Mappings of Wikidata Properties to Biolink

[RichardBruskiewich]

Translator (and Knowledge Beacons) are striving to standardize on the Biolink Model and on a common set of predicates. We need to somehow map beacon-specific predicates onto this emerging list.

As a case study, the "Reference Beacon" is a prototype beacon which wrapped the "legacy" Knowledge.Bio Release 3.0 Neo4j database which mainly contained content from the NIH Semantic Medline Database and a small drug-disease data set. The Release 3.0 standardized concepts and predicates around Wikidata (entity and property) concept identifiers.

Thus, the /predicates call of this beacon (https://rkb.ncats.io/swagger-ui.html#!/metadata/getPredicatesUsingGET) returns a modest list of Wikidata properties (see below). We need to map these properties onto the Translator Biolink (RO? SIO?) predicates list.

wd:P3356,positive diagnostic predictor
wd:P129,physically interacts with
wd:P279,subclass of
wd:P276,location
wd:P1557,manifestation of
wd:P361,part of
wd:P156,followed by
wd:P1056,product or material produced
wd:P2888,exact match
wd:P2175,medical condition treated
wd:P2283,uses
wd:P1542,has effect
kb:P2176,drug used for treatment
wd:P703,found in taxon
wd:P688,encodes
wd:P684,ortholog
wd:P682,biological process
wd:P681,cell component
wd:P680,molecular function
wd:P3433,biological variant of
wd:P2293,genetic association
wd:P1552,has quality
wd:P128,regulates (molecular biology)

[mbrush]

Does it make sense to add these to the predicate alignment spreadsheet here:
https://docs.google.com/spreadsheets/d/1zXitcR1QjHyh6WocukgshSR7IoAVg7MJQG-HNh96Jec/edit#gid=3366698

This would illustrate how they map to the predicates used natively in the reasoner KGs and the 'standardized' predicates we have defined so far. It would keep all predicate standardization work in the spreadsheet for now, which would serve as the single source of for KGs implementation efforts for now. Once the predicate spec is tested in the KGs and refined as needed, we can implement in Biolink and obsolete the spreadsheet.

If this makes sense, I can take a pass at integrating this list of Wikidata predicates into the spreadsheet. I suspect that there will be several that don’t map to any of the existing predicates and will require new ones to be created.

[RichardBruskiewich]

Hi Matt,

Sure... sounds reasonable to add these to the master predicate sheet. If you don't mind (since you are the "expert" of the sheet), please do go ahead and take a pass at integrating them.

I think Ben Good originally mapped these onto the Semantic Medline Database and other drug-disease data in our Knowledge.Bio iteration that predated our involvement in Translator, but I guess they all look pretty legitimate to the concerns of Translator.

Our beacon software is already Biolink Model aware, so we look forward to full integration.

[mbrush]

some progress on mapping wd properties to blm . . .
https://docs.google.com/spreadsheets/d/1rFEeBv1nyx95TSyi3YxwG8KKcoI1kgPXwRtm7rMaeDw/edit#gid=1473124732