[Obo-cell-type] Annotations to cell types (using OBO-Cell)

[Chris Mungall]

There's no sense in you adding the name too, that would only create  
more work for you. What you have below looks great.

By the way we should have a new oboedit interface for editing data  
such as pairwise ID mappings using the phenote interface (giving us  
term completion and all that good stuff)

On Mar 7, 2007, at 12:06 PM, Pankaj Jaiswal wrote:

> Chris,
>
> Do you want us to add the cell terms in PO as Xrefs.
>
> xref_analog: CL:ID
> e.g
> xref_analog: CL:0000540
>
>
> [Term]
> id: PO:0000293
> name: guard cell
> namespace: plant_structure
> def: "One of a pair of cells flanking the stomatal pore." [ISBN: 
> 0471245208]
> comment: They cause the opening and closing of the pore by changes  
> in turgor.
> xref_analog: CL:0000292--->CHECK THIS FOR SUGGESTED ADDITION
> is_a: PO:0004013 ! epidermal cell
> relationship: develops_from PO:0000351 ! guard mother cell
> relationship: part_of PO:0002000 ! stomatal complex
>
> Is it good to have only the ID or do you want us to add the term  
> name as well. Is there a better way?
>
> Pankaj
>
>
> Chris Mungall wrote:
>> again, with attachment
>> On Jan 16, 2007, at 7:31 AM, Chris Mungall wrote:
>>>
>>> Why not add links to CL from PO as xrefs? This will help keep the  
>>> two
>>> ontologies in sync, see
>>> http://www.bioontology.org/wiki/index.php/CL:Aligning_species-
>>> specific_anatomy_ontologies_with_CL
>>>
>>> See attached for a first pass at some automated mappings
>>>
>>> Hmm, according to OBO-Cell, zygote (CL:0000365) is both a plant and
>>> animal cell!
>>>
>>> I think the PO<->CL coordination effort could do with revisiting...
>>>
>>> On Jan 15, 2007, at 3:58 PM, Sue Rhee wrote:
>>>
>>>> Chris,
>>>>
>>>> The Plant Ontology has a number of cell types under its Plant
>>>> Structure branch and I think (though someone should confirm) that
>>>> the Cell Type ontology's plant cell type terms have PO IDs as
>>>> secondary IDs. Actually I think that this should be made
>>>> bidirectional but am not sure if the PO terms have CT IDs as
>>>> secondary IDs. In any case, there are 264 annotations to terms
>>>> under plant cell, which are downloadable from the PO website
>>>> (www.plantontology.org).
>>>>
>>>> Sue
>>>>
>>>> Chris Mungall wrote:
>>>>> Is anyone aware of downloadable annotations to CL IDs? I know
>>>>> that  MGI provide cell type localisation info as qualifiers to
>>>>> their GO  annotations; this will be available through AmiGO
>>>>> sometime this year.
>>>>> There is also the FlyBase/ZFIN/NCBO phenotype annotations, many
>>>>> of  which are described as qualities borne by types of cell (eg
>>>>> spermatocyte lacks asters)
>>>>> EVOC provides associations to dbEST libraries.
>>>>> Any others?
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>>>>
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>
> -- 
> Pankaj Jaiswal
> G-15, Bradfield Hall
> Dept. of Plant Breeding and Genetics
> Cornell University
> Ithaca, NY-14853, USA
>
> Ph. +1-607-255-3103 / 4199
> fax: +1-607-255-6683
>