Re: bioGUID

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
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Received on Friday, 30 March 2007 11:09:39 UTC