- From: Pat Hayes <phayes@ihmc.us>
- Date: Wed, 1 Feb 2006 12:41:00 -0600
- To: Eric Miller <em@w3.org>
- Cc: chris mungall <cjm@fruitfly.org>, Alf Eaton <lists@hubmed.org>, public-semweb-lifesci@w3.org
>On Jan 31, 2006, at 5:05 PM, chris mungall wrote: > >> >>On Jan 31, 2006, at 1:46 PM, Eric Miller wrote: >> >>> >>> >>>On Jan 31, 2006, at 3:56 PM, Alf Eaton wrote: >>> >>>> >>>>Eric Jain wrote: >>>>>Joanne Luciano wrote: >>>>>>An MD I met with last week mentioned briefly the desire to >>>>>>obtain homologs >>>>>>for yeast proteins with the GO ID 0031930. With it was a >>>>>>request for other >>>>>>suggestions for querying proteins with this ontology assignment >>>>>>(looking for >>>>>>mammalian homologs). >>>>>> >>>>>>Can the semantic web help with this or is it already basic and solved, in >>>>>>which case, can someone point me or fill in the details? Where >>>>>>should I go? >>>>>>What questions should I ask? >>>>>Semantic web technologies can help make certain things simpler >>>>>to implement -- and therefore allow things to be implemented >>>>>that would not have been feasible otherwise. But tasks such as >>>>>listing all proteins for an organism that have been tagged with >>>>>a specific term are simple enough to be supported even without >>>>>any semantic web magic, see http://pir.uniprot.org/, for >>>>>example. This site also allows you to run similarity searches on >>>>>the matching entries to find homologs. >>>>>Now in this particular case it looks like you are out of luck: >>>>>No yeast proteins have been associated with GO:0031930. Often >>>>>the main limiting factor are not the tools, but the available >>>>>data... >>>> >>>>There are S. cerevisiae proteins assigned to GO:0031930 though, >>>>you can see them here: <http://tinyurl.com/d2dm9> >>> >>>I started writing a piggy bank [1] scraper using solvent [2] to >>>make explicit the data thats implied in the HTML tables when I >>>noticed the XML link [3] at the bottom of the page. >> >>surely screen scraping should be a last resort, such as when the >>underlying database has no APIs or download option > >Agreed! > >>all the data underlying amigo is available in a number of hopefully >>more sensible ways. See http://www.godatabase.org/dev > >Good to know. Do you think people just "know" the fact that the >underlying amigo is available? The link is helpful at the bottom of >the page, but a *consistent* convention this community could adopt >to clearly associate the data corresponding to the HTML page would >be extremely valuable. > >More specifically, I'd suggest for this page, the following template be used > ><link rel="meta" type="application/rdf+xml" title="Data for >GO:0031930" >href="http://www.godatabase.org/cgi-bin/amigo/go.cgiformat=xml&view=details&search_constraint=terms&depth=0&session_id=412b1138742957&query=GO:0031930" >/> > >and help define such a consistent linking mechanism. Seems like RDF/A should be relevant here. It will be a draft recommendation very soon, time to get ahead of the game? See http://www.w3.org/2001/sw/BestPractices/HTML/2005-rdfa-syntax Pat -- --------------------------------------------------------------------- IHMC (850)434 8903 or (650)494 3973 home 40 South Alcaniz St. (850)202 4416 office Pensacola (850)202 4440 fax FL 32502 (850)291 0667 cell phayesAT-SIGNihmc.us http://www.ihmc.us/users/phayes
Received on Wednesday, 1 February 2006 18:41:09 UTC