[ome-users] DBLocation in STD definitions

[Graham Klyne]

At 11:58 27/07/05 -0400, Ilya Goldberg wrote:


>On Jul 25, 2005, at 12:16 PM, Graham Klyne wrote:
>
>>At 10:40 25/07/05 -0400, Ilya Goldberg wrote:
>>
>>
>>>On Jul 22, 2005, at 10:36 AM, Graham Klyne wrote:
>>>
>>>>I see that the definition of a STD requires a DBLoication attribute, 
>>>>which I assume is a reference to where the corresponding datum is 
>>>>stored in the relational DB schema.
>>>
>>>This is a declaration of where in the DB you would like to store your 
>>>data - not a declaration of where the data is already stored.  In other 
>>>words, the DBLocation should be a new table/column for your data.
>>
>>Ah yes, of course.
>
>Its actually slightly more than what I said.  The system won't complain if 
>the tables/columns already exist, it will only add what it needs to 
>represent things as STs.  You can in fact use this to describe an existing 
>DB (though we haven't tested this mode of operation very much).

Interesting!  I was going to ask something like that, with reference to my 
earlier question about retracting semantic types.  For now, while I 
experiment, I tried defining a new ST with a new DB table, but I was 
wondering if I could create a new ST that overlays an existing DB 
table;  your comment suggests this is so.

Following my previous attempts to remove STD MEXes, I tried creating a new 
ST (with a new SB table).  Importing the new ST was *very* slow (took a 
luchtime to complete), and when I try to create an annotation the system 
seems to hang -- i.e. the browser gets no response to the request.  I don't 
have clean enough data to report a bug (which I think this must be, since 
whatever I did I don't think OME should stop responding like this), so this 
is merely by way of a heads-up.

I am about to reset my OME database.  My current plan is to use psql to 
drop the ome database, then re-run the install script to re-create it.  Is 
there an easier way?

#g



---
Graham Klyne
Image Bioinformatics Research Group (http://www.bioimage.org/)
Department of Zoology, University of Oxford
South Parks Road, Oxford OX1 3PS, UK
E-mail: <Graham.Klyne at zoo.ox.ac.uk>
Direct phone: +44-(0)1865-281991
Departmental fax: +44-(0)1865-310447