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

[Chih-Wei Tung]

Hi Chris.

I just added the cell type terms in PO as Xref: CL:ID, please go to   
http://brebiou.cshl.edu/viewcvs/Poc/ontology/OBO_format/po_anatomy.obo
to download the file "po_anatomy.obo revision 1.39"

The following cell type terms I didn't add in PO, either the  
definitions don't match, or they are not plant cell.
CL:0000019 sperm --> PO:0000084 sperm cell
CL:0000202 hair cell --> PO:0000262 trichoblast
CL:0000372	tormogen cell --> PO:0000115 socket cell
CL:0000374	thrichogen cell -->  PO:0000262 trichoblast
CL:0000380 thecogen cell --> PO:0004531 sheath cell

Please let me know if there is any inconsistence about it.

Chih-Wei




On Mar 7, 2007, at 3:51 PM, Chris Mungall wrote:

>
> 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
>>
>