Dear Jun,
I guess what Matt means is that he is expecting a kind of naming
scheme for the URIs from your site http://bioguid.info. For
example, the LSID authories listed at http://lsid.biopathways.org/
authorities.shtml use a consistent schema to publish a LSID for a
bio-entity. Sorry for pulling out LSIDs again:(.
OK, basically it is "http://bioguid.info/" + namespace + ':' +
identifier
For example, the DOI doi:10.1109/mis.2006.62 becomes
http://bioguid.info/doi:10.1109/mis.2006.62
Where possible I use existing namespaces, such as "hdl", "gi", and
"pmid". For other cases I make it up. One strategy to make this
slightly more formal might be to use the info URI scheme, but they
don't have all the identifiers I need.
If and when I add support for LSIDs, I would just append the full
LSID to http://bioguid.info/.
I am not sure I quite see this cross-reference happening from your
demo. I am expecting, as what you have shown on your blog (http://
semant.blogspot.com/2006/06/discovering-new-things.html), to see a
cross-reference between the different URIs of the same entity,
either hosted in the same database or different databases. Did I
miss anything? If you are able to do this type of cross-reference,
it would be very interesting to know how you achieved this:)
The extent of cross linking depends on the sources, although I'm
looking at uploading additional links. Much of the crosslinking will
be discovered by SPARQL queries, rather than the RDF for an
identifier. The examples on my blogs are from earlier triple stores
that were fully populated with relevant data.
For example, http://bioguid.info/pmid:15619443 is a PubMed paper,
which has 62 sequences linked to it. One of these is http://
bioguid.info/gi:55418360, which displays the link back to http://
bioguid.info/pmid:1561944, as well as a link to the organism http://
bioguid.info/taxon:299664, and to the voucher specimen http://
bioguid.info/KU:Herps:195181. These individual items don't display
all the links, but these can be recovered from the triple store.
If you want all the cross links, that would require that I follow
through all the links and store them in the triple store. This could
be done, but at this stage I'm leaving that for external scripts to
do (I'll try and post some examples in the near future). Of course, I
guess one could have a background process that followed the links and
populated the triple store. I'll think about this.
Are you interested in making http://bioguid.info/ as a community
gateway for the experts to submit their own statements about a bio-
entity? I have a user case in mind: in our project, we have many
experimental data that are *gathered* from the bioinformatics
resources. These data are associated with some RDF statements that
describe how they were processed by the scientists. It would be
nice for the scientists to subscribe this experimental metadata to
your gateway and then enables them to view both the domain
knowledge about these data and their experimental information.
Hmmm, I think I'd prefer to have links to such statements, if that's
what you mean. In other words, somebody else hosts the facility to
make statements, but these could be linked via bioguids. For example,
an obvious lightweight way to do this would be to use blogs as
annotation tools, and have the blog entry contain a link to the bioguid.
Can you see any points for making http://bioguid.info/ a service,
which can be deployed by people locally?
It could, although I regard it as a bit of a stopgap measure in the
absence of "real" GUIDS.
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