Open matentzn opened 2 months ago
@matentzn How would you like to see this done?
Here's an example of a term w/ a definition now (DOID:0081461 ):
slurp/doid.tsv : |
mondo_id | mondo_label | xref | xref_source | original_label | definition | parents |
---|---|---|---|---|---|---|---|
ID | LABEL | A oboInOwl:hasDbXref | >A oboInOwl:source SPLIT=" | A IAO:0000115 | SC % | ||
MONDO:0971037 | thyroid gland spindle epithelial tumor with thymus-like elements | DOID:0081461 | MONDO:equivalentTo | thyroid gland spindle epithelial tumor with thymus-like elements | A thyroid gland carcinoma that is characterized by a lobulated architectural pattern and the presence of a biphasic cellular population composed of spindle epithelial cells and glandular cells. | MONDO:0015075 |
components/doid.owl
:
<owl:Class rdf:about="http://purl.obolibrary.org/obo/DOID_0081461">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DOID_3963"/>
<obo:IAO_0000115>A thyroid gland carcinoma that is characterized by a lobulated architectural pattern and the presence of a biphasic cellular population composed of spindle epithelial cells and glandular cells.</obo:IAO_0000115>
<oboInOwl:hasDbXref>NCI:C46105</oboInOwl:hasDbXref>
<oboInOwl:hasExactSynonym>SETTLE</oboInOwl:hasExactSynonym>
...
<rdfs:label xml:lang="en">thyroid gland spindle epithelial tumor with thymus-like elements</rdfs:label>
</owl:Class>
The definition in the TSV is:
A thyroid gland carcinoma that is characterized by a lobulated architectural pattern and the presence of a biphasic cellular population composed of spindle epithelial cells and glandular cells.
Are you saying that we should append any oio:hasDbXref
(or potentially other predicates) to the definitions?
See definition_evidence
column
mondo_id | mondo_label | xref | xref_source | original_label | definition | definition_evidence | parents |
---|---|---|---|---|---|---|---|
ID | LABEL | A oboInOwl:hasDbXref | >A oboInOwl:source SPLIT=| | A IAO:0000115 | >A oboInOwl:hasDbXref SPLIT=| | SC % | |
MONDO:0971037 | thyroid gland spindle epithelial tumor with thymus-like elements | DOID:0081461 | MONDO:equivalentTo | thyroid gland spindle epithelial tumor with thymus-like elements | A thyroid gland carcinoma that is characterized by a lobulated architectural pattern and the presence of a biphasic cellular population composed of spindle epithelial cells and glandular cells. | DOID:0081461 | MONDO:0015075 |
Ahhh, I see. That will be very easy to add.
Although note, I see it has SPLIT=|
. The way that the migrate pipeline works currently, if I add this, I think it's only ever going to have 1 CURIE in that column, the same curie as in the xref
column. I assume that is OK.
No harm with the SPLIT=|
just a reflex to making it future proof.
Right now the migration (slurp) tables dont add provenance to definitions, they should!