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:
http://stitch.embl.de/services/iteminfo?node=9606.ENSP00000186982
http://stitch.embl.de/services/iteminfo?node=CID2244
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.
Tuesday, March 4, 2008
Embedding protein/chemical information into other web pages
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Can I ask a question about STITCH database here?
ReplyDeleteThe Network control under the graphical representation, one of the buttons is interactive view. I am interesting in this mode, but I can't figure out how it works? When I click the SHAKE button, I can see the graphical motion, but I don't know what is the main purpose for this interacton.
Could you help me with this problem?
Thank you very much.
The interactive view lets you drag nodes around so that you can place them in any order. The Shake command tries to find an optimal placement of the nodes, but this placement doesn't have any biological significance.
ReplyDeleteWe will soon provide more options for downloading the networks, so that you can for example use Cytoscape.