[MOBY] [MOBY-l] Services on MOBYClient

[Mark Wilkinson]

On Mon, 2003-12-08 at 15:47, Simon Twigger wrote:

Hey Simon!  thanks for your patience!

> I wondered about this too but when you look at the Object list  
> (http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects) Global_Keyword is  
> also listed there as an Object which was why I was trying to do it that  
> way.

Is it?!?  Good heavens... someone is due for a good spanking!  ;-)


> Not really, it should take a broader range of inputs and not just  
> regurgitate what you put in with a little bit more info. Though, if one  
> went with the idea of extending the objects like we have in sequence -  
> VirtualGene, GenericGene, FullyAnnotatedGene, etc. (going from bare  
> minimum info - symbol, name and ID to every annotation under the sun)  
> this might have a use.

Yup - I think this is the way to go.  There's nothing wrong with what
you are doing **at all**.  Passing in a gene ID and returning that gene
ID with a bunch of cross-references is a legitimate and useful
service... I just didn't understand why you were outputting a string.

The alternative - if you find that you really are just regurgitating the
input, is to output a collection of Object's representing what you
currently output as CrossRef's.  That would be an equivalent service.

> Mentally I tend to distinguish identifiers from symbols which perhaps  
> colors my thinking - For me, Identifiers are stable accession numbers,  
> id numbers, etc. (eg RGD:12345), symbols are much less stable and are  
> closer to a keyword than anything else.

I think in the context of genetics a gene name (e.g. CDC25) is acting as
an identifier... this is certainly how we identify genes in publications
(barring the problem of multiple names for genes).  My loci in DragonDB
(an AceDB instance) use the Gene Name as the primary key for the record,
so for me it is absolutely acting as an identifier :-)

> There is a danger of biting off too much in one go and I would opt for  
> breaking this up into multiple services that could wrapped up and  
> called as an uber-service (that hopefully ran the various searches in  
> parallel before merging at the end).

I'm starting to worry about the wisdom of the Global_Keyword namespace
at all... but keyword searches are *so* common!  It just tempts people
to create peculiar services... If you do a registry query for services
that consume Global_Keyword right now you end up with a surprisingly
large number of them already, and the registry is still quite small!
Moreover, most of them are completely useless w.r.t. the keyword that
you have in your hand at that moment!  The problem is that these kinds
of services have very little semantic information, since a keyword lacks
semantic information...  I can see the usefulness of doing keyword
searches on GO, and on PubMed, but in many cases it doesn't seem so
useful...

Anyway, it's a public registry :-)  People will register whatever they
like, at the end of the day!

M