[Obo-cell-type] Annotations to cell types (using OBO-Cell)
Chris Mungall
cjm at fruitfly.org
Thu Mar 8 19:51:15 EST 2007
Great, thanks!
I have found 44 inconsistencies between PO and CL, see attached.
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inconsistency_by_alignment PO:0000081-axial cell is_a+ PO:0009002-plant cell CL:0000363-axial cell not-is_a+ CL:0000610-plant cell
inconsistency_by_alignment PO:0000084-sperm cell is_a+ PO:0009002-plant cell CL:0000366-sperm cell (sensu Viridiplantae) not-is_a+ CL:0000610-plant cell
inconsistency_by_alignment PO:0000115-socket cell is_a+ PO:0004013-epidermal cell CL:0000297-socket cell not-is_a+ CL:0000362-epidermal cell
inconsistency_by_alignment PO:0000115-socket cell is_a+ PO:0009002-plant cell CL:0000297-socket cell not-is_a+ CL:0000610-plant cell
inconsistency_by_alignment PO:0000244-functional megaspore is_a+ PO:0009002-plant cell CL:0000433-functional megaspore not-is_a+ CL:0000610-plant cell
inconsistency_by_alignment PO:0000245-degenerate megaspore is_a+ PO:0009002-plant cell CL:0000475-degenerate megaspore not-is_a+ CL:0000610-plant cell
inconsistency_by_alignment PO:0000262-trichoblast is_a+ PO:0004013-epidermal cell CL:0000299-trichoblast not-is_a+ CL:0000362-epidermal cell
inconsistency_by_alignment PO:0000263-atrichoblast is_a+ PO:0004013-epidermal cell CL:0000332-atrichoblast not-is_a+ CL:0000362-epidermal cell
inconsistency_by_alignment PO:0000273-xylem element is_a+ PO:0009002-plant cell CL:0000298-xylem element not-is_a+ CL:0000610-plant cell
inconsistency_by_alignment PO:0000273-xylem element is_a+ PO:0009002-plant cell CL:0000298-xylem element not-is_a+ CL:0000610-plant cell
inconsistency_by_alignment PO:0000282-trichome is_a+ PO:0004013-epidermal cell CL:0000282-trichome not-is_a+ CL:0000362-epidermal cell
inconsistency_by_alignment PO:0000282-trichome is_a+ PO:0009002-plant cell CL:0000282-trichome not-is_a+ CL:0000610-plant cell
inconsistency_by_alignment PO:0000284-subsidiary cell is_a+ PO:0004013-epidermal cell CL:0000270-subsidiary cell not-is_a+ CL:0000362-epidermal cell
inconsistency_by_alignment PO:0000290-tracheary element is_a+ PO:0000273-xylem element CL:0000672-tracheary element not-is_a+ CL:0000298-xylem element
inconsistency_by_alignment PO:0000290-tracheary element is_a+ PO:0000081-axial cell CL:0000672-tracheary element not-is_a+ CL:0000363-axial cell
inconsistency_by_alignment PO:0000293-guard cell is_a+ PO:0004013-epidermal cell CL:0000292-guard cell not-is_a+ CL:0000362-epidermal cell
inconsistency_by_alignment PO:0000293-guard cell is_a+ PO:0009002-plant cell CL:0000292-guard cell not-is_a+ CL:0000610-plant cell
inconsistency_by_alignment PO:0000301-tracheid is_a+ PO:0000273-xylem element CL:0000331-tracheid not-is_a+ CL:0000298-xylem element
inconsistency_by_alignment PO:0000301-tracheid is_a+ PO:0000081-axial cell CL:0000331-tracheid not-is_a+ CL:0000363-axial cell
inconsistency_by_alignment PO:0000332-pavement cell is_a+ PO:0004013-epidermal cell CL:0000400-pavement cell not-is_a+ CL:0000362-epidermal cell
inconsistency_by_alignment PO:0000332-pavement cell is_a+ PO:0009002-plant cell CL:0000400-pavement cell not-is_a+ CL:0000610-plant cell
inconsistency_by_alignment PO:0000351-guard mother cell is_a+ PO:0004013-epidermal cell CL:0000262-guard mother cell not-is_a+ CL:0000362-epidermal cell
inconsistency_by_alignment PO:0000351-guard mother cell is_a+ PO:0009002-plant cell CL:0000262-guard mother cell not-is_a+ CL:0000610-plant cell
inconsistency_by_alignment PO:0000355-fiber tracheid is_a+ PO:0000273-xylem element CL:0000258-fiber tracheid not-is_a+ CL:0000298-xylem element
inconsistency_by_alignment PO:0000355-fiber tracheid is_a+ PO:0000081-axial cell CL:0000258-fiber tracheid not-is_a+ CL:0000363-axial cell
inconsistency_by_alignment PO:0002002-basal cell is_a+ PO:0009002-plant cell CL:0000646-basal cell not-is_a+ CL:0000610-plant cell
inconsistency_by_alignment PO:0004011-initial cell is_a+ PO:0004010-meristematic cell CL:0000034-stem cell not-is_a+ CL:0000685-meristematic cell
inconsistency_by_alignment PO:0004011-initial cell is_a+ PO:0009002-plant cell CL:0000034-stem cell not-is_a+ CL:0000610-plant cell
inconsistency_by_alignment PO:0004013-epidermal cell is_a+ PO:0009002-plant cell CL:0000362-epidermal cell not-is_a+ CL:0000610-plant cell
inconsistency_by_alignment PO:0004531-sheath cell is_a+ PO:0009002-plant cell CL:0000618-sheath cell not-is_a+ CL:0000610-plant cell
inconsistency_by_alignment PO:0020019-megaspore is_a+ PO:0009002-plant cell CL:0000250-megaspore not-is_a+ CL:0000610-plant cell
inconsistency_by_alignment PO:0020048-microspore is_a+ PO:0009002-plant cell CL:0000252-microspore not-is_a+ CL:0000610-plant cell
inconsistency_by_alignment CL:0000266-meristemoid is_a+ CL:0000034-stem cell PO:0000070-meristemoid not-is_a+ PO:0004011-initial cell
inconsistency_by_alignment CL:0000299-trichoblast is_a+ CL:0000538-epidermal initial PO:0000262-trichoblast not-is_a+ PO:0000349-epidermal initial
inconsistency_by_alignment CL:0000299-trichoblast is_a+ CL:0000685-meristematic cell PO:0000262-trichoblast not-is_a+ PO:0004010-meristematic cell
inconsistency_by_alignment CL:0000299-trichoblast is_a+ CL:0000034-stem cell PO:0000262-trichoblast not-is_a+ PO:0004011-initial cell
inconsistency_by_alignment CL:0000332-atrichoblast is_a+ CL:0000538-epidermal initial PO:0000263-atrichoblast not-is_a+ PO:0000349-epidermal initial
inconsistency_by_alignment CL:0000332-atrichoblast is_a+ CL:0000685-meristematic cell PO:0000263-atrichoblast not-is_a+ PO:0004010-meristematic cell
inconsistency_by_alignment CL:0000332-atrichoblast is_a+ CL:0000034-stem cell PO:0000263-atrichoblast not-is_a+ PO:0004011-initial cell
inconsistency_by_alignment CL:0000543-sieve tube member is_a+ CL:0000268-sieve element PO:0000289-sieve tube member not-is_a+ PO:0000289-sieve tube member
inconsistency_by_alignment CL:0000292-guard cell is_a+ CL:0000262-guard mother cell PO:0000293-guard cell not-is_a+ PO:0000351-guard mother cell
inconsistency_by_alignment CL:0000258-fiber tracheid is_a+ CL:0000672-tracheary element PO:0000355-fiber tracheid not-is_a+ PO:0000290-tracheary element
inconsistency_by_alignment CL:0000646-basal cell is_a+ CL:0000034-stem cell PO:0002002-basal cell not-is_a+ PO:0004011-initial cell
inconsistency_by_alignment CL:0000685-meristematic cell is_a+ CL:0000034-stem cell PO:0004010-meristematic cell not-is_a+ PO:0004011-initial cell
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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
>>>
>>
>
>
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