NOTICE: ** You do not have BioPerl installed ** BioPerl and Digest::MD5 are required if you wish to install AmiGO. They are also required for some applications involving sequences. If you don't care about these, then you can ignore this message. If you do care about these, you can still ignore this message for now and install both BioPerl and Digest::MD5 later on Checking if your kit is complete... Looks good Writing Makefile for GO cp GO/Model/Modification.pm blib/lib/GO/Model/Modification.pm cp GO/xsl/oboxml_to_owl.xsl blib/lib/GO/xsl/oboxml_to_owl.xsl cp GO/Parsers/obj_emitter.pm blib/lib/GO/Parsers/obj_emitter.pm cp GO/Model/GraphIterator.pm blib/lib/GO/Model/GraphIterator.pm cp GO/Model/TreeIterator.pm blib/lib/GO/Model/TreeIterator.pm cp GO/Model/Association.pm blib/lib/GO/Model/Association.pm cp GO/Handlers/lexanalysis2sql.pm blib/lib/GO/Handlers/lexanalysis2sql.pm cp GO/Parsers/generic_tagval_parser.pm blib/lib/GO/Parsers/generic_tagval_parser.pm cp GO/Parsers/mgi_assoc_parser.pm blib/lib/GO/Parsers/mgi_assoc_parser.pm cp GO/IO/Blast.pm blib/lib/GO/IO/Blast.pm cp GO/Handlers/obj_storable.pm blib/lib/GO/Handlers/obj_storable.pm cp go-perl.pod blib/lib/go-perl.pod cp GO/Model/DB.pm blib/lib/GO/Model/DB.pm cp GO/Parser.pm blib/lib/GO/Parser.pm cp GO/Model/GeneProduct.pm blib/lib/GO/Model/GeneProduct.pm cp GO/Handlers/obj_yaml.pm blib/lib/GO/Handlers/obj_yaml.pm cp GO/Parsers/go_def_parser.pm blib/lib/GO/Parsers/go_def_parser.pm cp GO/Parsers/obo_text_parser.pm blib/lib/GO/Parsers/obo_text_parser.pm cp GO/Model/Root.pm blib/lib/GO/Model/Root.pm cp GO/xsl/chadoxml_to_oboxml.xsl blib/lib/GO/xsl/chadoxml_to_oboxml.xsl cp GO/xsl/oboxml_filter.xsl blib/lib/GO/xsl/oboxml_filter.xsl cp GO/Handlers/obo.pm blib/lib/GO/Handlers/obo.pm cp GO/Parsers/obj_yaml_parser.pm blib/lib/GO/Parsers/obj_yaml_parser.pm cp GO/xsl/owl_to_oboxml.xsl blib/lib/GO/xsl/owl_to_oboxml.xsl cp GO/Handlers/lexanalysis.pm blib/lib/GO/Handlers/lexanalysis.pm cp GO/Handlers/go_xref.pm blib/lib/GO/Handlers/go_xref.pm cp GO/xsl/oboxml_to_chadoxml.xsl blib/lib/GO/xsl/oboxml_to_chadoxml.xsl cp GO/Parsers/mesh_parser.pm blib/lib/GO/Parsers/mesh_parser.pm cp GO/Parsers/go_xref_parser.pm blib/lib/GO/Parsers/go_xref_parser.pm cp GO/Parsers/obj_storable_parser.pm blib/lib/GO/Parsers/obj_storable_parser.pm cp GO/Handlers/obo_text.pm blib/lib/GO/Handlers/obo_text.pm cp GO/Handlers/sxpr.pm blib/lib/GO/Handlers/sxpr.pm cp GO/Model/Relationship.pm blib/lib/GO/Model/Relationship.pm cp GO/Handlers/obo_godb_flat.pm blib/lib/GO/Handlers/obo_godb_flat.pm cp GO/Parsers/refgenomes_parser.pm blib/lib/GO/Parsers/refgenomes_parser.pm cp GO/IO/XML.pm blib/lib/GO/IO/XML.pm cp GO/xsl/oboxml_to_godb_prestore.xsl blib/lib/GO/xsl/oboxml_to_godb_prestore.xsl cp GO/Model/Ontology.pm blib/lib/GO/Model/Ontology.pm cp GO/Handlers/abstract_prolog_writer.pm blib/lib/GO/Handlers/abstract_prolog_writer.pm cp GO/Model/CrossProduct.pm blib/lib/GO/Model/CrossProduct.pm cp GO/Parsers/go_ids_parser.pm blib/lib/GO/Parsers/go_ids_parser.pm cp GO/IO/Analysis.pm blib/lib/GO/IO/Analysis.pm cp GO/Model/GraphNodeInstance.pm blib/lib/GO/Model/GraphNodeInstance.pm cp GO/IO/Dotty.pm blib/lib/GO/IO/Dotty.pm cp GO/Model/Restriction.pm blib/lib/GO/Model/Restriction.pm cp GO/Handlers/obo_html.pm blib/lib/GO/Handlers/obo_html.pm cp GO/Handlers/owl_to_obo_text.pm blib/lib/GO/Handlers/owl_to_obo_text.pm cp GO/Basic.pm blib/lib/GO/Basic.pm cp GO/Handlers/godb_prestore.pm blib/lib/GO/Handlers/godb_prestore.pm cp GO/Parsers/go_assoc_parser.pm blib/lib/GO/Parsers/go_assoc_parser.pm cp GO/Model/Evidence.pm blib/lib/GO/Model/Evidence.pm cp GO/Parsers/obo_xml_parser.pm blib/lib/GO/Parsers/obo_xml_parser.pm cp GO/Parsers/ncbi_taxonomy_parser.pm blib/lib/GO/Parsers/ncbi_taxonomy_parser.pm cp GO/Handlers/obj.pm blib/lib/GO/Handlers/obj.pm cp GO/xsl/oboxml_to_racer.xsl blib/lib/GO/xsl/oboxml_to_racer.xsl cp GO/Model/Property.pm blib/lib/GO/Model/Property.pm cp GO/Model/Xref.pm blib/lib/GO/Model/Xref.pm cp GO/Handlers/base.pm blib/lib/GO/Handlers/base.pm cp GO/xsl/oboxml_to_obotext.xsl blib/lib/GO/xsl/oboxml_to_obotext.xsl cp GO/xsl/oboxml_to_simple_owl.xsl blib/lib/GO/xsl/oboxml_to_simple_owl.xsl cp GO/Parsers/references_parser.pm blib/lib/GO/Parsers/references_parser.pm cp GO/Handlers/go_def.pm blib/lib/GO/Handlers/go_def.pm cp GO/Handlers/tbl.pm blib/lib/GO/Handlers/tbl.pm cp GO/Handlers/prolog.pm blib/lib/GO/Handlers/prolog.pm cp GO/Model/LogicalDefinition.pm blib/lib/GO/Model/LogicalDefinition.pm cp GO/ObjFactory.pm blib/lib/GO/ObjFactory.pm cp GO/Utils.pm blib/lib/GO/Utils.pm cp GO/IO/go_assoc.pm blib/lib/GO/IO/go_assoc.pm cp GO/Handlers/text_html.pm blib/lib/GO/Handlers/text_html.pm cp GO/Parsers/xrf_abbs_parser.pm blib/lib/GO/Parsers/xrf_abbs_parser.pm cp GO/Handlers/go_ont.pm blib/lib/GO/Handlers/go_ont.pm cp GO/Handlers/obo_xml.pm blib/lib/GO/Handlers/obo_xml.pm cp GO/Model/Graph.pm blib/lib/GO/Model/Graph.pm cp GO/Model/Term.pm blib/lib/GO/Model/Term.pm cp GO/Parsers/ParserEventNames.pm blib/lib/GO/Parsers/ParserEventNames.pm cp GO/Model/Path.pm blib/lib/GO/Model/Path.pm cp GO/Handlers/xml.pm blib/lib/GO/Handlers/xml.pm cp GO/Handlers/summary.pm blib/lib/GO/Handlers/summary.pm cp GO/IO/ObanOwl.pm blib/lib/GO/IO/ObanOwl.pm cp GO/Model/Species.pm blib/lib/GO/Model/Species.pm cp GO/xsl/ipr_to_oboxml.xsl blib/lib/GO/xsl/ipr_to_oboxml.xsl cp GO/xsl/oboxml_to_dig.xsl blib/lib/GO/xsl/oboxml_to_dig.xsl cp GO/Model/Seq.pm blib/lib/GO/Model/Seq.pm cp GO/Parsers/unknown_format_parser.pm blib/lib/GO/Parsers/unknown_format_parser.pm cp GO/Handlers/obo_sxpr.pm blib/lib/GO/Handlers/obo_sxpr.pm cp GO/IO/RDFXML.pm blib/lib/GO/IO/RDFXML.pm cp GO/Parsers/go_ont_parser.pm blib/lib/GO/Parsers/go_ont_parser.pm cp GO/Handlers/pathlist.pm blib/lib/GO/Handlers/pathlist.pm cp GO/Parsers/ncbi_taxon_names_parser.pm blib/lib/GO/Parsers/ncbi_taxon_names_parser.pm cp GO/Handlers/abstract_sql_writer.pm blib/lib/GO/Handlers/abstract_sql_writer.pm cp GO/IO/OBDXML.pm blib/lib/GO/IO/OBDXML.pm cp GO/Handlers/rdf.pm blib/lib/GO/Handlers/rdf.pm cp GO/ObjCache.pm blib/lib/GO/ObjCache.pm cp GO/Handlers/xsl_base.pm blib/lib/GO/Handlers/xsl_base.pm cp GO/Parsers/owl_parser.pm blib/lib/GO/Parsers/owl_parser.pm cp GO/Parsers/base_parser.pm blib/lib/GO/Parsers/base_parser.pm cp GO/Parsers/locuslink_parser.pm blib/lib/GO/Parsers/locuslink_parser.pm cp GO/xsl/oboxml_to_summary_table.xsl blib/lib/GO/xsl/oboxml_to_summary_table.xsl cp GO/Handlers/owl.pm blib/lib/GO/Handlers/owl.pm cp GO/Parsers/obo_parser.pm blib/lib/GO/Parsers/obo_parser.pm cp GO/xsl/oboxml_to_obd_prestore.xsl blib/lib/GO/xsl/oboxml_to_obd_prestore.xsl cp scripts/go2pathlist blib/script/go2pathlist /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2pathlist cp scripts/go2godb_prestore blib/script/go2godb_prestore /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2godb_prestore cp scripts/go-show-paths-to-root.pl blib/script/go-show-paths-to-root.pl /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go-show-paths-to-root.pl cp scripts/go2chadoxml blib/script/go2chadoxml /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2chadoxml cp scripts/go2obo blib/script/go2obo /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2obo cp scripts/go-apply-xslt blib/script/go-apply-xslt /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go-apply-xslt cp scripts/go2summary blib/script/go2summary /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2summary cp scripts/go2rdf blib/script/go2rdf /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2rdf cp scripts/go-export-prolog.pl blib/script/go-export-prolog.pl /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go-export-prolog.pl cp scripts/go2error_report blib/script/go2error_report /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2error_report cp scripts/go2prolog blib/script/go2prolog /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2prolog cp scripts/go2text_html blib/script/go2text_html /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2text_html cp scripts/go2owl blib/script/go2owl /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2owl cp scripts/go-show-assocs-by-node.pl blib/script/go-show-assocs-by-node.pl /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go-show-assocs-by-node.pl cp scripts/go2obo_html blib/script/go2obo_html /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2obo_html cp scripts/go2sxpr blib/script/go2sxpr /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2sxpr cp scripts/go2obo_text blib/script/go2obo_text /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2obo_text cp scripts/go-dag-summary.pl blib/script/go-dag-summary.pl /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go-dag-summary.pl cp scripts/go2tbl blib/script/go2tbl /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2tbl cp scripts/go-export-graph.pl blib/script/go-export-graph.pl /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go-export-graph.pl cp scripts/go2rdfxml blib/script/go2rdfxml /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2rdfxml cp scripts/go2xml blib/script/go2xml /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2xml cp scripts/map2slim blib/script/map2slim /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/map2slim cp scripts/go-filter-subset.pl blib/script/go-filter-subset.pl /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go-filter-subset.pl cp scripts/go2fmt.pl blib/script/go2fmt.pl /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2fmt.pl cp scripts/go2obo_xml blib/script/go2obo_xml /export/home/cpanrun/build/5.6.1/bin/perl -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -MExtUtils::MakeMaker -e "MY->fixin(shift)" blib/script/go2obo_xml Manifying blib/man3/GO::Model::Modification.3 Manifying blib/man3/GO::Parsers::obj_emitter.3 Manifying blib/man3/GO::Model::GraphIterator.3 Manifying blib/man3/GO::Model::TreeIterator.3 Manifying blib/man3/GO::Model::Association.3 Manifying blib/man3/GO::Parsers::generic_tagval_parser.3 Manifying blib/man3/GO::Parsers::mgi_assoc_parser.3 Manifying blib/man3/GO::IO::Blast.3 Manifying blib/man3/go-perl.3 Manifying blib/man3/GO::Model::DB.3 Manifying blib/man3/GO::Parser.3 Manifying blib/man3/GO::Model::GeneProduct.3 Manifying blib/man3/GO::Parsers::go_def_parser.3 Manifying blib/man3/GO::Parsers::obo_text_parser.3 Manifying blib/man3/GO::Model::Root.3 Manifying blib/man1/go-filter-subset.pl.1 Manifying blib/man1/go2fmt.pl.1 Manifying blib/man3/GO::Handlers::go_xref.3 Manifying blib/man3/GO::Parsers::mesh_parser.3 Manifying blib/man3/GO::Parsers::go_xref_parser.3 Manifying blib/man3/GO::Handlers::obo_text.3 Manifying blib/man1/go-show-assocs-by-node.pl.1 Manifying blib/man3/GO::Handlers::obo_godb_flat.3 Manifying blib/man3/GO::Model::Relationship.3 Manifying blib/man3/GO::Parsers::refgenomes_parser.3 Manifying blib/man1/go-export-graph.pl.1 Manifying blib/man3/GO::Model::Ontology.3 Manifying blib/man3/GO::Model::CrossProduct.3 Manifying blib/man3/GO::Parsers::go_ids_parser.3 Manifying blib/man3/GO::IO::Analysis.3 Manifying blib/man3/GO::Model::GraphNodeInstance.3 Manifying blib/man3/GO::IO::Dotty.3 Manifying blib/man3/GO::Model::Restriction.3 Manifying blib/man3/GO::Handlers::obo_html.3 Manifying blib/man3/GO::Handlers::owl_to_obo_text.3 Manifying blib/man3/GO::Basic.3 Manifying blib/man3/GO::Handlers::godb_prestore.3 Manifying blib/man3/GO::Parsers::go_assoc_parser.3 Manifying blib/man3/GO::Model::Evidence.3 Manifying blib/man3/GO::Parsers::obo_xml_parser.3 Manifying blib/man3/GO::Parsers::ncbi_taxonomy_parser.3 Manifying blib/man3/GO::Handlers::obj.3 Manifying blib/man1/go-show-paths-to-root.pl.1 Manifying blib/man3/GO::Model::Property.3 Manifying blib/man3/GO::Model::Xref.3 Manifying blib/man3/GO::Handlers::base.3 Manifying blib/man3/GO::Parsers::references_parser.3 Manifying blib/man3/GO::Handlers::go_def.3 Manifying blib/man3/GO::Handlers::tbl.3 Manifying blib/man3/GO::Model::LogicalDefinition.3 Manifying blib/man3/GO::Utils.3 Manifying blib/man3/GO::ObjFactory.3 Manifying blib/man3/GO::Handlers::text_html.3 Manifying blib/man3/GO::IO::go_assoc.3 Manifying blib/man3/GO::Handlers::go_ont.3 Manifying blib/man3/GO::Parsers::xrf_abbs_parser.3 Manifying blib/man1/map2slim.1 Manifying blib/man3/GO::Model::Graph.3 Manifying blib/man3/GO::Parsers::ParserEventNames.3 Manifying blib/man3/GO::Model::Term.3 Manifying blib/man3/GO::Model::Path.3 Manifying blib/man3/GO::Handlers::summary.3 Manifying blib/man3/GO::IO::ObanOwl.3 Manifying blib/man3/GO::Model::Species.3 Manifying blib/man3/GO::Model::Seq.3 Manifying blib/man3/GO::Parsers::unknown_format_parser.3 Manifying blib/man3/GO::IO::RDFXML.3 Manifying blib/man3/GO::Parsers::go_ont_parser.3 Manifying blib/man3/GO::Parsers::ncbi_taxon_names_parser.3 Manifying blib/man3/GO::IO::OBDXML.3 Manifying blib/man3/GO::ObjCache.3 Manifying blib/man1/go-dag-summary.pl.1 Manifying blib/man3/GO::Handlers::xsl_base.3 Manifying blib/man3/GO::Parsers::owl_parser.3 Manifying blib/man3/GO::Parsers::base_parser.3 Manifying blib/man3/GO::Parsers::locuslink_parser.3 Manifying blib/man3/GO::Handlers::owl.3 PERL_DL_NONLAZY=1 /export/home/cpanrun/build/5.6.1/bin/perl -Iblib/arch -Iblib/lib -I/export/home/cpanrun/build/5.6.1/lib/5.6.1/sun4-solaris-thread-multi -I/export/home/cpanrun/build/5.6.1/lib/5.6.1 -e 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests @ARGV;' t/*.t t/t010build.........1..6 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok t/t020paths.........1..7 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok t/t030detecterror...1..4 ok 1 ok 2 '(error (message "\"synonym:krebs cycle\" doesn't look valid") (file "./t/data/test_bad_function.dat") (line " %high-potential iron-sulfur carrier ; synonym:krebs cycle" ) (line_no "6") (parse_class "GO::Parsers::go_ont_parser")) '(error (message "clash on GO:0015000; was 'obsolete' now 'not-polyferredoxin'" ) (file "./t/data/test_bad_function.dat") (line "%not-polyferredoxin ; GO:0015000") (line_no "8") (parse_class "GO::Parsers::go_ont_parser")) ok 3 '(error (message "\"synonym:krebs cycle\" doesn't look valid") (file "./t/data/test_bad_function.dat") (line " %high-potential iron-sulfur carrier ; synonym:krebs cycle" ) (line_no "6") (parse_class "GO::Parsers::go_ont_parser")) '(error (message "clash on GO:0015000; was 'obsolete' now 'not-polyferredoxin'" ) (file "./t/data/test_bad_function.dat") (line "%not-polyferredoxin ; GO:0015000") (line_no "8") (parse_class "GO::Parsers::go_ont_parser")) ok 4 ok t/t050oboformat.....1..6 ok 1 ok 2 ROOT: molecular_function ROOT: biological_process ROOT: cellular_component ok 3 ok 4 EDGE|GO:0000182|GO:0003677|is_a EDGE|GO:0008534|GO:0008578|is_a EDGE|GO:0008461|GO:0003824|is_a EDGE|GO:0007628|GO:0008344|is_a EDGE|GO:0007629|GO:0008344|is_a EDGE|GO:0008464|GO:0003824|is_a EDGE|GO:0000299|GO:0005624|is_a EDGE|GO:0003709|GO:0003700|is_a EDGE|GO:0003701|GO:0003700|is_a EDGE|GO:0003710|GO:0003700|is_a EDGE|GO:0003702|GO:0003700|is_a EDGE|GO:0003711|GO:0003700|is_a EDGE|GO:0003715|GO:0003700|is_a EDGE|GO:0003700|GO:0003677|is_a EDGE|GO:0003701|GO:0003700|is_a EDGE|GO:0003703|GO:0003702|is_a EDGE|GO:0003704|GO:0003702|is_a EDGE|GO:0003705|GO:0003702|is_a EDGE|GO:0003706|GO:0003702|is_a EDGE|GO:0003702|GO:0003700|is_a EDGE|GO:0003703|GO:0003702|is_a EDGE|GO:0004844|GO:0008578|is_a EDGE|GO:0008263|GO:0008578|is_a EDGE|GO:0003907|GO:0008578|is_a EDGE|GO:0008534|GO:0008578|is_a EDGE|GO:0008578|GO:0003824|is_a EDGE|GO:0003704|GO:0003702|is_a EDGE|GO:0003705|GO:0003702|is_a EDGE|GO:0003707|GO:0003706|is_a EDGE|GO:0003708|GO:0003706|is_a EDGE|GO:0003706|GO:0003702|is_a EDGE|GO:0003707|GO:0003706|is_a EDGE|GO:0003707|GO:0004879|is_a EDGE|GO:0003708|GO:0003706|is_a EDGE|GO:0003708|GO:0004879|is_a EDGE|GO:0003709|GO:0003700|is_a EDGE|GO:0000150|GO:0003690|is_a EDGE|GO:0003676|GO:0003674|is_a EDGE|GO:0003824|GO:0003674|is_a EDGE|GO:0003677|GO:0003676|is_a EDGE|GO:0003676|GO:0003674|is_a EDGE|GO:0008148|GO:0003711|is_a EDGE|GO:0003692|GO:0003677|is_a EDGE|GO:0003684|GO:0003677|is_a EDGE|GO:0003693|GO:0003677|is_a EDGE|GO:0003685|GO:0003677|is_a EDGE|GO:0003694|GO:0003677|is_a EDGE|GO:0003678|GO:0003677|is_a EDGE|GO:0000182|GO:0003677|is_a EDGE|GO:0003695|GO:0003677|is_a EDGE|GO:0003687|GO:0003677|is_a EDGE|GO:0003696|GO:0003677|is_a EDGE|GO:0003697|GO:0003677|is_a EDGE|GO:0003700|GO:0003677|is_a EDGE|GO:0003720|GO:0003677|is_a EDGE|GO:0008301|GO:0003677|is_a EDGE|GO:0003680|GO:0003677|is_a EDGE|GO:0000217|GO:0003677|is_a EDGE|GO:0003681|GO:0003677|is_a EDGE|GO:0003682|GO:0003677|is_a EDGE|GO:0003690|GO:0003677|is_a EDGE|GO:0003677|GO:0003676|is_a EDGE|GO:0007636|GO:0007630|is_a EDGE|GO:0007630|GO:0008344|is_a EDGE|GO:0003678|GO:0003677|is_a EDGE|GO:0003678|GO:0004386|is_a EDGE|GO:0005624|GO:0000267|is_a EDGE|GO:0005626|GO:0000267|is_a EDGE|GO:0000267|GO:0005623|part_of EDGE|GO:0007636|GO:0007630|is_a EDGE|GO:0007636|GO:0007635|is_a EDGE|GO:0003710|GO:0003700|is_a EDGE|GO:0008148|GO:0003711|is_a EDGE|GO:0008159|GO:0003711|is_a EDGE|GO:0003711|GO:0003700|is_a EDGE|GO:0008111|GO:0003824|is_a EDGE|GO:0048148|GO:0042220|is_a EDGE|GO:0048148|GO:0030534|is_a EDGE|GO:0048149|GO:0045471|is_a EDGE|GO:0048149|GO:0030534|is_a EDGE|GO:0008343|GO:0030534|is_a EDGE|GO:0008344|GO:0030534|is_a EDGE|GO:0048148|GO:0030534|is_a EDGE|GO:0048149|GO:0030534|is_a EDGE|GO:0048150|GO:0030534|is_a EDGE|GO:0030534|GO:0007610|is_a EDGE|GO:0003717|GO:0003715|is_a EDGE|GO:0003718|GO:0003715|is_a EDGE|GO:0003716|GO:0003715|is_a EDGE|GO:0003715|GO:0003700|is_a EDGE|GO:0043025|GO:0005623|part_of EDGE|GO:0003716|GO:0003715|is_a EDGE|GO:0003717|GO:0003715|is_a EDGE|GO:0003718|GO:0003715|is_a EDGE|GO:0003839|GO:0003824|is_a EDGE|GO:0008416|GO:0003824|is_a EDGE|GO:0003686|GO:0003824|is_a EDGE|GO:0008336|GO:0003824|is_a EDGE|GO:0008461|GO:0003824|is_a EDGE|GO:0008464|GO:0003824|is_a EDGE|GO:0008456|GO:0003824|is_a EDGE|GO:0008488|GO:0003824|is_a EDGE|GO:0008578|GO:0003824|is_a EDGE|GO:0008111|GO:0003824|is_a EDGE|GO:0003904|GO:0003824|is_a EDGE|GO:0003905|GO:0003824|is_a EDGE|GO:0003832|GO:0003824|is_a EDGE|GO:0003840|GO:0003824|is_a EDGE|GO:0003906|GO:0003824|is_a EDGE|GO:0003833|GO:0003824|is_a EDGE|GO:0003825|GO:0003824|is_a EDGE|GO:0003834|GO:0003824|is_a EDGE|GO:0003826|GO:0003824|is_a EDGE|GO:0003908|GO:0003824|is_a EDGE|GO:0003837|GO:0003824|is_a EDGE|GO:0003824|GO:0003674|is_a EDGE|GO:0007610|GO:0008150|is_a EDGE|GO:0003825|GO:0003824|is_a EDGE|GO:0003826|GO:0003824|is_a EDGE|GO:0003680|GO:0003677|is_a EDGE|GO:0003681|GO:0003677|is_a EDGE|GO:0003683|GO:0003682|is_a EDGE|GO:0003682|GO:0003677|is_a EDGE|GO:0003683|GO:0003682|is_a EDGE|GO:0003684|GO:0003677|is_a EDGE|GO:0003686|GO:0003685|is_a EDGE|GO:0003685|GO:0003677|is_a EDGE|GO:0004844|GO:0003686|is_a EDGE|GO:0004844|GO:0008578|is_a EDGE|GO:0004844|GO:0003686|is_a EDGE|GO:0008263|GO:0003686|is_a EDGE|GO:0003907|GO:0003686|is_a EDGE|GO:0003686|GO:0003685|is_a EDGE|GO:0003686|GO:0003824|is_a EDGE|GO:0008263|GO:0003686|is_a EDGE|GO:0008263|GO:0008578|is_a EDGE|GO:0003688|GO:0003687|is_a EDGE|GO:0003689|GO:0003687|is_a EDGE|GO:0003687|GO:0003677|is_a EDGE|GO:0008336|GO:0003824|is_a EDGE|GO:0005623|GO:0005575|is_a EDGE|GO:0003688|GO:0003687|is_a EDGE|GO:0008159|GO:0003711|is_a EDGE|GO:0003689|GO:0003687|is_a EDGE|GO:0005935|GO:0005933|part_of EDGE|GO:0005934|GO:0005933|part_of EDGE|GO:0005933|GO:0005623|part_of EDGE|GO:0000133|GO:0005934|part_of EDGE|GO:0005934|GO:0000134|is_a EDGE|GO:0005934|GO:0005933|part_of EDGE|GO:0000133|GO:0005935|part_of EDGE|GO:0000142|GO:0005935|part_of EDGE|GO:0005935|GO:0000134|is_a EDGE|GO:0005935|GO:0005933|part_of EDGE|GO:0048150|GO:0045472|is_a EDGE|GO:0048150|GO:0030534|is_a EDGE|GO:0008488|GO:0003824|is_a EDGE|GO:0003721|GO:0003720|is_a EDGE|GO:0003691|GO:0003720|is_a EDGE|GO:0003720|GO:0003677|is_a EDGE|GO:0003721|GO:0003720|is_a EDGE|GO:0003721|GO:0003964|is_a EDGE|GO:0008301|GO:0003677|is_a EDGE|GO:0003904|GO:0003824|is_a EDGE|GO:0003904|GO:0003913|is_a EDGE|GO:0000133|GO:0005935|part_of EDGE|GO:0000133|GO:0005938|part_of EDGE|GO:0000133|GO:0005934|part_of EDGE|GO:0003832|GO:0003824|is_a EDGE|GO:0003905|GO:0003824|is_a EDGE|GO:0003833|GO:0003824|is_a EDGE|GO:0003906|GO:0003824|is_a EDGE|GO:0003907|GO:0003686|is_a EDGE|GO:0003907|GO:0008578|is_a EDGE|GO:0003834|GO:0003824|is_a EDGE|GO:0003908|GO:0008172|is_a EDGE|GO:0003908|GO:0003824|is_a EDGE|GO:0001662|GO:0007610|is_a EDGE|GO:0030534|GO:0007610|is_a EDGE|GO:0007610|GO:0008150|is_a EDGE|GO:0000150|GO:0003690|is_a EDGE|GO:0003691|GO:0003690|is_a EDGE|GO:0003690|GO:0003677|is_a EDGE|GO:0003691|GO:0003720|is_a EDGE|GO:0003691|GO:0003690|is_a EDGE|GO:0003837|GO:0003824|is_a EDGE|GO:0003692|GO:0003677|is_a EDGE|GO:0003693|GO:0003677|is_a EDGE|GO:0003839|GO:0003824|is_a EDGE|GO:0008343|GO:0007631|is_a EDGE|GO:0008343|GO:0030534|is_a EDGE|GO:0003694|GO:0003677|is_a EDGE|GO:0008416|GO:0003824|is_a EDGE|GO:0007628|GO:0008344|is_a EDGE|GO:0007629|GO:0008344|is_a EDGE|GO:0007630|GO:0008344|is_a EDGE|GO:0008344|GO:0030534|is_a EDGE|GO:0008344|GO:0007626|is_a EDGE|GO:0003695|GO:0003677|is_a EDGE|GO:0003696|GO:0003677|is_a EDGE|GO:0003697|GO:0003677|is_a EDGE|GO:0008456|GO:0003824|is_a EDGE|GO:0001662|GO:0042596|is_a EDGE|GO:0001662|GO:0007610|is_a EDGE|GO:0003840|GO:0003824|is_a EDGE|GO:0000144|GO:0000142|part_of EDGE|GO:0000142|GO:0005935|part_of EDGE|GO:0000142|GO:0030480|is_a EDGE|GO:0005933|GO:0005623|part_of EDGE|GO:0000267|GO:0005623|part_of EDGE|GO:0043025|GO:0005623|part_of EDGE|GO:0005623|GO:0005575|is_a EDGE|GO:0000299|GO:0005624|is_a EDGE|GO:0005624|GO:0000267|is_a EDGE|GO:0000144|GO:0030481|is_a EDGE|GO:0000144|GO:0000142|part_of EDGE|GO:0000217|GO:0003677|is_a EDGE|GO:0005626|GO:0000267|is_a total parent rels:118 total (both ways):218 ok 5 ok 6 ok t/t060oboformat2....1..36 ok 1 Parsing: ./t/data/go-truncated.obo ok 2 ROOT: 1-phosphatidylinositol-4-phosphate kinase ROOT: spermidine catabolism to deoxyhypusine, using deoxyhypusine synthase ROOT: root ROOT: Part of TERMS: 29 SYNS:behavioral response to drought|behavioral response to thirst DEFXREFS:GO:jl EDGE|GO:0042630|GO:0009414|is_a EDGE|GO:0042630|GO:0007610|is_a DEFXREFS:GO:jic|ISBN:0198606907 EDGE|GO:0007636|GO:0007630|is_a EDGE|GO:0007630|GO:0008344|is_a DEFXREFS:GO:mah EDGE|GO:0008343|GO:0007631|is_a EDGE|GO:0008343|GO:0030534|is_a SYNS:drinking|eating DEFXREFS:GO:mah EDGE|GO:0042595|GO:0007631|is_a EDGE|GO:0008343|GO:0007631|is_a EDGE|GO:0042755|GO:0007631|is_a EDGE|GO:0042756|GO:0007631|is_a EDGE|GO:0007631|GO:0007610|is_a DEFXREFS:GO:ai EDGE|GO:0007628|GO:0008344|is_a EDGE|GO:0007629|GO:0008344|is_a EDGE|GO:0007630|GO:0008344|is_a EDGE|GO:0008344|GO:0030534|is_a EDGE|GO:0008344|GO:0007626|is_a DEFXREFS:GO:curators EDGE|GO:0007636|GO:0007635|is_a EDGE|GO:0007637|GO:0007635|is_a EDGE|GO:0042048|GO:0007635|is_a EDGE|GO:0007635|GO:0007610|is_a DEFXREFS:ISBN:0198506732|FB:bf EDGE|GO:0035095|GO:0030534|is_a EDGE|GO:0035095|GO:0035094|is_a DEFXREFS:GO:jic EDGE|GO:0007636|GO:0007630|is_a EDGE|GO:0007636|GO:0007635|is_a DEFXREFS:GO:jic|ISBN:0198606907 EDGE|GO:0007628|GO:0008344|is_a DEFXREFS:GO:jic|FBrf:0044924|URL:http://fbserver.gen.cam.ac.uk EDGE|GO:0007637|GO:0007635|is_a DEFXREFS:GO:jic|ISBN:0198606907 EDGE|GO:0007629|GO:0008344|is_a DEFXREFS:ISBN:01928006X|GO:jl EDGE|GO:0043050|GO:0042755|is_a EDGE|GO:0042755|GO:0007631|is_a DEFXREFS:URL:http://cancerweb.ncl.ac.uk/|GO:jl EDGE|GO:0042756|GO:0007631|is_a DEFXREFS:GO:jic EDGE|GO:0048150|GO:0045472|is_a EDGE|GO:0048150|GO:0030534|is_a DEFXREFS:GO:curators EDGE|GO:0042595|GO:0007631|is_a EDGE|GO:0042595|GO:0042594|is_a SYNS:FAKE:0001|class I PI3K|fake synonym EXACT SYNS:fake synonym COMMENT:To update annotations, consider the molecular function term '1-phosphatidylinositol-4-phosphate 5-kinase activity ; GO:0016308'. DEFXREFS:GO:curators|EC:2.7.1.68 DEFXREFS:MGI:dph|MEDLINE:99119440 EDGE|GO:0001662|GO:0042596|is_a EDGE|GO:0001662|GO:0007610|is_a SYNS:[eIF-5A]-deoxyhypusine synthase|deoxyhypusine synthase|spermidine dehydrogenase XREFS:EC:2.5.1.46|MetaCyc:2.5.1.46-RXN COMMENT:Note that this reaction is catalyzed by a single enzyme but since it has multiple steps, it appears in the process ontology. DEFXREFS:MetaCyc:1.1.1.249-RXN EDGE|GO:0050983|GO:0046203|is_a EDGE|GO:0008150|root|is_a DEFXREFS:GO:jic EDGE|GO:0048148|GO:0042220|is_a EDGE|GO:0048148|GO:0030534|is_a DEFXREFS:GO:mah|ISBN:0877797099 EDGE|GO:0035095|GO:0030534|is_a EDGE|GO:0008343|GO:0030534|is_a EDGE|GO:0008344|GO:0030534|is_a EDGE|GO:0048148|GO:0030534|is_a EDGE|GO:0048149|GO:0030534|is_a EDGE|GO:0048150|GO:0030534|is_a EDGE|GO:0030534|GO:0007610|is_a DEFXREFS:GO:jic EDGE|GO:0048149|GO:0045471|is_a EDGE|GO:0048149|GO:0030534|is_a SYNS:pumping behavior DEFXREFS:PMID:2181052|WB:cab EDGE|GO:0043051|GO:0043050|part_of EDGE|GO:0043050|GO:0042755|is_a DEFXREFS:WB:cab|PMID:2181052 EDGE|GO:0043051|GO:0043050|part_of DEFXREFS:GO:jic EDGE|GO:0042048|GO:0007635|is_a DEFXREFS:GO:jic|URL:http://cancerweb.ncl.ac.uk EDGE|GO:0048266|GO:0048265|is_a EDGE|GO:0048266|GO:0007610|is_a DEFXREFS:GO:curators EDGE|GO:0007610|GO:0008150|is_a EDGE|GO:0008150|root|is_a SYNS:behaviour DEFXREFS:WB:ems|ISBN:0395448956 EDGE|GO:0042630|GO:0007610|is_a EDGE|GO:0048266|GO:0007610|is_a EDGE|GO:0001662|GO:0007610|is_a EDGE|GO:0007631|GO:0007610|is_a EDGE|GO:0030534|GO:0007610|is_a EDGE|GO:0007635|GO:0007610|is_a EDGE|GO:0007610|GO:0008150|is_a total defs:27 total def xrefs:42 total xrefs:2 total comments:2 total syns:12 total EXACT syns:1 total obs:1 total parent rels:37 total (both ways):64 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ./t/data/go-truncated.obo from:obo_text to:obo_xml ok 13 Parsing: ./t/data/go-truncated.obo.obo_xml ok 14 ROOT: 1-phosphatidylinositol-4-phosphate kinase ROOT: spermidine catabolism to deoxyhypusine, using deoxyhypusine synthase ROOT: root ROOT: Part of TERMS: 29 SYNS:behavioral response to drought|behavioral response to thirst DEFXREFS:GO:jl EDGE|GO:0042630|GO:0009414|is_a EDGE|GO:0042630|GO:0007610|is_a DEFXREFS:GO:jic|ISBN:0198606907 EDGE|GO:0007636|GO:0007630|is_a EDGE|GO:0007630|GO:0008344|is_a DEFXREFS:GO:mah EDGE|GO:0008343|GO:0007631|is_a EDGE|GO:0008343|GO:0030534|is_a SYNS:drinking|eating DEFXREFS:GO:mah EDGE|GO:0042595|GO:0007631|is_a EDGE|GO:0008343|GO:0007631|is_a EDGE|GO:0042755|GO:0007631|is_a EDGE|GO:0042756|GO:0007631|is_a EDGE|GO:0007631|GO:0007610|is_a DEFXREFS:GO:ai EDGE|GO:0007628|GO:0008344|is_a EDGE|GO:0007629|GO:0008344|is_a EDGE|GO:0007630|GO:0008344|is_a EDGE|GO:0008344|GO:0030534|is_a EDGE|GO:0008344|GO:0007626|is_a DEFXREFS:GO:curators EDGE|GO:0007636|GO:0007635|is_a EDGE|GO:0007637|GO:0007635|is_a EDGE|GO:0042048|GO:0007635|is_a EDGE|GO:0007635|GO:0007610|is_a DEFXREFS:ISBN:0198506732|FB:bf EDGE|GO:0035095|GO:0030534|is_a EDGE|GO:0035095|GO:0035094|is_a DEFXREFS:GO:jic EDGE|GO:0007636|GO:0007630|is_a EDGE|GO:0007636|GO:0007635|is_a DEFXREFS:GO:jic|ISBN:0198606907 EDGE|GO:0007628|GO:0008344|is_a DEFXREFS:GO:jic|FBrf:0044924|URL:http://fbserver.gen.cam.ac.uk EDGE|GO:0007637|GO:0007635|is_a DEFXREFS:GO:jic|ISBN:0198606907 EDGE|GO:0007629|GO:0008344|is_a DEFXREFS:ISBN:01928006X|GO:jl EDGE|GO:0043050|GO:0042755|is_a EDGE|GO:0042755|GO:0007631|is_a DEFXREFS:URL:http://cancerweb.ncl.ac.uk/|GO:jl EDGE|GO:0042756|GO:0007631|is_a DEFXREFS:GO:jic EDGE|GO:0048150|GO:0045472|is_a EDGE|GO:0048150|GO:0030534|is_a DEFXREFS:GO:curators EDGE|GO:0042595|GO:0007631|is_a EDGE|GO:0042595|GO:0042594|is_a SYNS:FAKE:0001|class I PI3K|fake synonym EXACT SYNS:fake synonym COMMENT:To update annotations, consider the molecular function term '1-phosphatidylinositol-4-phosphate 5-kinase activity ; GO:0016308'. DEFXREFS:GO:curators|EC:2.7.1.68 DEFXREFS:MGI:dph|MEDLINE:99119440 EDGE|GO:0001662|GO:0042596|is_a EDGE|GO:0001662|GO:0007610|is_a SYNS:[eIF-5A]-deoxyhypusine synthase|deoxyhypusine synthase|spermidine dehydrogenase XREFS:EC:2.5.1.46|MetaCyc:2.5.1.46-RXN COMMENT:Note that this reaction is catalyzed by a single enzyme but since it has multiple steps, it appears in the process ontology. DEFXREFS:MetaCyc:1.1.1.249-RXN EDGE|GO:0050983|GO:0046203|is_a EDGE|GO:0008150|root|is_a DEFXREFS:GO:jic EDGE|GO:0048148|GO:0042220|is_a EDGE|GO:0048148|GO:0030534|is_a DEFXREFS:GO:mah|ISBN:0877797099 EDGE|GO:0035095|GO:0030534|is_a EDGE|GO:0008343|GO:0030534|is_a EDGE|GO:0008344|GO:0030534|is_a EDGE|GO:0048148|GO:0030534|is_a EDGE|GO:0048149|GO:0030534|is_a EDGE|GO:0048150|GO:0030534|is_a EDGE|GO:0030534|GO:0007610|is_a DEFXREFS:GO:jic EDGE|GO:0048149|GO:0045471|is_a EDGE|GO:0048149|GO:0030534|is_a SYNS:pumping behavior DEFXREFS:PMID:2181052|WB:cab EDGE|GO:0043051|GO:0043050|part_of EDGE|GO:0043050|GO:0042755|is_a DEFXREFS:WB:cab|PMID:2181052 EDGE|GO:0043051|GO:0043050|part_of DEFXREFS:GO:jic EDGE|GO:0042048|GO:0007635|is_a DEFXREFS:GO:jic|URL:http://cancerweb.ncl.ac.uk EDGE|GO:0048266|GO:0048265|is_a EDGE|GO:0048266|GO:0007610|is_a DEFXREFS:GO:curators EDGE|GO:0007610|GO:0008150|is_a EDGE|GO:0008150|root|is_a SYNS:behaviour DEFXREFS:WB:ems|ISBN:0395448956 EDGE|GO:0042630|GO:0007610|is_a EDGE|GO:0048266|GO:0007610|is_a EDGE|GO:0001662|GO:0007610|is_a EDGE|GO:0007631|GO:0007610|is_a EDGE|GO:0030534|GO:0007610|is_a EDGE|GO:0007635|GO:0007610|is_a EDGE|GO:0007610|GO:0008150|is_a total defs:27 total def xrefs:42 total xrefs:2 total comments:2 total syns:12 total EXACT syns:1 total obs:1 total parent rels:37 total (both ways):64 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ./t/data/go-truncated.obo.obo_xml from:obo_xml to:obo_text ok 25 Parsing: ./t/data/go-truncated.obo.obo_xml.obo_text ok 26 ROOT: 1-phosphatidylinositol-4-phosphate kinase ROOT: spermidine catabolism to deoxyhypusine, using deoxyhypusine synthase ROOT: root ROOT: Part of TERMS: 29 SYNS:behavioral response to drought|behavioral response to thirst DEFXREFS:GO:jl EDGE|GO:0042630|GO:0009414|is_a EDGE|GO:0042630|GO:0007610|is_a DEFXREFS:GO:jic|ISBN:0198606907 EDGE|GO:0007636|GO:0007630|is_a EDGE|GO:0007630|GO:0008344|is_a DEFXREFS:GO:mah EDGE|GO:0008343|GO:0007631|is_a EDGE|GO:0008343|GO:0030534|is_a SYNS:drinking|eating DEFXREFS:GO:mah EDGE|GO:0042595|GO:0007631|is_a EDGE|GO:0008343|GO:0007631|is_a EDGE|GO:0042755|GO:0007631|is_a EDGE|GO:0042756|GO:0007631|is_a EDGE|GO:0007631|GO:0007610|is_a DEFXREFS:GO:ai EDGE|GO:0007628|GO:0008344|is_a EDGE|GO:0007629|GO:0008344|is_a EDGE|GO:0007630|GO:0008344|is_a EDGE|GO:0008344|GO:0030534|is_a EDGE|GO:0008344|GO:0007626|is_a DEFXREFS:GO:curators EDGE|GO:0007636|GO:0007635|is_a EDGE|GO:0007637|GO:0007635|is_a EDGE|GO:0042048|GO:0007635|is_a EDGE|GO:0007635|GO:0007610|is_a DEFXREFS:ISBN:0198506732|FB:bf EDGE|GO:0035095|GO:0030534|is_a EDGE|GO:0035095|GO:0035094|is_a DEFXREFS:GO:jic EDGE|GO:0007636|GO:0007630|is_a EDGE|GO:0007636|GO:0007635|is_a DEFXREFS:GO:jic|ISBN:0198606907 EDGE|GO:0007628|GO:0008344|is_a DEFXREFS:GO:jic|FBrf:0044924|URL:http://fbserver.gen.cam.ac.uk EDGE|GO:0007637|GO:0007635|is_a DEFXREFS:GO:jic|ISBN:0198606907 EDGE|GO:0007629|GO:0008344|is_a DEFXREFS:ISBN:01928006X|GO:jl EDGE|GO:0043050|GO:0042755|is_a EDGE|GO:0042755|GO:0007631|is_a DEFXREFS:URL:http://cancerweb.ncl.ac.uk/|GO:jl EDGE|GO:0042756|GO:0007631|is_a DEFXREFS:GO:jic EDGE|GO:0048150|GO:0045472|is_a EDGE|GO:0048150|GO:0030534|is_a DEFXREFS:GO:curators EDGE|GO:0042595|GO:0007631|is_a EDGE|GO:0042595|GO:0042594|is_a SYNS:class I PI3K|FAKE:0001|fake synonym EXACT SYNS:fake synonym COMMENT:To update annotations, consider the molecular function term '1-phosphatidylinositol-4-phosphate 5-kinase activity ; GO:0016308'. DEFXREFS:GO:curators|EC:2.7.1.68 DEFXREFS:MGI:dph|MEDLINE:99119440 EDGE|GO:0001662|GO:0042596|is_a EDGE|GO:0001662|GO:0007610|is_a SYNS:[eIF-5A]-deoxyhypusine synthase|deoxyhypusine synthase|spermidine dehydrogenase XREFS:EC:2.5.1.46|MetaCyc:2.5.1.46-RXN COMMENT:Note that this reaction is catalyzed by a single enzyme but since it has multiple steps, it appears in the process ontology. DEFXREFS:MetaCyc:1.1.1.249-RXN EDGE|GO:0050983|GO:0046203|is_a EDGE|GO:0008150|root|is_a DEFXREFS:GO:jic EDGE|GO:0048148|GO:0042220|is_a EDGE|GO:0048148|GO:0030534|is_a DEFXREFS:GO:mah|ISBN:0877797099 EDGE|GO:0035095|GO:0030534|is_a EDGE|GO:0008343|GO:0030534|is_a EDGE|GO:0008344|GO:0030534|is_a EDGE|GO:0048148|GO:0030534|is_a EDGE|GO:0048149|GO:0030534|is_a EDGE|GO:0048150|GO:0030534|is_a EDGE|GO:0030534|GO:0007610|is_a DEFXREFS:GO:jic EDGE|GO:0048149|GO:0045471|is_a EDGE|GO:0048149|GO:0030534|is_a SYNS:pumping behavior DEFXREFS:PMID:2181052|WB:cab EDGE|GO:0043051|GO:0043050|part_of EDGE|GO:0043050|GO:0042755|is_a DEFXREFS:WB:cab|PMID:2181052 EDGE|GO:0043051|GO:0043050|part_of DEFXREFS:GO:jic EDGE|GO:0042048|GO:0007635|is_a DEFXREFS:GO:jic|URL:http://cancerweb.ncl.ac.uk EDGE|GO:0048266|GO:0048265|is_a EDGE|GO:0048266|GO:0007610|is_a DEFXREFS:GO:curators EDGE|GO:0007610|GO:0008150|is_a EDGE|GO:0008150|root|is_a SYNS:behaviour DEFXREFS:WB:ems|ISBN:0395448956 EDGE|GO:0042630|GO:0007610|is_a EDGE|GO:0048266|GO:0007610|is_a EDGE|GO:0001662|GO:0007610|is_a EDGE|GO:0007631|GO:0007610|is_a EDGE|GO:0030534|GO:0007610|is_a EDGE|GO:0007635|GO:0007610|is_a EDGE|GO:0007610|GO:0008150|is_a total defs:27 total def xrefs:42 total xrefs:2 total comments:2 total syns:12 total EXACT syns:1 total obs:1 total parent rels:37 total (both ways):64 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok t/t070parseannot2obj.1..5 ok 1 ok 2 TERM: GO:0003673 Gene_Ontology *DEEP: 86 TERM: GO:0008150 biological_process *DEEP: 52 TERM: GO:0007610 behavior *DEEP: 0 TERM: GO:0000004 biological_process unknown PROD: ziplock *DEEP: 1 TERM: GO:0007154 cell communication *DEEP: 3 TERM: GO:0008037 cell recognition *DEEP: 0 TERM: GO:0007267 cell-cell signaling *DEEP: 0 TERM: GO:0030383 host-pathogen interaction *DEEP: 0 TERM: GO:0009719 response to endogenous stimulus PROD: zip *DEEP: 1 TERM: GO:0009605 response to external stimulus *DEEP: 0 TERM: GO:0009628 response to abiotic stimulus *DEEP: 0 TERM: GO:0009607 response to biotic stimulus *DEEP: 0 TERM: GO:0007165 signal transduction PROD: zpg PROD: Zyx102EF *DEEP: 2 TERM: GO:0008151 cell growth and/or maintenance *DEEP: 18 TERM: GO:0007049 cell cycle PROD: zip PROD: zwilch *DEEP: 2 TERM: GO:0016049 cell growth *DEEP: 0 TERM: GO:0019725 cell homeostasis *DEEP: 0 TERM: GO:0016043 cell organization and biogenesis *DEEP: 3 TERM: GO:0007028 cytoplasm organization and biogenesis *DEEP: 3 TERM: GO:0006996 organelle organization and biogenesis *DEEP: 3 TERM: GO:0007010 cytoskeleton organization and biogenesis PROD: zip PROD: zip PROD: Zyx102EF *DEEP: 3 TERM: GO:0007005 mitochondrion organization and biogenesis *DEEP: 0 TERM: GO:0008283 cell proliferation PROD: zip *DEEP: 1 TERM: GO:0006943 chemi-mechanical coupling *DEEP: 0 TERM: GO:0008152 metabolism *DEEP: 10 TERM: GO:0006519 amino acid and derivative metabolism *DEEP: 0 TERM: GO:0009058 biosynthesis *DEEP: 0 TERM: GO:0005975 carbohydrate metabolism PROD: Zw *DEEP: 1 TERM: GO:0009056 catabolism PROD: Zw *DEEP: 1 TERM: GO:0006731 coenzymes and prosthetic group metabolism PROD: Zw *DEEP: 1 TERM: GO:0006118 electron transport *DEEP: 0 TERM: GO:0006091 energy pathways PROD: Zw *DEEP: 1 TERM: GO:0006629 lipid metabolism *DEEP: 0 TERM: GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism PROD: Zw *DEEP: 6 TERM: GO:0006259 DNA metabolism *DEEP: 0 TERM: GO:0006350 transcription PROD: zfh2 PROD: Zfrp8 PROD: Zn72D PROD: Zpr1 PROD: Zyx102EF *DEEP: 5 TERM: GO:0019538 protein metabolism *DEEP: 0 TERM: GO:0006412 protein biosynthesis *DEEP: 0 TERM: GO:0006464 protein modification *DEEP: 0 TERM: GO:0019748 secondary metabolism *DEEP: 0 TERM: GO:0006950 response to stress *DEEP: 0 TERM: GO:0006810 transport *DEEP: 2 TERM: GO:0006811 ion transport PROD: ZIP1 PROD: Zip3 *DEEP: 2 TERM: GO:0015031 protein transport *DEEP: 0 TERM: GO:0016265 death *DEEP: 2 TERM: GO:0008219 cell death PROD: Zfrp8 PROD: zip *DEEP: 2 TERM: GO:0007275 development PROD: zip *DEEP: 23 TERM: GO:0030154 cell differentiation PROD: zip *DEEP: 1 TERM: GO:0009790 embryonic development PROD: zip PROD: zip PROD: zip PROD: zip PROD: zip *DEEP: 5 TERM: GO:0040007 growth *DEEP: 0 TERM: GO:0009653 morphogenesis PROD: zfh2 PROD: zfh2 PROD: zip PROD: zip PROD: zip PROD: zip PROD: zip PROD: zip PROD: zip PROD: zip PROD: Zwim *DEEP: 11 TERM: GO:0040029 regulation of gene expression, epigenetic *DEEP: 0 TERM: GO:0000003 reproduction PROD: zip PROD: ziti PROD: zpg PROD: zpg PROD: zuc *DEEP: 5 TERM: GO:0007582 physiological processes PROD: zip PROD: zip PROD: zip PROD: zormin PROD: Zyx102EF *DEEP: 5 TERM: GO:0016032 viral life cycle *DEEP: 0 TERM: GO:0005575 cellular_component *DEEP: 13 TERM: GO:0005623 cell PROD: zpg *DEEP: 11 TERM: GO:0005622 intracellular *DEEP: 10 TERM: GO:0005694 chromosome *DEEP: 0 TERM: GO:0005929 cilium *DEEP: 0 TERM: GO:0005737 cytoplasm PROD: zip *DEEP: 4 TERM: GO:0000229 cytoplasmic chromosome *DEEP: 0 TERM: GO:0016023 cytoplasmic vesicle *DEEP: 0 TERM: GO:0005856 cytoskeleton PROD: zip PROD: zip PROD: Zyx102EF *DEEP: 3 TERM: GO:0005829 cytosol *DEEP: 0 TERM: GO:0005783 endoplasmic reticulum *DEEP: 0 TERM: GO:0005768 endosome *DEEP: 0 TERM: GO:0005794 Golgi apparatus *DEEP: 0 TERM: GO:0005811 lipid particle *DEEP: 0 TERM: GO:0005815 microtubule organizing center *DEEP: 0 TERM: GO:0005739 mitochondrion *DEEP: 0 TERM: GO:0005777 peroxisome *DEEP: 0 TERM: GO:0009536 plastid *DEEP: 0 TERM: GO:0005840 ribosome *DEEP: 0 TERM: GO:0005773 vacuole *DEEP: 0 TERM: GO:0005764 lysosome *DEEP: 0 TERM: GO:0005634 nucleus PROD: zfh2 PROD: zfh2 PROD: Zfrp8 *DEEP: 4 TERM: GO:0000228 nuclear chromosome *DEEP: 0 TERM: GO:0005635 nuclear membrane *DEEP: 0 TERM: GO:0005730 nucleolus PROD: Zpr1 *DEEP: 1 TERM: GO:0005654 nucleoplasm *DEEP: 0 TERM: GO:0005886 plasma membrane PROD: zpg PROD: zpg *DEEP: 2 TERM: GO:0009579 thylakoid *DEEP: 0 TERM: GO:0008372 cellular_component unknown PROD: ziplock PROD: ziti *DEEP: 2 TERM: GO:0030312 external encapsulating structure *DEEP: 0 TERM: GO:0030313 cell envelope *DEEP: 0 TERM: GO:0005618 cell wall *DEEP: 0 TERM: GO:0005576 extracellular *DEEP: 0 TERM: GO:0005578 extracellular matrix *DEEP: 0 TERM: GO:0005615 extracellular space *DEEP: 0 TERM: GO:0005941 unlocalized *DEEP: 0 TERM: GO:0003674 molecular_function *DEEP: 21 TERM: GO:0016209 antioxidant activity *DEEP: 0 TERM: GO:0016329 apoptosis regulator activity *DEEP: 0 TERM: GO:0005488 binding *DEEP: 6 TERM: GO:0005509 calcium ion binding *DEEP: 0 TERM: GO:0030246 carbohydrate binding *DEEP: 0 TERM: GO:0008289 lipid binding *DEEP: 0 TERM: GO:0003676 nucleic acid binding *DEEP: 5 TERM: GO:0003677 DNA binding PROD: zfh2 PROD: zfh2 PROD: Zfrp8 *DEEP: 4 TERM: GO:0003682 chromatin binding PROD: Zfrp8 *DEEP: 1 TERM: GO:0003700 transcription factor activity *DEEP: 0 TERM: GO:0004518 nuclease activity *DEEP: 0 TERM: GO:0003723 RNA binding PROD: Zn72D *DEEP: 1 TERM: GO:0008135 translation factor activity, nucleic acid binding *DEEP: 0 TERM: GO:0000166 nucleotide binding *DEEP: 0 TERM: GO:0019825 oxygen binding *DEEP: 0 TERM: GO:0005515 protein binding *DEEP: 1 TERM: GO:0008092 cytoskeletal protein binding PROD: zip *DEEP: 1 TERM: GO:0003779 actin binding *DEEP: 0 TERM: GO:0003824 catalytic activity PROD: Zw PROD: Zw *DEEP: 4 TERM: GO:0016787 hydrolase PROD: zip *DEEP: 1 TERM: GO:0008233 peptidase activity *DEEP: 0 TERM: GO:0004721 protein phosphatase activity *DEEP: 0 TERM: GO:0016301 kinase *DEEP: 1 TERM: GO:0004672 protein kinase activity PROD: Zwim *DEEP: 1 TERM: GO:0016740 transferase *DEEP: 0 TERM: GO:0005194 cell adhesion molecule activity *DEEP: 0 TERM: GO:0003754 chaperone activity *DEEP: 0 TERM: GO:0030188 chaperone regulator activity *DEEP: 0 TERM: GO:0003793 defense/immunity protein activity *DEEP: 0 TERM: GO:0030234 enzyme regulator activity *DEEP: 0 TERM: GO:0005554 molecular_function unknown PROD: ziplock PROD: ziti *DEEP: 2 TERM: GO:0003774 motor activity PROD: zip *DEEP: 1 TERM: GO:0045735 nutrient reservoir activity *DEEP: 0 TERM: GO:0017028 protein stabilization activity *DEEP: 0 TERM: GO:0008638 protein tagging activity *DEEP: 0 TERM: GO:0004871 signal transducer activity *DEEP: 0 TERM: GO:0004872 receptor activity *DEEP: 0 TERM: GO:0005102 receptor binding *DEEP: 0 TERM: GO:0005198 structural molecule activity PROD: zip PROD: zormin PROD: Zyx102EF *DEEP: 3 TERM: GO:0030528 transcription regulator activity PROD: zfh2 PROD: Zyx102EF *DEEP: 2 TERM: GO:0045182 translation regulator *DEEP: 0 TERM: GO:0005215 transporter activity PROD: ZIP1 PROD: Zip3 PROD: zpg *DEEP: 3 TERM: GO:0005489 electron transporter activity *DEEP: 0 TERM: GO:0005216 ion channel activity *DEEP: 0 TERM: GO:0005326 neurotransmitter transporter activity *DEEP: 0 TERM: GO:0030533 triplet codon-amino acid adaptor activity *DEEP: 0 TERM: part_of part_of *DEEP: 0 ok 3 ok 4 Type:gene Type:gene Type:gene Type:gene Type:gene Type:gene Type:gene Type:gene Type:gene Type:gene Type:gene Type:gene Type:gene Type:gene Type:gene Type:gene ok 5 ok t/t080gofmt2........1..3 ok 1 ok 2 '(term (id "GO:0003673") (name "Gene_Ontology") (is_root "1") (namespace "Gene_Ontology")) '(term (id "GO:0003674") (name "molecular_function") (namespace "molecular_function") (relationship (type "part_of") (to "GO:0003673"))) '(term (id "X:1") (name "zoo") (namespace "molecular_function") (is_a "GO:0003674")) '(term (id "X:2") (name "goo") (namespace "molecular_function") (relationship (type "inverse_of") (to "X:1"))) '(term (id "X;3") (name "poo") (namespace "molecular_function") (relationship (type "disjoint_from") (to "X:2"))) '(term (id "X:5") (name "ooh") (namespace "molecular_function") (relationship (type "star") (to "X;3"))) '(term (id "X:6") (name "moo") (namespace "molecular_function") (relationship (type "hash") (to "X:5"))) ok 3 ok t/t100roundtrip.....1..2 ok 1 # XML::Writer not installed ok 2 # XML::Writer not installed ok t/t110basic.........1..4 GO:0016604 GO:0016604 ok 1 PARENTS nucleoplasm ok 2 Gene_Ontology cell cellular_component intracellular nucleoplasm nucleus ok 3 GO:0005654 RENT complex chromatin remodeling complex chromatin silencing complex nuclear body nuclear speck ok 4 GO:0005654 ok t/t130relations.....1..7 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 OBO_REL:part_of ok 7 ok t/t140subgraph......1..1 $Gene_Ontology ; GO:0003673 %molecular_function ; GO:0003674 %nucleic acid binding ; GO:0003676 %DNA binding ; GO:0003677 %transcription factor ; GO:0003700 ; synonym:GO:0000130 ok 1 ok t/t150xref..........1..2 ok 1 ok 2 ok t/t160logicaldef....1..5 ok 1 ns: biological_process ok 2 ldef ns: foo ok 3 GO:0007626 OBOL:during FBdv:00005336 GO:0007626 ok 4 ok 5 ok t/t170chadoxml......1..9 ok 1 # XML::Writer not installed ok 2 # XML::Writer not installed ok 3 # XML::Writer not installed ok 4 # XML::Writer not installed ok 5 # XML::Writer not installed ok 6 # XML::Writer not installed ok 7 # XML::Writer not installed ok 8 # XML::Writer not installed ok 9 # XML::Writer not installed ok t/t180ncbi_taxonomy.1..4 ./t/data/sample.ncbi_taxonomy from:ncbi_taxonomy to:obo ok 1 ok 2 ok 3 Phenylobacterium immobile {test} ok 4 ok t/t200impliedlinks..1..2 ok 1 ok 2 ok t/t210cache.........1..6 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok t/t220xref_esc......1..6 ok 1 ok 2 ok 3 UM-BBD_pathwayID:2,4,5-t UM-BBD_pathwayID:2,4,5-t ok 4 ok 5 ok 6 ok t/t230term_expression.1..1 GO:1234 part_of CL:abc GO:1234 part_of CL:abc part_of AO:999 GO:1234 part_of CL:abc part_of AO:999 has_coordinate x:left GO:1234 results_in_output_of CHEBI:765 ^part_of CL:abc part_of AO:999 has_coordinate x:left ok 1 ok t/t240ga2obj........1..3 ok 1 ok 2 ok 3 ok All tests successful. Files=20, Tests=119, 55 wallclock secs (49.93 cusr + 3.91 csys = 53.84 CPU) Installing /export/home/cpanrun/build/5.6.1/lib/site_perl/5.6.1/go-perl.pod Installing /export/home/cpanrun/build/5.6.1/lib/site_perl/5.6.1/GO/Parser.pm Installing /export/home/cpanrun/build/5.6.1/lib/site_perl/5.6.1/GO/Basic.pm Installing /export/home/cpanrun/build/5.6.1/lib/site_perl/5.6.1/GO/ObjFactory.pm Installing /export/home/cpanrun/build/5.6.1/lib/site_perl/5.6.1/GO/Utils.pm Installing /export/home/cpanrun/build/5.6.1/lib/site_perl/5.6.1/GO/ObjCache.pm Installing /export/home/cpanrun/build/5.6.1/lib/site_perl/5.6.1/GO/IO/Blast.pm Installing /export/home/cpanrun/build/5.6.1/lib/site_perl/5.6.1/GO/IO/XML.pm Installing /export/home/cpanrun/build/5.6.1/lib/site_perl/5.6.1/GO/IO/Analysis.pm Installing /export/home/cpanrun/build/5.6.1/lib/site_perl/5.6.1/GO/IO/Dotty.pm Installing /export/home/cpanrun/build/5.6.1/lib/site_perl/5.6.1/GO/IO/go_assoc.pm Installing 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