Unique identifiers assigned to Plant Ontology developer groups

[Pankaj Jaiswal]

Doreen and Lincoln, please correct me here.
I think for the purpose of DB, we will be putting up our complete poc-DB up for 
download same as Gene Ontology DB. Right !

As far as what Mary is asking, I don't mind putting up another file with a dump 
using OBO adapter. Perhaps, this can be scheduled only with the DB release and 
not every time we modify the flat files in the CVS.

Pankaj


Mary Polacco wrote:

> Hi Pankaj,
> This is very useful!
> 
> What does it take to post this on the downloads section so that other folks
> who wish to import the terms into databases could have this without having
> to figure out DAG EDIT?
>     -mary
> 
> On 11/5/03 10:29 AM, "Pankaj Jaiswal" <pj37 at cornell.edu> wrote:
> 
> 
>>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
******************************************