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

[Chris Mungall]

Great, thanks!

I have found 44 inconsistencies between PO and CL, see attached.
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On Mar 8, 2007, at 12:33 PM, Chih-Wei Tung wrote:

> 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
>>>
>>
>
>