Class: Mapping

name: mapping
description: Represents an individual mapping between a pair of entities
from_schema: https://w3id.org/sssom/schema/
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
- semantic_similarity_score
- semantic_similarity_measure
- see_also
- issue_tracker_item
- other
- comment
class_uri: owl:Axiom

name: mapping
description: Represents an individual mapping between a pair of entities
from_schema: https://w3id.org/sssom/schema/
attributes:
  subject_id:
    name: subject_id
    description: The ID of the subject of the mapping.
    examples:
    - value: HP:0009894
      description: The CURIE denoting the Human Phenotype Ontology concept of 'Thickened
        ears'
    from_schema: https://w3id.org/sssom/schema/
    mappings:
    - owl:annotatedSource
    rank: 1000
    slot_uri: owl:annotatedSource
    alias: subject_id
    owner: mapping
    domain_of:
    - mapping
    range: EntityReference
    required: true
  subject_label:
    name: subject_label
    description: The label of subject of the mapping
    examples:
    - value: Thickened ears
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: subject_label
    owner: mapping
    domain_of:
    - mapping
    range: string
    recommended: true
  subject_category:
    name: 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.
    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.)
    from_schema: https://w3id.org/sssom/schema/
    see_also:
    - https://github.com/mapping-commons/sssom/issues/13
    - https://github.com/mapping-commons/sssom/issues/256
    rank: 1000
    alias: subject_category
    owner: mapping
    domain_of:
    - mapping
    range: string
  predicate_id:
    name: predicate_id
    description: The ID of the predicate or relation that relates the subject and
      object of this match.
    examples:
    - value: skos:exactMatch
    from_schema: https://w3id.org/sssom/schema/
    mappings:
    - owl:annotatedProperty
    rank: 1000
    slot_uri: owl:annotatedProperty
    alias: predicate_id
    owner: mapping
    domain_of:
    - mapping
    - literal mapping
    range: EntityReference
    required: true
  predicate_label:
    name: predicate_label
    description: The label of the predicate/relation of the mapping
    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.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: predicate_label
    owner: mapping
    domain_of:
    - mapping
    - literal mapping
    range: string
  predicate_modifier:
    name: predicate_modifier
    description: A modifier for negating the prediate. See https://github.com/mapping-commons/sssom/issues/40
      for discussion
    examples:
    - value: Not
      description: Negates the predicate, see documentation of predicate_modifier_enum
    from_schema: https://w3id.org/sssom/schema/
    see_also:
    - https://github.com/mapping-commons/sssom/issues/107
    rank: 1000
    alias: predicate_modifier
    owner: mapping
    domain_of:
    - mapping
    - literal mapping
    range: predicate_modifier_enum
  object_id:
    name: object_id
    description: The ID of the object of the mapping.
    examples:
    - value: HP:0009894
      description: The CURIE denoting the Human Phenotype Ontology concept of 'Thickened
        ears'
    from_schema: https://w3id.org/sssom/schema/
    mappings:
    - owl:annotatedTarget
    rank: 1000
    slot_uri: owl:annotatedTarget
    alias: object_id
    owner: mapping
    domain_of:
    - mapping
    - literal mapping
    range: EntityReference
    required: true
  object_label:
    name: object_label
    description: The label of object of the mapping
    examples:
    - value: Thickened ears
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: object_label
    owner: mapping
    domain_of:
    - mapping
    - literal mapping
    range: string
    recommended: true
  object_category:
    name: 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.
    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.)
    from_schema: https://w3id.org/sssom/schema/
    see_also:
    - https://github.com/mapping-commons/sssom/issues/13
    - https://github.com/mapping-commons/sssom/issues/256
    rank: 1000
    alias: object_category
    owner: mapping
    domain_of:
    - mapping
    - literal mapping
    range: string
  mapping_justification:
    name: 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.
    examples:
    - value: semapv:LexicalMatching
    - value: semapv:ManualMappingCuration
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: mapping_justification
    owner: mapping
    domain_of:
    - mapping
    - literal mapping
    range: EntityReference
    required: true
    pattern: ^semapv:(MappingReview|ManualMappingCuration|LogicalReasoning|LexicalMatching|CompositeMatching|UnspecifiedMatching|SemanticSimilarityThresholdMatching|LexicalSimilarityThresholdMatching|MappingChaining)$
    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
  author_id:
    name: author_id
    description: Identifies the persons or groups responsible for asserting the mappings.
      Recommended to be a list of ORCIDs or otherwise identifying URIs.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    slot_uri: pav:authoredBy
    multivalued: true
    alias: author_id
    owner: mapping
    domain_of:
    - mapping
    - literal mapping
    range: EntityReference
  author_label:
    name: author_label
    description: A string identifying the author of this mapping. In the spirit of
      provenance, consider using author_id instead.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    multivalued: true
    alias: author_label
    owner: mapping
    domain_of:
    - mapping
    - literal mapping
    range: string
  reviewer_id:
    name: 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.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    multivalued: true
    alias: reviewer_id
    owner: mapping
    domain_of:
    - mapping
    - literal mapping
    range: EntityReference
  reviewer_label:
    name: reviewer_label
    description: A string identifying the reviewer of this mapping. In the spirit
      of provenance, consider using reviewer_id instead.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    multivalued: true
    alias: reviewer_label
    owner: mapping
    domain_of:
    - mapping
    - literal mapping
    range: string
  creator_id:
    name: 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.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    slot_uri: dcterms:creator
    multivalued: true
    alias: creator_id
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    - literal mapping
    range: EntityReference
  creator_label:
    name: creator_label
    description: A string identifying the creator of this mapping. In the spirit of
      provenance, consider using creator_id instead.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    multivalued: true
    alias: creator_label
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    - literal mapping
    range: string
  license:
    name: license
    description: A url to the license of the mapping. In absence of a license we assume
      no license.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    slot_uri: dcterms:license
    alias: license
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    - literal mapping
    range: uri
  subject_type:
    name: subject_type
    description: The type of entity that is being mapped.
    examples:
    - value: owl:Class
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: subject_type
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    range: entity_type_enum
  subject_source:
    name: subject_source
    description: URI of vocabulary or identifier source for the subject.
    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.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: subject_source
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    range: EntityReference
  subject_source_version:
    name: subject_source_version
    description: Version IRI or version string of the source of the subject term.
    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')
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: subject_source_version
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    range: string
  object_type:
    name: object_type
    description: The type of entity that is being mapped.
    examples:
    - value: owl:Class
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: object_type
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    - literal mapping
    range: entity_type_enum
  object_source:
    name: object_source
    description: URI of vocabulary or identifier source for the object.
    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.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: object_source
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    - literal mapping
    range: EntityReference
  object_source_version:
    name: object_source_version
    description: Version IRI or version string of the source of the object term.
    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')
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: object_source_version
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    - literal mapping
    range: string
  mapping_provider:
    name: 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.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: mapping_provider
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    - literal mapping
    range: uri
  mapping_source:
    name: 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.
    examples:
    - value: MONDO_MAPPINGS:mondo_exactmatch_ncit.sssom.tsv
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: mapping_source
    owner: mapping
    domain_of:
    - mapping
    - literal mapping
    range: EntityReference
  mapping_cardinality:
    name: 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.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: mapping_cardinality
    owner: mapping
    domain_of:
    - mapping
    - literal mapping
    range: mapping_cardinality_enum
  mapping_tool:
    name: 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.
    examples:
    - value: https://github.com/AgreementMakerLight/AML-Project
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: mapping_tool
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    - literal mapping
    range: string
  mapping_tool_version:
    name: mapping_tool_version
    description: Version string that denotes the version of the mapping tool used.
    examples:
    - value: v3.2
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: mapping_tool_version
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    - literal mapping
    range: string
  mapping_date:
    name: 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.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    slot_uri: pav:authoredOn
    alias: mapping_date
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    - literal mapping
    range: date
  publication_date:
    name: publication_date
    description: The date the mapping was published. This is different from the date
      the mapping was asserted.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    slot_uri: dcterms:created
    alias: publication_date
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    range: date
  confidence:
    name: confidence
    description: A score between 0 and 1 to denote the confidence or probability that
      the match is correct, where 1 denotes total confidence.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: confidence
    owner: mapping
    domain_of:
    - mapping
    - literal mapping
    range: double
  curation_rule:
    name: 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.
    from_schema: https://w3id.org/sssom/schema/
    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
    rank: 1000
    multivalued: true
    alias: curation_rule
    owner: mapping
    domain_of:
    - mapping
    range: EntityReference
  curation_rule_text:
    name: 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.
    from_schema: https://w3id.org/sssom/schema/
    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
    rank: 1000
    multivalued: true
    alias: curation_rule_text
    owner: mapping
    domain_of:
    - mapping
    range: string
  subject_match_field:
    name: subject_match_field
    description: A list of properties (term annotations on the subject) that was used
      for the match.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    multivalued: true
    alias: subject_match_field
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    range: EntityReference
  object_match_field:
    name: object_match_field
    description: A list of properties (term annotations on the object) that was used
      for the match.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    multivalued: true
    alias: object_match_field
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    - literal mapping
    range: EntityReference
  match_string:
    name: 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.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    multivalued: true
    alias: match_string
    owner: mapping
    domain_of:
    - mapping
    - literal mapping
    range: string
  subject_preprocessing:
    name: 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.
    examples:
    - value: semapv:Stemming
    - value: semapv:StopWordRemoval
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    multivalued: true
    alias: subject_preprocessing
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    range: EntityReference
  object_preprocessing:
    name: 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.
    examples:
    - value: semapv:Stemming
    - value: semapv:StopWordRemoval
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    multivalued: true
    alias: object_preprocessing
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    - literal mapping
    range: EntityReference
  semantic_similarity_score:
    name: semantic_similarity_score
    description: A score between 0 and 1 to denote the semantic similarity, where
      1 denotes equivalence.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: semantic_similarity_score
    owner: mapping
    domain_of:
    - mapping
    range: double
  semantic_similarity_measure:
    name: semantic_similarity_measure
    description: The measure used for computing the the semantic similarity score.
      To make processing this field as unambiguous as possible, we recommend using
      wikidata identifiers, but wikipedia pages could also be acceptable.
    examples:
    - value: https://www.wikidata.org/wiki/Q865360
      description: (the Wikidata identifier for the Jaccard index measure).
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: semantic_similarity_measure
    owner: mapping
    domain_of:
    - mapping
    range: string
  see_also:
    name: 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
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    slot_uri: rdfs:seeAlso
    multivalued: true
    alias: see_also
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    - literal mapping
    range: string
  issue_tracker_item:
    name: issue_tracker_item
    description: The issue tracker item discussing this mapping.
    examples:
    - value: SSSOM_GITHUB_ISSUE:166
      description: (A URL resolving to an issue discussing a new SSSOM element request)
    from_schema: https://w3id.org/sssom/schema/
    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
    rank: 1000
    alias: issue_tracker_item
    owner: mapping
    domain_of:
    - mapping
    range: EntityReference
  other:
    name: 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.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    alias: other
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    - literal mapping
    range: string
  comment:
    name: comment
    description: Free text field containing either curator notes or text generated
      by tool providing additional informative information.
    from_schema: https://w3id.org/sssom/schema/
    rank: 1000
    slot_uri: rdfs:comment
    alias: comment
    owner: mapping
    domain_of:
    - mapping set
    - mapping
    - literal mapping
    range: string
class_uri: owl:Axiom