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

Fri Dec 2 19:21:43 UTC 2011

My apologies if this is tangential, but I came late to this conversation on taxonomy and am trying to reconstruct the thread.

I work on the team that manages paleodb.org which maintains the taxonomic information of fossils. I am working on a new architecture for an application that will offer paleodb's taxonomic information RESTfully and compliant with all the current best practices.

Perhaps a separate list would be worthwhile to discuss/share ideas on creating taxonomy applications.

On Dec 2, 2011, at 11:46 AM, Peter Murray-Rust wrote:

> 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
> From recent conversations stemming from the biohackathon in Kyoto, I
> surmise that the NCBI taxonomy, presumably with a bias toward human
> and model organisms, as well as its adoption by Uniprot, should be the
> preferred choice for expressing taxon info in the context of
> biomedical knowledge?
> 
> Next question (thinking that I know the answer) is how to integrate
> datasets that use one of each: NCBI and Darwin? Of course, we can
> shelve this and come back to it some other year, if we want to dig
> into something more specifically biomedical. The issue will eventually
> come back to haunt us in any case. For example, with chemical
> identifiers..
> 
> Also, is taxon out of scope for Identifier.org ?
> 
> Cheers,
> Scott
> 
> ===================================
> [Jerven]
> Hi All,
> 
> Don't wish to spam the mailing list about which taxonomy to use. However if
> you actually look at the darwin and uniprot taxonomy "schema" then they are
> very similar. And even in the taxonomy world it doesn't have that many
> controversies.
> 
> Its the instances that get hairy.
> i.e. is it
> 
> Dugu is a rodentia
> <purl.uniprot.org/taxonomy/10160> rdfs:subClassOf <
> purl.uniprot.org/taxonomy/9989>
> or
> Dugu is a Caviomorpha
> <purl.uniprot.org/taxonomy/10160> rdfs:subClassOf <
> http://dbpedia.org/resource/Caviomorpha>
> 
> Which gets taxonomist all exited :)
> 
> Mapping schemas is easy to do here. Its mapping instances that get the
> feuds started :D
> 
> Regards,
> Jerven
> 
> ============================================
> PMR comment - this isn't spam, it's science!
> ============================================
> PMR - thanks for this. If we can make progress on identifiers it makes *me*
> happy!
> -- 
> Peter Murray-Rust
> Reader in Molecular Informatics
> Unilever Centre, Dep. Of Chemistry
> University of Cambridge
> CB2 1EW, UK
> +44-1223-763069
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