[Obo-cell-type] Annotations to cell types (using OBO-Cell)
Chris Mungall
cjm at fruitfly.org
Thu Mar 8 22:38:32 EST 2007
sorry about the lack of instructions!
gotta run off in a minute so i'll attempt a quick breakdown
let's take the first one:
>>> inconsistency_by_alignment PO:0000081-axial cell is_a+ PO:0009002-
>>> plant cell CL:0000363-axial cell not-is_a+ CL:0000610-plant cell
what it's saying is we have in PO:
/ PO:0009011 plant structure
is_a PO:0009002 plant cell
is_a PO:0000081 axial cell
And in CL:
/ CL:0000000 cell
is_a CL:0000003 cell in vivo
is_a CL:0000012 cell by class
is_a CL:0000144 cell by function
is_a CL:0000293 structural cell
is_a CL:0000363 axial cell
it is not under plant_cell
HOWEVER, there is nothing to worry about here. This is just a case of
the PO term being more specific (ie plant specific), which is normal.
Sorry for the false alarm; I will run this again later taking into
account the PO term is more specific
the ones with CL on the left hand side MAY be worth checking
On Mar 8, 2007, at 7:13 PM, chih-wei tung wrote:
> 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?
>>>>>>>>>> -------------------------------------------------------------
>>>>>>>>>> --- -----
>>>>>>>>>> ----
>>>>>>>>>> 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