query flexibility

[ajbrene...@dundee.ac.uk]

First of all, i'd like to say this looks like a very promising resource! But was writing a thread as what I need may be a bit different to what is provided at the moment.

Im looking for a way to programatically access protein data from uniprot. This service would seem to the trick, however it has some limitations the old uniprot api did not. For example the old uniprot api would let me define specific columns, such as go for Gene Ontology information mapped to the protein, and cross references into external databases such as reactome, wormbase, kegg ... It allowed for a more flexible set of queries, this service seems to be more focused and constrained.

Im fairly certain you guys have this mapping well solved, just don't know if I can access this through here, or if the table joins required for this escape the scope of this specific project, if so, what would you suggest?

Many thanks!

[Xavier Watkins]

Hello, and many thanks for your message. 

This API was initially designed as an "add-on” to distribute data not currently available through the current UniProt API (large scale variants, proteomics etc…). In the future we are planning on integrating the 2 APIs better, but in the meantime both the current UniProt API [1] and this API [2] can be accessed separately. JSON-LD is (unofficially) supported by the UniProt API if you need it [3]. These types of APIs are generaly designed to be as generic as possible, allowing programmatic clients to mash-up data from different end-points.

In regards to your use case, I would recommend looking into using the SPARQL endpoint, which would allow you to retrieve data for more complex queries [4].

Please don’t hesitate to post to this mailing list if you had any questions or feedback.

Regards,

Xavier

[1] http://www.uniprot.org/help/programmatic_access

[2] http://www.ebi.ac.uk/uniprot/api/doc/

[3] http://www.uniprot.org/uniprot/P12345.jsonld

[4] http://sparql.uniprot.org/