| 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. |
| curation_rule |
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. |
| curation_rule_text |
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. |
| 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_description |
The description of a mapping registry. |
| mapping_registry_id |
The unique identifier of a mapping registry. |
| mapping_registry_title |
The title 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_title |
The display name of a 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. 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. |
| 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 reviewer_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. 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. |
| 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. |