Semantic Web for the Life Sciences: topic
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BioGUID
Egon Willighagen
Thursday, 22 March 2007 15:16 UTC
http://bioguid.info/
A start with enabling life sciences with RDF information. I have not been able to play with it. But it does not seem to link between entries in any kind. A start nevertheless… are there other initiatives in life sciences for use of RDF?
Any recommendations on a RDF browser to use? Is this DISCO browser mention on that webpage any good?
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Replies
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There are links between entries, but these depend on the underlying sources. For example, the DOI http://bioguid.info/doi:10.1109/mis.2006.62 has no links because the CrossRef service I use doesn’t provide any. However, PubMed and GenBank records do have links. I good example is http://bioguid.info/gi:90296310 (the sequence DQ283141), which has links to the source organism, the publication, and the voucher specimen. These last two links (a DOI and a specimen id) are not in the original GenBank record, they are constructed. In the case of the DOI, I wrote a web service that parses the reference and looks for a DOI in CrossRef.
The metadata bioGUID extracts goes into a triple store. At some point it would be useful to expand the metadata returned. For example, one could add to the metadata for http://bioguid.info/doi:10.1206/0003-0090(2006)297%5B0001:TATOL%5D2.0.CO;2 the fact that it references the sequence DQ283141. I haven’t done this as the metadata would be incomplete unless I include all the sequences that paper refers to. I’m also trying to separate a GUID resolution service from a Semantic Web browser.
Disco is a nice tool. It’s 2 second timeout can case problems with bioGUID, because it often takes more than two seconds the first time a GUID is resolved (especially if more than one web service call is made). However, reloading the URI will usually get a result.
When I get the chance I will document bioGUID a bit more fully.
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Roderic,
I want to play a bit with RDF in (bio)chemistry, after having read enough about the theory of things. DISCO seems to be a webpage(service) to do things. Do you know something GUI on one’s desktop instead, to work around those time out issues inherit to HTTP? Or does one directly have to go to tools like Jena?
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I found some time to play with RDF and set up a bioGUID-like service for molecules (InChIs to be precise):
http://cb.openmolecules.net/rdf/?InChI=1/CH4/h1H4
Roderic, what about:
inchi:InChI=1/CH4/h1H4
?
I’m sorry about the “InChI=” duplication, but that is an integral part of the InChI.
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