Changes between Version 8 and Version 9 of OntologiesInUse


Ignore:
Timestamp:
Jun 6, 2012, 5:41:50 PM (9 years ago)
Author:
gomidori
Comment:

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  • OntologiesInUse

    v8 v9  
    11Ontologies used for extensions
    22
    3 ||'''ontology'''||'''abbr'''||URL||
    4 ||Cell Ontology||CL||https://sourceforge.net/tracker/?group_id=76834&atid=925065 ||
    5 ||CHEBI||CHEBI||-||
    6 ||PSI-MOD||MOD||-||
    7 ||Sequence Ontology||SO||-||
    8 ||PFAM||PF||||
    9 ||PATO|| ||-||
     3||'''ontology'''||'''abbr'''||tracker URL||
     4||[http://cellontology.org/ Cell Ontology]||CL||http://sourceforge.net/tracker/?group_id=76834&atid=925065||
     5||[http://www.ebi.ac.uk/chebi CHEBI]||CHEBI||http://sourceforge.net/tracker/?group_id=125463&atid=703818||
     6||[http://www.geneontology.org/ Gene Ontology]||GO||https://sourceforge.net/tracker/?atid=440764&group_id=36855||
     7||[http://obofoundry.org/wiki/index.php/PATO:Main_Page PATO]||PATO||http://sourceforge.net/tracker/?group_id=76834&atid=595654||
     8||[http://pfam.sanger.ac.uk/ Pfam]||Pfam||N/A, but contact helpdesk - pfam-help at sanger.ac.uk||
     9||[http://pir.georgetown.edu/pro/ Protein Ontology]||PR||http://sourceforge.net/tracker/?group_id=266825&atid=1135711||
     10||[http://psidev.cvs.sourceforge.net/psidev/psi/mod/data/PSI-MOD.obo PSI-MOD]||MOD||https://sourceforge.net/tracker/?group_id=65472&atid=776607||
     11||[http://sequenceontology.org/ Sequence Ontology]||SO||http://sourceforge.net/tracker/?group_id=72703&atid=810408||
    1012
    1113
    12 An example of each "type " of relation used should be added here:
     14An example of each relation used should be added here:
    1315
    1416https://sourceforge.net/apps/trac/pombase/wiki/ListOfRelations
    1517
    1618
    17 The term should be added to
    18 
    19  /mini-ontologies
     19For some ontologies, terms used should be added to the collection of ontology subsets that we plan to maintain (proposed as a /mini-ontologies/ sub-directory of the pombe-embl svn repository)
    2020
    2121  * chebi.obo
     
    2323  * cl.obo
    2424
    25 For these ontologies
    26 
    27 please edit the isa to point to PATO:0000001 ("quality"), CL:0000000 ("cell") or CHEBI:24431 ("chemical entity") as appropriate.
    28 
     25For these ontologies please edit the is_a parent to point to PATO:0000001 ("quality"), CL:0000000 ("cell"), or CHEBI:24431 ("chemical entity") as appropriate.