Class: MappingSet
Represents a set of mappings
URI: sssom:MappingSet
classDiagram
class MappingSet
MappingSet : comment
MappingSet : creator_id
MappingSet : creator_label
MappingSet : curie_map
MappingSet --|> prefix : curie_map
MappingSet : extension_definitions
MappingSet --|> extension definition : extension_definitions
MappingSet : issue_tracker
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 : mapping_tool_version
MappingSet : mappings
MappingSet --|> mapping : mappings
MappingSet : object_match_field
MappingSet : object_preprocessing
MappingSet : object_source
MappingSet : object_source_version
MappingSet : object_type
MappingSet --|> entity_type_enum : object_type
MappingSet : other
MappingSet : publication_date
MappingSet : see_also
MappingSet : subject_match_field
MappingSet : subject_preprocessing
MappingSet : subject_source
MappingSet : subject_source_version
MappingSet : subject_type
MappingSet --|> entity_type_enum : subject_type
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
curie_map | * Prefix |
A dictionary that contains prefixes as keys and their URI expansions as value... | direct |
mappings | * recommended Mapping |
Contains a list of mapping objects | direct |
mapping_set_id | 1 Uri |
A globally unique identifier for the mapping set (not each individual mapping... | direct |
mapping_set_version | 0..1 String |
A version string for the mapping | direct |
mapping_set_source | * Uri |
A mapping set or set of mapping set that was used to derive the mapping set | direct |
mapping_set_title | 0..1 String |
The display name of a mapping set | direct |
mapping_set_description | 0..1 String |
A description of the mapping set | direct |
creator_id | * EntityReference |
Identifies the persons or groups responsible for the creation of the mapping | direct |
creator_label | * String |
A string identifying the creator of this mapping | direct |
license | 1 Uri |
A url to the license of the mapping | direct |
subject_type | 0..1 EntityTypeEnum |
The type of entity that is being mapped | direct |
subject_source | 0..1 EntityReference |
URI of vocabulary or identifier source for the subject | direct |
subject_source_version | 0..1 String |
Version IRI or version string of the source of the subject term | direct |
object_type | 0..1 EntityTypeEnum |
The type of entity that is being mapped | direct |
object_source | 0..1 EntityReference |
URI of vocabulary or identifier source for the object | direct |
object_source_version | 0..1 String |
Version IRI or version string of the source of the object term | direct |
mapping_provider | 0..1 Uri |
URL pointing to the source that provided the mapping, for example an ontology... | direct |
mapping_tool | 0..1 String |
A reference to the tool or algorithm that was used to generate the mapping | direct |
mapping_tool_version | 0..1 String |
Version string that denotes the version of the mapping tool used | direct |
mapping_date | 0..1 Date |
The date the mapping was asserted | direct |
publication_date | 0..1 Date |
The date the mapping was published | direct |
subject_match_field | * EntityReference |
A list of properties (term annotations on the subject) that was used for the ... | direct |
object_match_field | * EntityReference |
A list of properties (term annotations on the object) that was used for the m... | direct |
subject_preprocessing | * EntityReference |
Method of preprocessing applied to the fields of the subject | direct |
object_preprocessing | * EntityReference |
Method of preprocessing applied to the fields of the object | direct |
see_also | * String |
A URL specific for the mapping instance | direct |
issue_tracker | 0..1 Uri |
A URL location of the issue tracker for this entity | direct |
other | 0..1 String |
Pipe separated list of key value pairs for properties not part of the SSSOM s... | direct |
comment | 0..1 String |
Free text field containing either curator notes or text generated by tool pro... | direct |
extension_definitions | * ExtensionDefinition |
A list that defines the extension slots used in the mapping set | direct |
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 Source
Direct
name: mapping set
description: Represents a set of mappings
from_schema: https://w3id.org/sssom/schema/
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
slot_usage:
license:
name: license
domain_of:
- mapping set
- mapping
required: true
Induced
name: mapping set
description: Represents a set of mappings
from_schema: https://w3id.org/sssom/schema/
slot_usage:
license:
name: license
domain_of:
- mapping set
- mapping
required: true
attributes:
curie_map:
name: curie_map
description: A dictionary that contains prefixes as keys and their URI expansions
as values.
from_schema: https://w3id.org/sssom/schema/
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
rank: 1000
multivalued: true
alias: curie_map
owner: mapping set
domain_of:
- mapping set
range: prefix
inlined: true
mappings:
name: mappings
description: Contains a list of mapping objects
from_schema: https://w3id.org/sssom/schema/
rank: 1000
multivalued: true
alias: mappings
owner: mapping set
domain_of:
- 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/
rank: 1000
alias: mapping_set_id
owner: mapping set
domain_of:
- mapping set
- mapping set reference
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/
rank: 1000
slot_uri: owl:versionInfo
alias: mapping_set_version
owner: mapping set
domain_of:
- 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/
rank: 1000
slot_uri: prov:wasDerivedFrom
multivalued: true
alias: mapping_set_source
owner: mapping set
domain_of:
- 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/
rank: 1000
slot_uri: dcterms:title
alias: mapping_set_title
owner: mapping set
domain_of:
- 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/
rank: 1000
slot_uri: dcterms:description
alias: mapping_set_description
owner: mapping set
domain_of:
- 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 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 set
domain_of:
- mapping set
- 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 set
domain_of:
- mapping set
- 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 set
domain_of:
- mapping set
- mapping
range: uri
required: true
subject_type:
name: subject_type
instantiates:
- sssom:Propagatable
annotations:
propagated:
tag: propagated
value: true
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 set
domain_of:
- mapping set
- mapping
range: entity_type_enum
subject_source:
name: subject_source
instantiates:
- sssom:Propagatable
annotations:
propagated:
tag: propagated
value: true
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 set
domain_of:
- mapping set
- mapping
range: EntityReference
subject_source_version:
name: subject_source_version
instantiates:
- sssom:Propagatable
annotations:
propagated:
tag: propagated
value: true
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 set
domain_of:
- mapping set
- mapping
range: string
object_type:
name: object_type
instantiates:
- sssom:Propagatable
annotations:
propagated:
tag: propagated
value: true
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 set
domain_of:
- mapping set
- mapping
range: entity_type_enum
object_source:
name: object_source
instantiates:
- sssom:Propagatable
annotations:
propagated:
tag: propagated
value: true
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 set
domain_of:
- mapping set
- mapping
range: EntityReference
object_source_version:
name: object_source_version
instantiates:
- sssom:Propagatable
annotations:
propagated:
tag: propagated
value: true
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 set
domain_of:
- mapping set
- mapping
range: string
mapping_provider:
name: mapping_provider
instantiates:
- sssom:Propagatable
annotations:
propagated:
tag: propagated
value: true
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 set
domain_of:
- mapping set
- mapping
range: uri
mapping_tool:
name: mapping_tool
instantiates:
- sssom:Propagatable
annotations:
propagated:
tag: propagated
value: true
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 set
domain_of:
- mapping set
- mapping
range: string
mapping_tool_version:
name: mapping_tool_version
instantiates:
- sssom:Propagatable
annotations:
propagated:
tag: propagated
value: true
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 set
domain_of:
- mapping set
- mapping
range: string
mapping_date:
name: mapping_date
instantiates:
- sssom:Propagatable
annotations:
propagated:
tag: propagated
value: true
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 set
domain_of:
- mapping set
- 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 set
domain_of:
- mapping set
- mapping
range: date
subject_match_field:
name: subject_match_field
instantiates:
- sssom:Propagatable
annotations:
propagated:
tag: propagated
value: true
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 set
domain_of:
- mapping set
- mapping
range: EntityReference
object_match_field:
name: object_match_field
instantiates:
- sssom:Propagatable
annotations:
propagated:
tag: propagated
value: true
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 set
domain_of:
- mapping set
- mapping
range: EntityReference
subject_preprocessing:
name: subject_preprocessing
instantiates:
- sssom:Propagatable
annotations:
propagated:
tag: propagated
value: true
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 set
domain_of:
- mapping set
- mapping
range: EntityReference
object_preprocessing:
name: object_preprocessing
instantiates:
- sssom:Propagatable
annotations:
propagated:
tag: propagated
value: true
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 set
domain_of:
- mapping set
- mapping
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/
rank: 1000
slot_uri: rdfs:seeAlso
multivalued: true
alias: see_also
owner: mapping set
domain_of:
- mapping set
- mapping
range: string
issue_tracker:
name: issue_tracker
description: A URL location of the issue tracker for this entity.
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)
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.sssom.tsv
rank: 1000
alias: issue_tracker
owner: mapping set
domain_of:
- mapping set
- mapping registry
range: uri
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 set
domain_of:
- mapping set
- 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 set
domain_of:
- mapping set
- mapping
range: string
extension_definitions:
name: extension_definitions
description: A list that defines the extension slots used in the mapping set.
from_schema: https://w3id.org/sssom/schema/
see_also:
- https://github.com/mapping-commons/sssom/issues/328
- https://github.com/mapping-commons/sssom/blob/master/examples/schema/extension-slots.sssom.tsv
rank: 1000
multivalued: true
alias: extension_definitions
owner: mapping set
domain_of:
- mapping set
range: extension definition