Re: [Treebase-devel] [eX-purgate bulk]: taxonomic query telecon

[Rutger V. <rut...@gm...>]

On Thu, May 28, 2009 at 7:56 PM, William Piel <wil...@ya...> wrote:
>
> On May 28, 2009, at 5:20 PM, Rutger Vos wrote:
>
> Here's a doodle poll to pick a date/time: http://doodle.com/7x5aykszup954ysa
>
> I will be in London until the 5th. Conceivably I can Skype from London, but
> not knowing the conference schedule, I can't commit.

Obviously you're a key participant so let's just play it by ear; I
suppose we can start the discussion by email and either call in next
week or whenever you can make it.

> It's my understanding that we have not yet imported ncbi's classification
> into TreeBASE2? Is this correct? If so, then "containing any Primates" is
> not an option at the moment -- although it should be eventually (I'm putting
> it in our poster!) -- and it should be an easy thing to add.

Absolutely, not yet - but very important. A propos, what would be the
right way to do this? I've thought about it a little bit and imagined
importing the NCBI taxonomy as a very large tree against whose
topology we run queries would be a way to do this that doesn't require
schema changes. Reasonable? Silly?

> Hilmar objects to the use of multiple terms, and would rather that I just
> use "taxonIdentifier", but then have some special namespace for what I'm
> searching on. (e.g. "taxonIdentifier any ncbi_taxid:12345" vs
> "taxonIdentifier any ubio_namebankid:12345").

I can see the point of that: it would make inclusion into CDAO easier
if all we need is a generic taxonIdentifier object. On the other hand,
it would imply overloading the identifier string, with the namespacing
smuggling some amount of extra semantics into something that really
ought to be an opaque string.

> PhyloWS seems to be missing a specification on how to  search on a tree
> topology.

The wiki floats the idea of using PhyloCode for that, but I'm not sure
if it can satisfy all our requirements.

Rutger



-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com