Unique identifiers assigned to Plant Ontology developer groups

[Mary Polacco]

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
>>> 
>>> 
>> 
>> 
>>