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sssom

Datamodel for Simple Standard for Sharing Ontological Mappings (SSSOM)

URI: https://w3id.org/sssom/schema/ Name: sssom

Classes

Class Description
Mapping Represents an individual mapping between a pair of entities
MappingRegistry A registry for managing mapping sets. It holds a set of mapping set references, and can import other registries.
MappingSet Represents a set of mappings
MappingSetReference 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

Slot Description
author_id Identifies the persons or groups responsible for asserting the mappings. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible.
author_label A string identifying the author of this mapping. In the spirit of provenance, consider to use author_id instead.
comment Free text field containing either curator notes or text generated by tool providing additional informative information.
confidence A score between 0 and 1 to denote the confidence or probability that the match is correct, where 1 denotes total confidence.
creator_id 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 A string identifying the creator of this mapping. In the spirit of provenance, consider to use creator_id instead.
documentation A URL to the documentation of this mapping commons.
homepage A URL to a homepage of this mapping commons.
imports A list of registries that should be imported into this one.
last_updated The date this reference was last updated.
license A url to the license of the mapping. In absence of a license we assume no license.
local_name The local name assigned to file that corresponds to the downloaded mapping set.
mapping_cardinality 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.
mapping_date The date the mapping was asserted. This is different from the date the mapping was published or compiled in a SSSOM file.
mapping_justification A mapping justification is an action (or the written representation of that action) of showing a mapping to be right or reasonable.
mapping_provider 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_registry_id The unique identifier of a mapping registry.
mapping_set_description A description of the mapping set.
mapping_set_group Set by the owners of the mapping registry. A way to group .
mapping_set_id A globally unique identifier for the mapping set (not each individual mapping). Should be IRI, ideally resolvable.
mapping_set_references A list of mapping set references.
mapping_set_source A mapping set or set of mapping set that was used to derive the mapping set.
mapping_set_version A version string for the mapping.
mapping_source 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.
mapping_tool 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_tool_version Version string that denotes the version of the mapping tool used.
mappings Contains a list of mapping objects
match_string Strings that are shared by subj/obj. It is recommended to indicate the fields for the match using the object and subject_match_field slots.
mirror_from A URL location from which to obtain a resource, such as a mapping set.
object_category The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary.
object_id The ID of the object of the mapping.
object_label The label of object of the mapping
object_match_field A tuple of fields (term annotations on the object) that was used for the match.
object_preprocessing 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.
object_source IRI of ontology source for the object. Version IRI preferred.
object_source_version Version IRI or version string of the source of the object term.
object_type The type of entity that is being mapped.
other Pipe separated list of key value pairs for properties not part of the SSSOM spec. Can be used to encode additional provenance data.
predicate_id The ID of the predicate or relation that relates the subject and object of this match.
predicate_label The label of the predicate/relation of the mapping
predicate_modifier A modifier for negating the prediate. See https://github.com/mapping-commons/sssom/issues/40 for discussion
predicate_type The type of entity that is being mapped.
publication_date The date the mapping was published. This is different from the date the mapping was asserted.
registry_confidence 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.
reviewer_id Identifies the persons or groups that reviewed and confirmed 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.
reviewer_label A string identifying the reviewer of this mapping. In the spirit of provenance, consider to use author_id instead.
see_also 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
semantic_similarity_measure 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.
semantic_similarity_score A score between 0 and 1 to denote the semantic similarity, where 1 denotes equivalence.
subject_category The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary.
subject_id The ID of the subject of the mapping.
subject_label The label of subject of the mapping
subject_match_field A tuple of fields (term annotations on the subject) that was used for the match.
subject_preprocessing 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.
subject_source URI of ontology source for the subject.
subject_source_version Version IRI or version string of the source of the subject term.
subject_type The type of entity that is being mapped.

Enumerations

Enumeration Description
EntityTypeEnum None
MappingCardinalityEnum None
PredicateModifierEnum None

Subsets

Subset Description