diff --git a/mkdocs.yml b/mkdocs.yml index 0f0fe992..3b0b728b 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -50,6 +50,7 @@ nav: - 5-Star Entity Mappings - Cheatsheet: 5star-mappings.md - Update schema/context and release: update.md - Matching tool implementation guide: matching-tool-implementation-guide.md + - SSSOM profiles: sssom-profiles.md - Glossary: glossary.md site_url: https://mapping-commons.github.io/sssom/ diff --git a/src/docs/sssom-profiles.md b/src/docs/sssom-profiles.md new file mode 100644 index 00000000..b46e838d --- /dev/null +++ b/src/docs/sssom-profiles.md @@ -0,0 +1,17 @@ +## SSSOM Profiles + +- [Literal Mappings](#literal) + + + +### Literal Mappings + +The SSSOM profile for literal mappings is a version of SSSOM that allows the dissemination and standardisation of mappings between identifers and literals. + +As of 01.08.2023, the first version of this profile has been published, and it is still subject to change. We recommend to reach out on the [SSSOM issue tracker](https://github.com/mapping-commons/sssom/issues) if you are interested in using the literal profile. Note: we dont expect there to be any major breaking changes. + +**Demand better docs now**: https://github.com/mapping-commons/sssom/issues + +- [Slides](https://docs.google.com/presentation/d/1mBZK6KS7JgmXlEtszQiOa_Cl7SXg_Z8wRp0tZHaL57Y/edit) +- [PR](https://github.com/mapping-commons/sssom/pull/235) +- [Recording/discussion](events/mc2023.md) \ No newline at end of file diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml index d005cf39..b35c9f45 100644 --- a/src/sssom_schema/schema/sssom_schema.yaml +++ b/src/sssom_schema/schema/sssom_schema.yaml @@ -13,6 +13,7 @@ prefixes: pav: http://purl.org/pav/ prov: http://www.w3.org/ns/prov# skos: http://www.w3.org/2004/02/skos/core# + xsd: http://www.w3.org/2001/XMLSchema# semapv: https://w3id.org/semapv/vocab/ see_also: - https://github.com/mapping-commons/sssom @@ -121,6 +122,26 @@ slots: examples: - value: HP:0009894 description: The CURIE denoting the Human Phenotype Ontology concept of 'Thickened ears' + literal: + description: The literal being mapped + range: string + required: true + mappings: + - owl:annotatedSource + slot_uri: owl:annotatedSource + examples: + - value: "Alzheimer" + description: A string referring to some thing. + literal_datatype: + description: The datatype of the literal being mapped + range: uri + required: false + mappings: + - rdf:datatype + slot_uri: rdf:datatype + examples: + - value: xsd:string + description: A string referring to some thing. subject_label: description: The label of subject of the mapping range: string @@ -350,6 +371,20 @@ slots: examples: - value: http://purl.obolibrary.org/obo/mondo/releases/2021-01-30/mondo.owl description: (A persistent Version IRI pointing to the Mondo version '2021-01-30') + literal_source: + description: URI of ontology source for the literal. + range: EntityReference + examples: + - value: obo:mondo.owl + description: A persistent OBO CURIE pointing to the latest version of the Mondo ontology. + - value: wikidata:Q7876491 + description: A Wikidata identifier for the Uberon ontology resource. + literal_source_version: + description: Version IRI or version string of the source of the literal. + range: string + examples: + - value: http://purl.obolibrary.org/obo/mondo/releases/2021-01-30/mondo.owl + description: (A persistent Version IRI pointing to the Mondo version '2021-01-30') object_source: description: URI of vocabulary or identifier source for the object. range: EntityReference @@ -444,6 +479,13 @@ slots: examples: - value: semapv:Stemming - value: semapv:StopWordRemoval + literal_preprocessing: + description: Method of preprocessing applied to the literal. + range: EntityReference + multivalued: true + examples: + - value: semapv:Stemming + - value: semapv:StopWordRemoval curation_rule: description: A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping. Curation rules often involve complex domain-specific considerations, which are hard to capture in an automated fashion. The curation @@ -479,6 +521,18 @@ slots: examples: - value: https://www.wikidata.org/wiki/Q865360 description: (the Wikidata identifier for the Jaccard index measure). + similarity_score: + description: A score between 0 and 1 to denote the similarity, where + 1 denotes equivalence. + range: double + similarity_measure: + description: The measure used for computing the the similarity score. + To make processing this field as unambiguous as possible, we recommend using + wikidata identifiers, but wikipedia pages could also be acceptable. + range: string + examples: + - value: https://www.wikidata.org/wiki/Q865360 + description: (the Wikidata identifier for the Jaccard index measure). issue_tracker_item: description: The issue tracker item discussing this mapping. range: EntityReference @@ -598,6 +652,50 @@ classes: - other - comment class_uri: owl:Axiom + literal mapping: + description: Represents an individual mapping between a literal and an entity. + Note that this schema has been created on 01.08.2023 and is subject to change. + see_also: + - https://mapping-commons.github.io/sssom/sssom-profiles/ + slots: + - literal + - literal_datatype + - predicate_id + - predicate_label + - predicate_modifier + - object_id + - object_label + - object_category + - mapping_justification + - author_id + - author_label + - reviewer_id + - reviewer_label + - creator_id + - creator_label + - license + - literal_source + - literal_source_version + - object_type + - object_source + - object_source_version + - mapping_provider + - mapping_source + - mapping_cardinality + - mapping_tool + - mapping_tool_version + - mapping_date + - confidence + - object_match_field + - match_string + - literal_preprocessing + - object_preprocessing + - similarity_score + - similarity_measure + - see_also + - other + - comment + class_uri: owl:Axiom mapping registry: description: A registry for managing mapping sets. It holds a set of mapping set references, and can import other registries.