sssom_schema.yaml

id: https://w3id.org/sssom/schema/
name: sssom
description: Datamodel for Simple Standard for Sharing Ontological Mappings (SSSOM)
imports:
- linkml:types
prefixes:
  dcterms: http://purl.org/dc/terms/
  linkml: https://w3id.org/linkml/
  sssom: https://w3id.org/sssom/
  rdfs: http://www.w3.org/2000/01/rdf-schema#
  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
  oboInOwl: http://www.geneontology.org/formats/oboInOwl#
  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
- https://mapping-commons.github.io/sssom/home/
default_curi_maps:
- semweb_context
- obo_context
default_prefix: sssom
default_range: string

enums:
  entity_type_enum:
    permissible_values:
      owl class:
        meaning: owl:Class
      owl object property:
        meaning: owl:ObjectProperty
      owl data property:
        meaning: owl:DataProperty
      owl annotation property:
        meaning: owl:AnnotationProperty
      owl named individual:
        meaning: owl:NamedIndividual
      skos concept:
        meaning: skos:Concept
      rdfs resource:
        meaning: rdfs:Resource
      rdfs class:
        meaning: rdfs:Class
      rdfs literal:
        meaning: rdfs:Literal
        description: This value indicates that the entity being mapped is not a semantic entity with a distinct identifier, but is instead represented entirely by its literal label. This value MUST NOT be used in the predicate_type slot.
        see_also:
        - https://mapping-commons.github.io/sssom/spec-model/#literal-mappings
        - https://github.com/mapping-commons/sssom/issues/234
        - https://github.com/mapping-commons/sssom/blob/master/examples/schema/literals.sssom.tsv
      rdfs datatype:
        meaning: rdfs:Datatype
      rdf property:
        meaning: rdf:Property
      composed entity expression:
        description: This value indicates that the entity ID does not represent a single entity, but a composite involving several individual entities. This value MUST NOT be used in the predicate_type slot. This specifications does not prescribe how an ID representing a composite entity should be interpreted; this is left at the discretion of applications.
        see_also:
        - https://github.com/mapping-commons/sssom/issues/402
        - https://github.com/mapping-commons/sssom/blob/master/examples/schema/composite-entities.sssom.tsv
        
  predicate_modifier_enum:
    permissible_values:
      Not: Negating the mapping predicate. The meaning of the triple becomes subject_id is not a predicate_id match to object_id.
  mapping_cardinality_enum:
    permissible_values:
      "1:1": One-to-one mapping
      "1:n": One-to-many mapping
      "n:1": Many-to-one mapping
      "1:0": One-to-none mapping
      "0:1": None-to-one mapping
      "n:n": Many-to-many mapping

types:
 EntityReference:
    typeof: uriorcurie
    description: |
      A reference to an entity involved in the mapping.
    base: str
    uri: rdfs:Resource
    see_also:
      - https://mapping-commons.github.io/sssom/spec/#tsv

slots:
  prefix_name:
    key: true
    range: ncname
  prefix_url:
    range: uri
  curie_map:
    description: A dictionary that contains prefixes as keys and their URI expansions as values.
    range: prefix
    multivalued: true
    inlined: true
    see_also:
      - https://github.com/mapping-commons/sssom/issues/225
      - https://github.com/mapping-commons/sssom/pull/349
      - https://github.com/mapping-commons/sssom/blob/master/examples/schema/curie_map.sssom.tsv
  mirror_from:
    description: A URL location from which to obtain a resource, such as a mapping set.
    range: uri
  registry_confidence:
    description: This value is set by the registry that indexes the mapping set. It reflects the confidence the registry has in the correctness of the mappings in the mapping set.
    range: double
  last_updated:
    description: The date this reference was last updated.
    range: date
  local_name:
    description: The local name assigned to file that corresponds to the downloaded mapping set.
    range: string
  mapping_set_references:
    description: A list of mapping set references.
    range: mapping set reference
    multivalued: true
    recommended: true
  mapping_registry_id:
    description: The unique identifier of a mapping registry.
    range: EntityReference
    required: true
  mapping_registry_title:
    description: The title of a mapping registry.
    range: string
  mapping_registry_description:
    description: The description of a mapping registry.
    range: string
  imports:
    description: A list of registries that should be imported into this one.
    multivalued: true
    range: uri
  documentation:
    description: A URL to the documentation of this mapping commons.
    range: uri
  homepage:
    description: A URL to a homepage of this mapping commons.
    range: uri
  mappings:
    description: Contains a list of mapping objects.
    range: mapping
    multivalued: true
    inlined_as_list: true
    recommended: true
  subject_id:
    description: The ID of the subject of the mapping.
    range: EntityReference
    mappings:
    - owl:annotatedSource
    slot_uri: owl:annotatedSource
    examples:
      - value: HP:0009894
        description: The CURIE denoting the Human Phenotype Ontology concept of 'Thickened ears'
  subject_label:
    description: The label of subject of the mapping.
    range: string
    examples:
      - value: Thickened ears
    recommended: true
  subject_category:
    description: The conceptual category to which the subject belongs to. This can
      be a string denoting the category or a term from a controlled vocabulary.
      This slot is deliberately underspecified. Conceptual categories can range from
      those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve
      as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this
      optional field is documentation for human reviewers - when a category is known
      and documented clearly, the cost of interpreting and evaluating the mapping decreases.
    range: string
    see_also:
      - https://github.com/mapping-commons/sssom/issues/13
      - https://github.com/mapping-commons/sssom/issues/256
    examples:
      - value: UBERON:0001062
        description: The CURIE of the Uberon term for "anatomical entity".
      - value: anatomical entity
        description: A string, rather than ID, describing the "anatomical entity" category. This is possible, but less preferred than using an ID.
      - value: biolink:Gene
        description: The CURIE of the biolink class for genes.
  subject_type:
    description: The type of entity that is being mapped.
    range: entity_type_enum
    instantiates: sssom:Propagatable
    annotations:
      propagated: true
    examples:
      - value: owl:Class
  predicate_id:
    description: The ID of the predicate or relation that relates the subject and
      object of this match.
    mappings:
    - owl:annotatedProperty
    range: EntityReference
    required: true
    slot_uri: owl:annotatedProperty
    examples:
      - value: owl:sameAs
        description: The subject and the object are instances (owl individuals), and the two instances are the same.
      - value: owl:equivalentClass
        description: The subject and the object are classes (owl class), and the two classes are the same.
      - value: owl:equivalentProperty
        description: The subject and the object are properties (owl object, data, annotation properties), and the two properties are the same.
      - value: rdfs:subClassOf
        description: The subject and the object are classes (owl class), and the subject is a subclass of the object.
      - value: rdfs:subPropertyOf
        description: The subject and the object are properties (owl object, data, annotation properties), and the subject is a subproperty of the object.
      - value: skos:relatedMatch
        description: The subject and the object are associated in some unspecified way.
      - value: skos:closeMatch
        description: The subject and the object are sufficiently similar that they can be used interchangeably in some information retrieval applications.
      - value: skos:exactMatch
        description: The subject and the object can, with a high degree of confidence, be used interchangeably across a wide range of information retrieval applications.
      - value: skos:narrowMatch
        description: "From the SKOS primer: A triple skos:narrower (and skos:narrowMatch) asserts that , the object of the triple, is a narrower concept than , the subject of the triple."
      - value: skos:broadMatch
        description: "From the SKOS primer: A triple skos:broader (and skos:broadMatch) asserts that , the object of the triple, is a broader concept than , the subject of the triple."
      - value: oboInOwl:hasDbXref
        description: Two terms are related in some way. The meaning is frequently consistent across a single set of mappings. Note this property is often overloaded even where the terms are of a different nature (e.g. interpro2go).
      - value: rdfs:seeAlso
        description: The subject and the object are associated in some unspecified way. The object IRI often resolves to a resource on the web that provides additional information.
  predicate_modifier:
    description: A modifier for negating the predicate. See https://github.com/mapping-commons/sssom/issues/40 for discussion
    range: predicate_modifier_enum
    see_also:
      - https://github.com/mapping-commons/sssom/issues/107
    examples:
      - value: Not
        description: Negates the predicate, see documentation of predicate_modifier_enum
  predicate_label:
    description: The label of the predicate/relation of the mapping.
    range: string
    examples:
      - value: has cross-reference
        description: The label of the oboInOwl:hasDbXref property to represent cross-references.
  predicate_type:
    description: The type of entity that is being mapped.
    range: entity_type_enum
    examples:
      - value: owl:AnnotationProperty
      - value: owl:ObjectProperty
  object_id:
    description: The ID of the object of the mapping.
    mappings:
    - owl:annotatedTarget
    range: EntityReference
    slot_uri: owl:annotatedTarget
    examples:
      - value: HP:0009894
        description: The CURIE denoting the Human Phenotype Ontology concept of 'Thickened ears'.
  object_label:
    description: The label of object of the mapping.
    range: string
    examples:
      - value: Thickened ears
    recommended: true
  object_category:
    description: The conceptual category to which the subject belongs to. This can
      be a string denoting the category or a term from a controlled vocabulary.
      This slot is deliberately underspecified. Conceptual categories can range from
      those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve
      as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this
      optional field is documentation for human reviewers - when a category is known
      and documented clearly, the cost of interpreting and evaluating the mapping decreases.
    range: string
    see_also:
      - https://github.com/mapping-commons/sssom/issues/13
      - https://github.com/mapping-commons/sssom/issues/256
    examples:
      - value: UBERON:0001062
        description: The CURIE of the Uberon term for "anatomical entity".
      - value: anatomical entity
        description: A string, rather than ID, describing the "anatomical entity" category. This is possible, but less preferred than using an ID.
      - value: biolink:Gene
        description: The CURIE of the biolink class for genes.
  mapping_justification:
    description: A mapping justification is an action (or the written representation of that action) of showing a mapping to be right or reasonable.
    range: EntityReference
    pattern: "^semapv:(MappingReview|ManualMappingCuration|LogicalReasoning|LexicalMatching|CompositeMatching|UnspecifiedMatching|SemanticSimilarityThresholdMatching|LexicalSimilarityThresholdMatching|MappingChaining)$"
    required: true
    any_of:
      - equals_string: semapv:LexicalMatching
      - equals_string: semapv:LogicalReasoning
      - equals_string: semapv:CompositeMatching
      - equals_string: semapv:UnspecifiedMatching
      - equals_string: semapv:SemanticSimilarityThresholdMatching
      - equals_string: semapv:LexicalSimilarityThresholdMatching
      - equals_string: semapv:MappingChaining
      - equals_string: semapv:MappingReview
      - equals_string: semapv:ManualMappingCuration
    examples:
      - value: semapv:LexicalMatching
      - value: semapv:ManualMappingCuration
  object_type:
    description: The type of entity that is being mapped.
    range: entity_type_enum
    instantiates: sssom:Propagatable
    annotations:
      propagated: true
    examples:
      - value: owl:Class
  mapping_set_id:
    description: A globally unique identifier for the mapping set (not each individual
      mapping). Should be IRI, ideally resolvable.
    required: true
    range: uri
    examples:
      - value: http://purl.obolibrary.org/obo/mondo/mappings/mondo_exactmatch_ncit.sssom.tsv
        description: A persistent URI pointing to the latest version of the Mondo - NCIT mapping in the Mondo namespace.
  mapping_set_version:
    description: A version string for the mapping.
    range: string
    slot_uri: owl:versionInfo
    examples:
      - value: "2020-01-01"
        description: A date-based version that indicates that the mapping was published on the 1st January in 2021.
      - value: "1.2.1"
        description: "(A semantic version tag that indicates that this is the 1st major, 2nd minor version, patch 1 (https://semver.org/).)"
  mapping_set_group:
    description: Set by the owners of the mapping registry. A way to group related mapping sets for example for UI purposes.
    range: string
  mapping_set_title:
    description: The display name of a mapping set.
    range: string
    slot_uri: dcterms:title
    examples:
      - value: "The Mondo-OMIM mappings by Monarch Initiative."
  mapping_set_description:
    description: A description of the mapping set.
    range: string
    slot_uri: dcterms:description
    examples:
      - value: "This mapping set was produced to integrate human and mouse phenotype data at the IMPC. It is primarily used for making mouse phenotypes searchable by human synonyms at https://mousephenotype.org/."
  creator_id:
    description: Identifies the persons or groups responsible for the creation of
      the mapping. The creator is the agent that put the mapping in its published form, 
      which may be different from the author, which is a person that was actively involved
      in the assertion of the mapping.
      Recommended to be a list of ORCIDs or otherwise
      identifying URIs.
    slot_uri: dcterms:creator
    range: EntityReference
    multivalued: true
    examples:
      - value: orcid:0000-0002-7356-1779|orcid:0000-0002-6601-2165
        description: The ORCID of the (multiple) creators of the mapping.
      - value: orcid:0000-0002-7356-1779
        description: The ORCID of the creator of the mapping.
  creator_label:
    description: A string identifying the creator of this mapping. In the spirit of
      provenance, consider using creator_id instead.
    range: string
    multivalued: true
    examples:
      - value: Nicolas Matentzoglu|Chris Mungall
        description: The human-readable names of the (multiple) creators of the mapping.
      - value: Nicolas Matentzoglu
        description: The human-readable name of the creator of the mapping.
  author_id:
    description: Identifies the persons or groups responsible for asserting the mappings.
      Recommended to be a list of ORCIDs or otherwise
      identifying URIs.
    slot_uri: pav:authoredBy
    range: EntityReference
    multivalued: true
    examples:
      - value: orcid:0000-0002-7356-1779|orcid:0000-0002-6601-2165
        description: The ORCID of the (multiple) authors of the mapping.
      - value: orcid:0000-0002-7356-1779
        description: The ORCID of the author of the mapping.
  author_label:
    description: A string identifying the author of this mapping. In the spirit of
      provenance, consider using author_id instead.
    range: string
    multivalued: true
    examples:
      - value: Nicolas Matentzoglu|Chris Mungall
        description: The human-readable names of the (multiple) authors of the mapping.
      - value: Nicolas Matentzoglu
        description: The human-readable name of the author of the mapping.
  reviewer_id:
    description: Identifies the persons or groups that reviewed and confirmed the mapping.
      Recommended to be a list of ORCIDs or otherwise
      identifying URIs.
    range: EntityReference
    multivalued: true
    examples:
      - value: orcid:0000-0002-7356-1779|orcid:0000-0002-6601-2165
        description: The ORCID of the (multiple) reviewers of the mapping.
      - value: orcid:0000-0002-7356-1779
        description: The ORCID of the reviewer of the mapping.
  reviewer_label:
    description: A string identifying the reviewer of this mapping. In the spirit of
      provenance, consider using reviewer_id instead.
    range: string
    multivalued: true
    examples:
      - value: Nicolas Matentzoglu|Chris Mungall
        description: The human-readable names of the (multiple) reviewers of the mapping.
      - value: Nicolas Matentzoglu
        description: The human-readable name of the reviewer of the mapping.
  license:
    description: A url to the license of the mapping. In absence of a license we assume
      no license.
    range: uri
    slot_uri: dcterms:license
    examples:
      - value: https://creativecommons.org/licenses/by/4.0/
        description: The URI of the Creative Commons Attribution 4.0 International license.
  subject_source:
    description: URI of vocabulary or identifier source for the subject.
    range: EntityReference
    instantiates: sssom:Propagatable
    annotations:
      propagated: true
    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.
  subject_source_version:
    description: Version IRI or version string of the source of the subject term.
    range: string
    instantiates: sssom:Propagatable
    annotations:
      propagated: true
    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
    instantiates: sssom:Propagatable
    annotations:
      propagated: true
    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.
  object_source_version:
    description: Version IRI or version string of the source of the object term.
    range: string
    instantiates: sssom:Propagatable
    annotations:
      propagated: true
    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'
  mapping_provider:
    description: URL pointing to the source that provided the mapping, for example
      an ontology that already contains the mappings, or a database from which it was derived.
    range: uri
    instantiates: sssom:Propagatable
    annotations:
      propagated: true
    examples:
      - value: https://www.ohdsi.org/
        description: A URL pointing to the Observational Health Data Sciences and Informatics initiative.
      - value: https://monarchinitiative.org/
        description: A URL pointing to the Monarch Initiative Resource.
  mapping_set_source:
    description: A mapping set or set of mapping set that was used to derive the mapping set.
    slot_uri: prov:wasDerivedFrom
    range: uri
    multivalued: true
    examples:
      - value: http://purl.obolibrary.org/obo/mondo/mappings/2022-05-20/mondo_exactmatch_ncit.sssom.tsv
        description: A persistent, ideally versioned, link to the mapping set from which the current mapping set is derived.
  mapping_source:
    description: The mapping set this mapping was originally defined in. mapping_source is used for example when merging multiple
      mapping sets or deriving one mapping set from another.
    range: EntityReference
    examples:
      - value: MONDO_MAPPINGS:mondo_exactmatch_ncit.sssom.tsv
        description: A reference to the mapping set that originally contained this mapping.
  mapping_cardinality:
    description: A string indicating whether this mapping is from a 1:1 (the subject_id
      maps to a single object_id), 1:n (the subject maps to more than one object_id), 
      n:1, 1:0, 0:1 or n:n group. Note that this is a convenience field that should be derivable 
      from the mapping set.
    range: mapping_cardinality_enum
    examples:
      - value: "1:1"
        description: A one-to-one mapping.
      - value: "1:n"
        description: A one-to-many mapping.
  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.
    range: string
    instantiates: sssom:Propagatable
    annotations:
      propagated: true
    examples:
      - value: https://github.com/AgreementMakerLight/AML-Project
        description: A URL pointing to the AgreementMakerLight project.
      - value: AgreementMakerLight
        description: A string (name) denoting the AgreementMakerLight project.
  mapping_tool_version:
    description: Version string that denotes the version of the mapping tool used.
    range: string
    instantiates: sssom:Propagatable
    annotations:
      propagated: true
    examples:
      - value: v3.2
  mapping_date:
    description: The date the mapping was asserted. This is different from the date the mapping was published or compiled in a SSSOM file.
    slot_uri: pav:authoredOn
    range: date
    instantiates: sssom:Propagatable
    examples:
      - value: 2021-01-01
    annotations:
      propagated: true
  publication_date:
    description: The date the mapping was published. This is different from the date the mapping was asserted.
    slot_uri: dcterms:created
    range: date
    examples:
      - value: 2021-01-01
  confidence:
    description: A score between 0 and 1 to denote the confidence or probability that
      the match is correct, where 1 denotes total confidence.
    range: double
    minimum_value: 0.0
    maximum_value: 1.0
    examples:
      - value: 0.95
        description: A confidence score of 0.95, indicating 95% confidence.
  subject_match_field:
    description: A list of properties (term annotations on the subject) that was used
      for the match.
    range: EntityReference
    multivalued: true
    instantiates: sssom:Propagatable
    annotations:
      propagated: true
    examples:
      - value: rdfs:label
        description: "The RDFS label property (rdfs:label) was used to match the subject."
      - value: skos:prefLabel
        description: "The SKOS preferred label property (skos:prefLabel) was used to match the subject."
  object_match_field:
    description: A list of properties (term annotations on the object) that was used
      for the match.
    range: EntityReference
    multivalued: true
    instantiates: sssom:Propagatable
    annotations:
      propagated: true
    examples:
      - value: rdfs:label
        description: "The RDFS label property (rdfs:label) was used to match the object."
      - value: skos:prefLabel
        description: "The SKOS preferred label property (skos:prefLabel) was used to match the object."
  match_string:
    description: String that is shared by subj/obj. It is recommended to indicate the 
      fields for the match using the object and subject_match_field slots.
    range: string
    multivalued: true
    examples:
      - value: "gala"
        description: "The 'gala' string was matched for both subject and object."
  subject_preprocessing:
    description: Method of preprocessing applied to the fields of the subject. 
      If different preprocessing steps were performed on different fields, it is
      recommended to store the match in separate rows.
    range: EntityReference
    multivalued: true
    instantiates: sssom:Propagatable
    annotations:
      propagated: true
    examples:
      - value: semapv:Stemming
      - value: semapv:StopWordRemoval
  object_preprocessing:
    description: Method of preprocessing applied to the fields of the object. 
      If different preprocessing steps were performed on different fields, it is
      recommended to store the match in separate rows.
    range: EntityReference
    multivalued: true
    instantiates: sssom:Propagatable
    annotations:
      propagated: 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
      rule is captured as a resource rather than a string, which enables higher levels of transparency and sharing across mapping sets.
      The URI representation of the curation rule is expected to be a resolvable identifier which provides details about the nature of the curation rule.
    range: EntityReference
    multivalued: true
    examples:
      - value: DISEASE_MAPPING_COMMONS_RULES:MPR2
        description: A reference to the Disease Mapping Commons rule with the ID MPR2.
    see_also: 
      - https://github.com/mapping-commons/sssom/issues/166
      - https://github.com/mapping-commons/sssom/pull/258
      - https://github.com/mapping-commons/sssom/blob/master/examples/schema/curation_rule.sssom.tsv
  curation_rule_text:
    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
      rule should be captured as a resource (entity reference) rather than a string (see curation_rule element), which enables higher levels of transparency and sharing across mapping sets.
      The textual representation of curation rule is intended to be used in cases where (1) the creation of a resource is not practical from the
      perspective of the mapping_provider and (2) as an additional piece of metadata to augment the curation_rule element with a human readable text.
    range: string
    multivalued: true
    examples:
      - value: "The two phenotypes inhere in homologous structures and exhibit the same phenotypic quality."
      - value: "The two diseases are used synonymous in the medical literature."
    see_also:
      - https://github.com/mapping-commons/sssom/issues/166
      - https://github.com/mapping-commons/sssom/pull/258
      - https://github.com/mapping-commons/sssom/blob/master/examples/schema/curation_rule_text.sssom.tsv
  similarity_score:
    description: A score between 0 and 1 to denote the similarity between two entities, where
      1 denotes equivalence, and 0 denotes disjointness. The score is meant to be used in conjunction 
      with the similarity_measure field, to document, for example, the lexical or semantic match
      of a matching algorithm.
    range: double
    minimum_value: 0.0
    maximum_value: 1.0
    examples:
      - value: 0.95
        description: A similarity score of 0.95, indicating 95% similarity.
    see_also:
      - https://github.com/mapping-commons/sssom/issues/385
      - https://github.com/mapping-commons/sssom/pull/386
      - https://github.com/mapping-commons/sssom/blob/master/examples/schema/similarity_score.sssom.tsv
  similarity_measure:
    description: The measure used for computing a similarity score.
      This field is meant to be used in conjunction with the similarity_score field, to document,
      for example, the lexical or semantic match of a matching algorithm.
      To make processing this field as unambiguous as possible, we recommend using 
      wikidata CURIEs, but the type of this field is deliberately unspecified.
    range: string
    examples:
      - value: https://www.wikidata.org/entity/Q865360
        description: the Wikidata IRI for the Jaccard index measure).
      - value: wikidata:Q865360
        description: the Wikidata CURIE for the Jaccard index measure).
      - value: Levenshtein distance
        description: a score to measure the distance between two character sequences).
    see_also:
      - https://github.com/mapping-commons/sssom/issues/385
      - https://github.com/mapping-commons/sssom/pull/386
      - https://github.com/mapping-commons/sssom/blob/master/examples/schema/similarity_score.sssom.tsv
  issue_tracker_item:
    description: The issue tracker item discussing this mapping.
    range: EntityReference
    examples:
      - value: SSSOM_GITHUB_ISSUE:166
        description: A URL resolving to an issue discussing a new SSSOM element request
    see_also: 
      - https://github.com/mapping-commons/sssom/issues/78
      - https://github.com/mapping-commons/sssom/pull/259
      - https://github.com/mapping-commons/sssom/blob/master/examples/schema/issue_tracker_item.sssom.tsv
  issue_tracker:
    description: A URL location of the issue tracker for this entity.
    range: uri
    examples:
      - value: https://github.com/mapping-commons/mh_mapping_initiative/issues
        description: A URL resolving to the issue tracker of the Mouse-Human mapping initiative
    see_also: 
      - https://github.com/mapping-commons/sssom/issues/78
      - https://github.com/mapping-commons/sssom/pull/259
      - https://github.com/mapping-commons/sssom/blob/master/examples/schema/issue_tracker.sssom.tsv
  see_also:
    description: A URL specific for the mapping instance. E.g. for kboom we have a
      per-mapping image that shows surrounding axioms that drive probability. Could
      also be a github issue URL that discussed a complicated alignment
    slot_uri: rdfs:seeAlso
    examples:
      - value: https://github.com/mapping-commons/mh_mapping_initiative/pull/41
        description: A URL pointing to the pull request that introduced the mapping.
    range: string
    multivalued: true
  other:
    description: "Pipe separated list of key value pairs for properties not part of
      the SSSOM spec. Can be used to encode additional provenance data. NOTE. This
      field is not recommended for general use, and should be used sparingly. See
      https://github.com/mapping-commons/sssom/blob/master/examples/schema/extension-slots.sssom.tsv
      for an alternative approach based on extension slots."
    range: string
  comment:
    description: Free text field containing either curator notes or text generated
      by tool providing additional informative information.
    slot_uri: rdfs:comment
    range: string
    examples:
      - value: This mapping is weird in that the hierarchical position of the two terms
          is very different.
        description: A comment explaining a mapping authors reservation on a mapping.
  extension_definitions:
    description: A list that defines the extension slots used in the mapping set.
    range: extension definition
    multivalued: true
    see_also:
      - https://github.com/mapping-commons/sssom/issues/328
      - https://github.com/mapping-commons/sssom/blob/master/examples/schema/extension-slots.sssom.tsv
classes:
  mapping set:
    description: Represents a set of mappings.
    slot_usage:
      license:
        required: true
    slots:
    - curie_map
    - mappings
    - mapping_set_id
    - mapping_set_version
    - mapping_set_source
    - mapping_set_title
    - mapping_set_description
    - creator_id
    - creator_label
    - license
    - subject_type
    - subject_source
    - subject_source_version
    - object_type
    - object_source
    - object_source_version
    - mapping_provider
    - mapping_tool
    - mapping_tool_version
    - mapping_date
    - publication_date
    - subject_match_field
    - object_match_field
    - subject_preprocessing
    - object_preprocessing
    - see_also
    - issue_tracker
    - other
    - comment
    - extension_definitions
  mapping:
    description: Represents an individual mapping between a pair of entities.
    slots:
    - subject_id
    - subject_label
    - subject_category
    - 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
    - subject_type
    - subject_source
    - subject_source_version
    - object_type
    - object_source
    - object_source_version
    - mapping_provider
    - mapping_source
    - mapping_cardinality
    - mapping_tool
    - mapping_tool_version
    - mapping_date
    - publication_date
    - confidence
    - curation_rule
    - curation_rule_text
    - subject_match_field
    - object_match_field
    - match_string
    - subject_preprocessing
    - object_preprocessing
    - similarity_score
    - similarity_measure
    - see_also
    - issue_tracker_item
    - other
    - comment
    class_uri: owl:Axiom
    rules:
      - preconditions:
          slot_conditions:
            subject_type: 
              equals_string: "rdfs literal"
        postconditions:
          slot_conditions:
            subject_label:
              required: true
      - preconditions:
          slot_conditions:
            subject_type:
              none_of:
                equals_string: "rdfs literal"
        postconditions:
          slot_conditions:
            subject_id:
              required: true
      - preconditions:
          slot_conditions:
            object_type: 
              equals_string: "rdfs literal"
        postconditions:
          slot_conditions:
            object_label:
              required: true
      - preconditions:
          slot_conditions:
            object_type:
              none_of:
                equals_string: "rdfs literal"
        postconditions:
          slot_conditions:
            object_id:
              required: true
  mapping registry:
    description: A registry for managing mapping sets. It holds a set of 
      mapping set references, and can import other registries.
    slots:
      - mapping_registry_id
      - mapping_registry_title
      - mapping_registry_description
      - imports
      - mapping_set_references
      - documentation
      - homepage
      - issue_tracker
  mapping set reference:
    description: A reference to a mapping set. It allows to augment mapping 
      set metadata from the perspective of the registry, for example, providing 
      confidence, or a local filename or a grouping.
    slots:
      - mapping_set_id
      - mirror_from
      - registry_confidence
      - mapping_set_group
      - last_updated
      - local_name
  prefix:
    slots:
      - prefix_name
      - prefix_url
  extension definition:
    description: A definition of an extension (non-standard) slot.
    attributes:
      slot_name:
        description: The name of the extension slot.
        range: ncname
        required: true
      property:
        description: The property associated with the extension slot. It is
          intended to provide a non-ambiguous meaning to the slot (contrary
          to the slot_name, which for brevity reasons may be ambiguous).
        range: uriorcurie
      type_hint:
        description: Expected type of the values of the extension slot.
        range: uriorcurie
  Propagatable:
    class_uri: sssom:Propagatable
    description: Metamodel extension class to describe slots whose value can be
      propagated down from the MappingSet class to the Mapping class.
    see_also:
      - https://github.com/mapping-commons/sssom/issues/305
    attributes:
      propagated:
        description: Indicates whether a slot can be propagated from a mapping
          down to individual mappings.
        range: boolean
  NoTermFound:
    class_uri: sssom:NoTermFound
    description: sssom:NoTermFound can be used in place of a subject_id or object_id
      when the corresponding entity could not be found. It SHOULD be used in conjuction with
      a corresponding subject_source or object_source to signify where the term was not found.
    see_also:
      - https://github.com/mapping-commons/sssom/issues/28
      - https://github.com/mapping-commons/sssom/blob/master/examples/schema/no_term_found.sssom.tsv