Sync JSON-LD context with JSON-LD output from vocab

[ariutta]

I had been using a JSON-LD context, but it appears we can generate JSON-LD from our RDFa? Maybe these should be synced.

[AlasdairGray]

It would definitely be good to have these synced, otherwise we are prone to them diverging.

There is a recently published working draft on Microdata that has a section on converting between Microdata, RDFa, and JSON-LD.

[ariutta]

I started trying to sync the BridgeDb vocab with these three items:

• datasources_headers.txt (see pretty view), which describes datasources.txt (see pretty view)
• Swagger doc for webservice
• JSON-LD context for webservice

Action Items:

• [ ] do the about and datatype columns look correct in datasources_headers.txt?
• [ ] the response to this webservice query is ENSG00000160791 Ensembl. Is ENSG00000160791 an identifier, an ID or something else? This would be for use in the Swagger doc and JSON-LD context.
• [ ] what is the IRI for identifier (or whatever we want to call it)? Maybe rdf:ID or schema:identifier (suggested by @AlasdairGray) or biopax:id or http://www.rdaregistry.info/Elements/u/#P60052?
• [ ] for that same query, is Ensembl an instance of bdb:conventionalName?
• [ ] if we have multiple instances of CCR5 in a pathway, what name should we use to set ENSG00000160791 and Ensembl as properties of each instance? How about {"dataSourceConventionalName": "ENSG00000160791", "dataSourceIdentifier": "ENSG00000160791"}?

[AlasdairGray]

It might be worth using some Schema terms in the JSON-LD, e.g. schema:identifier. You could look at the Bioschemas specifications [fixed link - AR] for suggestions for marking up various types resources.

[ariutta]

@AlasdairGray, I support using terms from Schema/Bioschemas.

Action Items

• [ ] Do we have a consensus on using terms from Schema/Bioschemas?
• [ ] Should there be any bdb terms that are exact matches with terms from Schema/Bioschemas? Is bdb:DataSource an exact match for schema:Dataset?

[AlasdairGray]

bdb:DataSource and schema:Dataset are not exactly the same thing. The bdb:DataSource includes notions of the schema:DataCatalog, which would be the issuer of the identifiers.

The question is then whether they are operationally equivalent for most circumstances?

[ariutta]

Once @egonw finishes up some other deadlines, maybe he can weigh in on bdb:DataSource vs. schema:Dataset vs. schema:DataCatalog. I'm happy to use whatever the rest of the BridgeDb community prefers.