[Obo-cell-type] Annotations to cell types (using OBO-Cell)
chih-wei tung
cwt6 at cornell.edu
Thu Mar 8 22:13:47 EST 2007
Hi Chris,
It appears to me these 44 inconsistencies were the ones I created
Xref in PO according to the cell-vs-po.matches files. I guess I am
really confused by this "inconsistency_by_aligment", I am very
curious how did you generate this file?
Chih-Wei
On Mar 8, 2007, at 8:12 PM, Pankaj Jaiswal wrote:
> 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?
>>>>>>>>> --------------------------------------------------------------
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>>>>>>>>> _______________________________________________
>>>>>>>>> Obo-cell-type mailing list
>>>>>>>>> Obo-cell-type at lists.sourceforge.net
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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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