Class: MappingSet
Represents a set of mappings
URI: sssom:MappingSet
classDiagram
class MappingSet
MappingSet : comment
MappingSet : creator_id
MappingSet : creator_label
MappingSet : license
MappingSet : mapping_date
MappingSet : mapping_provider
MappingSet : mapping_set_description
MappingSet : mapping_set_id
MappingSet : mapping_set_source
MappingSet : mapping_set_title
MappingSet : mapping_set_version
MappingSet : mapping_tool
MappingSet : mappings
MappingSet : object_match_field
MappingSet : object_preprocessing
MappingSet : object_source
MappingSet : object_source_version
MappingSet : object_type
MappingSet : other
MappingSet : see_also
MappingSet : subject_match_field
MappingSet : subject_preprocessing
MappingSet : subject_source
MappingSet : subject_source_version
MappingSet : subject_type
Slots
Name | Range | Cardinality | Description | Info |
---|---|---|---|---|
mappings | Mapping | 0..* recommended | Contains a list of mapping objects | . |
mapping_set_id | xsd:anyURI | 1..1 | A globally unique identifier for the mapping set (not each individual mapping). Should be IRI, ideally resolvable. | . |
mapping_set_version | xsd:string | 0..1 | A version string for the mapping. | . |
mapping_set_source | xsd:anyURI | 0..* | A mapping set or set of mapping set that was used to derive the mapping set. | . |
mapping_set_title | xsd:string | 0..1 | The display name of a mapping set. | . |
mapping_set_description | xsd:string | 0..1 | A description of the mapping set. | . |
creator_id | EntityReference | 0..* | 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 (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible. | . |
creator_label | xsd:string | 0..* | A string identifying the creator of this mapping. In the spirit of provenance, consider to use creator_id instead. | . |
license | xsd:anyURI | 1..1 | A url to the license of the mapping. In absence of a license we assume no license. | . |
subject_type | EntityTypeEnum | 0..1 | The type of entity that is being mapped. | . |
subject_source | EntityReference | 0..1 | URI of ontology source for the subject. | . |
subject_source_version | xsd:string | 0..1 | Version IRI or version string of the source of the subject term. | . |
object_type | EntityTypeEnum | 0..1 | The type of entity that is being mapped. | . |
object_source | EntityReference | 0..1 | IRI of ontology source for the object. Version IRI preferred. | . |
object_source_version | xsd:string | 0..1 | Version IRI or version string of the source of the object term. | . |
mapping_provider | xsd:anyURI | 0..1 | 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. | . |
mapping_tool | xsd:string | 0..1 | 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. | . |
mapping_date | xsd:date | 0..1 | The date the mapping was asserted. This is different from the date the mapping was published or compiled in a SSSOM file. | . |
subject_match_field | EntityReference | 0..* | A tuple of fields (term annotations on the subject) that was used for the match. | . |
object_match_field | EntityReference | 0..* | A tuple of fields (term annotations on the object) that was used for the match. | . |
subject_preprocessing | EntityReference | 0..* | 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. | . |
object_preprocessing | EntityReference | 0..* | 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. | . |
see_also | xsd:string | 0..* | 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 | . |
other | xsd:string | 0..1 | Pipe separated list of key value pairs for properties not part of the SSSOM spec. Can be used to encode additional provenance data. | . |
comment | xsd:string | 0..1 | Free text field containing either curator notes or text generated by tool providing additional informative information. | . |
Usages
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/sssom/schema/
Mappings
Mapping Type | Mapped Value |
---|---|
self | ['sssom:MappingSet'] |
native | ['sssom:MappingSet'] |
LinkML Specification
Direct
name: mapping set
description: Represents a set of mappings
from_schema: https://w3id.org/sssom/schema/
slots:
- 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_date
- subject_match_field
- object_match_field
- subject_preprocessing
- object_preprocessing
- see_also
- other
- comment
slot_usage:
license:
name: license
required: true
Induced
name: mapping set
description: Represents a set of mappings
from_schema: https://w3id.org/sssom/schema/
slot_usage:
license:
name: license
required: true
attributes:
mappings:
name: mappings
description: Contains a list of mapping objects
from_schema: https://w3id.org/sssom/schema/
multivalued: true
alias: mappings
owner: mapping set
range: mapping
recommended: true
inlined_as_list: true
mapping_set_id:
name: mapping_set_id
description: A globally unique identifier for the mapping set (not each individual
mapping). Should be IRI, ideally resolvable.
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.)
from_schema: https://w3id.org/sssom/schema/
alias: mapping_set_id
owner: mapping set
range: uri
required: true
mapping_set_version:
name: mapping_set_version
description: A version string for the mapping.
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/).)
from_schema: https://w3id.org/sssom/schema/
slot_uri: owl:versionInfo
alias: mapping_set_version
owner: mapping set
range: string
mapping_set_source:
name: mapping_set_source
description: A mapping set or set of mapping set that was used to derive the mapping
set.
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.
from_schema: https://w3id.org/sssom/schema/
slot_uri: prov:wasDerivedFrom
multivalued: true
alias: mapping_set_source
owner: mapping set
range: uri
mapping_set_title:
name: mapping_set_title
description: The display name of a mapping set.
examples:
- value: The Mondo-OMIM mappings by Monarch Initiative.
from_schema: https://w3id.org/sssom/schema/
slot_uri: dc:title
alias: mapping_set_title
owner: mapping set
range: string
mapping_set_description:
name: mapping_set_description
description: A description of the mapping set.
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/.
from_schema: https://w3id.org/sssom/schema/
slot_uri: dc:description
alias: mapping_set_description
owner: mapping set
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 (pipe-separated)
list of ORCIDs or otherwise identifying URLs, but any identifying string (such
as name and affiliation) is permissible.
from_schema: https://w3id.org/sssom/schema/
slot_uri: dc:creator
multivalued: true
alias: creator_id
owner: mapping set
range: EntityReference
creator_label:
name: creator_label
description: A string identifying the creator of this mapping. In the spirit of
provenance, consider to use creator_id instead.
from_schema: https://w3id.org/sssom/schema/
multivalued: true
alias: creator_label
owner: mapping set
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/
slot_uri: dcterms:license
alias: license
owner: mapping set
range: uri
required: true
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/
alias: subject_type
owner: mapping set
range: entity_type_enum
subject_source:
name: subject_source
description: URI of ontology 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/
alias: subject_source
owner: mapping set
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/
alias: subject_source_version
owner: mapping set
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/
alias: object_type
owner: mapping set
range: entity_type_enum
object_source:
name: object_source
description: IRI of ontology source for the object. Version IRI preferred.
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/
alias: object_source
owner: mapping set
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/
alias: object_source_version
owner: mapping set
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/
alias: mapping_provider
owner: mapping set
range: uri
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/
alias: mapping_tool
owner: mapping set
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/
slot_uri: pav:authoredOn
alias: mapping_date
owner: mapping set
range: date
subject_match_field:
name: subject_match_field
description: A tuple of fields (term annotations on the subject) that was used
for the match.
from_schema: https://w3id.org/sssom/schema/
multivalued: true
alias: subject_match_field
owner: mapping set
range: EntityReference
object_match_field:
name: object_match_field
description: A tuple of fields (term annotations on the object) that was used
for the match.
from_schema: https://w3id.org/sssom/schema/
multivalued: true
alias: object_match_field
owner: mapping set
range: EntityReference
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/
multivalued: true
alias: subject_preprocessing
owner: mapping set
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/
multivalued: true
alias: object_preprocessing
owner: mapping set
range: EntityReference
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/
slot_uri: rdfs:seeAlso
multivalued: true
alias: see_also
owner: mapping set
range: string
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/
alias: other
owner: mapping set
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/
slot_uri: rdfs:comment
alias: comment
owner: mapping set
range: string