making it easier for databases to use the PO

[Pankaj Jaiswal]

I think Mary wants something like they have for GO
Tab-delimited GO.terms_and_ids file containing GO term IDs, names and 
ontologies in the following format

GO:0000001 mitochondrion inheritance P
GO:0000002 mitochondrial genome maintenance P

http://www.geneontology.org/doc/GO.terms_and_ids

However, I would suggest Mary to generate a file for MaizeGDB and POC's 
reference like a mapping file namely MaizeGDB2PO. MaizeGDB can decide on 
how often they would like to update this and can help her in automating 
the association dump.

Here is a more precise suggestion on format of this file. Shuly you can 
put this into your SOPs for creating mappings to the external 
vocabularies. This was taken from Go documents and updated for PO purposes.

reference: ftp://ftp.geneontology.org/pub/go/external2go

-Pankaj



-----------------------------
Indices of Other Classification Systems to PO

PO is not the only attempt to build structured controlled vocabularies
for plant anatomical and growth stage annotation. Nor is it the only 
such series of catalogs in current use. We have, in a series of files in 
the folder

    /external2go--->[SHULY : create this in CVS]

attempted to make translation tables between these catalogs and PO. We
caution that these mappings are neither complete nor exact; they are
to be used as a guide and is the sole responsibility of the curator or 
the information resource that generates them. One reason for this is 
absence of definitions from many of the other catalogs and of a complete 
set of definitions in PO itself. The line:

!Uses:

e.g.
!Uses:Source name and URL if possible

gives the source of the external file.

The line syntax is:

database:<identifier> > PO:<term> ; PO:<PO_id>

e.g.:

MaizeGDB:123456 > PO:seed ; PO:0009010
MaizeGDB:123457 > PO:seed coat ; PO:0009088

_________________________________________





Shuly Avraham wrote:

> Hi Mary,
> 
> This kind of list is very easy to generate. If all you need is a flat 
> list of terms organized alphabetically, I can generate the list and 
> place the file on our (soon to come) FTP site.
> If there are other kinds of requsets or database queries, I can generate 
> those as well.
> In addition, in the near future we will have a mysql database dump on 
> the ftp site, so you can create a local copy of the database, and query 
> it as you need.
> 
> Shuly.
> 
> Mary Polacco wrote:
> 
>> Hi all
>>
>> Is there any reason not to post a list of the PO accessions and the 
>> terms,
>> alphabetically - ie no ontology structure?
>>
>> It makes it easier for database folks such as myself both to retrofit, 
>> and
>> use the approved terms and their the accession IDs.
>>
>> Attached is a list - from last fall, the CVS dump of terms with 
>> accessions
>> and ontology structure, that I used to help map to MaizeGDB. Missing 
>> terms,
>> eg synonyms for husk, I mapped using the PO AmiGO browser.  It should be
>> trivial for a regular update of this sort to be dumped from the AmiGO
>> database.
>>
>>  mary
>>  
>>
> 

-- 
************************
Pankaj Jaiswal, PhD
G15-Bradfield Hall
Dept. of Plant Breeding
Cornell University
Ithaca, NY-14853, USA

Tel: +1-607-255-3103
      +1-607-255-4109
Fax: +1-607-255-6683
http://www.gramene.org
************************