Process of "following your nose"

Hello,

I am working on a bioinformatics data integration project with the objective of linking biological pathway data from our non-profit research group with gene annotation data from another research group. This gene annotation data is currently represented as a list named "unificationXrefs" in our documents. You can see a proof of concept for pathway WP531 <http://wikipathways.org/index.php/Pathway:WP531> published at the JSON-LD playground: <http://json-ld.org/playground/index.html#startTab=tab-expanded&json-ld=http%3A%2F%2Ftest2.wikipathways.org%2Fv2%2Fpathways%2FWP531%2F.json>.

The JSON-LD processor automatically deferences the IRI <http://test2.wikipathways.org/v2/contexts/pathway.jsonld> in the context, but it does not automatically dereference the unificationXrefs IRIs, such as <http://pointer.ucsf.edu:8080/ensembl/ENSG00000105486/UnificationXref>, in the body of the document. I understand this further dereferencing does not happen automatically, because it must be requested by a developer or machine. "Follow your nose" is an important part of JSON-LD, but how exactly are developers and machines supposed to do this? For example, let's say a user wants to find all instances of <http://www.identifiers.org/ncbigene/3978> in pathway WP531. Manually going to <http://pointer.ucsf.edu:8080/ensembl/ENSG00000105486/UnificationXref> will show one instance, but to do this automatically, would a developer who had never before seen our data need to first figure out that the unificationXrefs IRIs are JSON-LD documents and then write code to dereference every unificationXrefs IRI to check for the presence of <http://www.identifiers.org/ncbigene/3978>?

Thanks.
Anders Riutta
Gladstone Institutes

Received on Thursday, 29 May 2014 04:32:54 UTC