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go-perl-0.05
River stage one • 1 direct dependent • 1 total dependent

Changes for version 0.05

  • 2005-12-01 - [cjm] more docs for map2slim. made -b option safe' new convenience methods in Graph and GeneProduct added create_handler to Parser improved POD docs new test t140
  • 2006-02-12 - [cjm] added methods for new obo Typedef tag is_transitive, transitive_over etc
  • 2006-03-29 - [cjm] added GO::Model::LogicalDefinition
  • 2006-04-19 - [cjm] added new test for chadoxml
  • 2006-07-14 - [cjm] support for idspace tag
  • 2006-07-24 - [cjm] support for synonymtypedef tag [cjm] more synonym info from ncbi_taxonomy_parser 2006-08-25 - [cjm] added checks to dbxref parsing
  • 2006-09-11 - [cjm] exports subsetdefs in obo format fixed definition dbxref parsing (was only getting 1 dbxref)
  • 2006-10-18 - [cjm] finalised code for GO::Model::LogicalDefinition added Relationship->complete
    • [cjm] removed some cruft

Documentation

go-perl
perl modules for GO and other OBO ontologies
go-dag-summary
go-export-graph.pl
go-filter-subset.pl
extracts a subgraph from an ontology file
go-make-slim.pl
generates a slim file based on association file
go-show-assocs-by-node.pl
find association for a GO term
go-show-paths-to-root.pl
shows all possible paths from a term to the top
go2fmt.pl
map2slim
maps gene associations to a 'slim' ontology

Modules

GO::Basic
basic procedural interface to go-perl
GO::Handlers::base
GO::Handlers::go_def
GO::Handlers::go_ont
GO::Handlers::go_xref
GO::Handlers::godb_prestore
transforms OBO XML to GODB XML
GO::Handlers::obj
parses GO files into GO object model
GO::Handlers::obo_html
GO::Handlers::obo_text
GO::Handlers::owl
writes OWL
GO::Handlers::owl_to_obo_text
GO::Handlers::summary
GO::Handlers::tbl
GO::Handlers::text_html
GO::Handlers::xsl_base
GO::IO::Analysis
preliminary analysis object
GO::IO::Blast
Gene Ontology Blast Reports DEPRECATED
GO::Model::Graph
a collection of relationships over terms
GO::Model::GraphNodeInstance
a graph node located in a tree
GO::Model::Relationship
GO::Model::Root
GO::Model::Term
a term or concept in an ontology
GO::ObjFactory
GO Object Factory
GO::Parser
parses all GO files formats and types
GO::Parsers::ParserEventNames
exports constants corresponding to XML
GO::Parsers::base_parser
base class for parsers
GO::Parsers::go_assoc_parser
syntax parsing of GO gene-association flat files
GO::Parsers::go_def_parser
syntax parsing of GO .def flat files
GO::Parsers::go_ont_parser
syntax parsing of GO .ontology flat files
GO::Parsers::go_xref_parser
syntax parsing of GO xref flat files (eg eg2go, metacyc2go)
GO::Parsers::locuslink_parser
GO::Parsers::mesh_parser
Parses Mesh ascii text files
GO::Parsers::mgi_assoc_parser
parses MGI gene assoc stanza files
GO::Parsers::ncbi_taxon_names_parser
OBO Flat file parser object
GO::Parsers::ncbi_taxonomy_parser
GO::Parsers::obj_emitter
GO::Parsers::obo_text_parser
OBO Flat file parser object
GO::Parsers::obo_xml_parser
Parses xml made from events
GO::Parsers::owl_parser
turns OWL XML into event stream
GO::Parsers::unknown_format_parser
base class for parsers

Provides

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

Other files