id go_xp_regulation type logical_definitions title GO regulation logical definitions namespace GO_XP_REGULATION extends biological_process foundry NA status Draft download ftp://ftp.geneontology.org/pub/go/scratch/regulates_xp_live/go_reglive_withPosNeg_withPF.obo source home http://www.geneontology.org documentation http://wiki.geneontology.org/index.php/Regulation_cross-products contact Chris Mungall obo-crossproduct lists.sourceforge.net format obo description Logical definitions for GO Biological Regulation types - regulation of BP and MF. Auto-generated by oboedit2 semantic parser. These are high quality due to the consistency in term name syntax for regulation terms. Also includes inter-ontology links. Note for regulation of biological qualities you should see the obol page - http://www.berkeleybop.org/obol id bp_xp_cellular_component type logical_definitions title GO biological_process x cellular_component logical definitions namespace BP_XP_CC extends biological_process uses cellular_component uses relationship uses ro_proposed foundry NA status Draft download ftp://ftp.geneontology.org/pub/go/scratch/xps/biological_process_xp_cellular_component.obo source home http://www.geneontology.org documentation http://wiki.geneontology.org/index.php/XP:biological_process_xp_cellular_component contact go-editors go geneontology.org format obo description Logical definitions for GO Biological Processes using GO cellular component. These were sourced from auto-generated results, but then vetted manually. They may still be incomplete. The relations used may also change. These xps are internal to GO - no external OBO ontologies are used (with the exception of the OBO relation ontology and ro_proposed). Example: actin filament organization = organization and biogenesis THAT results_in_structural_change_to actin filament. id bp_xp_cell type logical_definitions title GO biological_process x cell logical definitions namespace BP_XP_CL extends biological_process uses cell uses relationship uses ro_proposed foundry NA status Draft download ftp://ftp.geneontology.org/pub/go/scratch/xps/biological_process_xp_cell.obo source home http://www.geneontology.org documentation http://wiki.geneontology.org/index.php/XP:biological_process_xp_cell contact go-editors go geneontology.org format obo description Logical definitions for GO Biological Processes using OBO-Cell. These were sourced from auto-generated results, but then vetted manually. They may still be incomplete. The relations used may also change. osteoblast differentiation = cell differentiation THAT results_in_acquisition_of_features_of osteoblast id go_xp_chebi type logical_definitions title GO x chemical entity logical definitions namespace go_to_chebi extends biological_process extends molecular_function uses chebi uses ro_ucdhsc uses relationship foundry NA status Draft download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/cross_products/go_chebi_xp/GO_to_ChEBI.obo source home documentation http://wiki.geneontology.org/index.php/XP:biological_process_xp_chebi contact Mike Bada mike.bada uchsc.edu format obo description Logical definitions for GO Biological Processes and CHEBI id ro_proposed type relations title Proposed new relations for RO namespace ro_proposed extends relationship foundry NA status Draft download ro_proposed|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro_proposed.obo source home documentation contact Chris Mungall cjm berkeleybop.org format obo description Relations under discussion. Candidates for inclusion in RO id ro_ucdhsc type relations title UCDHSC Relations namespace ro_ucdhsc extends relationship foundry NA status Draft download ro_ucdhsc|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/cross_products/go_chebi_xp/ro_ucdhsc.obo source home documentation contact Mike Bada mike.bada uchsc.edu format obo description Relations proposed by UCDHSC, potential RO inclusion candidates. Used in go_xp_chebi id plant_trait_xp type logical_definitions title plant_trait logical definitions namespace TO_XP extends plant_trait uses ro_proposed uses relationship uses quality uses po_anatomy uses chebi uses plant_environment uses biological_process foundry NA status Draft download plant_trait_xp.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/plant_traits/plant_trait_xp.obo source home Gramene Ontology database website|http://www.gramene.org/plant_ontology/ documentation http://www.bioontology.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating contact OBO phenotype group obo-phenotype lists.sourceforge.net format obo description plant_trait is an ontology of pre-composed phenotype terms specifically for plants. This mapping decomposes these phenotypes into constituent terms using PATO id mammalian_phenotype_xp type logical_definitions title mammalian_phenotype logical definitions namespace MP_XP extends mammalian_phenotype uses quality uses ro_proposed uses relationship uses adult_mouse_anatomy uses chebi uses cell uses biological_process uses cellular_component uses emap uses mouse_pathology foundry NA status Draft download mammalian_phenotype_xp.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mammalian_phenotype_xp.obo source home Mammalian Phenotype Browser|http://www.informatics.jax.org/searches/MP_form.shtml documentation http://www.bioontology.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating contact OBO phenotype group obo-phenotype lists.sourceforge.net format obo description mammalian_phenotype is an ontology of pre-composed phenotype terms for mouse/mammals. This mapping decomposes these phenotypes into constituent terms using PATO. This mapping is at the alpha stage - it has not yet been approved by MP curators id worm_phenotype_xp type logical_definitions title worm_phenotype logical definitions namespace WP_XP extends worm_phenotype uses quality uses ro_proposed uses relationship uses worm_anatomy uses worm_development uses chebi uses cell uses biological_process uses cellular_component foundry NA status Draft download worm_phenotype_xp.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype_xp.obo source home http://www.berkeleybop.org/obol documentation http://www.bioontology.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating contact OBO phenotype group obo-phenotype lists.sourceforge.net format obo description worm_phenotype is an ontology of pre-composed phenotype terms for C elegans. This mapping decomposes these phenotypes into constituent terms using PATO. This mapping is at the alpha stage - it has not yet been approved by WP curators id sequence_xp type logical_definitions title Sequence Ontology logical definitions namespace SO_XP extends sequence uses sequence foundry NA status Implementation release download so-xp.obo|http://song.cvs.sourceforge.net/*checkout*/song/ontology/so-xp.obo source http://song.cvs.sourceforge.net/*checkout*/song/ontology/so-xp.obo home SO home|http://song.sourceforge.net/ documentation contact SO developers song-devel lists.sourceforge.net format obo description Logical definitions (cross-products) for composite terms in SO. NOTE: these are now included in the main SO file. The so-xp file contains logical definitions WITHOUT implied links id ro_bfo_bridge type bridge title RO BFO domain and range constraints namespace OBO_REL_BFO_BRIDGE extends relationship uses bfo foundry NA status Draft download source http://www.obofoundry.org/ro/ro_bfo1-1_bridge.obo home OBO Relation Ontology|http://www.obofoundry.org/ro documentation contact Chris Mungall cjm fruitfly.org format obo description specifies which OBO relations can be used with which BFO types id quality_bfo_bridge type bridge title PATO BFO constraints namespace PATO_BFO_BRIDGE extends quality uses bfo foundry NA status Draft download quality_bfo_bridge.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality_bfo_bridge.obo source home documentation contact Chris Mungall cjm fruitfly.org format obo description Links upper level terms in PATO with BFO - eg quality of a continuant id caro_to_bfo type bridge title CARO to BFO is_a mappings namespace caro_to_bfo extends caro uses bfo foundry NA status Draft download caro_to_bfo.obo|http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro_to_bfo.obo source home documentation contact Chris Mungall cjm fruitfly.org format obo description CARO types are sub-types of more general BFO types; for example, cells are types of BFO:Object. This bridge file makes the is_a links explicit id bfo type ontology external yes title Basic Formal Ontology namespace bfo extends relationship uses bfo foundry NA status Implementation download bfo.owl|http://www.ifomis.org/bfo/1.0 source home BFO|http://www.ifomis.uni-saarland.de/bfo/ documentation contact BFO discuss bfo-discuss googlegroups.com format owl description The theory behind BFO has been developed and formulated by Barry Smith and Pierre Grenon in a series of publications. BFO grows out of a philosophical orientation which overlaps with that of DOLCE and SUMO. Unlike these, however, it is narrowly focused on the task of providing a genuine upper ontology which can be used in support of domain ontologies developed for scientific research, as for example in biomedicine within the framework of the OBO Foundry. Thus BFO does not contain physical, chemical, biological or other terms which would properly fall within the domain of the special sciences. BFO's current implementation in OWL has been developed by Holger Stenzhorn with contributions from Andrew Spear. id cog2go type mappings title cog2go mapping namespace COG2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/cog2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of cog2go to GO id ec2go type mappings title ec2go mapping namespace EC2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/ec2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of ec2go to GO id egad2go type mappings title egad2go mapping namespace EGAD2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/egad2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of egad2go to GO id genprotec2go type mappings title genprotec2go mapping namespace GENPROTECGO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/genprotec2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of genprotec2go to GO id hamap2go type mappings title hamap2go mapping namespace HAMAP2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/hamap2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of hamap2go to GO id interpro2go type mappings title interpro2go mapping namespace INTERPRO2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/interpro2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of interpro2go to GO id metacyc2go type mappings title metacyc2go mapping namespace METACYC2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/metacyc2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of metacyc2go to GO id mips2go type mappings title mips2go mapping namespace MIPS2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/mips2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of mips2go to GO id multifun2go type mappings title multifun2go mapping namespace MULTIFUN2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/multifun2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of multifun2go to GO id pfam2go type mappings title pfam2go mapping namespace PFAM2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/pfam2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of pfam2go to GO id prints2go type mappings title prints2go mapping namespace PRINTS2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/prints2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of prints2go to GO id prodom2go type mappings title prodom2go mapping namespace PRODOM2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/prodom2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of prodom2go to GO id prosite2go type mappings title prosite2go mapping namespace PROSITE2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/prosite2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of prosite2go to GO id reactome2go type mappings title reactome2go mapping namespace REACTOM2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/reactome2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of reactome2go to GO id rfam2go type mappings title rfam2go mapping namespace RFAMGO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/rfam2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of rfam2go to GO id smart2go type mappings title smart2go mapping namespace SMART2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/smart2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of smart2go to GO id spkw2go type mappings title spkw2go mapping namespace SPKW2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/spkw2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of spkw2go to GO id tigr2go type mappings title tigr2go mapping namespace TIGR2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/tigr2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of tigr2go to GO id tigrfams2go type mappings title tigrfams2go mapping namespace TIGRFAMS2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/tigrfams2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of tigrfams2go to GO id um-bbd_enzymeid2go type mappings title um-bbd_enzymeid2go mapping namespace UMBBDENZYMEID2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/um-bbd_enzymeid2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of um-bbd_enzymeid2go to GO id um-bbd_pathwayid2go type mappings title um-bbd_pathwayid2go mapping namespace UMBBDPATHWAYID2GO extends GO foundry NA status Implementation release download source ftp://ftp.geneontology.org/pub/go/external2go/um-bbd_pathwayid2go home GO|http://www.geneontology.org/ documentation contact Gene Ontology|go.org format go_xref description Mappings of um-bbd_pathwayid2go to GO