[MOBY-l] lengthy missive on MOBY status after ISMB/I3C

[mwilkinson at gene.pbi.nrc.ca]

Phillip Lord wrote:

>   Mark> I met with Carole Gobel at the I3C meeting and we had some
>   Mark> deep chats about myGrid & MOBY.
>
> I presume this means you went to the bar and got drunk?

no, but we flirted like mad!


>   Mark> I also spent several hours with Philip Lord and
>   Mark> Robert Stevens, who are "in the trenches" of the myGrid
>   Mark> project.
>
> I know this means we went to the bar and got drunk...

I don't remember that... very well...

>  If
> your ontology, for instance, does not distinguish between a Blast
> service which takes a sequence, and one which takes an ID, you could
> give the wrong stuff to the wrong service.

I don't think this can happen if you are using MOBY corectly.  Only
services that *can* use your input will be presented to you if you pose
the query based on your in-hand object type.


> Or you could give an ID to
> the wrong database, such as giving an SWISS-PROT id to a TAIR only
> search facility.

again, since service providers register both the object types *and* the
namespaces that they deal with, this should never happen either... touch
wood!


> I think this is a slightly separate issue from where the data
> stored. To me it makes sense to have all the metadata about a service
> in one place, rather than have some of it in one place, and some in
> another.

insofar as it is all part of a single registration, it is all in one
place-  a couple of joins on the database tells you everything you need
to know about the service.

> With your system, you would have to ask both the class
> directory to get information about BLAST services, and then the
> instance repository to get information about the instances, and which
> ones could cope with TAIR ID's, which with sequences, and so on.

the query is:   locateServiceByInput(Object, [Namespace, Servicetype,
Provider, maximum_return...])

This query simply returns all services that can use your in-hand object.
You can further filter this by namespace, service-type, etc., but it is a
single query on the database.


> If you have loosely defined datatypes then the system will tell you
> what you can do with it, and include things that, in fact, you can
> not. Like for instance giving a SW ID, to a TAIR blast search.

again, I don't think this is true if you are using the registry correctly
(and if the service provider has thought carefully about their
registration)


> Or is there a
> more generic problem that you haven't worked out how to link parts of
> a "multi-part" query, to parts of a multi-part answer, whether that
> answer is a result, or a failure report?

precisely.

M



--
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"Speed is subsittute fo accurancy."
________________________________

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

phone : (306) 975 5279
pager : (306) 934 2322
mobile: markw_mobile at illuminae.com