From 45799e3441d7771206262b610aad8d76252be3ca Mon Sep 17 00:00:00 2001 From: raphaelgazzotti Date: Thu, 26 Feb 2026 16:39:28 +0100 Subject: [PATCH 1/8] Update of ontology identifiers. --- schemas/controlledTerm.schema.tpl.json | 23 ++++++++++++++++++++++- 1 file changed, 22 insertions(+), 1 deletion(-) diff --git a/schemas/controlledTerm.schema.tpl.json b/schemas/controlledTerm.schema.tpl.json index dca6ce22..8f2e40c6 100644 --- a/schemas/controlledTerm.schema.tpl.json +++ b/schemas/controlledTerm.schema.tpl.json @@ -6,6 +6,15 @@ "name" ], "properties": { + "databaseCrossReferences": { + "minItems": 1, + "type": "array", + "uniqueItems": true, + "items": { + "type": "string" + }, + "_instruction": "Enter each cross-reference as a CURIE-style string in the format 'SOURCE:IDENTIFIER' (e.g., 'WIKIDATA:Q31703', 'MESH:D000544', 'KS:some-id')." + }, "definition": { "type": "string", "_instruction": "Enter one sentence for defining this term." @@ -39,13 +48,25 @@ ], "_instruction": "Enter the internationalized resource identifier (IRI) pointing to the preferred ontological term." }, + "ontologyIdentifiers": { + "minItems": 1, + "type": "array", + "uniqueItems": true, + "_instruction": "Enter all internationalized resource identifiers (IRIs) pointing to ontology entries that are equivalent to this term (e.g., from UBERON, MeSH, DOID, NCI Thesaurus). Do not repeat the preferred ontology identifier entered above.", + "items": { + "type": "string", + "_formats": [ + "iri" + ] + } + }, "synonym": { "type": "array", "minItems": 1, "uniqueItems": true, "_instruction": "Enter one or several synonyms (including abbreviations) for this controlled term.", "items": { - "type": "string" + "type": "iri" } } } From 8d1774d4a0a0b55dd52877465bcbfd1f914c4830 Mon Sep 17 00:00:00 2001 From: raphaelgazzotti Date: Thu, 26 Feb 2026 17:30:22 +0100 Subject: [PATCH 2/8] Embed GenericIdentifier. --- schemas/controlledTerm.schema.tpl.json | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/schemas/controlledTerm.schema.tpl.json b/schemas/controlledTerm.schema.tpl.json index 8f2e40c6..ed6db8a9 100644 --- a/schemas/controlledTerm.schema.tpl.json +++ b/schemas/controlledTerm.schema.tpl.json @@ -6,14 +6,14 @@ "name" ], "properties": { - "databaseCrossReferences": { + "crossReferences": { "minItems": 1, "type": "array", "uniqueItems": true, - "items": { - "type": "string" - }, - "_instruction": "Enter each cross-reference as a CURIE-style string in the format 'SOURCE:IDENTIFIER' (e.g., 'WIKIDATA:Q31703', 'MESH:D000544', 'KS:some-id')." + "_embeddedTypes": [ + "core:GenericIdentifier" + ], + "_instruction": "Enter all known cross-references to external databases or registries for this term." }, "definition": { "type": "string", From b85dd069c581fad28ae5044b7df85956a3c10fce Mon Sep 17 00:00:00 2001 From: raphaelgazzotti Date: Thu, 26 Feb 2026 17:34:32 +0100 Subject: [PATCH 3/8] Revert to type string. --- schemas/controlledTerm.schema.tpl.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schemas/controlledTerm.schema.tpl.json b/schemas/controlledTerm.schema.tpl.json index ed6db8a9..510e6ced 100644 --- a/schemas/controlledTerm.schema.tpl.json +++ b/schemas/controlledTerm.schema.tpl.json @@ -66,7 +66,7 @@ "uniqueItems": true, "_instruction": "Enter one or several synonyms (including abbreviations) for this controlled term.", "items": { - "type": "iri" + "type": "string" } } } From 8715cfe7c1f551a4b5d30009a436a8d16859f150 Mon Sep 17 00:00:00 2001 From: raphaelgazzotti Date: Thu, 26 Feb 2026 18:25:33 +0100 Subject: [PATCH 4/8] Updated crossReferences type as _linkedTypes --- schemas/controlledTerm.schema.tpl.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schemas/controlledTerm.schema.tpl.json b/schemas/controlledTerm.schema.tpl.json index 510e6ced..483a4360 100644 --- a/schemas/controlledTerm.schema.tpl.json +++ b/schemas/controlledTerm.schema.tpl.json @@ -10,7 +10,7 @@ "minItems": 1, "type": "array", "uniqueItems": true, - "_embeddedTypes": [ + "_linkedTypes": [ "core:GenericIdentifier" ], "_instruction": "Enter all known cross-references to external databases or registries for this term." From 748d772b1a9d6fcf543739bb53a0578eaa8491d5 Mon Sep 17 00:00:00 2001 From: Raphael-Gazzotti <125291580+Raphael-Gazzotti@users.noreply.github.com> Date: Mon, 2 Mar 2026 14:23:00 +0100 Subject: [PATCH 5/8] Change to _embeddedTypes for crossReferences --- schemas/controlledTerm.schema.tpl.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schemas/controlledTerm.schema.tpl.json b/schemas/controlledTerm.schema.tpl.json index 483a4360..510e6ced 100644 --- a/schemas/controlledTerm.schema.tpl.json +++ b/schemas/controlledTerm.schema.tpl.json @@ -10,7 +10,7 @@ "minItems": 1, "type": "array", "uniqueItems": true, - "_linkedTypes": [ + "_embeddedTypes": [ "core:GenericIdentifier" ], "_instruction": "Enter all known cross-references to external databases or registries for this term." From 2d928c60a6465d0213e1b7b7d296db91552b9f20 Mon Sep 17 00:00:00 2001 From: Raphael-Gazzotti <125291580+Raphael-Gazzotti@users.noreply.github.com> Date: Mon, 2 Mar 2026 14:44:34 +0100 Subject: [PATCH 6/8] Remove properties to interlex and kgspace --- schemas/controlledTerm.schema.tpl.json | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/schemas/controlledTerm.schema.tpl.json b/schemas/controlledTerm.schema.tpl.json index 510e6ced..7be086a0 100644 --- a/schemas/controlledTerm.schema.tpl.json +++ b/schemas/controlledTerm.schema.tpl.json @@ -23,20 +23,6 @@ "type": "string", "_instruction": "Enter a short text describing this term." }, - "interlexIdentifier": { - "type": "string", - "_formats": [ - "iri" - ], - "_instruction": "Enter the internationalized resource identifier (IRI) pointing to the integrated ontology entry in the InterLex project." - }, - "knowledgeSpaceLink": { - "type": "string", - "_formats": [ - "iri" - ], - "_instruction": "Enter the internationalized resource identifier (IRI) pointing to the wiki page of the corresponding term in the KnowledgeSpace." - }, "name": { "type": "string", "_instruction": "Controlled term originating from a defined terminology." From ed5f2e4ad53838aaf0c34625971badacacdec32e Mon Sep 17 00:00:00 2001 From: raphaelgazzotti Date: Fri, 6 Mar 2026 14:07:56 +0100 Subject: [PATCH 7/8] Updated with suggestions from @lzehl --- schemas/controlledTerm.schema.tpl.json | 34 +++++++++++++++++--------- 1 file changed, 22 insertions(+), 12 deletions(-) diff --git a/schemas/controlledTerm.schema.tpl.json b/schemas/controlledTerm.schema.tpl.json index 7be086a0..eed71cb4 100644 --- a/schemas/controlledTerm.schema.tpl.json +++ b/schemas/controlledTerm.schema.tpl.json @@ -6,15 +6,6 @@ "name" ], "properties": { - "crossReferences": { - "minItems": 1, - "type": "array", - "uniqueItems": true, - "_embeddedTypes": [ - "core:GenericIdentifier" - ], - "_instruction": "Enter all known cross-references to external databases or registries for this term." - }, "definition": { "type": "string", "_instruction": "Enter one sentence for defining this term." @@ -32,13 +23,32 @@ "_formats": [ "iri" ], - "_instruction": "Enter the internationalized resource identifier (IRI) pointing to the preferred ontological term." + "_instruction": "Enter the internationalized resource identifier (IRI) pointing to the preferred ontological term (e.g., InterLex)." + }, + "preferredCrossReference": { + "type": "string", + "_formats": [ + "iri" + ], + "_instruction": "Enter the internationalized resource identifier (IRI) pointing to the preferred cross-reference to an external database or registry (e.g., KnowledgeSpace)." + }, + "otherOntologyIdentifier": { + "minItems": 1, + "type": "array", + "uniqueItems": true, + "_instruction": "Enter all internationalized resource identifiers (IRIs) pointing to ontology entries that are equivalent to this term (e.g., UBERON). Do not repeat the preferred ontology identifier.", + "items": { + "type": "string", + "_formats": [ + "iri" + ] + } }, - "ontologyIdentifiers": { + "otherCrossReference": { "minItems": 1, "type": "array", "uniqueItems": true, - "_instruction": "Enter all internationalized resource identifiers (IRIs) pointing to ontology entries that are equivalent to this term (e.g., from UBERON, MeSH, DOID, NCI Thesaurus). Do not repeat the preferred ontology identifier entered above.", + "_instruction": "Enter all internationalized resource identifiers (IRIs) pointing to cross-references to external databases or registries that are equivalent to this term (e.g., Wikidata). Do not repeat the preferred cross-reference.", "items": { "type": "string", "_formats": [ From 7636238edce7c3a22fd082715ab48d4ebb691bf5 Mon Sep 17 00:00:00 2001 From: raphaelgazzotti Date: Fri, 6 Mar 2026 14:11:13 +0100 Subject: [PATCH 8/8] Sort properties --- schemas/controlledTerm.schema.tpl.json | 28 +++++++++++++------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/schemas/controlledTerm.schema.tpl.json b/schemas/controlledTerm.schema.tpl.json index eed71cb4..72e65e90 100644 --- a/schemas/controlledTerm.schema.tpl.json +++ b/schemas/controlledTerm.schema.tpl.json @@ -18,20 +18,6 @@ "type": "string", "_instruction": "Controlled term originating from a defined terminology." }, - "preferredOntologyIdentifier": { - "type": "string", - "_formats": [ - "iri" - ], - "_instruction": "Enter the internationalized resource identifier (IRI) pointing to the preferred ontological term (e.g., InterLex)." - }, - "preferredCrossReference": { - "type": "string", - "_formats": [ - "iri" - ], - "_instruction": "Enter the internationalized resource identifier (IRI) pointing to the preferred cross-reference to an external database or registry (e.g., KnowledgeSpace)." - }, "otherOntologyIdentifier": { "minItems": 1, "type": "array", @@ -56,6 +42,20 @@ ] } }, + "preferredOntologyIdentifier": { + "type": "string", + "_formats": [ + "iri" + ], + "_instruction": "Enter the internationalized resource identifier (IRI) pointing to the preferred ontological term (e.g., InterLex)." + }, + "preferredCrossReference": { + "type": "string", + "_formats": [ + "iri" + ], + "_instruction": "Enter the internationalized resource identifier (IRI) pointing to the preferred cross-reference to an external database or registry (e.g., KnowledgeSpace)." + }, "synonym": { "type": "array", "minItems": 1,