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

[Pankaj Jaiswal]

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

-- 
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