Re: bioGUID

Hi Roderic.

Do you have any publications that outline the motivation here (except
the LSIDs don't work for the semantic web argument you have outlined
in your online material)?

What are the rules for generating a URI for a particular database
record? For example:
http://bioguid.info/rdf/GO:0003674 does not work, and neither does
http://bioguid.info/rdf/go:0003674 ... is the gene ontology not
referenced yet? or do I have the rule wrong?

Are you trying to achieve a mechanism for uniquely identifying links
to important bioinformatic records by URI?

Would you imagine this might become a primary conduit for people to
locate a database record when they have database record IDs, rdf
tools, but no idea how to use these tools to access the record data
(I'm not suggesting the record data is itself RDF).

Are you trying to achieve a cross referencing system for database
records? And if so, on what basis is a cross-reference made? (for
example the record referenced itself back references the record making
this reference)

How would people apply to have their databases added?

The immediate use-case that springs to mind is being able to drop the
crop of libraries one needs to interpret records in one database to
find accession numbers for another database and so on until you find
sort of what you are looking for in the actual database you want.

cheers
Matt


On 3/30/07, Roderic Page <r.page@bio.gla.ac.uk> wrote:
>
> I've put together a web site called http://bioguid.info which, rather
> grandly, is an attempt to bootstrap the biodiversity Semantic Web by
> providing resolvable URIs for biological objects, such as publications,
> taxonomic names, nucleotide sequences, and specimens.
>
> These URIs (or "GUIDs") can be resolved by a web browser to display
> HTML, but under the hood are resolved to RDF (which you can see by
> viewing the source of the web page you get for a URI).
>
> The web interface is really window dressing, I just wanted a way to
> display RDF that wouldn't frighten people (me included). For some URIs
> all I do is grab XML and reformat it (e.g., DOIs). For GenBank records,
> all manner of agony is involved in trying to extract specimen and
> publication links.
>
> A good place to get a sense of what bioguid.info is about is to start
> with this Pubmed record: http://bioguid.info/pmid:17079492. From this,
> you can get a list of sequences. If you click on one of those, you'll
> see a link to a specimen, which you can then look at. For some
> specimens there are maps, you'll need Firefox 1.5, Camino, Webkkit, or
> a browser with a SVG plugin for the full effect (e.g.,
> http://bioguid.info/FMNH:Mammals:175377).
>
> What I'm trying to do generate enough RDF that can be linked together
> to start building applications that can start with a publication, an
> from that navigate through sequences, specimens, and evolutionary trees
> (or do the reverse, given a locality recover sequences and
> phylogenies).
>
> It's a toy, but I'd welcome any comments. There's some related
> commentary on http://www.nodalpoint.org/2007/03/21/bioguid_info
>
> Regards
>
> Rod
>
> ------------------------------------------------------------------------
> ----------------------------------------
> Professor Roderic D. M. Page
> Editor, Systematic Biology
> DEEB, IBLS
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QP
> United Kingdom
>
> Phone:    +44 141 330 4778
> Fax:      +44 141 330 2792
> email:    r.page@bio.gla.ac.uk
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>
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> Rod's rants on phyloinformatics: http://iphylo.blogspot.com
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>
>
>
>

Received on Friday, 30 March 2007 04:53:13 UTC