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12 Jun 2013 16:22:41 UTC
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perl modules for GO and other OBO ontologiesextracts a subgraph from an ontology filegenerates a slim file based on association filefind association for a GO termshows all possible paths from a term to the topmaps gene associations to a 'slim' ontologyModules
basic procedural interface to go-perltransforms OBO XML to GODB XMLparses GO files into GO object modelwrites OWLpreliminary analysis objectGene Ontology Blast Reports DEPRECATEDSpecies info for data used by Panther Clustersa collection of relationships over termsa graph node located in a treea term or concept in an ontologyGO Object Factoryparses all GO files formats and typesexports constants corresponding to XMLbase class for parserssyntax parsing of GO .def flat filessyntax parsing of GO gene-association flat filessyntax parsing of GO .def flat filessyntax parsing of flat files containing GO IDs.syntax parsing of GO .ontology flat filessyntax parsing of GO xref flat files (eg eg2go, metacyc2go)Parses Mesh ascii text filesparses MGI gene assoc stanza filesOBO Flat file parser objectOBO Flat file parser objectParses xml made from eventsturns OWL XML into event streamsyntax parsing of GO.refences filessyntax parsing of GO .def flat filesbase class for parserssyntax parsing of GO xrf_abbs flat filesProvides
in GO/Handlers/abstract_prolog_writer.pmin GO/Handlers/abstract_sql_writer.pmin GO/Handlers/lexanalysis.pmin GO/Handlers/lexanalysis2sql.pmin GO/Handlers/obj_storable.pmin GO/Handlers/obj_yaml.pmin GO/Handlers/obo.pmin GO/Handlers/obo_sxpr.pmin GO/Handlers/obo_xml.pmin GO/Handlers/pathlist.pmin GO/Handlers/prolog.pmin GO/Handlers/rdf.pmin GO/Handlers/sxpr.pmin GO/Handlers/xml.pmin GO/IO/Dotty.pmin GO/IO/OBDXML.pmin GO/IO/ObanOwl.pmin GO/IO/RDFXML.pmin GO/IO/XML.pmin GO/IO/go_assoc.pmin GO/Model/Association.pmin GO/Model/CrossProduct.pmin GO/Model/DB.pmin GO/Model/Evidence.pmin GO/Model/GeneProduct.pmin GO/Model/GraphIterator.pmin GO/Model/LogicalDefinition.pmin GO/Model/Modification.pmin GO/Model/Ontology.pmin GO/Model/Path.pmin GO/Model/Property.pmin GO/Model/Restriction.pmin GO/Model/Seq.pmin GO/Model/Species.pmin GO/Model/TreeIterator.pmin GO/Model/Xref.pmin GO/ObjCache.pmin GO/Parsers/obj_storable_parser.pmin GO/Parsers/obj_yaml_parser.pmin GO/Parsers/obo_parser.pmin GO/Utils.pmModule Install Instructions
To install GO::Utils, copy and paste the appropriate command in to your terminal.
cpanm GO::Utils
perl -MCPAN -e shell install GO::Utils
For more information on module installation, please visit the detailed CPAN module installation guide.