[open-science] HACKATHON-Semantic Web Identifiers for bioscience

Peter Murray-Rust pm286 at cam.ac.uk
Fri Dec 2 17:46:18 GMT 2011


Jenny has highlighted that we shall be using this list to discuss the
hackathon. I suggest we use a separate title for each thread, prefaced by
HACKATHON-

My problem is how to create indentiers for (say) viruses. If you look at
Wikipedia it doesn't give IDs. But I then discovered (by chance) taxid:
which gives numbers. But the pages don't give static URIs (they contain
cgi). I am cutting and pasing the discussion (and I shal;l refer any others
to here.

Jerven Bollema


Hi Peter, All,

All taxons in the UniProt taxonomy can be found via (
http://purl.uniprot.org/taxonomy/10305). This is synchronized with the NCBI
taxonomy and is the same in the public version (release delta excepted).
Some limited NCBI taxonomy curation happens at the Swiss-Prot group which
also does the UniProt rdf work (Guess where I work ;).

In this case you actually have an link in rdf from the herpes virus to its
hosts. The proteins it encodes (might not be all for each virus isolate
e.g. in this case only a single virion membrane protein is known) and links
to relevant papers as well as related virion proteins.
Will love to show you all how you can get this data in RDF and work with it
using SPARQL.

Regards,
Jerven
=============================================

M. Scott Marshall
show details 11:36 AM (6 hours ago)

Dear Peter and Jerven,

Nice blog with dawg and frog!

Thanks for the answer Jerven. I'm looking forward to this.

Not wanting to start (too much) commotion but also bumped into this
for taxons: http://rs.tdwg.org/dwc/index.htm


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