Merge pull request #656 from sneumann/fix/issue652

[WIP] Add DefinedTerm profile

DefinedTerm/README.md

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+# Profile for DefinedTerm and DefinedTermSet
+
+The two SchemaOrg types DefinedTerm and DefinedTermSet
+are allowed in many places as property values.
+
+In e.g. the life-sciences, there are a number of controlled vocabularies
+and ontologies, which are often used as source of the DefinedTerms.
+Many of the, can be browsed and accessed through terminology and lookup services or portals.
+
+For linked data applications it is sufficient for an entity
+with `@type="DefinedTerm"` to link to an `@id` pointing to the IRI
+of the referenced concept.
+
+In other cases, more information is needed to search and view defined term information
+without having to lookup external resources. E.g., a domain-specific search engine
+can create faceted search based on the `name` property, like e.g. done in TeSS.
+Aforementioned terminology services also offer linking and query interfaces
+beyond IRIs as parameters.
+
+Another possible use of a conformant `DefinedTerm`
+is to enable creating hyperlinks to other web ressources, e.g.
+https://bio.tools/t?inputDataFormatID=%22format_3244%22
+or provide tool-tips if the `description` is provided.
+
+Some typical OBO ontologies can be taken as inspiration of properties that should be
+required or recommended in a Bioschema DefinedTerm profile. We also provide
+some mapping information between properties of `DefinedTerm`
+and those from OBO, OWL and SKOS, following work in https://doi.org/10.1186/2041-1480-2-S1-S3.
+
+It is not intended to duplicate the content and expressivity
+of powerful ontology representations and serialisations like OWL or RDF.

DefinedTerm/examples/0.1-DRAFT/ECO-xray.jsonld

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+{
+  "@type": "DefinedTerm",
+  "@id": "http://purl.bioontology.org/ontology/ECO/ECO:0005670",
+  "termCode": "0005670",
+  "name": "x-ray crystallography evidence used in manual assertion",
+  "url": "http://purl.bioontology.org/ontology/ECO/ECO:0005670",
+  "inDefinedTermSet": {
+    "@type": "DefinedTermSet",
+    "@id": "http://purl.obolibrary.org/obo/eco.owl",
+    "name": "Evidence & Conclusion Ontology (ECO)",
+    "url": "https://bioportal.bioontology.org/ontologies/ECO"
+  },
+  "sameAs": [
+    "http://purl.obolibrary.org/obo/ECO_0005670",
+    "https://identifiers.org/ECO:0005670",
+    "https://www.ebi.ac.uk/ols4/ontologies/eco/terms?obo_id=ECO:0005670"
+  ]
+}

DefinedTerm/examples/0.1-DRAFT/EDAM-sequence_analysis.jsonld

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+{
+  "@type": "DefinedTerm",
+  "@id": "http://purl.bioontology.org/ontology/EDAM/topic_0080",
+  "termCode": "topic_0080",
+  "name": "Sequence analysis",
+  "url": "http://purl.bioontology.org/ontology/EDAM/topic_0080",
+  "inDefinedTermSet": {
+    "@type": "DefinedTermSet",
+    "@id": "http://edamontology.org",
+    "name": "EDAM ontology",
+    "url": "https://bioportal.bioontology.org/ontologies/EDAM"
+  },
+  "sameAs": [
+    "https://identifiers.org/edam:topic_0080",
+    "https://www.ebi.ac.uk/ols/ontologies/edam/terms?short_form=topic_0080"
+  ]
+}

DefinedTerm/examples/0.1-DRAFT/GO-protein_binding.jsonld

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+{
+  "@type": "DefinedTerm",
+  "@id": "http://amigo.geneontology.org/amigo/term/GO:0005515",
+  "termCode": "0005515",
+  "name": "protein binding",
+  "url": "http://amigo.geneontology.org/amigo/term/GO:0005515",
+  "inDefinedTermSet": {
+    "@type": "DefinedTermSet",
+    "@id": "http://purl.obolibrary.org/obo/go.owl",
+    "name": "Gene Ontology",
+    "url": "https://bioportal.bioontology.org/ontologies/GO"
+  },
+  "sameAs": [
+    "http://purl.obolibrary.org/obo/GO_0005515",
+    "http://purl.bioontology.org/ontology/GO/GO:0005515",
+    "https://identifiers.org/GO:0005515",
+    "https://www.ebi.ac.uk/ols4/ontologies/go/terms?obo_id=GO:0005515",
+    "https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0005515"
+  ]
+}

DefinedTerm/examples/0.1-DRAFT/NCBITAXON-human.jsonld

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+{
+  "@type": "DefinedTerm",
+  "@id": "http://purl.bioontology.org/ontology/NCBITAXON/9606",
+  "termCode": "9606",
+  "name": "Homo sapiens",
+  "url": "http://purl.bioontology.org/ontology/NCBITAXON/9606",
+  "inDefinedTermSet": {
+    "@type": "DefinedTermSet",
+    "@id": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+    "name": "NCBI taxon",
+    "url": "https://bioportal.bioontology.org/ontologies/NCBITAXON"
+  },
+  "sameAs": [
+    "http://purl.uniprot.org/taxonomy/9606",
+    "https://identifiers.org/taxonomy:9606",
+    "http://purl.obolibrary.org/obo/NCBITaxon_9606"
+  ]
+}

DefinedTerm/jsonld/DefinedTerm_v0.1-DRAFT.jsonld

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+{
+  "@context": {
+    "schema": "http://schema.org/",
+    "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
+    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+    "bioschemasdrafts": "https://discovery.biothings.io/view/DefinedTerm/"
+  },
+  "@graph": [
+    {
+      "@id": "bioschemasdrafts:DefinedTerm",
+      "@type": "rdfs:Class",
+      "rdfs:comment": "A word, name, acronym, phrase, etc. with a formal definition. Use the name property for the term being defined, use termCode if the term has an alpha-numeric code allocated, use description to provide the definition of the term. This Bioschemas profile specifically helps reusing terms from terminology and ontology services.",
+      "rdfs:label": "DefinedTerm",
+      "rdfs:subClassOf": {
+        "@id": "schema:DefinedTerm"
+      },
+      "$validation": {
+        "$schema": "http://json-schema.org/draft-07/schema#",
+        "type": "object",
+        "properties": {
+          "termCode": {
+            "description": "A code that identifies this [[DefinedTerm]] within a [[DefinedTermSet]]",
+            "type": "string",
+            "owl:cardinality": "one"
+          },
+          "inDefinedTermSet": {
+            "description": "A [[DefinedTermSet]] that contains this term.",
+            "type": "string",
+            "owl:cardinality": "one"
+          },
+          "description": {
+            "description": "A description of the item.",
+            "type": "string",
+            "owl:cardinality": "one"
+          },
+          "identifier": {
+            "description": "The identifier property represents any kind of identifier for any kind of [[Thing]], such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](/docs/datamodel.html#identifierBg) for more details.\n        ",
+            "type": "string",
+            "owl:cardinality": "one"
+          },
+          "name": {
+            "description": "The name of the item.",
+            "type": "string",
+            "owl:cardinality": "one"
+          },
+          "sameAs": {
+            "description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.",
+            "owl:cardinality": "many"
+          },
+          "url": {
+            "description": "URL of the item.",
+            "oneOf": [
+              {
+                "type": "string",
+                "format": "uri"
+              },
+              {
+                "type": "array",
+                "items": {
+                  "type": "string",
+                  "format": "uri"
+                }
+              }  
+            ],
+            "owl:cardinality": "many"
+          }
+        },
+        "required": [
+          "inDefinedTermSet"
+        ],
+        "recommended": [
+          "termCode",    
+          "sameAs",
+          "name"      
+        ],
+        "optional": [
+          "description"          
+        ]
+      },
+      "schemaVersion": [
+        "https://schema.org/docs/releases.html#v23.0"
+      ]
+    }
+  ]
+}