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Author image Chris Mungall

Documentation

perl modules for GO and other OBO ontologies
extracts a subgraph from an ontology file
generates a slim file based on association file
find association for a GO term
shows all possible paths from a term to the top
maps gene associations to a 'slim' ontology

Modules

basic procedural interface to go-perl
transforms OBO XML to GODB XML
parses GO files into GO object model
writes OWL
preliminary analysis object
Gene Ontology Blast Reports DEPRECATED
Species info for data used by Panther Clusters
a collection of relationships over terms
a graph node located in a tree
a term or concept in an ontology
GO Object Factory
parses all GO files formats and types
exports constants corresponding to XML
base class for parsers
syntax parsing of GO .def flat files
syntax parsing of GO gene-association flat files
syntax parsing of GO .def flat files
syntax parsing of flat files containing GO IDs.
syntax parsing of GO .ontology flat files
syntax parsing of GO xref flat files (eg eg2go, metacyc2go)
Parses Mesh ascii text files
parses MGI gene assoc stanza files
OBO Flat file parser object
OBO Flat file parser object
Parses xml made from events
turns OWL XML into event stream
syntax parsing of GO.refences files
syntax parsing of GO .def flat files
base class for parsers
syntax parsing of GO xrf_abbs flat files

Provides

in GO/Handlers/abstract_prolog_writer.pm
in GO/Handlers/abstract_sql_writer.pm
in GO/Handlers/lexanalysis.pm
in GO/Handlers/lexanalysis2sql.pm
in GO/Handlers/obj_storable.pm
in GO/Handlers/obj_yaml.pm
in GO/Handlers/obo.pm
in GO/Handlers/obo_sxpr.pm
in GO/Handlers/obo_xml.pm
in GO/Handlers/pathlist.pm
in GO/Handlers/prolog.pm
in GO/Handlers/rdf.pm
in GO/Handlers/sxpr.pm
in GO/Handlers/xml.pm
in GO/IO/Dotty.pm
in GO/IO/OBDXML.pm
in GO/IO/ObanOwl.pm
in GO/IO/RDFXML.pm
in GO/IO/XML.pm
in GO/IO/go_assoc.pm
in GO/Model/Association.pm
in GO/Model/CrossProduct.pm
in GO/Model/DB.pm
in GO/Model/Evidence.pm
in GO/Model/GeneProduct.pm
in GO/Model/GraphIterator.pm
in GO/Model/LogicalDefinition.pm
in GO/Model/Modification.pm
in GO/Model/Ontology.pm
in GO/Model/Path.pm
in GO/Model/Property.pm
in GO/Model/Restriction.pm
in GO/Model/Seq.pm
in GO/Model/Species.pm
in GO/Model/TreeIterator.pm
in GO/Model/Xref.pm
in GO/ObjCache.pm
in GO/Parsers/obj_storable_parser.pm
in GO/Parsers/obj_yaml_parser.pm
in GO/Parsers/obo_parser.pm
in GO/Utils.pm