Dear Matt,
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)?
No publication as yet on bioGUID, but I'm working on some rough notes.
In essence the motivation is to get biodiversity informatics using RDF,
and I don't think LSIDs are the best way to get us there. For something
related you could look at my article "Taxonomic names, metadata, and
the Semantic Web"
(http://jbi.nhm.ku.edu/index.php/jbi/article/view/25).
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?
bioGUID needs to know how to resolve the identifier, which in turn
means that there is some way to get metadata about the identifier
(although I will resort to having local copies of databases if I have
too).
To resolve a GO identifier there needs to be a service somewhere that
takes a GO identifier and returns metadata either in RDF, or in a
format that can be converted to RDF. Is there any such service? If not,
I would have to host a copy of GO here, and write something to output a
GO term in RDF.
Are you trying to achieve a mechanism for uniquely identifying links
to important bioinformatic records by URI?
I guess I'm trying to show the value of having such URIs, because my
sense is that -- within the biodiversity informatics community at least
-- people haven't bought the argument yet. It's hard to make the case
without real demos. Plus my own work depends on having such an
infrastructure in place.
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).
Ideally no, because I would hope data providers would have their own
URIs that are stable and return RDF. For example, the database record
that a user has should itself be a URI. However, as an interim step,
yes, bioGUID can be a way to locate a record in the absence of knowing
how to do that, and in some cases, it may be the only currently
existing way to do that, unless you want to write your own code. For
example, accessing a museum specimen record requires writing a XML
document and embedding that in a URL (gack).
Are you trying to achieve a cross referencing system for database
records? And if so, on what basis is a cross-reference made?
The cross reference uses bioGUIDs. For example, if a PubMed record
contains a DOI, the RDF will have a triple linking the PubMed and the
DOI using rdfs:sameAs. If a PubMed record lists sequence ids, they are
converted to bioGUIDs. I use bioGUIDs so that the link can be navigated
by a Semantic Web browser.
(for
example the record referenced itself back references the record making
this reference)
Um, huh? Do you mean, if a PubMed record references a sequence, does
the sequence reference the PubMed record? The answer is it depends. In
the case of a PubMed record and a sequence, in most cases yes, hence
for http://bioguid.info/pmid:17079492 there is a triple
<dcterms:references rdf:resource="http://bioguid.info/gi:117652796"; />
and for http://bioguid.info/gi:117652796 there is a triple
<dcterms:isReferencedBy
rdf:resource="http://bioguid.info/pmid:17079492"/>
These are easy because the PubMed and the GenBank records refer to each
other. In other cases both links don't exist -- for example, a specimen
has no idea whether a sequence links to it. I could add the reverse
link in these cases, but I'd sort of assumed that people could use a
SPARQL query to get these.
How would people apply to have their databases added?
Basically just ask me. So far I'm adding data sources that are directly
relevant to my own work, but since that includes sequences, that pretty
much opens up most things in bioinformatics. I'm also looking at adding
list of triples (such as citation links) to the underlying triple
store, so the bioGUID records become richer than just a remote database
lookup.
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.
Not totally sure I understand this. My own immediate use case is to
have a script that will fetch a record with a bioGUID, and have that
script fetch every linked record referred to by that record (i.e., RDF
spidering). For example, if I start with a PubMed identifier, the
script would pull out all the sequences in that paper, any specimens
linked to those sequences, the taxonomy of the organisms, and the
papers cited by the PubMed paper. I would then have a local triple
store for this information, and be able to do stuff like plot a
geographical map of the sequences based on the georeferenced specimen
records.
Regards
Rod
------------------------------------------------------------------------
----------------------------------------
Professor Roderic D. M. Page
Editor, Systematic Biology
DEEB, IBLS
Graham Kerr Building
University of Glasgow
Glasgow G12 8QP
United Kingdom
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Fax: +44 141 330 2792
email: [EMAIL PROTECTED]
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