Process of "following your nose"


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 <> published at the JSON-LD playground: <>.

The JSON-LD processor automatically deferences the IRI <> in the context, but it does not automatically dereference the unificationXrefs IRIs, such as <>, 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 <> in pathway WP531. Manually going to <> 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 <>?

Anders Riutta
Gladstone Institutes

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