From SchaefferM at missouri.edu  Mon Jul 28 11:31:02 2008
From: SchaefferM at missouri.edu (Mary (Polacco) Schaeffer)
Date: Mon, 28 Jul 2008 10:31:02 -0500
Subject: [Po-dev] FW: sure is a problem with obo-edit
In-Reply-To: <BBB39EAD-CC8B-4722-B18C-B32C3432B673@missouri.edu>
Message-ID: <C4B35066.1D207%SchaefferM@missouri.edu>

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
> 
> or
> 
> sperm cell < male gametophyte
>          male gametophyte % plant cell
> 
> 
> ?
> 
> This case is not covered in the documentation ;-).
> 
> 
> thanks and cheers,
> 
> Toni

------ End of Forwarded Message

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/po-dev/attachments/20080728/0526f878/attachment.html>

From pj37 at cornell.edu  Mon Jul 28 13:06:54 2008
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Mon, 28 Jul 2008 13:06:54 -0400
Subject: [Po-dev] Re: FW: sure is a problem with obo-edit
In-Reply-To: <C4B35066.1D207%SchaefferM@missouri.edu>
References: <C4B35066.1D207%SchaefferM@missouri.edu>
Message-ID: <488DFCAE.8050406@cornell.edu>

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


From jdeegan at ebi.ac.uk  Tue Jul 29 05:26:10 2008
From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark))
Date: Tue, 29 Jul 2008 10:26:10 +0100
Subject: [Po-dev] Re: FW: sure is a problem with obo-edit
In-Reply-To: <488DFCAE.8050406@cornell.edu>
References: <C4B35066.1D207%SchaefferM@missouri.edu>
	<488DFCAE.8050406@cornell.edu>
Message-ID: <488EE232.8010309@ebi.ac.uk>

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