From 63700434a0d60fccedb22d232124594333103b04 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 12 Jun 2025 08:25:19 +0300 Subject: [PATCH 1/6] Add mapping_tool_id slot to model Adding mapping_tool_id as an entity reference. Added a note the mapping_tool that mapping_tool_id should be preferred for a stronger level of standardisation --- src/sssom_schema/schema/sssom_schema.yaml | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml index 6b4973ca..8e2b3f3a 100644 --- a/src/sssom_schema/schema/sssom_schema.yaml +++ b/src/sssom_schema/schema/sssom_schema.yaml @@ -548,6 +548,7 @@ slots: mapping_tool: description: A reference to the tool or algorithm that was used to generate the mapping. Should be a URL pointing to more info about it, but can be free text. + Consider using the mapping_tool_id slot for a more standardised reference. range: string instantiates: sssom:Propagatable annotations: @@ -557,6 +558,19 @@ slots: description: A URL pointing to the AgreementMakerLight project. - value: AgreementMakerLight description: A string (name) denoting the AgreementMakerLight project. + mapping_tool_id: + description: The ID (entity reference) of the tool or algorithm that was used to generate the + mapping. + range: EntityReference + instantiates: sssom:Propagatable + annotations: + propagated: true + examples: + - value: wikidata:Q58057366 + description: A wikidata PURL identifying the AgreementMakerLight project. + see_also: + - https://github.com/mapping-commons/sssom/blob/master/examples/schema/mapping_tool_id.sssom.tsv + - https://github.com/mapping-commons/sssom/issues/449 mapping_tool_version: description: Version string that denotes the version of the mapping tool used. range: string @@ -807,6 +821,7 @@ classes: - predicate_type - mapping_provider - mapping_tool + - mapping_tool_id - mapping_tool_version - mapping_date - publication_date @@ -851,6 +866,7 @@ classes: - mapping_source - mapping_cardinality - mapping_tool + - mapping_tool_id - mapping_tool_version - mapping_date - publication_date From 7a02f67034eb4fde25e9602317339f12d9d960f7 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 12 Jun 2025 08:25:30 +0300 Subject: [PATCH 2/6] Add example for mapping_tool_id --- examples/schema/mapping_tool_id.sssom.tsv | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 examples/schema/mapping_tool_id.sssom.tsv diff --git a/examples/schema/mapping_tool_id.sssom.tsv b/examples/schema/mapping_tool_id.sssom.tsv new file mode 100644 index 00000000..f11118be --- /dev/null +++ b/examples/schema/mapping_tool_id.sssom.tsv @@ -0,0 +1,14 @@ +#curie_map: +# HP: http://purl.obolibrary.org/obo/HP_ +# MP: http://purl.obolibrary.org/obo/MP_ +# orcid: https://orcid.org/ +# wikidata: https://www.wikidata.org/wiki/ +#mapping_set_id: https://w3id.org/sssom/commons/examples/mapping_tool_id.sssom.tsv +#license: "https://creativecommons.org/publicdomain/zero/1.0/" +#creator_id: orcid:0000-0002-7356-1779 +#mapping_provider: "https://w3id.org/sssom/core_team" +#issue_tracker: "https://github.com/mapping-commons/mh_mapping_initiative/issues" +#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated. +subject_id predicate_id object_id mapping_justification mapping_tool_id +HP:0009124 skos:exactMatch MP:0000003 semapv:ManualMappingCuration wikidata:Q58057366 +HP:0008551 skos:exactMatch MP:0000018 semapv:ManualMappingCuration wikidata:Q58057366 From 6fa928179659d86b9de034b49815e76bfad3ffde Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 12 Jun 2025 08:27:33 +0300 Subject: [PATCH 3/6] Update changelog, adding mapping_tool_id --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3e001623..27c22a91 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,8 +7,8 @@ - Add `similarity_measure` slot to the `MappingSet` class ([issue](https://github.com/mapping-commons/sssom/issues/411)). - Add `sssom_version` slot to the `MappingSet` class ([issue](https://github.com/mapping-commons/sssom/issues/439)). - Change the type of the `see_also` slot to `xsd:anyURI` ([issue](https://github.com/mapping-commons/sssom/issues/422)). -- Add `mappings_set_confidence` slot to the `MappingSet` class ([issue](https://github.com/mapping-commons/sssom/issues/438)). -- TBD +- Add `mapping_set_confidence` slot to the `MappingSet` class ([issue](https://github.com/mapping-commons/sssom/issues/438)). +- Add `mapping_tool_id` slot to the `Mapping` and `MappingSet` classes ([issue](https://github.com/mapping-commons/sssom/issues/449)). ## SSSOM version 1.0.0 From ea98d542921e8841121461c36dabbe0a2c6114ab Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 12 Jun 2025 08:28:34 +0300 Subject: [PATCH 4/6] Add added_in annotation to mapping_tool_id slot --- src/sssom_schema/schema/sssom_schema.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml index 8e2b3f3a..eeb41045 100644 --- a/src/sssom_schema/schema/sssom_schema.yaml +++ b/src/sssom_schema/schema/sssom_schema.yaml @@ -565,6 +565,7 @@ slots: instantiates: sssom:Propagatable annotations: propagated: true + added_in: "1.1" examples: - value: wikidata:Q58057366 description: A wikidata PURL identifying the AgreementMakerLight project. From 4a2cccaa91c38e08d8b6700d4a85b1a1612ddf1e Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 12 Jun 2025 11:24:57 +0300 Subject: [PATCH 5/6] fix creator_id in mapping_tool_id.sssom.tsv Co-authored-by: Damien Goutte-Gattat --- examples/schema/mapping_tool_id.sssom.tsv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/examples/schema/mapping_tool_id.sssom.tsv b/examples/schema/mapping_tool_id.sssom.tsv index f11118be..d14adc1c 100644 --- a/examples/schema/mapping_tool_id.sssom.tsv +++ b/examples/schema/mapping_tool_id.sssom.tsv @@ -5,7 +5,8 @@ # wikidata: https://www.wikidata.org/wiki/ #mapping_set_id: https://w3id.org/sssom/commons/examples/mapping_tool_id.sssom.tsv #license: "https://creativecommons.org/publicdomain/zero/1.0/" -#creator_id: orcid:0000-0002-7356-1779 +#creator_id: +# - orcid:0000-0002-7356-1779 #mapping_provider: "https://w3id.org/sssom/core_team" #issue_tracker: "https://github.com/mapping-commons/mh_mapping_initiative/issues" #comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated. From a8529d01fbc2d41bb2837098ddf21c7db31563b0 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 12 Jun 2025 11:25:49 +0300 Subject: [PATCH 6/6] add versionable instantiation to mapping_tool_id slot Co-authored-by: Damien Goutte-Gattat --- src/sssom_schema/schema/sssom_schema.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml index eeb41045..9d97b703 100644 --- a/src/sssom_schema/schema/sssom_schema.yaml +++ b/src/sssom_schema/schema/sssom_schema.yaml @@ -562,7 +562,9 @@ slots: description: The ID (entity reference) of the tool or algorithm that was used to generate the mapping. range: EntityReference - instantiates: sssom:Propagatable + instantiates: + - sssom:Propagatable + - sssom:Versionable annotations: propagated: true added_in: "1.1"