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[bioontology-support] [BioPortal] Cereal plant gross anatomy Parsing Failed

Trish Whetzel whetzel at stanford.edu
Wed Jul 25 10:28:44 PDT 2012


Ok, the format looks a bit odd (see below) and the URL to obtain the file is:
http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/gramene/obsolete/anatomy_gramene.ontology?view=co&content-type=text/plain

Do you know if this file loads in the current version of OBO-Edit? I didn't see any error messages from OBO-Edit yet I do not see the ontology either. If this "version" was pulled only because of the change in metadata I believe we can remove this latest entry to leave the previous version viewable and accessible via the Web services.

Trish 



Ontology file snippet:
!autogenerated-by:     DAG-Edit version 1.306-beta-1
!saved-by:             pj37
!date:                 Tue Jul 22 11:58:24 EDT 2003
!version: $Revision: 1.1.1.1 $
!Editors: Pankaj Jaiswal (Gramene), Leonore Reiser & Jonathan Clarke (TAIR), Dom Paolillo Jr. (Cornell Univ.)
!Relationship types: % (ISA), < (PART OF), ~ (DERIVED/DEVELOPS_FROM)
!Disclaimer: Copyright 2002 Gramene Database
!Title: Cereal Plant Anatomy
$cereal plant ontology ; GRO:0080001
 %plant anatomy ontology ; GRO:0005297
  %whole plant ; GRO:0005000
   %embryo ; GRO:0005343 < seed ; GRO:0005339
    <basal cell ; GRO:0000179
    <cotyledon ; GRO:0005358
     %scutellum ; GRO:0005344
    <cotyledon primordium ; GRO:0000365 % initial cell ; GRO:0005825 % organ primordium ; GRO:0000136
    <embryonic axis ; GRO:0000387
     <epicotyl ; GRO:0005383 ; synonym:plumule
      <coleoptile ; GRO:0005373
    <embryonic ground tissue ; GRO:0000367
    <epiblast ; GRO:0005345
    <hypocotyl ; GRO:0005342
    <meristem primary ; GRO:0005613 ; synonym:primary meristem
    <procambium ; GRO:0000345 ; synonym:provascular tissue < primary meristematic tissues ; GRO:0005753
    <protoderm ; GRO:0000182 < primary meristematic tissues ; GRO:0005753
    <protophloem ; GRO:0000346
    <protoxylem ; GRO:0000272 < xylem primary ; GRO:0005849
    <ptyxis ; GRO:0005108 ; synonym:embryonic leaf
     <bud scale ; GRO:0005379
     <first leaf ; GRO:0005375
     <second leaf ; GRO:0005377
     <ventral scale ; GRO:0005371


On Jul 25, 2012, at 7:14 PM, Laurel Cooper wrote:

> We can probably clear this up with a quick skype call.  I am only here today and tomorrow and i know you are at icbo.
> It seems there was a mix-up when the purls were fixed, and then I tried to fix it from my end and I think I broke something.
> Laurel
> 
> On 7/24/12 11:30 AM, support at bioontology.org wrote:
>> Cereal plant gross anatomy parsing failed.
>> 
>> The BioPortal team is investigating the issue.
>> 
>> Please contact support at bioontology.org if you have questions.
>> 
>> Thank you,
>> The BioPortal Team 
> 
> -- 
> **********************************************************
> Laurel (Lol) Cooper, PhD
> Coordinator, Plant Ontology Consortium
> Dept. of Botany and Plant Pathology
> Rm 3086, Cordley Hall
> Oregon State University
> Corvallis, OR 97331
> Web: www.plantontology.org
> 
> Phone: 541-737-5272
> Fax: 541-737-3573
> Skype: cooperlol910
> ***********************************************************
> 
> 
> 



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