[MOBY-l] Suzi + Alan = Solution

[Mark Wilkinson]

Alan Robinson wrote:

> If MOBY needs a vocabulary for databases names & identifiers, I suggest
> that it adopts the same scheme as GO:

good call - thanks for the ref!


> You may ask, should I use the ID, AC or SV field in an EMBL record?
> Or the locus, accession, version or gi fields of GenBank?

I don't think we are going to be able to avoid letting people use whatever
they have in their hands.  Sometimes you just don't have a choice  :-)


Suzanna Lewis wrote:

> 1. id and idtype (an additional attribute)
> 2. id is structured (idtype:id) like (sp:P12345 or GO:1111)
> 3. id stands alone and the application sends it scattershot
>      to everything and sees what happens.
>
> #1 is cleanest, but people start ignoring the type because
> they 'know' what the application is doing and don't bother
> to check it.
>
> #2 is crude, but it forces you to deal with it and acknowledge
> it
>
> #3 is noisy and ugly, but simple minded enough that
> innocents don't complain too much
>

Of these, I think we can get away with #1 in our circumstance.  Since  id and
idtype are mandatory parts of the MOBY triple, there is no additional
overhead to going down this path.  For the same reason, (3) is simply not
possible (touch wood) under the MOBY system.

I think what I'll do is the following:

a.  Service registration will have an optional 'namespace(s)' attribute
(optinal because not all services will care what namespace they are being
sent... e.g. a Blast service only cares about the sequence, not the ID of
that sequence)
b.  When searching for a service you may provide the namespace for the ID
that you have in your hand if it is relevant.
c.  If you don't have the namespace in your hand you get back all services
that use that object-type, regardless of namespace
d.  If a Service has not registered a namespace, then the Service is
**obligated** to ensure that it checks/validates the namespace before it
attempts to use the object it has received, if this is relevant to that
service (to address Alan's 1/15 Million issue)

If anyone objects to this please say so ASAP, as I am going to start doing
the relevant coding right away,

Cheers all!  If things go well, I'll have a sequence retrieval service up and
running by the end of the day (thanks also to Paul Kulchenko who answered
some of my SOAP::Lite questions overnight)

M


--
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"Speed is subsittute fo accurancy."
________________________________

Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK
Canada