Tuesday, March 4, 2008

Embedding protein/chemical information into other web pages

One of the nice things about STRING/STITCH is that you can click on any item and be presented with a helpful pop-up describing the item in question. :-)

As you can see, for a protein, we show links to different servers, the domain structure and if possible a representative PDB structure. For a chemical we currently only show the structure and link to PubChem.

In order to use the same pop-up in Reflect (a cool tool that recognizes and annotates proteins and chemical any web page), we made a service out of it. The functionality is going to change in the future, but here are two working examples:

The idea is that you can take this raw HTML and put it into an iframe with JavaScript. (This is left as an exercise to the reader... future versions of STRING may use this technique to make the pages a bit smaller.) For now, it only accepts internal STRING identifiers, which you either get from our download files or from the API.

Monday, March 3, 2008

Servers may be unreachable today (March 3)

You might have trouble today accessing our servers today because of construction in the server rooms. We apologize and hope that everything will be done soon!

Update: We're back online.

Scope of the API and current plans

When I announced the API, I didn't devote much space to the intended scope of the API. To make things clearer:

  • REST/SOAP: We'll only provide a REST API plus a Soaplab2 wrapper for Taverna. Perhaps later dedicated programmers can add a SOAP interface if the demand is sufficiently high.
  • Queries for bulk data: For implementation and licensing reasons, we'll only provide methods to query by individual items, just like on the web site. If you need access to bulk data, you can download it.
  • Miscellaneous records: We want to add more query options later for retrieving information from the freely available files. For example: What are the synonyms of this item? To which orthologous group does this protein belong?