[Obo-cell-type] Annotations to cell types (using OBO-Cell)
Pankaj Jaiswal
pj37 at cornell.edu
Thu Mar 8 20:12:53 EST 2007
The inconsistency is in the PO or in CL in terms of missing ISA?
How do I interpret this file.
Pankaj
Chris Mungall wrote:
>
> Great, thanks!
>
> I have found 44 inconsistencies between PO and CL, see attached.
>
>
> ------------------------------------------------------------------------
>
> 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
>
>
> ------------------------------------------------------------------------
>
>
> 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?
>>>>>>>> ----------------------------------------------------------------
>>>>>>>> -----
>>>>>>>> ----
>>>>>>>> Take Surveys. Earn Cash. Influence the Future of IT
>>>>>>>> Join SourceForge.net's Techsay panel and you'll get the chance to
>>>>>>>> share your
>>>>>>>> opinions on IT & business topics through brief surveys - and earn
>>>>>>>> cash
>>>>>>>> http://www.techsay.com/default.php?
>>>>>>>> page=join.php&p=sourceforge&CID=DEVDEV
>>>>>>>> _______________________________________________
>>>>>>>> Obo-cell-type mailing list
>>>>>>>> Obo-cell-type at lists.sourceforge.net
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/obo-cell-type
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------
>>>>>> -------
>>>>>> Take Surveys. Earn Cash. Influence the Future of IT
>>>>>> Join SourceForge.net's Techsay panel and you'll get the chance to
>>>>>> share your
>>>>>> opinions on IT & business topics through brief surveys - and earn
>>>>>> cash
>>>>>> http://www.techsay.com/default.php?
>>>>>> page=join.php&p=sourceforge&CID=DEVDEV
>>>>>> _______________________________________________
>>>>>> Obo-cell-type mailing list
>>>>>> Obo-cell-type at lists.sourceforge.net
>>>>>> https://lists.sourceforge.net/lists/listinfo/obo-cell-type
>>>>>>
>>>>
>>>> --
>>>> 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
>>>>
>>>
>>
>>
>
More information about the Po-dev
mailing list