nlharris
commented
3 years ago This bug originated from the "Secret Disciples of the Mungall" working group. 😀
Closed matentzn closed 3 years ago
nlharris
commented
3 years ago This bug originated from the "Secret Disciples of the Mungall" working group. 😀
cmungall
commented
3 years ago OK, I may have misled Nico. We were confused as adding slot_uri to the license slot had no effect on the jsonld context, which was contrary to what I expected.
I'm trying to reduce to a simple test case and am a bit confused, will make a separate ticket
cmungall
commented
3 years ago Sorry haven't had tine to look. It's this a makefike bug? What target ate you expecting? Jason schema? Python data classes?
On Fri, Feb 19, 2021, 12:31 Nico Matentzoglu notifications@github.com wrote:
Describe the bug
I am trying to update my model https://github.com/cmungall/sssom-py/blob/f88c4146d784c2ac080700ac7a3891ae47181cb1/Makefile#L3from this yaml source:
id: http://example.org/sssom/schema/ name: sssom description: Datamodel for Simple Standard for Sharing Ontology Mappings (SSSOM) imports:
- biolinkml:types prefixes: biolinkml: https://w3id.org/biolink/biolinkml/ sssom: https://w3id.org/sssom/ dcterms: http://purl.org/dc/terms/ see_also:
- https://github.com/OBOFoundry/SSSOM default_curi_maps:
- semweb_context default_prefix: sssom slots: mappings: description: Contains a list of mapping objects range: mapping multivalued: true id: description: CURIE or IRI identifier identifier: true subject_id: description: The ID of the subject of the mapping. mappings:
- owl:annotatedSource range: entity slot_uri: owl:annotatedSource subject_label: description: The label of subject of the mapping range: string 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. range: string predicate_id: description: The ID of the predicate or relation that relates the subject and object of this match. mappings:
- owl:annotatedProperty range: entity slot_uri: owl:annotatedProperty predicate_label: description: The label of the predicate/relation of the mapping range: string object_id: description: The ID of the object of the mapping. mappings:
- owl:annotatedTarget range: entity slot_uri: owl:annotatedTarget object_label: description: The label of object of the mapping range: string 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. range: string match_type: description: ID from Match type (SSSOM:MatchType) branch of the SSSSOM Vocabulary. In the case of multiple match types for a single subject, predicate, object triplet, two seperate mappings must be specified. range: string mapping_set_id: description: A globally unique identifier for the mapping set (not each individual mapping). Should be IRI, ideally resolvable. range: entity mapping_set_version: description: A version string for the mapping. mappings:
- owl:versionInfo range: string creator_id: description: Identifies the persons or groups responsible for the creation 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. mappings:
- dc:creator range: entity creator_label: description: A string identifying the creator of this mapping. In the spirit of provenance, consider to use creator_id instead. range: string license: description: A url to the license of the mapping. In absence of a license we assume no license. slot_uri: dcterms:license mappings:
- dcterms:license range: string subject_source: description: IRI of ontology source for the subject. Version IRI preferred. range: string subject_source_version: description: Version IRI of the source of the subject term. range: string object_source: description: IRI of ontology source for the object. Version IRI preferred. range: string object_source_version: description: Version IRI of the source of the object term. range: string mapping_provider: description: URL pointing to the source that provided the mapping, for example an ontology that already contains the mappings. range: string 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. range: string mapping_date: description: The date the mapping was computed mappings:
- dc:date range: string confidence: description: A score between 0 and 1 to denote the confidence or probability that the match is correct, where 1 denotes total confidence. range: double subject_match_field: description: A tuple of fields (term annotations on the subject) that was used for the match. Should be used in conjunction with lexical and complexes matches, see SSSOM match types below. range: entity object_match_field: description: A tuple of fields (term annotations on the object) that was used for the match. Should be used in conjunction with lexical and complexes matches, see SSSOM match types below. range: entity match_string: description: String that is shared by subj/obj range: string subject_preprocessing: description: Method of preprocessing applied to the fields of the subject. Tuple of IDs from "Pre-processing method" (SSSOM:PreprocessingMethod) branch of the SSSSOM Vocabulary. range: string object_preprocessing: description: "Method of preprocessing applied to the fields of the object. Tuple\ \ of IDs from \u201CPre-processing method\u201D (SSSOM:PreprocessingMethod)\ \ branch of the SSSSOM Vocabulary." range: string match_term_type: description: Specifies what type of terms are being matched (class, property, or individual). Value should be ID from Term Match (SSSOM:TermMatch) branch of the SSSSOM Vocabulary. range: string semantic_similarity_score: description: A score between 0 and 1 to denote the semantic similarity, where 1 denotes equivalence. range: double information_content_mica_score: description: A score between 0 and 1 to denote the information content of the most informative common ancestor, where 1 denotes the maximum level of informativeness. range: double 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 mappings:
- rdfs:seeAlso range: string 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. range: string comment: description: Free text field containing either curator notes or text generated by tool providing additional informative information. range: string required: description: Indicates wether the SSSOM metadata element is required range: string metadata_element: description: All legal SSSOM metadata elements are subproperties of this. range: string scope: description: Indicates whether the metadata element has local, global or local-global scope. range: string rdf_example: description: An example value of the a SSSOM element in the TSV file. range: string tsv_example: description: An example value of the a SSSOM element in RDF. range: string equivalent_property: description: 'SSSOM property should be mapped to:' range: string classes: mapping set: description: Represents a set of mappings slots:
- mappings
- mapping_set_id
- mapping_set_version
- creator_id
- creator_label
- license
- subject_source
- subject_source_version
- object_source
- object_source_version
- mapping_provider
- mapping_tool
- mapping_date
- subject_match_field
- object_match_field
- subject_preprocessing
- object_preprocessing
- match_term_type
- see_also
- other
- comment mapping: description: Represents an individual mapping between a pair of entities slots:
- subject_id
- subject_label
- subject_category
- predicate_id
- predicate_label
- object_id
- object_label
- object_category
- match_type
- creator_id
- creator_label
- license
- subject_source
- subject_source_version
- object_source
- object_source_version
- mapping_provider
- mapping_tool
- mapping_date
- confidence
- subject_match_field
- object_match_field
- match_string
- subject_preprocessing
- object_preprocessing
- match_term_type
- semantic_similarity_score
- information_content_mica_score
- see_also
- other
- comment class_uri: owl:Axiom entity: description: Represents any entity that can be mapped, such as an OWL class or SKOS concept mappings:
- rdf:Resource slots:
- id
To Reproduce
- clone: https://github.com/cmungall/sssom-py
- edit schema/sssom.yaml with the changed yaml above
- run make all
Expected behavior My models should update, in particular, dcterms:license should appear as a slot_uri
What working group (or team) did this request originate from? This bug originated from the "Secret Disciples of the Mungall" working group.
Note: This is relevant for members of NCATS Translator.
Additional context
Tag relevant members for discussion @cmungall https://github.com/cmungall
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matentzn
commented
3 years ago It's been fixed - yes! Was Makefile bug!
Describe the bug
I am trying to update my model from this yaml source:
To Reproduce
make allExpected behavior My models should update, in particular, dcterms:license should appear as a
slot_uriWhat working group (or team) did this request originate from? This bug originated from the "Secret Disciples of the Mungall" working group.
Note: This is relevant for members of NCATS Translator.
Additional context
Tag relevant members for discussion @cmungall