Unique identifiers assigned to Plant Ontology developer groups

[Pankaj Jaiswal]

Hi Mary,

I am copying this message to Liya. I guess this can be pulled out from the 
Ontology DB tables. I am not so sure about the hierarchy, but here is what I 
did. By using the Dag-EDIT ver 1.407, I saved the gramene ontology+definition 
file by using the OBO adapter and I can get a complete record of terms as 
following. I hope this will work. Earlier versions of Dag-EDIT used to have an 
adapter for generating an RDF format, but this one seems better.


[Typedef]
id: part_of
name: Part of

[Typedef]
id: develops_from
name: develops from

[Term]
id: GRO:0005050
name: phelloderm
is_a: GRO:0005047
is_a: GRO:0005048

[Term]
id: GRO:0005279
name: floral primordium
is_a: GRO:0000136

[Term]
id: GRO:0005598
name: vascular cambium
is_a: GRO:0005597

[Term]
id: GRO:0005580
name: floral nectary
is_a: GRO:0005659

[Term]
id: GRO:0006107
name: microspore mother cell
is_a: GRO:0005825

[Term]
id: GRO:0005352
name: xylem
relationship: part_of GRO:0005369




Pankaj

Mary Polacco wrote:

> Pankaj,
> Is there an easy way to get a table of the terms and their POC identifiers
> other than writing a parser for the flat file that shows also the heirarchy?
> 
> -mary
> 
> On 11/4/03 6:15 PM, "Pankaj Jaiswal" <pj37 at cornell.edu> wrote:
> 
> 
>>Unique identifiers assigned to Plant Ontology developer groups
>>
>>Every term in the anatomy or developmental stage ontology is identified by a
>>unique identifier. Under the conventions that we have already established, the
>>syntax of a PO identifier is PO:nnnnnnn, where nnnnnnn is a zero-padded unique
>>integer of seven digits.
>>
>>In order to ensure database integrity, identifiers are never removed. Terms
>>that 
>>are retired(deleted) from the ontology are moved into the obsolete category.
>>To 
>>ensure that the same identifier is not used twice, each participating group
>>will 
>>be assigned non-overlapping ID ranges and listed on this page for
>>documentation 
>>purposes. These ranges will automatically act as (internal) identifiers for
>>the 
>>group that submitted the term. If you want the identifiers assigned to your
>>group, please send and e mail to po-dev at plantontology.org
>>
>>Group      identifier range (from-to)
>>TAIR     0000001-0005000
>>Gramene     0005001-0010000
>>IRRI     0010001-0015000
>>MaizeDB     0015001-0020000-->Change group name to MaizeGDB
>>
>>For the above 4 groups, the range was assigned prior to the award of this
>>project http://www.plantontology.org/doc/poc_project.html
>>
>>Toby Kellogg     0020001-0025000
>>Open     0025001-0030000
>>Open     0030001-0035000
>>Open     0035001-0040000
>>Open     0040001-0045000
>>Open     0045001-0050000
>>Open     0050001-0055000
>>
>>Setting your range of numbers within DAG-Edit.
>>
>>Once you have claimed a set of numbers from the ontology numbers file, you
>>must 
>>also set these numbers within the configuration file of DAG-Edit. To do this
>>you 
>>should open DAG-Edit, and chose from the 'plugins' menu the 'DAG-Edit
>>Configuration Manager'. Within this window you can now fill in your range of
>>numbers, starting in the 'start of id range' line and finishing in the 'End of
>>id range' line. Press 'Save Configuration' to save your changes.
>>
>>In order to avoid conflicts, any new term contributed by the group should
>>carry 
>>the Ontology term identifier from the assigned range.
>>
>>
>>
>>It is also an easy way to track the contribution.
>>
>>
>>Pankaj
>>
>>
> 
> 
> 

-- 
******************************************
Pankaj Jaiswal, Ph.D.
Research Associate
Dept. of Plant Breeding
Cornell University
Ithaca, NY-14853, USA

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org
******************************************