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 <[EMAIL PROTECTED]> 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: [EMAIL PROTECTED] web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html iChat: aim://rodpage1962 reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species: http://ispecies.org Rod's rants on phyloinformatics: http://iphylo.blogspot.com Rod's rants on ants: http://semant.blogspot.com
