[MOBY-l] MOBY Central database schema

[Mark Wilkinson]

Hi all,

I'm starting to build the Registry database today as I have now got the
MOBY-Central registry service running ~properly (according to the new
API) on my local machine... all it needs now is something to talk to,
and some objects to talk about :-)

The registry database schema is quite straightforward at the moment:

Table: Service
    id
    Name
    URL
    URI
    Type_id
    Description

Table: Parameter
    id
    Object_id
    Service_id
    IN_OUT (enum 'in', 'out')

Table:  Object
    ????

Table: Service
    ????

Those last two are the sticking points.  At the moment the objects and
services are in flat files, but I think we want them in  tables which
represent their ontology.  The GO database schema seems unnecessarily
heavy, but on the other hand we get the tools for free.  As Midori
mentioned, the GO database has tables for archiving changes, and if we
are changing the object/service hierarchy once MOBY is up and running we
will need that also...  Chris, how tightly are tools like DAG-Edit tied
to your schema?  Can we make a "light" version of it and still use the
tools?

For the moment I'll just make a set of simple tables with a third table
"term2term" like they have in GO... or something like that... just to
get us started.

After that, we need some actual XSD specifications for Objects.  Jason,
are you building some of the ones that we talked about at the meeting?
I'll also take a stab at a few on Monday just to make sure that I'm
generating the WSDL document correctly.  I can't think of a better way
to store these than in flat-files somewhere on MOBY-Central, since they
are going to be imported and modified during the creation of the WSDL
document... does anyone have a better suggestion?  In any case, that
will work for the time being.

 I'm going to go out on a limb and say that I hope to have MOBY-Central
available on a public server by the following Monday.... but please
don't hang me by my toes if I fail!

Midori, Jason - I've made a few requests to get you added as open-bio
developers, but I'm not getting any response.  I've just sent the
request to someone else to see if I get an answer.  Sorry it is taking
so long!

Best wishes all, and have a great weekend!!  I'm off to celebrate my
34th  :-)   don't wait up...

M


--
--------------------------------
"Speed is subsittute fo accurancy."
________________________________

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