Merge branch 'master' into 2023_12_21-18_03

_data/profile_versions.yaml

@@ -51,7 +51,7 @@ Dataset:
   name: Dataset
   status: active
 DefinedTerm:
-  latest_publication: 0.1 -DRAFT
+  latest_publication: 0.1-DRAFT
   latest_release: null
   name: DefinedTerm
   status: active

pages/_groups/Datasets.md

@@ -26,7 +26,7 @@ objectives:
 
 specifications:
   [
-    'Dataset', 'DataRecord'
+    'Dataset', 'DataRecord', 'DefinedTerm'
   ]
 
 types:

pages/_profiles/DefinedTerm/0.1-DRAFT.html

@@ -0,0 +1,118 @@
+---
+redirect_from:
+- "/profiles/DefinedTerm/"
+- "/profiles/DefinedTerm"
+# spec_info content generated using GOWeb
+# DO NOT MANUALLY EDIT THE CONTENT
+cross_walk_url: ''
+dde_ui_url: https://discovery.biothings.io/view/bioschemasdrafts/bioschemasdrafts:DefinedTerm
+gh_tasks: https://github.com/Bioschemas/specifications/labels/type%3A%20DefinedTerm
+group: data
+hierarchy:
+- Thing
+- Intangible
+- DefinedTerm
+json-ld_url: DefinedTerm/jsonld/DefinedTerm_v0.1-DRAFT.json
+live_deploy: /liveDeploys
+mapping:
+- bsc_description: ''
+  cardinality: ONE
+  controlled_vocab: ''
+  description: A [[DefinedTermSet]] that contains this term.
+  example: |-
+    {
+      "@type": "DefinedTerm",
+      "inDefinedTermSet": "http://purl.obolibrary.org/obo/ncbitaxon.owl"
+    }
+  expected_types:
+  - Text
+  marginality: Minimum
+  property: inDefinedTermSet
+  type: ''
+  type_url: ''
+- bsc_description: ''
+  cardinality: ONE
+  controlled_vocab: ''
+  description: A code that identifies this [[DefinedTerm]] within a [[DefinedTermSet]]
+  example: |-
+    {
+     "@type": "DefinedTerm",
+     "termCode": "GO:0005515"
+    }
+  expected_types:
+  - Text
+  marginality: Recommended
+  property: termCode
+  type: ''
+  type_url: ''
+- bsc_description: ''
+  cardinality: MANY
+  controlled_vocab: ''
+  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.
+  example: |-
+    {
+      "@type": "DefinedTerm",
+      "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"
+      ]
+    }
+  expected_types: []
+  marginality: Recommended
+  property: sameAs
+  type: ''
+  type_url: ''
+- bsc_description: ''
+  cardinality: ONE
+  controlled_vocab: ''
+  description: The name of the item.
+  example: |-
+    {
+      "@type": "DefinedTerm",
+      "termCode": "protein binding"
+    }
+  expected_types:
+  - Text
+  marginality: Recommended
+  property: name
+  type: ''
+  type_url: ''
+- bsc_description: ''
+  cardinality: ONE
+  controlled_vocab: ''
+  description: A description of the item.
+  example: |-
+    {
+      "@type": "DefinedTerm",
+      "termCode": "Binding to a protein"
+    }
+  expected_types:
+  - Text
+  marginality: Optional
+  property: description
+  type: ''
+  type_url: ''
+name: DefinedTerm
+parent_type: DefinedTerm
+previous_release: ''
+previous_version: ''
+spec_info:
+  description: 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.
+    Version 0.1-DRAFT. <h3>Summary of Changes</h3> None--this is the first draft.
+  full_example: https://github.com/BioSchemas/specifications/tree/master/DefinedTerm/examples
+  official_type: DefinedTerm
+  title: DefinedTerm
+  version: 0.1-DRAFT
+  version_date: 20231221T182915
+spec_type: Profile
+status: revision
+use_cases_url: /useCases/DefinedTerm
+---

pages/_useCases/DefinedTerm.md

@@ -0,0 +1,29 @@
+---
+layout: use-case
+name: DefinedTerm
+group: data
+active: true
+---
+
+The SchemaOrg type DefinedTerm is allowed in many places as property value.
+
+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 them 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. Those use cases are the target of this profile.
+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.
+
+It is not intended to duplicate the content and expressivity
+of powerful ontology representations and serialisations like OWL or RDF.