approximately true approximate be symbol - a serial number such as "12324X" - a stop sign - a written proper name such as "OBI" - An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - 20091104, MC: this needs work and will most probably change - 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). - PERSON: James A. Overton - PERSON: Jonathan Rees - based on Oxford English Dictionary + symbol @@ -2033,22 +1764,9 @@ JAR: A data item is an approximately justified approximately true approximate be - - - - - - information content entity - Examples of information content entites include journal articles, data, graphical layouts, and graphs. - A generically dependent continuant that is about some thing. - 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). - information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). - -Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. - PERSON: Chris Stoeckert - OBI_0000142 + information content entity @@ -2065,26 +1783,9 @@ Previous. An information content entity is a non-realizable information entity t - - - - 1 - - - - - - 1 - - - 10 feet. 3 ml. - + scalar measurement datum A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. - 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in -this case we explicitly refer to the singular form - Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot + scalar measurement datum @@ -2094,20 +1795,9 @@ this case we explicitly refer to the singular form - - - - - - - + directive information entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. - 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. - 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO - Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters + directive information entity @@ -2118,13 +1808,8 @@ this case we explicitly refer to the singular form algorithm - PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. - A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. - Philippe Rocca-Serra - PlanAndPlannedProcess Branch - OBI_0000270 - adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) + algorithm @@ -2156,30 +1841,12 @@ this case we explicitly refer to the singular form PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 + curation status specification - - - - - data set - Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). - - A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. - 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type - 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000042 - group:OBI - data set - - - - @@ -2187,6 +1854,7 @@ this case we explicitly refer to the singular form data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg + data about an ontology part @@ -2196,35 +1864,9 @@ this case we explicitly refer to the singular form - - - - - - - - - - - - plan specification - PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. - - A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2014-03-31: A plan specification can have other parts, such as conditional specifications. - Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved - Alan Ruttenberg - OBI Plan and Planned Process branch - OBI_0000344 - 2/3/2009 Comment from OBI review. - -Action specification not well enough specified. -Conditional specification not well enough specified. -Question whether all plan specifications have objective specifications. - -Request that IAO either clarify these or change definitions not to use them + A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. + plan specification @@ -2241,50 +1883,13 @@ Request that IAO either clarify these or change definitions not to use them measurement datum - Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. - A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. - 2/2/2009 is_specified_output of some assay? - person:Chris Stoeckert - OBI_0000305 - group:OBI + measurement datum - - - - - - - - - - - - - - - - - - - - - material information bearer - A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. - a brain - a hard drive - - A material entity in which a concretization of an information content entity inheres. - GROUP: IAO - material information bearer - - - - @@ -2296,6 +1901,7 @@ Request that IAO either clarify these or change definitions not to use them + @@ -2316,13 +1922,8 @@ Request that IAO either clarify these or change definitions not to use them textual entity - Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities - A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. - AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. - MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. - PERSON: Lawrence Hunter - text + textual entity @@ -2333,10 +1934,8 @@ Request that IAO either clarify these or change definitions not to use them document - A journal article, patent application, laboratory notebook, or a book - A collection of information content entities intended to be understood together as a whole - PERSON: Lawrence Hunter + document @@ -2347,10 +1946,8 @@ Request that IAO either clarify these or change definitions not to use them publication - A journal article or book - - A document that has been accepted by a publisher - PERSON: Lawrence Hunter + A document that is the output of a publishing process. + publication @@ -2383,24 +1980,9 @@ Request that IAO either clarify these or change definitions not to use them - - - - - - - - - - - - - - - + time measurement datum A scalar measurement datum that is the result of measuring a temporal interval - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg + time measurement datum @@ -2411,10 +1993,7 @@ Request that IAO either clarify these or change definitions not to use them email address - - Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583 - Person:Alan Ruttenberg - Person:Chris Stoeckart + email address @@ -2424,24 +2003,9 @@ Request that IAO either clarify these or change definitions not to use them - - - - - - - - - - - - - Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. - + documenting A planned process in which a document is created or added to by including the specified input in it. - 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape - Bjoern Peters - wikipedia http://en.wikipedia.org/wiki/Documenting + documenting @@ -2451,26 +2015,9 @@ Request that IAO either clarify these or change definitions not to use them - - - - - - - - - - - - - A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned. - + assigning a centrally registered identifier A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity - 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry. - Person:Alan Ruttenberg - Person:Bjoern Peters - Person:Melanie Courtot - assigning a CRID + assigning a centrally registered identifier @@ -2480,83 +2027,14 @@ Request that IAO either clarify these or change definitions not to use them - - - - - - - The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. - + centrally registered identifier symbol A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID symbol - Original proposal from Bjoern, discussions at IAO calls + centrally registered identifier symbol - - - - - - - - - - - - - - - - - - - - - - The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. - - An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. - 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). - Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. - - Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier - - - - - - - - - PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. - - A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID registry - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier registry - - - - @@ -2777,7 +2255,6 @@ Request that IAO either clarify these or change definitions not to use them planned process - planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. @@ -2788,7 +2265,6 @@ objectives is a planned process. branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - planned process @@ -2879,7 +2355,6 @@ objectives is a planned process. Could add specific objective specification Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS - investigation @@ -3545,7 +3020,6 @@ that has_part some material entity is a material entity. If we add as equivalent removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. branch derived 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. - study design execution @@ -6355,7 +5829,6 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from data analysis data processing Branch editors - data transformation @@ -6494,7 +5967,6 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. - CP4 study design @@ -7081,7 +6553,6 @@ realizes some 'host of immune response role' time unit - A unit which is a standard measure of the dimension in which events occur in sequence. CS7 time unit @@ -7124,14 +6595,13 @@ realizes some 'host of immune response role' - - + failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term - + @@ -7210,12 +6680,11 @@ realizes some 'host of immune response role' - - + placeholder removed placeholder removed - + @@ -7317,6 +6786,18 @@ realizes some 'host of immune response role' + + + + + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. + This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + + out of scope + + + + + geographic location A reference to a place on the Earth, by its name or by its geographical location. CS13 diff --git a/views/obi-base.owl b/views/obi-base.owl index c52c9b00..51cd9806 100644 --- a/views/obi-base.owl +++ b/views/obi-base.owl @@ -13,7 +13,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -80,7 +80,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2023-09-20 + 2024-05-03 @@ -462,12 +462,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - + + + + + @@ -3987,6 +3987,204 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -4215,6 +4413,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + planned process Injecting mice with a vaccine in order to test its efficacy @@ -4909,6 +5108,7 @@ objectives is a planned process. + @@ -5211,7 +5411,7 @@ Modification made by JZ. - + reagent role Buffer, dye, a catalyst, a solvating agent. @@ -7195,10 +7395,7 @@ for now. - - - - + @@ -7213,35 +7410,13 @@ for now. - - - - - - - - - - - - - - - - - - - - - intraperitoneal injection - is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe BP - intraperitoneal injection + intraperitoneal injection @@ -8911,16 +9086,13 @@ that has_part some material entity is a material entity. If we add as equivalent - - - - + - + @@ -8932,19 +9104,11 @@ that has_part some material entity is a material entity. If we add as equivalent - - - - - - - intraperitoneal administration Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h - The administration of a substance into the peritoneum of an organism Person:Bjoern Peters - intraperitoneal administration + intraperitoneal administration @@ -9847,7 +10011,6 @@ that has_part some material entity is a material entity. If we add as equivalent PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072 - check on definition ! solvent mixer @@ -10946,7 +11109,6 @@ that has_part some material entity is a material entity. If we add as equivalent PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055 - chromatography device, check on definition ! column cartridge @@ -11262,7 +11424,6 @@ that has_part some material entity is a material entity. If we add as equivalent PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054 - check on definition ! column cartridger @@ -11293,7 +11454,6 @@ that has_part some material entity is a material entity. If we add as equivalent PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065 - chromatography device, check on definition ! needle assembly @@ -17161,6 +17321,7 @@ http://en.wikipedia.org/wiki/Survival_rate + @@ -17175,20 +17336,6 @@ http://en.wikipedia.org/wiki/Survival_rate - - - - - - - - - - - - - - @@ -17196,9 +17343,7 @@ http://en.wikipedia.org/wiki/Survival_rate - oral ingestion of pill - An adding a material entity to target with the entity is a pill and the target is the mouth Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case @@ -19704,10 +19849,7 @@ Added duirng Mar 1, 2010 dev call - - - - + @@ -19739,15 +19881,7 @@ Added duirng Mar 1, 2010 dev call - - - - - - - intramuscular injection - is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe intramuscular injection @@ -19888,10 +20022,7 @@ Added duirng Mar 1, 2010 dev call - - - - + @@ -19923,15 +20054,7 @@ Added duirng Mar 1, 2010 dev call - - - - - - - intradermal injection - is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot intradermal injection @@ -20224,15 +20347,7 @@ Biochimie. 2010 Feb 18. - - - - - - - oral administration - An administering substance in vivo into the mouth of an organism PERSON: Melanie Courtot oral administration @@ -20270,10 +20385,7 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - - - - + @@ -20305,15 +20417,7 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - - - - - - - subcutaneous injection - is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot subcutaneous injection @@ -20950,10 +21054,7 @@ In the examples above, a reagent is an operational component of a device, but th - - - - + @@ -20971,15 +21072,7 @@ In the examples above, a reagent is an operational component of a device, but th - - - - - - - intranasal mucosal administration - The administration of a substance into the intranasal mucosis of an organism PERSON: Melanie Courtot intranasal mucosal administration @@ -21206,10 +21299,7 @@ In the examples above, a reagent is an operational component of a device, but th - - - - + @@ -21241,15 +21331,7 @@ In the examples above, a reagent is an operational component of a device, but th - - - - - - - intravenous injection - is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot intravenous injection @@ -25892,7 +25974,7 @@ All subtype will be defined by textual definition now. - + @@ -25901,9 +25983,7 @@ All subtype will be defined by textual definition now. passive immunization - Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. -Transferring epitope specific T cells from one mouse into another. - + Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. Transferring epitope specific T cells from one mouse into another. The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum adoptive transfer @@ -58902,12 +58982,12 @@ https://www.doi.org/ - Illumina Infinium MethylationEPIC BeadChip + Illumina Infinium MethylationEPIC v1.0 BeadChip An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. Person: Chris Stoeckert, Jason Hilton http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf - Illumina Infinium MethylationEPIC BeadChip + Illumina Infinium MethylationEPIC v1.0 BeadChip @@ -72722,7 +72802,8 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A specimen that is collected with a suctioning tube from the nasal cavity. Asiyah Yu Lin ORCID:0000-0003-2620-0345 - nasal wash specimen|nasopharyngeal aspirate + nasal wash specimen + nasopharyngeal aspirate Asiyah Yu Lin ORCID:0000-0003-2620-0345 nasal aspirate specimen @@ -76938,6 +77019,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + antibiotic administration process Administering substance in vivo where an antibiotic substance is administered to a living organism. Chris Stoeckert Cristian Cocos @@ -83137,6 +83219,290 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + MRI used for assessing structural integrity of brain axons and visualizing ischemia. + A type of magnetic resonance image data set collected using at least three diffusion gradients of some factor "b," which is a function of the amplitude, duration, and interval of the gradiants. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://github.com/obi-ontology/obi/issues/1481 + diffusion weighted magnetic resonance image data set + + + + + + + + + MRI used for assessing brain activity via blood oxygen level dependent signal. + An magnetic resonance image data set collected as a 4D time series representing changes in brain metabolism (i.e. BOLD), typically used as a proxy for brain activity. + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://github.com/obi-ontology/obi/issues/1481 + functional magnetic resonance image data set + + + + + + + + + An fMRI used for assessing functional connectivity of brain regions at rest. + A type of functional MRI in which the participant is not given a task, but just rests during acquisision + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://github.com/obi-ontology/obi/issues/1481 + resting state functional magnetic resonance image data set + + + + + + + + + fMRI type used for assessing brain activity while performing an action or in response to stimuli. + A type of functional MRI in which the participant is given a task or tasks, which are timed with the acquisition + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://github.com/obi-ontology/obi/issues/1481 + task-based functional magnetic resonance image data set + + + + + + + + + MRI used for evaluating ischemia. + An magnetic resonance image data set that captures volume and flow of blood in the brain. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://github.com/obi-ontology/obi/issues/1481 + perfusion weighted magnetic resonance image data set + + + + + + + + + MRI used for visualizing structure of tissue. + An magnetic resonance image data set in which the contrast emphasizes density of protons, supressing T1 and T2 effects + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://github.com/obi-ontology/obi/issues/1481 + proton density magnetic resonance image data set + + + + + + + + + MRI used for visualizing structure of tissue where fluid is hypointense. + An magnetic resonance image acquired using a T1 weighted magnetic resonance image acquisition sequence. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://github.com/obi-ontology/obi/issues/1481 + T1 weighted magnetic resonance image data set + + + + + + + + + MRI used for assessing breakdown of blood brain barrier. + A T1 weighted image data set where gadolidium contrast agent has been administered to the participant before image acquistion. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://github.com/obi-ontology/obi/issues/1481 + post-Gd T1 weighted magnetic resonance image data set + + + + + + + + + MRI used for computational research on the structure of tissue. + T1 weighted image data set collected using a gradient recall echo sequence. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://github.com/obi-ontology/obi/issues/1481 + T1 weighted GRE magnetic resonance image data set + + + + + + + + + MRI used for computational segmentation of tissue due to high quality. + A T1-weighted image data set acquired from an NMR/MRI machine with at least a 3 Tesla magnet and in which the voxel size is isotropic. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://github.com/obi-ontology/obi/issues/1481 + high resolution T1 weighted magnetic resonance image data set + + + + + + + + + First MRI acquired as part of longitudinal study. + A T1w image data set collected at an evaluant's first visit in a study. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://github.com/obi-ontology/obi/issues/1481 + baseline high resolution T1 weighted magnetic resonance image data set + + + + + + + + + MRI acquired after the first scan as part of longitudinal study. + A T1w image data set collected at a later time than the evaluant's first scan. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://github.com/obi-ontology/obi/issues/1481 + follow-up high resolution T1 weighted magnetic resonance image data set + + + + + + + + + MRI used for visualizing structure of tissue, often of lower quality than a GRE sequence. + A T1 weighted image data set acquired using a spin echo sequence. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://github.com/obi-ontology/obi/issues/1481 + T1 weighted SE magnetic resonance image data set + + + + + + + + + MRI used for visualizing structure of tissue where fluid is hyperintense. + A magnetic resonance image produced by a T2 weighted magnetic resonance image acquisition sequence. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://github.com/obi-ontology/obi/issues/1481 + T2 weighted magnetic resonance image data set + + + + + + + + + MRI used for visualizing lesions in multiple sclerosis. + A T2 weighted image data set collected using a FLAIR sequence. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://github.com/obi-ontology/obi/issues/1481 + T2 weighted FLAIR magnetic resonance image data set + + + + + + + + + MRI used for visualizing structure of tissue with fast acquisition times. + T2 weighted image collected using a fast/turbo spin echo sequence. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + T2 weighted TSE magnetic resonance image data set + https://github.com/obi-ontology/obi/issues/1481 + T2 weighted FSE magnetic resonance image data set + + + + + + + + + MRI used for visualizing structure of tissue, often longer acquisition than FSE sequence. + A type of T2-weighted image in which the acquisition is performed using a 2D spin-echo technique + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://github.com/obi-ontology/obi/issues/1481 + T2 weighted SE magnetic resonance image data set + + + + + + + + + MRI used for visualizing structure of tissue where signal from fat is suppressed. + A T2 weighted magnetic resonance image data set collected using a STIR sequence to suppress the signal coming from fat. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://github.com/obi-ontology/obi/issues/1481 + T2 weighted STIR magnetic resonance image data set + + + + + + + + + MRI better suited for identifying focal pathology than T2w SE sequences. + T2* weighted image data set collected using a gradient echo sequence. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://github.com/obi-ontology/obi/issues/1481 + T2* weighted GRE magnetic resonance image data set + + + + @@ -83220,6 +83586,118 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + The Desikan-Killiany brain region atlas used by the FreeSurfer software suite. + An image data set consisting of values computed from multiple image data sets encoded to represent the spatial location of individual functional or structural regions of a canonical brain. + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + https://github.com/obi-ontology/obi/issues/1481 + brain region atlas image data set + + + + + + + + + A brain atlas of resting-state functional networks derived from the probability that disparate brains regions are active at the same time. + A brain atlas consisting of weighted values that respresent the probability that a voxel X is part of some brain component Y, typically derived from multiple image data sets. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + https://github.com/obi-ontology/obi/issues/1481 + probabilistic brain region atlas image dataset + + + + + + + + + The JHU white-matter tractography atlas used for mapping brain connectomes. + A brain atlas consisting of discrete integer values where a value X denotes a voxel is part of some brain component Y. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + https://github.com/obi-ontology/obi/issues/1481 + deterministic brain region atlas image data set + + + + + + + + + The output of an algorithm that identifies pedestrians walking in a street from an image data set, where the output contains values only in the segment where the pedestrian is present. + An image data set of integer values in which each value corresponds to some shared characteristic or computed property. The values often belong to a group of pixels or voxels that share the same characteristic, such as a tissue type or anatomical region. + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + https://github.com/obi-ontology/obi/issues/1481 + image segmentation map + + + + + + + + + The output produced by a manual or automated segmentation of lesions from a brain MRI. + An image data set where voxel intensity values greater than zero encode the location of some brain lesion and voxels outside the lesion have an intensity value of zero. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://github.com/obi-ontology/obi/issues/1481 + lesion mask + + + + + + + + + The output produced by a manual or automated segmentation of lesions from a T1w MRI. + A lesion mask where the lesions are derived from a T1 weighted image data set. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://github.com/obi-ontology/obi/issues/1481 + T1 lesion mask + + + + + + + + + The output produced by a manual or automated segmentation of lesions from a T2w FLAIR MRI. + A lesion mask where the lesions are derived from a T2 FLAIR image data set. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://github.com/obi-ontology/obi/issues/1481 + T2 FLAIR lesion mask + + + + @@ -84027,6 +84505,12 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + An administration of substance in vivo with the intention to induce disease in the organism. IEDB IEDB @@ -84039,6 +84523,20 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + + An administration of substance in vivo with the intention to reduce the symptoms of or prevent development of a disease in the organism. IEDB IEDB @@ -84786,6 +85284,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + in vivo challenge The administration of a challenge to a live host. Hector Guzman-Orozco IEDB @@ -88258,6 +88757,650 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the stomach of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intragastric administration + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the colon of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intracolonic administration + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the vagina of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + vaginal administration + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance onto the surface of the skin of an organism. + Sebastian Duesing + percutaneous administration + transcutaneous administration + https://github.com/obi-ontology/obi/issues/1703 + topical administration + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance to the cervix of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + cervical administration + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance to the conjunctiva of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + conjunctival administration + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the trachea of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intratracheal administration + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the amnion of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intra-amniotic administration + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the artery of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intra-arterial administration + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the cerebrum of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intracerebral administration + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the cranium of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intracranial administration + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the epidermis of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intraepidermal administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the lymphatic system of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intralymphatic administration + + + + + + + + + + + + + + + + + + + + + + + + + An intralymphatic administration in which the substance is administered into a lymph node. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + lymph node administration + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the urethra of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + urethral administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An intraepidermal administration in which the skin is scratched before the substance is administered to the skin. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + skin scarification administration + + + + + + + + + + + + + + + + + + + + + + + + + An adminstration of a substance into the uterus of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intrauteral administration + + + + + + + + + + + + + + + + + + + + + + + + + An intra-arterial administration in which the substance is administered into the carotid artery. + Sebastian Duesing + i.c. + i.c. administration + https://github.com/obi-ontology/obi/issues/1703 + intracarotid administration + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance to the eye of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intraocular administration + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the placenta of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intraplacental administration + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the rectum of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intrarectal administration + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the spleen of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intrasplenic administration + + + + + + + + + A process in which the target material entity is scraped by another material entity. + Sebastian Duesing + abrading + https://github.com/obi-ontology/obi/issues/1703 + scratching + + + + @@ -89146,6 +90289,33 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + + + + + + + + + An administration of a substance into a tumor of an organism. + Sebastian Duesing + intratumoral administration + + + + @@ -89197,6 +90367,1182 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + An objective specification that is fulfilled by causing a disease in a particular organism. + Sebastian Duesing + disease causation objective + + + + + + + + + An objective specification that is fulfilled by reducing the severity of a disease in a particular organism. + Sebastian Duesing + disease severity reduction objective + + + + + + + + + An objective specification that is fulfilled by preventing the development of a disease in a particular organism. + Sebastian Duesing + disease prevention objective + + + + + + + + + A role borne by a biological or chemical entity that participates or has molecular components that participate in a chemical reaction. + Sebastian Duesing + reactant role + + + + + + + + + A role borne by a biological or chemical entity which serves as the core component of a chemical reaction process, upon which other reactants, like reagents or solvents, act. + Cameron More + Sebastian Duesing + precursor role + + + + + + + + + + + + + + + + + + + + + + + + + + + + An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a T cell epitope:MHC:TCR complex. + PERSON:Randi Vita, Sebastian Duesing, Bjoern Peters + IEDB + 3D structure|electron microscopy + electron microscopy assay determining the 3D structure of a T cell epitope:MHC:TCR complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a MHC:ligand complex. + PERSON:Randi Vita, Sebastian Duesing, Bjoern Peters + IEDB + 3D structure|electron microscopy + electron microscopy assay determining the 3D structure of a MHC:ligand complex + + + + + + + + + An objective specification that is fulfilled by reducing the prevalence of a disease in a population of organisms. + Sebastian Duesing + disease prevalence reduction objective + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A purification to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + antibody purification of MHC protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of MHC protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC class I protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of MHC class I protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of human MHC class I protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of human MHC class I protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A2 serotype, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of HLA protein complex with A2 serotype + + + + + + + + + + + + + + + + + + + An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A24 serotype, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of HLA protein complex with A24 serotype + + + + + + + + + + + + + + + + + + + + + + + + + + An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A2 serotype and/or HLA protein complex with A28 serotype, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of HLA protein complex with A2 serotype and/or HLA protein complex with A28 serotype + + + + + + + + + + + + + + + + + + + An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A29 serotype, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of HLA protein complex with A29 serotype + + + + + + + + + + + + + + + + + + + An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with B27 serotype, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of HLA protein complex with B27 serotype + + + + + + + + + + + + + + + + + + + An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA-C protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of HLA-C protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of pig MHC class I protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of pig MHC class I protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of cattle MHC class I protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of cattle MHC class I protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of rat MHC class I protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of rat MHC class I protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse MHC class I protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of mouse MHC class I protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Dd protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of H2-Dd protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Db protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of H2-Db protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Kd protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of H2-Kd protein complex + + + + + + + + + + + + + + + + + + + + + + + + + + + An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Ld protein complex, H2-Db protein complex, and/or H2-Dq protein complex while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of H2-Ld protein complex, H2-Db protein complex, and/or H2-Dq protein complex + + + + + + + + + + + + + + + + + + + + + + + + + + An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Dd protein complex and/or H2-Kd protein complex while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of H2-Dd protein complex and/or H2-Kd protein complex + + + + + + + + + + + + + + + + + + + + + + + + + + An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse MHC class I protein complex with H2-b haplotype and/or mouse MHC protein complex with H2-p haplotype while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of mouse MHC class I protein complex with H2-b haplotype and/or mouse MHC protein complex with H2-p haplotype + + + + + + + + + + + + + + + + + + + + + + + + + + + An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse H2-Kb protein complex, H2-Ks protein complex, and/or H2-Kq protein complex while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of H2-Kb protein complex, H2-Ks protein complex, and/or H2-Kq protein complex + + + + + + + + + + + + + + + + + + + + + + + + + + + An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of pig MHC class I protein complex, cattle MHC class I protein complex, and/or human MHC class I protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of pig MHC class I protein complex, cattle MHC class I protein complex, and/or human MHC class I protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of MHC protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC class II protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of MHC class II protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of cattle MHC class II protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of cattle MHC class II protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of human MHC class II protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of human MHC class II protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of human MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA-DP protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of HLA-DP protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of human MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA-DR protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of HLA-DR protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of human MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with DQ3 serotype, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of HLA protein complex with DQ3 serotype + + + + + + + + + + + + + + + + + + + An antibody purification of MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse MHC class II protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of mouse MHC class II protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of mouse MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-IA protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of H2-IA protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of mouse MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-IAg7 protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of H2-IAg7 protein complex + + + + + + + + + + + + + + + + + + + An antibody purification of mouse MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-IAd protein complex, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of H2-IAd protein complex + + + + + + + + + + + + + + + + + + + + + + + + + + An antibody purification of MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse MHC class II protein complex and/or rat MHC class II protein complex with RT1-A haplotype, while others contain impurities and are not of interest. + Randi Vita + Sebastian Duesing + Randi Vita + antibody purification of mouse MHC class II protein complex and/or rat MHC class II protein complex with RT1-A haplotype + + + + + + + + + + + + + + + + + + + + + + + + + + + + + tandem mass spectrometry analysis + Sebastian Duesing + A mass spectrometry analysis in which the data being analyzed is the result of a tandem mass spectrometry assay. + https://github.com/obi-ontology/obi/issues/1684 + tandem mass spectrometry analysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + liquid chromatography mass spectrometry analysis + Sebastian Duesing + A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography mass spectrometry assay. + https://github.com/obi-ontology/obi/issues/1684 + liquid chromatrography mass spectrometry analysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + liquid chromatography tandem mass spectrometry analysis + Sebastian Duesing + A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography tandem mass spectrometry assay. + https://github.com/obi-ontology/obi/issues/1684 + liquid chromatography-tandem mass spectrometry analysis + + + + + + + + + Illumina Infinium MethylationEPIC v2.0 BeadChip + An Illumina methylation BeadChip that targets 935,000 methylation sites per sample at single-nucleotide resolution. + Sebastian Duesing + https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html + https://github.com/obi-ontology/obi/issues/1665 + Illumina Infinium MethylationEPIC v2.0 BeadChip + + + + + + + + + A clinical data item that quantifies the severity of a person's fatigue as measured by a 20-item self-report instrument. + Sebastian Duesing + https://pubmed.ncbi.nlm.nih.gov/7636775/ DOI: 10.1016/0022-3999(94)00125-o + multidimensional fatigue inventory score + + + + + + + + + + + + + + + + + + + albumin-free serum + A blood serum specimen that contains no albumin. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/493 + Philippe Rocca-Serra + albumin-free serum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + fasting + Pre-test fasting is required or recommended for several blood tests, including glucose and C-peptide tests. 8–12 hours is typical for fasting duration. + A planned process in which an organism drinks only water and does not eat for a specified period of time. + Sebastian Duesing + A.M. Simundic et al., Standardization of collection requirements for fasting samples: For the Working Group on Preanalytical Phase (WG-PA) of the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM), Clinica Chimica Acta, Volume 432, 2014, Pages 33-37, ISSN 0009-8981, https://doi.org/10.1016/j.cca.2013.11.008. + https://github.com/obi-ontology/obi/issues/494 + Philippe Rocca-Serra + fasting + + + + + + + + + Overnight fasting commonly occurs prior to a blood draw scheduled in the morning. + A fasting with a duration of 8–12 hours, typically occurring overnight. + Sebastian Duesing + A.M. Simundic et al., Standardization of collection requirements for fasting samples: For the Working Group on Preanalytical Phase (WG-PA) of the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM), Clinica Chimica Acta, Volume 432, 2014, Pages 33-37, ISSN 0009-8981, https://doi.org/10.1016/j.cca.2013.11.008. + https://github.com/obi-ontology/obi/issues/494 + Philippe Rocca-Serra + overnight fasting + + + + + + + + + + + + + + + An organismal quality that inheres in an organism that has completed a fasting process, and which ceases to inhere in that organism once that organism drinks a liquid other than water or eats. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/494 + Philippe Rocca-Serra + fasted + + + + + + + + + An information content entity that indicates the smallest increment that can be resolved on the scale of a measurement instrument. + Sebastian Duesing + least count + https://en.wikipedia.org/wiki/Least_count + https://github.com/obi-ontology/obi/issues/506 + Philippe Rocca-Serra + minimum resolved unit of measurement + + + + @@ -89638,30 +91984,26 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - + + + + 0 + + + primary cultured cell population Spleen cells put directly into culture; Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934 cells that have been isolated from some organismal source, expanded in culture, but not undergone a complete passaging (ie are still in culture, or have been lifted from culture and frozen in aliquots for future use) A cultured cell population comprised of cells expanded directly from living tissue prior to being passaged. 2013-6-5 MHB: This OBI class was formerly called 'primary cell culture', but label changed and definition updated following CLO alignment work. Previous definition: 'a primary cell culture is a cell culture where the cells derive from a fresh tissue source.' + consider if we really want to be so strict here . . . ie maybe we we say that they have not been output from an 'establishing cell line' process, but in some cases a passage or two may be allowed for a primary culture. the establishing of a line requires some procedss that attains a degree of homogeneity in the culture. PERSON:Matthew Brush primary cell culture primary cell culture sample PERSON:Matthew Brush primary cultured cell population - - - 0 - - - - - - - consider if we really want to be so strict here . . . ie maybe we we say that they have not been output from an 'establishing cell line' process, but in some cases a passage or two may be allowed for a primary culture. the establishing of a line requires some procedss that attains a degree of homogeneity in the culture. - @@ -93962,7 +96304,7 @@ determinations of compounds. - + @@ -97653,6 +99995,7 @@ Manual editing of automatically recorded data in an anesthesia information manag + @@ -100609,11 +102952,10 @@ Possible ecological risks of transgenic organism release when transgenes affect administration in vivo with infectious agent - - is an administration of an infectious agent to a host organism - IEDB - IEDB - administration in vivo with infectious agent + is an administration of an infectious agent to a host organism + IEDB + IEDB + administration in vivo with infectious agent @@ -101365,7 +103707,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it IEDB adherent cell culture sample IEDB - cultured adherent cell populaiton + cultured adherent cell population @@ -101574,7 +103916,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + @@ -101613,7 +103955,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + @@ -101621,7 +103963,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + @@ -102686,14 +105028,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - CD8 receptor - + A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. - This term does not belong in ONTIE. It should be imported from PRO, but there seems to be no appropriate term as of 08/17/2009. CD8 - WEB: http://en.wikipedia.org/wiki/CD8 - CD8 receptor + https://github.com/obi-ontology/obi/issues/353 + + obsolete CD8 receptor + true @@ -130847,6 +133188,12 @@ realizes some 'host of immune response role' + + + + + + @@ -131019,6 +133366,12 @@ realizes some 'host of immune response role' + + + + + + @@ -131254,6 +133607,12 @@ realizes some 'host of immune response role' + + + + + + @@ -131362,6 +133721,12 @@ realizes some 'host of immune response role' + + + + + + @@ -131488,6 +133853,12 @@ realizes some 'host of immune response role' + + + + + + @@ -131524,6 +133895,12 @@ realizes some 'host of immune response role' + + + + + + @@ -131554,6 +133931,12 @@ realizes some 'host of immune response role' + + + + + + @@ -131578,6 +133961,12 @@ realizes some 'host of immune response role' + + + + + + @@ -131728,6 +134117,12 @@ realizes some 'host of immune response role' + + + + + + @@ -131740,6 +134135,12 @@ realizes some 'host of immune response role' + + + + + + diff --git a/views/obi.obo b/views/obi.obo index d45aef7d..72f402e1 100644 --- a/views/obi.obo +++ b/views/obi.obo @@ -1,6 +1,19 @@ format-version: 1.2 -data-version: 2024-01-09 -date: 09:01:2024 14:43 +data-version: 2024-05-03 +date: 03:05:2024 11:02 +synonymtypedef: OMO:0003000 "abbreviation" +synonymtypedef: OMO:0003001 "ambiguous synonym" +synonymtypedef: OMO:0003002 "dubious synonym" +synonymtypedef: OMO:0003003 "layperson synonym" +synonymtypedef: OMO:0003004 "plural form" +synonymtypedef: OMO:0003005 "UK spelling synonym" +synonymtypedef: OMO:0003006 "misspelling" +synonymtypedef: OMO:0003007 "misnomer" +synonymtypedef: OMO:0003008 "previous name" +synonymtypedef: OMO:0003009 "legal name" +synonymtypedef: OMO:0003010 "International Nonproprietary Name" +synonymtypedef: OMO:0003011 "latin term" +synonymtypedef: OMO:0003012 "acronym" remark: Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. ontology: obi property_value: defaultLanguage "en" xsd:string @@ -67,40 +80,7 @@ property_value: http://purl.org/dc/elements/1.1/subject "An ontology for the ann property_value: http://purl.org/dc/terms/license "http://creativecommons.org/licenses/by/4.0/" xsd:string property_value: http://purl.org/dc/terms/title "Ontology for Biomedical Investigations" xsd:string property_value: IAO:0000589 "Ontology for Biomedical Investigations" xsd:string -property_value: owl:versionInfo "2024-01-09" xsd:string - -[Term] -id: APOLLO_SV:00000008 -name: software development -def: "A planned process that has specified output a software product and that involves the creation of source code." [] -is_a: OBI:0000011 ! planned process - -[Term] -id: APOLLO_SV:00000032 -name: count -def: "A measurement datum that is the output of counting." [] -is_a: IAO:0000109 ! measurement datum - -[Term] -id: APOLLO_SV:00000033 -name: counting -def: "The planned process of finding the number of elements in a finite set of objects." [] -is_a: OBI:0000011 ! planned process - -[Term] -id: APOLLO_SV:00000522 -name: source code repository -def: "A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc." [] -comment: Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based -is_a: IAO:0000310 ! document - -[Term] -id: APOLLO_SV:00000796 -name: dataset creating -def: "A planned process that has a data set as its specified output." [] -synonym: "data set creation" EXACT [] -synonym: "dataset creation" EXACT [] -is_a: OBI:0000011 ! planned process +property_value: owl:versionInfo "2024-05-03" xsd:string [Term] id: BFO:0000001 @@ -125,39 +105,24 @@ id: BFO:0000004 name: independent continuant is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant -disjoint_from: BFO:0000031 ! generically dependent continuant - -[Term] -id: BFO:0000005 -name: obsolete dependent continuant -def: "A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities." [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true [Term] id: BFO:0000006 name: spatial region is_a: BFO:0000141 ! immaterial entity disjoint_from: BFO:0000029 ! site -disjoint_from: BFO:0000029 ! site -disjoint_from: BFO:0000140 ! continuant fiat boundary [Term] id: BFO:0000008 name: temporal region is_a: BFO:0000003 ! occurrent disjoint_from: BFO:0000011 ! spatiotemporal region -disjoint_from: BFO:0000011 ! spatiotemporal region -disjoint_from: BFO:0000015 ! process -disjoint_from: BFO:0000035 ! process boundary [Term] id: BFO:0000009 name: two-dimensional spatial region is_a: BFO:0000006 ! spatial region disjoint_from: BFO:0000018 ! zero-dimensional spatial region -disjoint_from: BFO:0000028 ! three-dimensional spatial region [Term] id: BFO:0000011 @@ -186,7 +151,6 @@ disjoint_from: BFO:0000019 ! quality id: BFO:0000018 name: zero-dimensional spatial region is_a: BFO:0000006 ! spatial region -disjoint_from: BFO:0000028 ! three-dimensional spatial region [Term] id: BFO:0000019 @@ -197,7 +161,6 @@ is_a: BFO:0000020 ! specifically dependent continuant id: BFO:0000020 name: specifically dependent continuant is_a: BFO:0000002 ! continuant -disjoint_from: BFO:0000031 ! generically dependent continuant [Term] id: BFO:0000023 @@ -207,14 +170,13 @@ is_a: BFO:0000017 ! realizable entity [Term] id: BFO:0000024 -name: fiat object part +name: fiat object is_a: BFO:0000040 ! material entity [Term] id: BFO:0000026 name: one-dimensional spatial region is_a: BFO:0000006 ! spatial region -disjoint_from: BFO:0000028 ! three-dimensional spatial region [Term] id: BFO:0000027 @@ -279,8 +241,6 @@ id: BFO:0000142 name: one-dimensional continuant fiat boundary is_a: BFO:0000140 ! continuant fiat boundary disjoint_from: BFO:0000146 ! two-dimensional continuant fiat boundary -disjoint_from: BFO:0000146 ! two-dimensional continuant fiat boundary -disjoint_from: BFO:0000147 ! zero-dimensional continuant fiat boundary [Term] id: BFO:0000144 @@ -2431,7 +2391,6 @@ is_a: IAO:0000009 ! datum label id: IAO:0000005 name: objective specification def: "A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved." [] -synonym: "goal specification" EXACT [] is_a: IAO:0000033 ! directive information entity [Term] @@ -2446,12 +2405,6 @@ name: action specification def: "A directive information entity that describes an action the bearer will take." [] is_a: IAO:0000033 ! directive information entity -[Term] -id: IAO:0000008 -name: obsolete_artifact -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true - [Term] id: IAO:0000009 name: datum label @@ -2464,62 +2417,16 @@ name: software def: "Software is a plan specification composed of a series of instructions that can be \ninterpreted by or directly executed by a processing unit." [] is_a: IAO:0000104 ! plan specification -[Term] -id: IAO:0000012 -name: obsolete2_digital entity -def: "A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical." [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true - -[Term] -id: IAO:0000013 -name: journal article -def: "A report that is published in a journal." [] -is_a: IAO:0000088 ! report - [Term] id: IAO:0000015 name: information carrier def: "A quality of an information bearer that imparts the information content" [] is_a: BFO:0000019 ! quality -[Term] -id: IAO:0000017 -name: model number -def: "A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots." [] -is_a: IAO:0000028 ! symbol - -[Term] -id: IAO:0000018 -name: obsolete_material_entity -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true - -[Term] -id: IAO:0000019 -name: obsolete2_binary digital entity -def: "A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters." [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true - -[Term] -id: IAO:0000024 -name: obsolete_unit of measure -def: "a unit of measure is the quality of some material entity compared to which another quality is some multiple of." [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true - -[Term] -id: IAO:0000025 -name: programming language -def: "A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it." [] -is_a: IAO:0000104 ! plan specification - [Term] id: IAO:0000027 name: data item def: "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] -synonym: "data" EXACT [] is_a: IAO:0000030 ! information content entity [Term] @@ -2528,24 +2435,12 @@ name: symbol def: "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." [] is_a: IAO:0000030 ! information content entity -[Term] -id: IAO:0000029 -name: numeral -def: "A symbol that denotes a number." [] -is_a: IAO:0000028 ! symbol - [Term] id: IAO:0000030 name: information content entity def: "A generically dependent continuant that is about some thing." [] is_a: BFO:0000031 ! generically dependent continuant -[Term] -id: IAO:0000031 -name: integer numeral -def: "A numeral that denotes an integer" [] -is_a: IAO:0000029 ! numeral - [Term] id: IAO:0000032 name: scalar measurement datum @@ -2558,19 +2453,6 @@ name: directive information entity def: "An information content entity whose concretizations indicate to their bearer how to realize them in a process." [] is_a: IAO:0000030 ! information content entity -[Term] -id: IAO:0000034 -name: time trigger -is_a: IAO:0000001 ! conditional specification - -[Term] -id: IAO:0000035 -name: obsolete_study interpretation -def: "A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses" [] -synonym: "conclusion" EXACT [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true - [Term] id: IAO:0000037 name: dot plot @@ -2583,43 +2465,18 @@ name: graph def: "A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way." [] is_a: IAO:0000309 ! diagram -[Term] -id: IAO:0000047 -name: obsolete2_text based digital entity -def: "A text based digital entity is a digital entity that is encoded so that it only contains text characters." [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true - [Term] id: IAO:0000055 name: rule def: "A rule is an executable which guides, defines, restricts actions." [] is_a: IAO:0000001 ! conditional specification -[Term] -id: IAO:0000057 -name: contour plot -is_a: IAO:0000038 ! graph - -[Term] -id: IAO:0000059 -name: obsolete2_report figure -def: "A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements" [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true - [Term] id: IAO:0000064 name: algorithm def: "A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata." [] is_a: IAO:0000104 ! plan specification -[Term] -id: IAO:0000065 -name: software interpreter -def: "A software interpreter is a software application that executes some specified input software." [] -is_a: IAO:0000064 ! algorithm - [Term] id: IAO:0000078 name: curation status specification @@ -2638,33 +2495,6 @@ name: report def: "A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)." [] is_a: IAO:0000310 ! document -[Term] -id: IAO:0000091 -name: obsolete_report element -def: "A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page)." [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true - -[Term] -id: IAO:0000093 -name: obsolete2_binary executable -def: "Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)" [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true - -[Term] -id: IAO:0000096 -name: source code module -def: "A source code module is a directive information entity that specifies, using a programming language, some algorithm." [] -is_a: IAO:0000033 ! directive information entity - -[Term] -id: IAO:0000097 -name: obsolete_report table -def: "A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content" [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true - [Term] id: IAO:0000098 name: data format specification @@ -2692,60 +2522,15 @@ is_a: IAO:0000027 ! data item [Term] id: IAO:0000104 name: plan specification -def: "A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified." [] -comment: 2/3/2009 Comment from OBI review.\n\nAction specification not well enough specified.\nConditional specification not well enough specified.\nQuestion whether all plan specifications have objective specifications.\n\nRequest that IAO either clarify these or change definitions not to use them +def: "A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified." [] is_a: IAO:0000033 ! directive information entity -[Term] -id: IAO:0000105 -name: obsolete2_digital document -def: "A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file." [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true - [Term] id: IAO:0000109 name: measurement datum def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." [] is_a: IAO:0000027 ! data item -[Term] -id: IAO:0000128 -name: obsolete_identifier -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true - -[Term] -id: IAO:0000129 -name: version number -def: "A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name." [] -is_a: IAO:0000028 ! symbol - -[Term] -id: IAO:0000131 -name: serial number -def: "A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots." [] -is_a: IAO:0000028 ! symbol - -[Term] -id: IAO:0000132 -name: lot number -def: "A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots." [] -synonym: "batch number" EXACT [] -is_a: IAO:0000028 ! symbol - -[Term] -id: IAO:0000140 -name: setting datum -def: "A settings datum is a datum that denotes some configuration of an instrument." [] -is_a: IAO:0000027 ! data item - -[Term] -id: IAO:0000141 -name: obsolete_digital quality -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true - [Term] id: IAO:0000144 name: conclusion textual entity @@ -2771,19 +2556,6 @@ name: heatmap def: "A heatmap is a report graph which is a graphical representation of data\nwhere the values taken by a variable(s) are shown as colors in a\ntwo-dimensional map." [] is_a: IAO:0000038 ! graph -[Term] -id: IAO:0000181 -name: Venn diagram -def: "A Venn diagram is a report graph showing all hypothetically possible\nlogical relations between a finite collection of sets." [] -is_a: IAO:0000038 ! graph - -[Term] -id: IAO:0000182 -name: obsolete_survival curve -def: "A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time." [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true - [Term] id: IAO:0000183 name: dendrogram @@ -2794,21 +2566,8 @@ is_a: IAO:0000038 ! graph id: IAO:0000184 name: scatter plot def: "A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis." [] -synonym: "scattergraph" EXACT [] is_a: IAO:0000038 ! graph -[Term] -id: IAO:0000185 -name: photograph -def: "A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc." [] -is_a: IAO:0000101 ! image - -[Term] -id: IAO:0000186 -name: photographic print -def: "A photographic print is a material entity upon which a photograph generically depends." [] -is_a: IAO:0000178 ! material information bearer - [Term] id: IAO:0000225 name: obsolescence reason specification @@ -2819,51 +2578,14 @@ is_a: IAO:0000102 ! data about an ontology part id: IAO:0000300 name: textual entity def: "A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc." [] -synonym: "text" EXACT [] is_a: IAO:0000030 ! information content entity -[Term] -id: IAO:0000301 -name: citation -def: "A textual entity intended to identify a particular publication." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000302 -name: author identification -def: "A textual entity intended to identify a particular author" [] -is_a: IAO:0000590 ! written name - -[Term] -id: IAO:0000303 -name: institutional identification -def: "A textual entity intended to identify a particular institution" [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000304 -name: caption -def: "A textual entity that describes a figure" [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000305 -name: document title -def: "A textual entity that names a document" [] -is_a: IAO:0000300 ! textual entity - [Term] id: IAO:0000306 name: table def: "A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions" [] is_a: IAO:0000300 ! textual entity -[Term] -id: IAO:0000307 -name: table of abbreviations -def: "A table where the constituent texts are abbreviations and their expansions" [] -is_a: IAO:0000306 ! table - [Term] id: IAO:0000308 name: figure @@ -2885,143 +2607,15 @@ is_a: IAO:0000030 ! information content entity [Term] id: IAO:0000311 name: publication -def: "A document that has been accepted by a publisher" [] +def: "A document that is the output of a publishing process." [] is_a: IAO:0000310 ! document [Term] id: IAO:0000312 name: publication about an investigation def: "A publication that is about an investigation" [] -synonym: "scientific publication" EXACT [] is_a: IAO:0000311 ! publication -[Term] -id: IAO:0000313 -name: patent -def: "A document that has been accepted by a patent authority" [] -is_a: IAO:0000310 ! document - -[Term] -id: IAO:0000314 -name: document part -def: "An information content entity that is part of a document." [] -is_a: IAO:0000030 ! information content entity - -[Term] -id: IAO:0000315 -name: abstract -def: "A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes." [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000316 -name: introduction to a publication about an investigation -def: "A part of a publication about an investigation that is about the objective specification (why the investigation is being done)" [] -synonym: "background" EXACT [] -synonym: "introduction" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000317 -name: methods section -def: "A part of a publication about an investigation that is about the study design of the investigation" [] -synonym: "experimental" EXACT [] -synonym: "experimental procedures" EXACT [] -synonym: "experimental section" EXACT [] -synonym: "methods" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000318 -name: results section -def: "A part of a publication about an investigation that is about a study design execution" [] -synonym: "results" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000319 -name: discussion section of a publication about an investigation -def: "A part of a publication about an investigation that is about the study interpretation of the investigation" [] -synonym: "discussion" EXACT [] -synonym: "discussion section" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000320 -name: references section -def: "A part of a document that has citations as parts" [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000321 -name: author list -def: "A part of a document that enumerates the authors of the document" [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000322 -name: institution list -def: "A part of a document that has parts that are institution identifications associated with the authors of the document" [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000323 -name: author contributions section -def: "A part of a publication that is about the specific contributions of each author" [] -synonym: "author contributions" EXACT [] -synonym: "contributions by the authors" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000324 -name: acknowledgements section -def: "Part of a publication that is about the contributions of people or institutions other than the authors." [] -synonym: "acknowledgements" EXACT [] -synonym: "acknowledgments" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000325 -name: footnote -def: "A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document." [] -synonym: "endnote" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000326 -name: supplementary material to a document -def: "A part of a document that is segregated from the rest of the document due to its size" [] -synonym: "additional information" EXACT [] -synonym: "appendix" EXACT [] -synonym: "supplemental information" EXACT [] -synonym: "supplementary material" EXACT [] -synonym: "supporting information" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000327 -name: table of contents -def: "A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred)." [] -is_a: IAO:0000306 ! table - -[Term] -id: IAO:0000328 -name: table of figures -def: "A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred)." [] -is_a: IAO:0000306 ! table - -[Term] -id: IAO:0000329 -name: running title -def: "A shorter version of a document title" [] -is_a: IAO:0000305 ! document title - -[Term] -id: IAO:0000330 -name: copyright section -def: "A document part that describes legal restrictions on making or distributing copies of the document" [] -is_a: IAO:0000314 ! document part - [Term] id: IAO:0000400 name: cartesian spatial coordinate datum @@ -3034,18 +2628,6 @@ name: one dimensional cartesian spatial coordinate datum def: "A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region" [] is_a: IAO:0000400 ! cartesian spatial coordinate datum -[Term] -id: IAO:0000402 -name: two dimensional cartesian spatial coordinate datum -def: "A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region" [] -is_a: IAO:0000400 ! cartesian spatial coordinate datum - -[Term] -id: IAO:0000403 -name: three dimensional cartesian spatial coordinate datum -def: "A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region" [] -is_a: IAO:0000400 ! cartesian spatial coordinate datum - [Term] id: IAO:0000408 name: length measurement datum @@ -3064,12 +2646,6 @@ name: mass measurement datum def: "A scalar measurement datum that is the result of measurement of mass quality" [] is_a: IAO:0000032 ! scalar measurement datum -[Term] -id: IAO:0000415 -name: hypothesis textual entity -def: "A textual entity that expresses an assertion that is intended to be tested." [] -is_a: IAO:0000300 ! textual entity - [Term] id: IAO:0000416 name: time measurement datum @@ -3087,18 +2663,6 @@ id: IAO:0000429 name: email address is_a: IAO:0000030 ! information content entity -[Term] -id: IAO:0000442 -name: author role -def: "A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name." [] -is_a: BFO:0000023 ! role - -[Term] -id: IAO:0000443 -name: data item extraction from journal article -def: "A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing" [] -is_a: OBI:0000011 ! planned process - [Term] id: IAO:0000572 name: documenting @@ -3109,93 +2673,25 @@ is_a: OBI:0000011 ! planned process id: IAO:0000573 name: line graph def: "A line graph is a type of graph created by connecting a series of data\npoints together with a line." [] -synonym: "line chart" EXACT [] is_a: IAO:0000038 ! graph [Term] id: IAO:0000574 name: assigning a centrally registered identifier def: "A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity" [] -synonym: "assigning a CRID" EXACT [] is_a: OBI:0000011 ! planned process -[Term] -id: IAO:0000575 -name: associating information with a centrally registered identifier in its registry -def: "A planned process in which a CRID registry associates an information content entity with a CRID symbol" [] -synonym: "associating information with a CRID in the CRID registry" EXACT [] -is_a: OBI:0000011 ! planned process - -[Term] -id: IAO:0000576 -name: obsolete_establishing a CRID registry -def: "a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID." [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true - [Term] id: IAO:0000577 name: centrally registered identifier symbol def: "A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry." [] -synonym: "CRID symbol" EXACT [] is_a: IAO:0000028 ! symbol -[Term] -id: IAO:0000578 -name: centrally registered identifier -def: "An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs." [] -synonym: "CRID" EXACT [] -is_a: IAO:0000030 ! information content entity - [Term] id: IAO:0000579 name: centrally registered identifier registry -def: "A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process." [] -synonym: "CRID registry" EXACT [] -is_a: IAO:0000100 ! data set - -[Term] -id: IAO:0000580 -name: looking up a centrally registered identifier -def: "A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol" [] -synonym: "looking up a CRID" EXACT [] -is_a: OBI:0000011 ! planned process - -[Term] -id: IAO:0000582 -name: time stamped measurement datum -is_a: IAO:0000109 ! measurement datum - -[Term] -id: IAO:0000584 -name: time sampled measurement data set -def: "A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time." [] -synonym: "experimental time series" EXACT [] -is_a: IAO:0000100 ! data set - -[Term] -id: IAO:0000590 -name: written name -def: "A textual entity that denotes a particular in reality." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000591 -name: software method -def: "A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task." [] -is_a: IAO:0000010 ! software - -[Term] -id: IAO:0000592 -name: software module -def: "A software module is software composed of a collection of software methods." [] -is_a: IAO:0000010 ! software - -[Term] -id: IAO:0000593 -name: software library -def: "A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application." [] -is_a: IAO:0000010 ! software +def: "A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process." [] +is_a: IAO:0020020 ! code set [Term] id: IAO:0000594 @@ -3204,346 +2700,9 @@ def: "A software application is software that can be directly executed by some p is_a: IAO:0000010 ! software [Term] -id: IAO:0000595 -name: software script -def: "A software script is software whose instructions can be executed using a software interpreter." [] -is_a: IAO:0000010 ! software - -[Term] -id: IAO:0000605 -name: abbreviation textual entity -def: "A textual entity listing abbreviations and their expansions that are used in a document." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000606 -name: abbreviations section -def: "A part of a document where abbreviations and their long-forms used within the document are listed." [] -synonym: "abbreviations" EXACT [] -synonym: "abbreviations list" EXACT [] -synonym: "abbreviations used" EXACT [] -synonym: "list of abbreviations" EXACT [] -synonym: "list of abbreviations used" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000607 -name: author information section -def: "A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document." [] -synonym: "author information" EXACT [] -synonym: "authors’ information" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000608 -name: author information textual entity -def: "A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000609 -name: author summary section -def: "A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers." [] -synonym: "author summary" EXACT [] -synonym: "summary" EXACT [] -synonym: "synopsis" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000610 -name: author summary textual entity -def: "A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000611 -name: availability section -def: "A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained." [] -synonym: "availability" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000612 -name: availability textual entity -def: "A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000613 -name: case report section -def: "A part of a document about the medical history of a specific patient as it relates to the topic of the document." [] -synonym: "case presentation" EXACT [] -synonym: "case report" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000614 -name: case report textual entity -def: "A textual entity that expresses a detailed account of a portion of the medical history for a specific patient." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000615 -name: conclusion section -def: "A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document." [] -synonym: "concluding remarks" EXACT [] -synonym: "conclusion" EXACT [] -synonym: "conclusions" EXACT [] -synonym: "findings" EXACT [] -synonym: "summary" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000616 -name: conflict of interest section -def: "A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document." [] -synonym: "competing interests" EXACT [] -synonym: "conflict of interest" EXACT [] -synonym: "conflict of interest statement" EXACT [] -synonym: "declaration of competing interests" EXACT [] -synonym: "disclosure of potential conflicts of interest" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000617 -name: conflict of interest textual entity -def: "A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000618 -name: consent section -def: "A part of a document about the consent process that was used to enroll patients in a study." [] -synonym: "consent" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000619 -name: consent textual entity -def: "A textual entity that documents the consenting process used to enroll patients in a study." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000620 -name: ethical approval section -def: "A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis." [] -synonym: "ethical approval" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000621 -name: ethical approval textual entity -def: "A textual entity that documents the ethical approval of some study design." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000622 -name: figures section -def: "A part of a document that contains one or more figures." [] -synonym: "figures" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000623 -name: funding source declaration section -def: "A part of a document used to detail information regarding the source of funding used in support of the generation of the document content." [] -synonym: "funding" EXACT [] -synonym: "funding information" EXACT [] -synonym: "funding sources" EXACT [] -synonym: "funding statement" EXACT [] -synonym: "funding/support" EXACT [] -synonym: "source of funding" EXACT [] -synonym: "sources of funding" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000624 -name: funding source declaration textual entity -def: "A textual entity documenting the source of funding that supported some study." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000625 -name: future directions section -def: "A part of a document detailing extensions of the described work that may be implemented at some future point in time." [] -synonym: "future challenges" EXACT [] -synonym: "future considerations" EXACT [] -synonym: "future developments" EXACT [] -synonym: "future directions" EXACT [] -synonym: "future outlook" EXACT [] -synonym: "future perspectives" EXACT [] -synonym: "future plans" EXACT [] -synonym: "future prospects" EXACT [] -synonym: "future research" EXACT [] -synonym: "future research directions" EXACT [] -synonym: "future studies" EXACT [] -synonym: "future work" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000626 -name: future directions textual entity -def: "A textual entity expressing ideas regarding future work relevant to work described in a document that could be done." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000627 -name: genome announcement section -def: "A document part announcing the publication of a novel draft genome sequence." [] -synonym: "genome announcement" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000628 -name: genome announcement textual entity -def: "A textual entity that describes the generation and public release of a novel, draft genome sequence." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000629 -name: keyword textual entity -def: "A textual entity listing keywords indicating the major theme(s) of a document." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000630 -name: keywords section -def: "A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed." [] -synonym: "keywords" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000631 -name: study limitations section -def: "A part of a document about biases or short comings related to the study design and execution." [] -synonym: "limitations" EXACT [] -synonym: "study limitations" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000632 -name: study limitations textual entity -def: "A textual entity addressing a shortcoming or bias of a study design or execution." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000633 -name: materials section -def: "A part of a document about the materials required to reproduce the content of the document." [] -synonym: "materials" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000634 -name: notes section -def: "A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc." [] -synonym: "footnotes" EXACT [] -synonym: "notes" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000635 -name: patients section -def: "A part of a document about the patients that participated in a study." [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000636 -name: patients textual entity -def: "A textual entity expressing information regarding the patients used in a study." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000637 -name: pre-publication history section -def: "A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors." [] -synonym: "notice of republication" EXACT [] -synonym: "pre-publication history" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000638 -name: pre-publication history textual entity -def: "A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000639 -name: related work section -def: "A part of a document about work in other publications that is relevant to the content of the document." [] -synonym: "related literature" EXACT [] -synonym: "related work" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000640 -name: related work textual entity -def: "A textual entity that discusses work from other publications and expresses their relevancy to the content of a document." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000641 -name: requirements section -def: "A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource." [] -synonym: "requirements" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000642 -name: requirements textual entity -def: "A textual entity that expresses the requirements necessary to use a resource, e.g. software." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000643 -name: statistical analysis textual entity -def: "A textual entity documenting statistical analysis tools and techniques employed." [] -is_a: IAO:0000300 ! textual entity - -[Term] -id: IAO:0000644 -name: statistical analysis section -def: "A part of the document used to describe the statistical methodologies employed in the work presented in the document." [] -synonym: "statistical analysis" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000645 -name: tables section -def: "A part of a document that contains one or more tables." [] -synonym: "tables" EXACT [] -is_a: IAO:0000314 ! document part - -[Term] -id: IAO:0000646 -name: postal code -def: "An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail." [] -is_a: IAO:0020000 ! identifier - -[Term] -id: IAO:0000647 -name: Postal delivery route -def: "A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region." [] -is_a: IAO:0000104 ! plan specification - -[Term] -id: IAO:0000648 -name: zone improvement plan code -def: "A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes." [] -synonym: "ZIP code" EXACT [] -is_a: IAO:0000646 ! postal code - -[Term] -id: IAO:0000650 -name: database extract, transform, and load process -def: "A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second." [] -synonym: "ETL" EXACT [] -is_a: OBI:0000011 ! planned process - -[Term] -id: IAO:0020000 -name: identifier -def: "An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." [] +id: IAO:0020020 +name: code set +def: "An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things." [] is_a: IAO:0000030 ! information content entity [Term] @@ -7277,7 +6436,6 @@ id: OBI:0000701 name: self-organizing map def: "A self-organizing map (SOM) is an artificial neural network with objective class discovery that uses a neighborhood function to preserve the topological properties of a dataset to produce low-dimensional (typically 2) discretized representation of the training data set. A set of artificial neurons learn to map points in an input space to coordinates in an output space. The input space can have different dimensions and topology from the output space, and the SOM will attempt to preserve these." [] synonym: "SOM" EXACT [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200175 ! class discovery data transformation [Term] @@ -7444,7 +6602,6 @@ id: OBI:0000727 name: k-nearest neighbors def: "A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned." [] synonym: "k-NN" EXACT [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200171 ! partitioning data transformation is_a: OBI:0200175 ! class discovery data transformation @@ -8673,7 +7830,7 @@ id: OBI:0000970 name: scalar score from composite inputs def: "A measurement datum which is the result of combining multiple datum. For example, a mean or summary score." [] synonym: "questionaire score" EXACT [] -is_a: IAO:0000032 ! scalar measurement datum +is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0000971 @@ -18451,7 +17608,6 @@ is_a: OBI:0200187 ! sequence analysis data transformation id: OBI:0002568 name: sequence data feature count tabulation def: "The counting of features (typically, genes) within aligned sequence data, and organization of these counts into one or more tables." [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200187 ! sequence analysis data transformation [Term] @@ -19868,7 +19024,8 @@ is_a: OBI:0002599 ! swab specimen id: OBI:0002780 name: nasal aspirate specimen def: "A specimen that is collected with a suctioning tube from the nasal cavity." [] -synonym: "nasal wash specimen|nasopharyngeal aspirate" EXACT [] +synonym: "nasal wash specimen" EXACT [] +synonym: "nasopharyngeal aspirate" EXACT [] is_a: OBI:0100051 ! specimen [Term] @@ -22981,7 +22138,6 @@ is_a: OBI:0200000 ! data transformation id: OBI:0003356 name: raw magnetic resonance image data set reconstruction def: "A process that transforms raw magnetic resonance image data from an NMR/MRI machine into a reconstructed magnetic resonance image data set." [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0003355 ! image data set analysis [Term] @@ -24616,6 +23772,37 @@ name: multidimensional fatigue inventory score def: "A clinical data item that quantifies the severity of a person's fatigue as measured by a 20-item self-report instrument." [] is_a: OGMS:0000123 ! clinical data item +[Term] +id: OBI:0003652 +name: albumin-free serum +def: "A blood serum specimen that contains no albumin." [] +is_a: OBI:0100017 ! blood serum specimen + +[Term] +id: OBI:0003653 +name: fasting +def: "A planned process in which an organism drinks only water and does not eat for a specified period of time." [] +is_a: OBI:0000011 ! planned process + +[Term] +id: OBI:0003654 +name: overnight fasting +def: "A fasting with a duration of 8–12 hours, typically occurring overnight." [] +is_a: OBI:0003653 ! fasting + +[Term] +id: OBI:0003655 +name: fasted +def: "An organismal quality that inheres in an organism that has completed a fasting process, and which ceases to inhere in that organism once that organism drinks a liquid other than water or eats." [] +is_a: PATO:0001995 ! organismal quality + +[Term] +id: OBI:0003657 +name: minimum resolved unit of measurement +def: "An information content entity that indicates the smallest increment that can be resolved on the scale of a measurement instrument." [] +synonym: "least count" EXACT [] +is_a: IAO:0000030 ! information content entity + [Term] id: OBI:0005246 name: injection function @@ -24797,7 +23984,6 @@ id: OBI:0200001 name: geometric mean calculation def: "A data transformation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations)." [] comment: A geometric mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations). -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200181 ! center calculation data transformation is_a: OBI:0200184 ! descriptive statistical calculation data transformation @@ -24829,7 +24015,6 @@ is_a: OBI:0200166 ! data transformation objective id: OBI:0200006 name: biexponential transformation def: "A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation." [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200072 ! curve fitting data transformation is_a: OBI:0200169 ! normalization data transformation @@ -24958,7 +24143,6 @@ is_a: OBI:0200169 ! normalization data transformation id: OBI:0200028 name: quantile transformation def: "A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles." [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200169 ! normalization data transformation is_a: OBI:0200181 ! center calculation data transformation @@ -25029,7 +24213,6 @@ is_a: OBI:0200080 ! network analysis id: OBI:0200041 name: k-means clustering def: "A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed)." [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200171 ! partitioning data transformation is_a: OBI:0200175 ! class discovery data transformation @@ -25037,7 +24220,6 @@ is_a: OBI:0200175 ! class discovery data transformation id: OBI:0200042 name: hierarchical clustering def: "A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root)." [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200175 ! class discovery data transformation [Term] @@ -25069,7 +24251,6 @@ id: OBI:0200050 name: dimensionality reduction def: "A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m." [] synonym: "data projection" EXACT [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200175 ! class discovery data transformation [Term] @@ -25188,7 +24369,6 @@ id: OBI:0200073 name: family wise error rate correction method def: "A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive." [] synonym: "FWER correction" EXACT [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200089 ! multiple testing correction method [Term] @@ -25226,7 +24406,6 @@ is_a: OBI:0200166 ! data transformation objective id: OBI:0200079 name: arithmetic mean calculation def: "An arithmetic mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment." [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200170 ! averaging data transformation is_a: OBI:0200181 ! center calculation data transformation is_a: OBI:0200184 ! descriptive statistical calculation data transformation @@ -25333,7 +24512,6 @@ is_a: OBI:0200169 ! normalization data transformation id: OBI:0200099 name: discriminant function analysis def: "Discriminant function analysis is a form of discriminant analysis used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome." [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0000663 ! class prediction data transformation is_a: OBI:0200106 ! discriminant analysis is_a: OBI:0200175 ! class discovery data transformation @@ -25350,7 +24528,6 @@ is_a: OBI:0200171 ! partitioning data transformation id: OBI:0200101 name: linear discriminant functional analysis def: "Linear discriminant functional analysis (LDFA) is a multivariate technique used in special applications where there are several intact groups (random assignment may be impossible) and they have been measured on several independent measures. Thus, you will want to describe how these groups differ on the basis of these measures. In this case, classification and prediction is the main objective." [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0000663 ! class prediction data transformation is_a: OBI:0200106 ! discriminant analysis is_a: OBI:0200175 ! class discovery data transformation @@ -25371,7 +24548,6 @@ is_a: OBI:0200102 ! regression analysis method id: OBI:0200104 name: principal component regression def: "The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores." [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200102 ! regression analysis method is_a: OBI:0200175 ! class discovery data transformation @@ -25405,7 +24581,6 @@ is_a: OBI:0200169 ! normalization data transformation id: OBI:0200109 name: b transformation def: "A b transformation is a data transformation obtained by applying the function B described in what follows to a (one dimensional) real number input. B(x)= a*exp(b*x)-c*exp(-d*x)+f, where exp denotes an exponential transformation and a, b, c, d, f are real constants with a, b, c, d positive with the objective of normalization." [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200169 ! normalization data transformation [Term] @@ -25426,7 +24601,6 @@ is_a: OBI:0000011 ! planned process id: OBI:0200113 name: similarity calculation def: "A similarity calculation is a data transformation that attaches to each pair of objects in the input a number that is meant to reflect how 'close' or 'similar' those objects are." [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0000663 ! class prediction data transformation is_a: OBI:0200175 ! class discovery data transformation @@ -25452,7 +24626,6 @@ is_a: OBI:0200072 ! curve fitting data transformation id: OBI:0200117 name: mode calculation def: "A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data." [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200181 ! center calculation data transformation is_a: OBI:0200184 ! descriptive statistical calculation data transformation @@ -25466,7 +24639,6 @@ is_a: OBI:0200184 ! descriptive statistical calculation data transformation id: OBI:0200119 name: median calculation def: "A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values." [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200181 ! center calculation data transformation is_a: OBI:0200184 ! descriptive statistical calculation data transformation @@ -25495,7 +24667,6 @@ is_a: OBI:0200184 ! descriptive statistical calculation data transformation id: OBI:0200123 name: skewness calculation def: "A skewness calculation is a descriptive statistics calculation defined as a parameter that describes how much a distribution (or a data set) varies from a bell-shaped curve. See http://www.riskglossary.com/link/skewness.htm for details. It is also known as the third central moment" [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200181 ! center calculation data transformation is_a: OBI:0200184 ! descriptive statistical calculation data transformation @@ -25710,7 +24881,6 @@ id: OBI:0200161 name: quantile number of false positives correction method def: "A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed'" [] synonym: "QNFP" EXACT [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200089 ! multiple testing correction method [Term] @@ -25725,7 +24895,6 @@ id: OBI:0200163 name: false discovery rate correction method def: "The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. ." [] synonym: "FDR correction method" EXACT [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200089 ! multiple testing correction method [Term] @@ -25733,7 +24902,6 @@ id: OBI:0200164 name: proportion of expected false positives correction method def: "A proportion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses." [] synonym: "PEFP correction method" EXACT [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200089 ! multiple testing correction method [Term] @@ -25741,7 +24909,6 @@ id: OBI:0200165 name: quantile proportion of false positives correction method def: "A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distribution of the proportion of false positives among the rejected hypothesis (false discovery rate)." [] synonym: "QPFP correction method" EXACT [] -is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200089 ! multiple testing correction method [Term] @@ -31271,7 +30438,7 @@ is_a: PATO:0000051 ! morphology id: PATO:0000122 name: length def: "A 1-D extent quality which is equal to the distance between two points." [] -is_a: PATO:0000051 ! morphology +is_a: PATO:0001708 ! 1-D extent [Term] id: PATO:0000125 @@ -31387,12 +30554,6 @@ name: physical object quality def: "A quality which inheres in a continuant." [] is_a: BFO:0000019 ! quality -[Term] -id: PATO:0001291 -name: electromagnetic (EM) radiation quality -def: "A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation." [] -is_a: PATO:0001739 ! radiation quality - [Term] id: PATO:0001296 name: luminous flux @@ -31403,7 +30564,7 @@ is_a: PATO:0001300 ! optical quality id: PATO:0001300 name: optical quality def: "An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light." [] -is_a: PATO:0001291 ! electromagnetic (EM) radiation quality +is_a: PATO:0070060 ! quality of interaction of a substance with electromagnetic radiation [Term] id: PATO:0001335 @@ -31523,7 +30684,7 @@ is_a: PATO:0001393 ! euploid id: PATO:0001396 name: cellular quality def: "A monadic quality of continuant that exists at the cellular level of organisation." [] -is_a: PATO:0001241 ! physical object quality +is_a: PATO:0070044 ! anatomical structure quality [Term] id: PATO:0001421 @@ -31568,23 +30729,23 @@ def: "A spatial quality inhering in a bearer by virtue of the bearer's being loc synonym: "frontal" EXACT [] is_a: PATO:0000140 ! position +[Term] +id: PATO:0001708 +name: 1-D extent +def: "A size quality inhering in an bearer by virtue of the bearer's extension in one dimension." [] +is_a: PATO:0000117 ! size + [Term] id: PATO:0001710 name: 3-D extent def: "A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions." [] is_a: PATO:0000117 ! size -[Term] -id: PATO:0001739 -name: radiation quality -def: "A quality that inheres in an bearer by virtue of how that bearer interacts with radiation." [] -is_a: PATO:0001018 ! physical quality - [Term] id: PATO:0001740 name: activity (of a radionuclide) def: "A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate." [] -is_a: PATO:0001739 ! radiation quality +is_a: PATO:0002198 ! quality of a substance [Term] id: PATO:0001741 @@ -31688,6 +30849,18 @@ name: fluid flow rate def: "A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time." [] is_a: PATO:0001574 ! flow rate +[Term] +id: PATO:0070044 +name: anatomical structure quality +def: "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." [] +is_a: PATO:0001241 ! physical object quality + +[Term] +id: PATO:0070060 +name: quality of interaction of a substance with electromagnetic radiation +def: "A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength." [] +is_a: PATO:0002198 ! quality of a substance + [Term] id: PR:000000001 name: protein @@ -32766,19 +31939,16 @@ is_a: UBERON:0000178 ! blood [Term] id: UO:0000001 name: length unit -def: "A unit which is a standard measure of the distance between two points." [] is_a: IAO:0000003 ! measurement unit label [Term] id: UO:0000002 name: mass unit -def: "A unit which is a standard measure of the amount of matter/energy of a physical object." [] is_a: IAO:0000003 ! measurement unit label [Term] id: UO:0000003 name: time unit -def: "A unit which is a standard measure of the dimension in which events occur in sequence." [] is_a: IAO:0000003 ! measurement unit label [Term] @@ -32906,78 +32076,34 @@ comment: Paraphrase of definition: a relation between an independent continuant [Typedef] id: IAO:0000039 name: has measurement unit label -range: IAO:0000003 ! measurement unit label is_functional: true is_a: BFO:0000051 ! has part -[Typedef] -id: IAO:0000135 -name: obsolete_specifically denotes -def: "c specifically denotes r =def \nr is a portion of reality\n& c is a particular quality\n& c depends specifically on some independent continuant b \n& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. \n\nMarked means there is a changed or additional quality of the bearer - the quality is the information carrier.\n\nCase 1\nMemory trace as mark created when reading some description of some friend. The trace can denote.\n\nCase 2\nPattern of ink arrayed on paper as mark when writing down a friend's name\n\nCase 3\nPattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file." [] -is_a: ObsoleteProperty -is_obsolete: true - [Typedef] id: IAO:0000136 name: is about def: "A (currently) primitive relation that relates an information artifact to an entity." [] -domain: IAO:0000030 ! information content entity - -[Typedef] -id: IAO:0000142 -name: mentions -def: "An information artifact IA mentions an entity E exactly when it has a component/part that denotes E" [] -is_a: IAO:0000136 ! is about [Typedef] id: IAO:0000219 name: denotes def: "A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically" [] -domain: IAO:0000030 ! information content entity -range: BFO:0000001 ! entity is_a: IAO:0000136 ! is about -inverse_of: IAO:0000235 ! denoted by - -[Typedef] -id: IAO:0000220 -name: obsolete_materially denotes -is_a: ObsoleteProperty -is_obsolete: true [Typedef] id: IAO:0000221 name: is quality measurement of def: "m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q" [] -domain: IAO:0000109 ! measurement datum -range: BFO:0000019 ! quality is_a: IAO:0000136 ! is about -inverse_of: IAO:0000417 ! is quality measured as - -[Typedef] -id: IAO:0000222 -name: obsolete_describes -is_a: ObsoleteProperty -is_obsolete: true - -[Typedef] -id: IAO:0000223 -name: obsolete_represents -is_a: ObsoleteProperty -is_obsolete: true [Typedef] id: IAO:0000235 name: denoted by def: "inverse of the relation 'denotes'" [] -domain: BFO:0000001 ! entity -range: IAO:0000030 ! information content entity [Typedef] id: IAO:0000407 name: has coordinate unit label -comment: relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point -domain: IAO:0000400 ! cartesian spatial coordinate datum -range: UO:0000001 ! length unit is_functional: true is_a: BFO:0000051 ! has part @@ -32985,43 +32111,8 @@ is_a: BFO:0000051 ! has part id: IAO:0000413 name: is duration of def: "relates a process to a time-measurement-datum that represents the duration of the process" [] -domain: IAO:0000416 ! time measurement datum -range: BFO:0000015 ! process is_a: IAO:0000136 ! is about -[Typedef] -id: IAO:0000417 -name: is quality measured as -def: "inverse of the relation of is quality measurement of" [] - -[Typedef] -id: IAO:0000418 -name: is quality specification of -def: "A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality." [] -is_a: IAO:0000136 ! is about -inverse_of: IAO:0000419 ! quality is specified as - -[Typedef] -id: IAO:0000419 -name: quality is specified as -def: "inverse of the relation of is quality specification of" [] - -[Typedef] -id: IAO:0000581 -name: has time stamp -def: "relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken" [] -domain: IAO:0000582 ! time stamped measurement datum -range: IAO:0000416 ! time measurement datum -is_functional: true -is_a: BFO:0000051 ! has part - -[Typedef] -id: IAO:0000583 -name: has measurement datum -def: "relates a time stamped measurement datum to the measurement datum that was measured" [] -domain: IAO:0000582 ! time stamped measurement datum -is_a: BFO:0000051 ! has part - [Typedef] id: OBI:0000107 name: provides_service_consumer_with @@ -33400,7 +32491,6 @@ id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] synonym: "has_function" EXACT [] -domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function is_a: RO:0000053 ! bearer of @@ -33421,20 +32511,6 @@ domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role is_a: RO:0000053 ! bearer of -[Typedef] -id: RO:0000091 -name: has disposition -def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] -domain: BFO:0000004 ! independent continuant -range: BFO:0000016 ! disposition -is_a: RO:0000053 ! bearer of -inverse_of: RO:0000092 ! disposition of - -[Typedef] -id: RO:0000092 -name: disposition of -is_a: RO:0000052 ! inheres in - [Typedef] id: RO:0001000 name: derives from diff --git a/views/obi_core.owl b/views/obi_core.owl index d31d305b..08b8a150 100644 --- a/views/obi_core.owl +++ b/views/obi_core.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -78,7 +78,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2024-01-09 + 2024-05-03 @@ -197,7 +197,7 @@ We don't have definitions of 'meaning' or 'expression' Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> @@ -240,12 +240,15 @@ We also have the outstanding issue of how to aim different definitions to differ - alternative term + alternative label - An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. + OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). + alternative label alternative term @@ -285,6 +288,12 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + @@ -390,7 +399,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation https://oborel.github.io/obo-relations/temporal-semantics/ @@ -523,6 +531,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part + has part @@ -569,17 +578,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - This document is about information artifacts and their representations - + is about A (currently) primitive relation that relates an information artifact to an entity. - 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. - -We will try to build it back up by elaborating the various subproperties that are more precisely defined. - -Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. - person:Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy + is about @@ -589,19 +590,9 @@ Some currently missing phenomena that should be considered "about" are - - - - A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. + denotes A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically - 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. -g denotes r =def -r is a portion of reality -there is some c that is a concretization of g -every c that is a concretization of g specifically denotes r - person:Alan Ruttenberg - Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan - + denotes @@ -610,11 +601,9 @@ every c that is a concretization of g specifically denotes r - - + denoted by inverse of the relation 'denotes' - Person: Jie Zheng, Chris Stoeckert, Mike Conlon - + denoted by @@ -640,16 +629,10 @@ every c that is a concretization of g specifically denotes r - - - - - has_specified_input - has_specified_input see is_input_of example_of_usage The inverse property of is_specified_input_of @@ -658,7 +641,6 @@ every c that is a concretization of g specifically denotes r PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot - has_specified_input @@ -683,23 +665,16 @@ every c that is a concretization of g specifically denotes r - - - - - has_specified_output - has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot - has_specified_output @@ -711,12 +686,10 @@ every c that is a concretization of g specifically denotes r is_specified_output_of - is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters - is_specified_output_of @@ -901,7 +874,6 @@ every c that is a concretization of g specifically denotes r - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence @@ -1005,12 +977,14 @@ every c that is a concretization of g specifically denotes r entity Entity + entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity @@ -1037,19 +1011,13 @@ every c that is a concretization of g specifically denotes r - - - - - - continuant Continuant continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) @@ -1061,24 +1029,6 @@ every c that is a concretization of g specifically denotes r continuant - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - @@ -1115,6 +1065,24 @@ every c that is a concretization of g specifically denotes r if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + + + + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + @@ -1122,12 +1090,6 @@ every c that is a concretization of g specifically denotes r - - - - - - occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. @@ -1193,8 +1155,6 @@ every c that is a concretization of g specifically denotes r - - ic IndependentContinuant a chair @@ -1397,7 +1357,7 @@ every c that is a concretization of g specifically denotes r the mass of this piece of gold. the shape of your nose the shape of your nostril - + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] @@ -1436,7 +1396,6 @@ every c that is a concretization of g specifically denotes r - sdc SpecificallyDependentContinuant specifically dependent continuant @@ -1455,7 +1414,7 @@ every c that is a concretization of g specifically denotes r b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - + (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] @@ -1736,7 +1695,7 @@ every c that is a concretization of g specifically denotes r - + cell line cell cell line cell 细胞系细胞 @@ -1751,14 +1710,14 @@ every c that is a concretization of g specifically denotes r cell line cell 细胞系细胞 - + - + 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. @@ -1882,17 +1841,8 @@ every c that is a concretization of g specifically denotes r measurement unit label - Examples of measurement unit labels are liters, inches, weight per volume. - A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. - 2009-03-16: provenance: a term measurement unit was -proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and -Cristian Cocos, and subsequently moved to IAO where the objective for -which the original term was defined was satisfied with the definition -of this, different, term. - 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot + measurement unit label @@ -1903,19 +1853,8 @@ of this, different, term. objective specification - In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. - A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." - 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. - Answers the question, why did you do this experiment? - PERSON: Alan Ruttenberg - PERSON: Barry Smith - PERSON: Bjoern Peters - PERSON: Jennifer Fostel - goal specification - OBI Plan and Planned Process/Roles Branch - OBI_0000217 + objective specification @@ -1925,11 +1864,9 @@ of this, different, term. - Pour the contents of flask 1 into flask 2 - + action specification A directive information entity that describes an action the bearer will take. - Alan Ruttenberg - OBI Plan and Planned Process branch + action specification @@ -1940,12 +1877,8 @@ of this, different, term. datum label - A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label - http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n - GROUP: IAO - 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. - + datum label @@ -1954,26 +1887,10 @@ of this, different, term. - - - - - - - - - - - information carrier - In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. - A quality of an information bearer that imparts the information content - 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. - 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. - PERSON: Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy + information carrier @@ -1984,24 +1901,8 @@ of this, different, term. data item - Data items include counts of things, analyte concentrations, and statistical summaries. - An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. - 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. - 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. - 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ - JAR: datum -- well, this will be very tricky to define, but maybe some -information-like stuff that might be put into a computer and that is -meant, by someone, to denote and/or to be interpreted by some -process... I would include lists, tables, sentences... I think I might -defer to Barry, or to Brian Cantwell Smith - -JAR: A data item is an approximately justified approximately true approximate belief - PERSON: Alan Ruttenberg - PERSON: Chris Stoeckert - PERSON: Jonathan Rees - data + data item @@ -2013,16 +1914,8 @@ JAR: A data item is an approximately justified approximately true approximate be symbol - a serial number such as "12324X" - a stop sign - a written proper name such as "OBI" - An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - 20091104, MC: this needs work and will most probably change - 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). - PERSON: James A. Overton - PERSON: Jonathan Rees - based on Oxford English Dictionary + symbol @@ -2032,22 +1925,9 @@ JAR: A data item is an approximately justified approximately true approximate be - - - - - - information content entity - Examples of information content entites include journal articles, data, graphical layouts, and graphs. - A generically dependent continuant that is about some thing. - 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). - information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). - -Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. - PERSON: Chris Stoeckert - OBI_0000142 + information content entity @@ -2058,20 +1938,9 @@ Previous. An information content entity is a non-realizable information entity t - - - - - - - + directive information entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. - 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. - 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO - Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters + directive information entity @@ -2082,13 +1951,8 @@ Previous. An information content entity is a non-realizable information entity t algorithm - PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. - A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. - Philippe Rocca-Serra - PlanAndPlannedProcess Branch - OBI_0000270 - adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) + algorithm @@ -2120,6 +1984,7 @@ Previous. An information content entity is a non-realizable information entity t PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 + curation status specification @@ -2130,15 +1995,8 @@ Previous. An information content entity is a non-realizable information entity t data set - Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). - A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. - 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type - 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000042 - group:OBI + data set @@ -2151,6 +2009,7 @@ Previous. An information content entity is a non-realizable information entity t data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg + data about an ontology part @@ -2160,35 +2019,9 @@ Previous. An information content entity is a non-realizable information entity t - - - - - - - - - - - - plan specification - PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. - - A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2014-03-31: A plan specification can have other parts, such as conditional specifications. - Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved - Alan Ruttenberg - OBI Plan and Planned Process branch - OBI_0000344 - 2/3/2009 Comment from OBI review. - -Action specification not well enough specified. -Conditional specification not well enough specified. -Question whether all plan specifications have objective specifications. - -Request that IAO either clarify these or change definitions not to use them + A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. + plan specification @@ -2205,13 +2038,8 @@ Request that IAO either clarify these or change definitions not to use them measurement datum - Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. - A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. - 2/2/2009 is_specified_output of some assay? - person:Chris Stoeckert - OBI_0000305 - group:OBI + measurement datum @@ -2220,30 +2048,10 @@ Request that IAO either clarify these or change definitions not to use them - - - - - - - - - - - - - - - - material information bearer - A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. - a brain - a hard drive - A material entity in which a concretization of an information content entity inheres. - GROUP: IAO + material information bearer @@ -2260,6 +2068,7 @@ Request that IAO either clarify these or change definitions not to use them + @@ -2280,10 +2089,8 @@ Request that IAO either clarify these or change definitions not to use them document - A journal article, patent application, laboratory notebook, or a book - A collection of information content entities intended to be understood together as a whole - PERSON: Lawrence Hunter + document @@ -2316,24 +2123,9 @@ Request that IAO either clarify these or change definitions not to use them - - - - - - - - - - - - - Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. - + documenting A planned process in which a document is created or added to by including the specified input in it. - 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape - Bjoern Peters - wikipedia http://en.wikipedia.org/wiki/Documenting + documenting @@ -2343,79 +2135,34 @@ Request that IAO either clarify these or change definitions not to use them - - - - - - - The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. - + centrally registered identifier symbol A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID symbol - Original proposal from Bjoern, discussions at IAO calls + centrally registered identifier symbol - + - - - - - - - - - - - - - - - - - - - - The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. - - An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. - 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). - Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. - - Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier + + + centrally registered identifier registry + A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. + + centrally registered identifier registry - + - - - PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. - - A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID registry - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier registry + + + code set + An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things. + + code set @@ -2603,7 +2350,6 @@ Request that IAO either clarify these or change definitions not to use them planned process - planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. @@ -2614,7 +2360,6 @@ objectives is a planned process. branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - planned process @@ -2692,7 +2437,6 @@ objectives is a planned process. Could add specific objective specification Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS - study investigation @@ -3280,7 +3024,6 @@ for now. removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. branch derived 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. - study design execution @@ -3939,7 +3682,6 @@ This issue is outside the scope of OBI. data analysis data processing Branch editors - data transformation @@ -3979,7 +3721,6 @@ This issue is outside the scope of OBI. PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. - study design @@ -4237,14 +3978,13 @@ realizes some 'host of immune response role' - - + failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term - + @@ -4323,12 +4063,11 @@ realizes some 'host of immune response role' - - + placeholder removed placeholder removed - + @@ -4430,6 +4169,20 @@ realizes some 'host of immune response role' + + + + + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. + This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/77 + https://orcid.org/0000-0001-5208-3432 + out of scope + + + + + geographic location A reference to a place on the Earth, by its name or by its geographical location. geographic location