Changes between Version 4 and Version 5 of FissionYeastPhenotypeOntology


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Timestamp:
Dec 28, 2012, 3:49:14 PM (9 years ago)
Author:
gomidori
Comment:

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  • FissionYeastPhenotypeOntology

    v4 v5  
    44The Fission Yeast Phenotype Ontology (FYPO) is a formal ontology of phenotypes observed in fission yeast.
    55
    6 FYPO is being developed to support the comprehensive and detailed representation of phenotypes in [http://www.pombase.org/ PomBase], the new online fission yeast resource. Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions.
     6FYPO is being developed to support the comprehensive and detailed representation of phenotypes in [http://www.pombase.org/ PomBase], the online fission yeast resource. Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions.
     7
     8== Availability ==
     9FYPO is maintained in a Subversion repository hosted at !SourceForge:
     10
     11https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/
     12
     13The main phenotype_ontology directory contains the editors' working file (fypo_edit.obo). FYPO curators use [http://code.google.com/p/owltools/wiki/Oort Oort] to manage the FYPO release process.
     14
     15A selection of OBO format files generated by Oort are archived in date-stamped releases in the releases subdirectory of the SVN repository. The current versions of these files are also available via HTTP at the curation.pombase.org site -- see table below.
     16
     17OWL files are also generated by Oort, and can be included in the FYPO releases if demand arises.
     18
     19=== Available files: ===
     20
     21||File||Description||SVN path||HTTP link||
     22||fypo.obo||Main FYPO file from Oort; implied links asserted||/phenotype_ontology/releases/latest/fypo.obo||[http://curation.pombase.org/ontologies/fypo/latest/fypo.obo fypo.obo]||
     23||fypo-merged.obo||implied links not asserted||/phenotype_ontology/releases/latest/fypo-merged.obo||[http://curation.pombase.org/ontologies/fypo/latest/fypo-merged.obo fypo-merged.obo]||
     24||fypo-simple.obo||logical definitions omitted||/phenotype_ontology/releases/latest/fypo-simple.obo||[http://curation.pombase.org/ontologies/fypo/latest/fypo-simple.obo fypo-simple.obo]||
     25||fypo-basic.obo||includes only is_a links||/phenotype_ontology/releases/latest/fypo-basic.obo||[http://curation.pombase.org/ontologies/fypo/latest/fypo-basic.obo fypo-basic.obo]||
     26
     27Note: We are aware that !SourceForge URLs for the 'latest' directory do not work with HTTP access (they do work with command-line svn). If this causes problems, use the curation.pombase.org URLs.
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    729
    830== External Ontologies ==
    9 FYPO uses these OBO ontologies in its cross-product definitions:
     31Most FYPO terms have logical definitions (aka computable definitions, cross-product definitions) following the entity-quality (EQ) model. FYPO uses these OBO ontologies in its cross-product definitions:
    1032 * [http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/phenotype/quality.obo PATO]
    1133 * [http://geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo Gene Ontology (GO)]
     
    1840
    1941== Using FYPO in !PomBase ==
    20 [wiki:CuratorDocumentation#Phenotypes Phenotype curation documentation]
     42The !PomBase online curation tool ([http://curation.pombase.org/ Canto]) uses FYPO terms for annotation of ''S. pombe'' phenotypes. FYPO terms are displayed on [http://www.pombase.org/ PomBase] gene pages, along with supporting evidence and allele and expression details.
     43
     44[wiki:CuratorDocumentation#Phenotypes Phenotype curation documentation] is under development.
    2145
    2246== Tracker ==
    23 https://sourceforge.net/tracker/?func=browse&group_id=65526&atid=2096431
     47https://sourceforge.net/p/pombase/fission-yeast-phenotype/
    2448
    2549----