[Po-dev] Re: FW: sure is a problem with obo-edit

[Jennifer Deegan (nee Clark)]

Hi,

You could put this on the OBO-Edit bug tracker:

https://sourceforge.net/tracker/?group_id=36855&atid=418257

Jen

Pankaj Jaiswal wrote:

> This looks right to me on the website
> http://plantontology.org/amigo/go.cgi?layout=1&graph_bgcolor=white&graph_textcolor=blue&graph_format=default&action=dotty&search_constraint=terms&view=details&query=PO%3A0000084 
> 
> 
> See my inserts.
> 
> Pankaj
> 
> Mary (Polacco) Schaeffer wrote:
> 
>> Hi Pankaj,
>> Toni Kazic, my colleague at MU in Computer Science is looking at the 
>> Plant Ontology, towards using it in a computational reasoner. ON 
>> Friday, she showed me a PO heirarchy pulled from the obo-editor and it 
>> looked very strange, /aka /wrong.  I can answer the below question, 
>> but wonder if there is something else to worry about with obo-edit 
>> that everyone knows, but is not documented,
>>   Best,
>>   mary
>> ------ Forwarded Message
>>
>>>  From: Toni Kazic <kazict at missouri.edu>
>>>  Date: Fri, 25 Jul 2008 20:41:39 -0500
>>>  To: Mary Schaeffer mu <schaefferm at missouri.edu>
>>>  Cc: Toni Kazic <kazict at missouri.edu>
>>>  Subject: sure is a problem with obo-edit
>>>
>>>  and maybe also the viewer at the POC web site.  Certainly obo-edit  
>>>  leaves out many, many nodes when navigating the display.
>>>
>>>  Question:  in the following
>>>
>>>  ~sperm cell ; PO:0000084, PO:0020098 ; CL:0000366 ; synonym:sperm  
>>>  nucleus < male gametophyte ; PO:0020091 % plant cell ; PO:0009002
>>>
>>>
>>>  does this mean
>>>
>>>  sperm cell < male gametophyte
>>>           sperm cell % plant cell
> 
> 
> 
> This is right
> 
> 
>>>
>>>  or
>>>
>>>  sperm cell < male gametophyte
>>>           male gametophyte % plant cell
> 
> 
> 
> This assertion is wrong. You should not be using the old GO format. Use 
> the OBO format
> http://brebiou.cshl.org/viewcvs/Poc/ontology/OBO_format/po_anatomy.obo?rev=HEAD&content-type=text/plain 
> 
> 
> [Term]
> id: PO:0000084
> name: sperm cell
> alt_id: PO:0020098
> namespace: plant_structure
> def: "A haploid male reproductive cell (usually two in number); during 
> double fertilization\, one fuses with the female gamete (egg cell) to 
> produce a zygote while another fusses with the two polar nuclei of the 
> central cell to give rise to endosperm." [TAIR:ki]
> subset: reference
> synonym: "sperm nucleus" []
> xref_analog: CL:0000366
> is_a: PO:0009002 ! plant cell
> relationship: develops_from PO:0020097 ! generative cell
> relationship: part_of PO:0020091 ! male gametophyte
> 
> [Term]
> id: PO:0020091
> name: male gametophyte
> alt_id: PO:0020007
> namespace: plant_structure
> def: "A plant body or cell lineage formed by vegetative growth of the 
> microspore\, producing male gametes." [APWeb:Glossary]
> subset: reference
> synonym: "microgametophyte" []
> synonym: "pollen" []
> synonym: "pollen grain" []
> is_a: PO:0009004 ! gametophyte
> 
> 
> 
>>>
>>>
>>>  ?
>>>
>>>  This case is not covered in the documentation ;-).
>>>
>>>
>>>  thanks and cheers,
>>>
>>>  Toni
>>
>>
>> ------ End of Forwarded Message
> 
> 

-- 
Jennifer Deegan (nee Clark)
EMBL-European Bioinformatics Institute
Gene Ontology Consortium