OBO Download Matrix
This page is for downloading OBO ontologies in a variety of formats, and for downloading reports from each of the ontologies. The data below is derived automatically from the primary sources, available from the main OBO website. This page is experimental. See below for caveats.
- Repository
- Documentation
Ontologies
| Ontology | ID Prefix | Files |
|---|---|---|
| AERO:Adverse Event Reporting Ontology | AERO | pro[45 kb md5] -- obo[25 kb md5] -- obo_xml[34 kb md5] -- owl[77 kb md5] -- tbl[12 kb md5] -- prolog[45 kb md5] -- obo.html[101 kb md5] -- |
| NIF_Cell:NIF Cell | NIF_Cell | pro[462 kb md5] -- obo[293 kb md5] -- obo_xml[536 kb md5] -- owl[460 kb md5] -- tbl[32 kb md5] -- prolog[462 kb md5] -- obo.html[1219 kb md5] -- |
| NIF_Dysfunction:NIF Dysfunction | NIF_Dysfunction | pro[106 kb md5] -- obo[56 kb md5] -- obo_xml[67 kb md5] -- owl[826 kb md5] -- tbl[19 kb md5] -- prolog[106 kb md5] -- obo.html[269 kb md5] -- |
| NIF_GrossAnatomy:NIF Gross Anatomy | NIF_GrossAnatomy | pro[754 kb md5] -- obo[496 kb md5] -- obo_xml[566 kb md5] -- owl[3030 kb md5] -- tbl[100 kb md5] -- prolog[754 kb md5] -- obo.html[2016 kb md5] -- |
| OGMS:Ontology for General Medical Science | OGMS | pro[25 kb md5] -- obo[17 kb md5] -- obo_xml[24 kb md5] -- owl[61 kb md5] -- tbl[11 kb md5] -- prolog[25 kb md5] -- obo.html[71 kb md5] -- |
| adult_mouse_anatomy:Mouse adult gross anatomy | MA | obo_xml[661 kb md5] -- obo[318 kb md5] -- owl[1439 kb md5] -- tbl[105 kb md5] -- prolog[754 kb md5] -- owl2[636 kb md5] -- |
| adverse_events:Ontology of Adverse Events | OAE | pro[647 kb md5] -- obo[345 kb md5] -- obo_xml[463 kb md5] -- owl[989 kb md5] -- tbl[149 kb md5] -- prolog[647 kb md5] -- obo.html[1415 kb md5] -- |
| aeo:Anatomical Entity Ontology | AEO | obo_xml[117 kb md5] -- obo[61 kb md5] -- owl[277 kb md5] -- tbl[30 kb md5] -- prolog[116 kb md5] -- owl2[0 kb md5] -- xref[6 kb md5] -- |
| amphibian_anatomy:Amphibian gross anatomy | AAO | obo_xml[680 kb md5] -- obo[368 kb md5] -- owl[1549 kb md5] -- tbl[173 kb md5] -- prolog[678 kb md5] -- owl2[779 kb md5] -- xref[29 kb md5] -- |
| amphibian_taxonomy:Amphibian taxonomy | ATO | Could not index: Source not available at specified URL as recognised format |
| animalhist:Animal natural history and life history | ADW | |
| ascomycete_phenotype:Ascomycete phenotype ontology | APO | obo_xml[138 kb md5] -- obo[83 kb md5] -- owl[317 kb md5] -- tbl[31 kb md5] -- prolog[173 kb md5] -- owl2[100 kb md5] -- xref[4 kb md5] -- |
| bfo:Basic Formal Ontology | BFO | pro[63 kb md5] -- obo[52 kb md5] -- obo_xml[74 kb md5] -- owl[44 kb md5] -- tbl[8 kb md5] -- prolog[63 kb md5] -- obo.html[151 kb md5] -- imports-local.obo[0 kb md5] -- imports-local.owl[4 kb md5] -- abduced-links.txt[0 kb md5] -- |
| bilateria_mrca:Bilateria anatomy | BILA | obo_xml[47 kb md5] -- obo[26 kb md5] -- owl[95 kb md5] -- tbl[10 kb md5] -- prolog[41 kb md5] -- stats[0 kb md5] -- owl2[39 kb md5] -- xref[2 kb md5] -- |
| biological_process:Biological process | GO | obo_xml[41151 kb md5] -- obo_xml[23397 kb md5] -- owl[50395 kb md5] -- tbl[7494 kb md5] -- prolog[26883 kb md5] -- owl2[0 kb md5] -- xref[1138 kb md5] -- |
| biological_process_prerelease:Biological process PRERELEASE | GO | obo_xml[41151 kb md5] -- obo[23842 kb md5] -- owl[89161 kb md5] -- tbl[11228 kb md5] -- prolog[46186 kb md5] -- owl2[0 kb md5] -- xref[2566 kb md5] -- |
| brenda:BRENDA tissue / enzyme source | BTO | obo_xml[2807 kb md5] -- obo[1772 kb md5] -- owl[6049 kb md5] -- tbl[792 kb md5] -- prolog[2783 kb md5] -- owl2[2823 kb md5] -- xref[293 kb md5] -- |
| caro:Common Anatomy Reference Ontology | CARO | obo_xml[22 kb md5] -- obo[12 kb md5] -- owl[68 kb md5] -- tbl[7 kb md5] -- prolog[21 kb md5] -- owl2[22 kb md5] -- xref[1 kb md5] -- |
| cdao:Comparative Data Analysis Ontology | CDAO | owl[133 kb md5] -- obo.html[0 kb md5] -- |
| cell:Cell type | CL | obo_xml[5242 kb md5] -- obo[2820 kb md5] -- tbl[925 kb md5] -- prolog[4940 kb md5] -- owl2[0 kb md5] -- xref[431 kb md5] -- |
| cell_prerelease:Cell type PRERELEASE | CL | obo_xml[5242 kb md5] -- obo[2820 kb md5] -- tbl[925 kb md5] -- prolog[4940 kb md5] -- owl2[0 kb md5] -- xref[431 kb md5] -- |
| cellular_component:Cellular component | GO | obo_xml[41151 kb md5] -- obo_xml[2348 kb md5] -- owl[5246 kb md5] -- tbl[775 kb md5] -- prolog[2340 kb md5] -- owl2[0 kb md5] -- xref[135 kb md5] -- |
| cereal_anatomy:Cereal Plant Gross Anatomy | GRO | obo_xml[1473 kb md5] -- obo[777 kb md5] -- owl[3231 kb md5] -- tbl[231 kb md5] -- prolog[1667 kb md5] -- owl2[0 kb md5] -- xref[56 kb md5] -- |
| chebi:Chemical entities of biological interest | CHEBI | obo_xml[61911 kb md5] -- obo[24082 kb md5] -- owl[138807 kb md5] -- tbl[12166 kb md5] -- prolog[91369 kb md5] -- owl2[0 kb md5] -- xref[1943 kb md5] -- |
| cheminf:Chemical Information Ontology | CHEMINF | pro[21 kb md5] -- obo[14 kb md5] -- obo_xml[22 kb md5] -- owl[110 kb md5] -- tbl[2 kb md5] -- prolog[21 kb md5] -- stats[0 kb md5] -- obo.html[55 kb md5] -- |
| clinical_measurement:Clinical measurement ontology | CMO | |
| cob:Protein covalent bond | RESID | |
| dendritic_cell:Dendritic cell | DC_CL | obo_xml[95 kb md5] -- obo[57 kb md5] -- owl[233 kb md5] -- tbl[12 kb md5] -- prolog[90 kb md5] -- stats[0 kb md5] -- owl2[104 kb md5] -- xref[4 kb md5] -- |
| dendritic_cell_prerelease:Dendritic cell PRERELEASE | DC_CL | obo_xml[95 kb md5] -- obo[57 kb md5] -- owl[233 kb md5] -- tbl[12 kb md5] -- prolog[90 kb md5] -- stats[0 kb md5] -- owl2[104 kb md5] -- |
| dictyostelium_discoideum_anatomy:Dictyostelium discoideum anatomy | DDANAT | obo_xml[113 kb md5] -- obo[60 kb md5] -- owl[273 kb md5] -- tbl[28 kb md5] -- prolog[110 kb md5] -- stats[0 kb md5] -- owl2[106 kb md5] -- xref[6 kb md5] -- |
| disease_ontology:Human disease ontology | DOID | obo_xml[9253 kb md5] -- obo[3713 kb md5] -- owl[24125 kb md5] -- tbl[1351 kb md5] -- prolog[9370 kb md5] -- owl2[3671 kb md5] -- xref[1069 kb md5] -- |
| emap:Mouse gross anatomy and development | EMAP | obo_xml[3236 kb md5] -- obo[1677 kb md5] -- owl[7369 kb md5] -- tbl[630 kb md5] -- prolog[3366 kb md5] -- stats[0 kb md5] -- owl2[3710 kb md5] -- |
| envo:Environment Ontology | ENVO | obo_xml[1044 kb md5] -- obo[451 kb md5] -- owl[2561 kb md5] -- tbl[211 kb md5] -- prolog[1034 kb md5] -- owl2[669 kb md5] -- xref[84 kb md5] -- |
| envo_prerelease:Environment Ontology PRERELEASE | ENVO | obo_xml[1044 kb md5] -- obo[451 kb md5] -- owl[2561 kb md5] -- tbl[211 kb md5] -- prolog[1034 kb md5] -- owl2[669 kb md5] -- xref[84 kb md5] -- |
| ero:eagle-i resource ontology | ERO | pro[1529 kb md5] -- obo[803 kb md5] -- obo_xml[1065 kb md5] -- owl[2783 kb md5] -- tbl[486 kb md5] -- prolog[1529 kb md5] -- obo.html[2897 kb md5] -- |
| event:Event (INOH pathway ontology) | IEV | obo_xml[2169 kb md5] -- obo[1226 kb md5] -- owl[5599 kb md5] -- tbl[380 kb md5] -- prolog[2079 kb md5] -- owl2[1290 kb md5] -- xref[239 kb md5] -- |
| evidence_code:Evidence codes | ECO | obo_xml[176 kb md5] -- obo[108 kb md5] -- owl[341 kb md5] -- tbl[45 kb md5] -- prolog[172 kb md5] -- owl2[0 kb md5] -- xref[5 kb md5] -- |
| evoc:eVOC (Expressed Sequence Annotation for Humans) | EV | obo_xml[170 kb md5] -- obo[69 kb md5] -- owl[353 kb md5] -- tbl[31 kb md5] -- prolog[204 kb md5] -- stats[0 kb md5] -- owl2[186 kb md5] -- |
| exo:Exposure ontology | ExO | obo[27 kb md5] -- |
| experimental_condition:Experimental condition ontology | XCO | |
| fix:Physico-chemical methods and properties | FIX | Could not index: Source not available at specified URL as recognised format |
| fly_anatomy:Drosophila gross anatomy | FBbt | obo_xml[5592 kb md5] -- obo[3257 kb md5] -- owl[12812 kb md5] -- tbl[1184 kb md5] -- prolog[5877 kb md5] -- owl2[0 kb md5] -- xref[320 kb md5] -- |
| fly_anatomy_prerelease:Drosophila gross anatomy PRERELEASE | FBbt | obo_xml[5592 kb md5] -- obo[3257 kb md5] -- owl[12812 kb md5] -- tbl[1184 kb md5] -- prolog[5877 kb md5] -- owl2[0 kb md5] -- xref[320 kb md5] -- |
| fly_development:Drosophila development | FBdv | obo_xml[114 kb md5] -- obo[67 kb md5] -- owl[268 kb md5] -- tbl[28 kb md5] -- prolog[112 kb md5] -- owl2[104 kb md5] -- xref[5 kb md5] -- |
| fly_taxonomy:Fly taxonomy | FBsp | obo_xml[1578 kb md5] -- obo[819 kb md5] -- owl[3159 kb md5] -- tbl[325 kb md5] -- prolog[2109 kb md5] -- stats[0 kb md5] -- owl2[1367 kb md5] -- xref[55 kb md5] -- |
| flybase_vocab:FlyBase Controlled Vocabulary | FBcv | obo_xml[374 kb md5] -- obo[242 kb md5] -- owl[771 kb md5] -- tbl[109 kb md5] -- prolog[399 kb md5] -- owl2[0 kb md5] -- xref[19 kb md5] -- |
| fma_lite:Foundational Model of Anatomy (subset) | FMA | obo_xml[21759 kb md5] -- obo[15337 kb md5] -- owl[45629 kb md5] -- tbl[5907 kb md5] -- prolog[28586 kb md5] -- stats[0 kb md5] -- owl2[22430 kb md5] -- |
| fma_lite_prerelease:Foundational Model of Anatomy (subset) PRERELEASE | FMA | obo_xml[21759 kb md5] -- obo[15337 kb md5] -- owl[45629 kb md5] -- tbl[5907 kb md5] -- prolog[28586 kb md5] -- owl2[22430 kb md5] -- |
| fungal_anatomy:Fungal gross anatomy | FAO | obo_xml[44 kb md5] -- obo[21 kb md5] -- owl[104 kb md5] -- tbl[12 kb md5] -- prolog[39 kb md5] -- owl2[41 kb md5] -- xref[3 kb md5] -- |
| fypo:Fission Yeast Phenotype Ontology | FYPO | obo_xml[1093 kb md5] -- obo[540 kb md5] -- owl[2497 kb md5] -- tbl[212 kb md5] -- prolog[1024 kb md5] -- owl2[0 kb md5] -- xref[29 kb md5] -- |
| gemina_symptom:Symptom Ontology | SYMP | obo_xml[311 kb md5] -- obo[165 kb md5] -- owl[706 kb md5] -- tbl[70 kb md5] -- prolog[325 kb md5] -- owl2[246 kb md5] -- xref[43 kb md5] -- |
| gene_regulation:Gene Regulation Ontology | BOOTStrep | pro[480 kb md5] -- obo[313 kb md5] -- obo_xml[413 kb md5] -- owl[418 kb md5] -- tbl[39 kb md5] -- prolog[480 kb md5] -- stats[0 kb md5] -- obo.html[1208 kb md5] -- |
| habronattus_courtship:Habronattus courtship | Could not index: Source not available at specified URL as recognised format | |
| homology_ontology:homology_ontology | HOM | obo_xml[63 kb md5] -- obo[32 kb md5] -- owl[138 kb md5] -- tbl[9 kb md5] -- prolog[52 kb md5] -- stats[0 kb md5] -- owl2[45 kb md5] -- xref[11 kb md5] -- |
| human-dev-anat-abstract:Human developmental anatomy, abstract version | EHDAA | obo_xml[521 kb md5] -- obo[215 kb md5] -- owl[1237 kb md5] -- tbl[65 kb md5] -- prolog[514 kb md5] -- stats[0 kb md5] -- owl2[474 kb md5] -- xref[1 kb md5] -- |
| human-dev-anat-abstract2:Human developmental anatomy, abstract version, v2 | EHDAA2 | obo_xml[1504 kb md5] -- obo[939 kb md5] -- owl[4061 kb md5] -- tbl[117 kb md5] -- prolog[1347 kb md5] -- owl2[2495 kb md5] -- xref[2 kb md5] -- |
| human-dev-anat-staged:Human developmental anatomy, timed version | EHDA | obo_xml[3235 kb md5] -- obo[1121 kb md5] -- owl[8902 kb md5] -- tbl[224 kb md5] -- prolog[2619 kb md5] -- stats[0 kb md5] -- owl2[1786 kb md5] -- xref[332 kb md5] -- |
| human_embryology_terminology:Terminology of Anatomy of Human Embryology | TAHE | Could not index: Source not available at specified URL as recognised format |
| human_histology_terminology:Terminology of Anatomy of Human Histology | TAHH | Could not index: Source not available at specified URL as recognised format |
| human_phenotype:human phenotype ontology | HP | obo_xml[4878 kb md5] -- obo[2981 kb md5] -- owl[9270 kb md5] -- tbl[1200 kb md5] -- prolog[5168 kb md5] -- owl2[0 kb md5] -- xref[244 kb md5] -- |
| hymenoptera_anatomy:Hymenoptera Anatomy Ontology | HAO | pro[1079 kb md5] -- obo[616 kb md5] -- obo_xml[1224 kb md5] -- owl[5120 kb md5] -- tbl[261 kb md5] -- prolog[1079 kb md5] -- obo.html[2559 kb md5] -- |
| image:Biological imaging methods | FBbi | obo_xml[155 kb md5] -- obo[96 kb md5] -- owl[258 kb md5] -- tbl[33 kb md5] -- prolog[153 kb md5] -- owl2[138 kb md5] -- xref[2 kb md5] -- |
| infectious_disease_ontology:Infectious disease | IDO | pro[186 kb md5] -- obo[134 kb md5] -- obo_xml[173 kb md5] -- owl[461 kb md5] -- tbl[60 kb md5] -- prolog[186 kb md5] -- obo.html[564 kb md5] -- |
| influenza_ontology:Influenza Ontology | FLU | pro[44 kb md5] -- obo[29 kb md5] -- obo_xml[44 kb md5] -- owl[124 kb md5] -- tbl[19 kb md5] -- prolog[44 kb md5] -- obo.html[131 kb md5] -- |
| information_artifact:Information Artifact Ontology | IAO | pro[78 kb md5] -- obo[54 kb md5] -- obo_xml[68 kb md5] -- owl[2 kb md5] -- tbl[20 kb md5] -- prolog[78 kb md5] -- stats[0 kb md5] -- obo.html[218 kb md5] -- |
| interpro:Protein Domains | IPR | Could not index: Source not available at specified URL as recognised format |
| kisao:Kinetic Simulation Algorithm Ontology | KISAO | owl[466 kb md5] -- obo.html[0 kb md5] -- |
| lipid:Lipid Ontology | LiPrO | pro[1035 kb md5] -- obo[559 kb md5] -- obo_xml[673 kb md5] -- owl[1327 kb md5] -- tbl[73 kb md5] -- prolog[1035 kb md5] -- stats[0 kb md5] -- obo.html[1792 kb md5] -- |
| loggerhead_nesting:Loggerhead nesting | obo_xml[91 kb md5] -- obo[42 kb md5] -- owl[214 kb md5] -- tbl[24 kb md5] -- prolog[90 kb md5] -- stats[0 kb md5] -- owl2[95 kb md5] -- xref[5 kb md5] -- | |
| malaria_ontology:Malaria Ontology | IDOMAL | obo_xml[1378 kb md5] -- obo[783 kb md5] -- owl[2939 kb md5] -- tbl[350 kb md5] -- prolog[1330 kb md5] -- owl2[1190 kb md5] -- xref[71 kb md5] -- |
| mammalian_phenotype:Mammalian phenotype | MP | obo_xml[6042 kb md5] -- obo[3474 kb md5] -- owl[12221 kb md5] -- tbl[2053 kb md5] -- prolog[6650 kb md5] -- owl2[5274 kb md5] -- xref[280 kb md5] -- |
| mao:Multiple alignment | MAO | obo_xml[65 kb md5] -- obo[33 kb md5] -- owl[154 kb md5] -- tbl[19 kb md5] -- prolog[59 kb md5] -- stats[0 kb md5] -- owl2[65 kb md5] -- xref[2 kb md5] -- |
| measurement_method:Measurement method ontology | MMO | |
| medaka_anatomy_development:Medaka fish anatomy and development | MFO | obo_xml[1018 kb md5] -- obo[500 kb md5] -- owl[2344 kb md5] -- tbl[188 kb md5] -- prolog[1055 kb md5] -- stats[0 kb md5] -- owl2[996 kb md5] -- xref[1 kb md5] -- |
| mged:Microarray experimental conditions | MO | pro[420 kb md5] -- obo[310 kb md5] -- obo_xml[547 kb md5] -- owl[556 kb md5] -- tbl[5 kb md5] -- prolog[420 kb md5] -- stats[0 kb md5] -- obo.html[1345 kb md5] -- |
| minimal_anatomical_terminology:Minimal anatomical terminology | MAT | obo_xml[190 kb md5] -- obo[99 kb md5] -- owl[432 kb md5] -- tbl[17 kb md5] -- prolog[254 kb md5] -- stats[0 kb md5] -- owl2[105 kb md5] -- |
| molecular_function:Molecular function | GO | obo_xml[41151 kb md5] -- obo_xml[15414 kb md5] -- owl[33545 kb md5] -- tbl[2957 kb md5] -- prolog[16970 kb md5] -- owl2[0 kb md5] -- xref[1247 kb md5] -- |
| molecule_role:Molecule role (INOH Protein name/family name ontology) | IMR | obo_xml[14711 kb md5] -- obo[4336 kb md5] -- owl[40365 kb md5] -- tbl[1415 kb md5] -- prolog[16995 kb md5] -- owl2[5831 kb md5] -- xref[192 kb md5] -- |
| mosquito_anatomy:Mosquito gross anatomy | TGMA | obo_xml[2063 kb md5] -- obo[948 kb md5] -- owl[4973 kb md5] -- tbl[466 kb md5] -- prolog[2226 kb md5] -- owl2[1528 kb md5] -- xref[57 kb md5] -- |
| mosquito_insecticide_resistance:Mosquito insecticide resistance | MIRO | obo_xml[1929 kb md5] -- obo[802 kb md5] -- owl[4657 kb md5] -- tbl[352 kb md5] -- prolog[1969 kb md5] -- owl2[1567 kb md5] -- xref[149 kb md5] -- |
| mouse_pathology:Mouse pathology | MPATH | obo_xml[378 kb md5] -- obo[203 kb md5] -- owl[820 kb md5] -- tbl[100 kb md5] -- prolog[367 kb md5] -- owl2[303 kb md5] -- xref[26 kb md5] -- |
| ncbi_taxonomy:NCBI organismal classification | NCBITaxon | obo_xml[242773 kb md5] -- obo[132203 kb md5] -- owl[568998 kb md5] -- tbl[45607 kb md5] -- prolog[260161 kb md5] -- owl2[222464 kb md5] -- |
| ncithesaurus:NCI Thesaurus | ncithesaurus | pro[302961 kb md5] -- obo[244308 kb md5] -- obo_xml[346983 kb md5] -- owl[224003 kb md5] -- tbl[6018 kb md5] -- prolog[302961 kb md5] -- obo.html[1116981 kb md5] -- |
| neuro_behavior_ontology:Neuro Behavior Ontology | NBO | obo_xml[738 kb md5] -- obo[428 kb md5] -- tbl[30 kb md5] -- prolog[518 kb md5] -- owl2[0 kb md5] -- |
| nmr:NMR-instrument specific component of metabolomics investigations | NMR | Could not index: Source not available at specified URL as recognised format |
| obi:Ontology for biomedical investigations | OBI | pro[3870 kb md5] -- obo[3349 kb md5] -- obo_xml[3488 kb md5] -- owl[6454 kb md5] -- tbl[626 kb md5] -- prolog[3870 kb md5] -- obo.html[12289 kb md5] -- |
| omrse:Ontology of Medically Related Social Entities | OMRSE | pro[10 kb md5] -- obo[5 kb md5] -- obo_xml[7 kb md5] -- owl[13 kb md5] -- tbl[2 kb md5] -- prolog[10 kb md5] -- stats[4 kb md5] -- obo.html[24 kb md5] -- |
| opl:Ontology for Parasite LifeCycle | OPL | pro[217 kb md5] -- obo[114 kb md5] -- obo_xml[150 kb md5] -- owl[391 kb md5] -- tbl[60 kb md5] -- prolog[217 kb md5] -- obo.html[417 kb md5] -- |
| pathway:Pathway ontology | PW | Could not index: Source not available at specified URL as recognised format |
| pharmacogenomics:Suggested Ontology for Pharmacogenomics | SOPHARM | pro[103 kb md5] -- obo[58 kb md5] -- obo_xml[69 kb md5] -- owl[127 kb md5] -- tbl[6 kb md5] -- prolog[103 kb md5] -- stats[0 kb md5] -- obo.html[177 kb md5] -- |
| plant_environment:Plant Environmental Conditions | EO | obo_xml[235 kb md5] -- obo[115 kb md5] -- owl[528 kb md5] -- tbl[73 kb md5] -- prolog[210 kb md5] -- stats[0 kb md5] -- owl2[216 kb md5] -- xref[12 kb md5] -- |
| plant_ontology:Plant Ontology | PO | obo_xml[1863 kb md5] -- obo[971 kb md5] -- owl[4125 kb md5] -- tbl[310 kb md5] -- prolog[2116 kb md5] -- owl2[0 kb md5] -- xref[67 kb md5] -- |
| plant_trait:Plant Trait Ontology | TO | obo_xml[623 kb md5] -- obo[324 kb md5] -- owl[1337 kb md5] -- tbl[155 kb md5] -- prolog[639 kb md5] -- owl2[523 kb md5] -- xref[29 kb md5] -- |
| plasmodium_life_cycle:Plasmodium life cycle | PLO | obo_xml[0 kb md5] -- owl[3 kb md5] -- owl2[4 kb md5] -- |
| platynereis_stage_ontology:Platynereis stage ontology | PD_ST | obo[15 kb md5] -- owl[39 kb md5] -- tbl[8 kb md5] -- prolog[18 kb md5] -- stats[0 kb md5] -- |
| po_anatomy:Plant Anatomy Ontology | PAO | obo_xml[1473 kb md5] -- obo[777 kb md5] -- owl[3231 kb md5] -- tbl[231 kb md5] -- prolog[1667 kb md5] -- owl2[0 kb md5] -- xref[56 kb md5] -- |
| po_temporal:Plant Growth and Development Stage | PGDSO | obo_xml[378 kb md5] -- obo[187 kb md5] -- owl[854 kb md5] -- tbl[78 kb md5] -- prolog[444 kb md5] -- owl2[0 kb md5] -- xref[11 kb md5] -- |
| poro:Porifera Ontology | PORO | pro[322 kb md5] -- obo[174 kb md5] -- obo_xml[228 kb md5] -- owl[956 kb md5] -- tbl[91 kb md5] -- prolog[322 kb md5] -- obo.html[695 kb md5] -- |
| protein:PRotein Ontology (PRO) | PR | obo_xml[23057 kb md5] -- obo[12082 kb md5] -- owl[48925 kb md5] -- tbl[5802 kb md5] -- prolog[26780 kb md5] -- owl2[0 kb md5] -- xref[724 kb md5] -- |
| protein_prerelease:PRotein Ontology (PRO) PRERELEASE | PR | obo[12082 kb md5] -- tbl[5037 kb md5] -- prolog[26780 kb md5] -- stats[0 kb md5] -- xref[724 kb md5] -- |
| provenance:Proteomics data and process provenance | ProPreO | pro[152 kb md5] -- obo[110 kb md5] -- obo_xml[147 kb md5] -- owl[229 kb md5] -- tbl[14 kb md5] -- prolog[152 kb md5] -- stats[0 kb md5] -- obo.html[420 kb md5] -- |
| psi-mi:Protein-protein interaction | MI | obo_xml[2076 kb md5] -- obo[1041 kb md5] -- owl[4624 kb md5] -- tbl[463 kb md5] -- prolog[2070 kb md5] -- owl2[1359 kb md5] -- xref[172 kb md5] -- |
| psi-mod:Protein modification | MOD | obo_xml[3771 kb md5] -- obo[1622 kb md5] -- owl[8629 kb md5] -- tbl[497 kb md5] -- prolog[3713 kb md5] -- owl2[1806 kb md5] -- xref[381 kb md5] -- |
| psi-ms:Mass spectrometry | MS | obo_xml[773 kb md5] -- obo[432 kb md5] -- owl[1778 kb md5] -- tbl[212 kb md5] -- prolog[763 kb md5] -- owl2[724 kb md5] -- xref[48 kb md5] -- |
| quality:Phenotypic quality | PATO | obo_xml[911 kb md5] -- obo[511 kb md5] -- owl[1948 kb md5] -- tbl[222 kb md5] -- prolog[953 kb md5] -- owl2[0 kb md5] -- xref[43 kb md5] -- |
| relationship:OBO relationship types (legacy) | OBO_REL | obo_xml[23 kb md5] -- obo[17 kb md5] -- owl[33 kb md5] -- prolog[24 kb md5] -- stats[0 kb md5] -- owl2[11 kb md5] -- xref[0 kb md5] -- |
| rex:Physico-chemical process | REX | obo_xml[214 kb md5] -- obo[127 kb md5] -- owl[472 kb md5] -- tbl[65 kb md5] -- prolog[211 kb md5] -- stats[0 kb md5] -- owl2[216 kb md5] -- xref[18 kb md5] -- |
| rnao:RNA ontology | RNAO | obo_xml[170 kb md5] -- obo[99 kb md5] -- owl[397 kb md5] -- tbl[40 kb md5] -- prolog[189 kb md5] -- owl2[196 kb md5] -- xref[1 kb md5] -- |
| ro:Relation ontology | RO | owl[91 kb md5] -- obo.html[0 kb md5] -- |
| sao:Subcellular anatomy ontology | SAO | pro[648 kb md5] -- obo[526 kb md5] -- obo_xml[862 kb md5] -- owl[857 kb md5] -- tbl[27 kb md5] -- prolog[648 kb md5] -- stats[0 kb md5] -- obo.html[2290 kb md5] -- |
| sep:Sample processing and separation techniques | SEP | obo_xml[1 kb md5] -- obo[275 kb md5] -- owl[3 kb md5] -- prolog[0 kb md5] -- owl2[0 kb md5] -- |
| sequence:Sequence types and features | SO | obo_xml[1320 kb md5] -- obo[703 kb md5] -- owl[2750 kb md5] -- tbl[335 kb md5] -- prolog[1415 kb md5] -- owl2[0 kb md5] -- xref[69 kb md5] -- |
| sequence_prerelease:Sequence types and features PRERELEASE | SO | obo_xml[1320 kb md5] -- obo[703 kb md5] -- owl[2750 kb md5] -- tbl[335 kb md5] -- prolog[1415 kb md5] -- owl2[0 kb md5] -- xref[69 kb md5] -- |
| software:Software ontology | SWO | pro[472 kb md5] -- obo[260 kb md5] -- obo_xml[345 kb md5] -- owl[1228 kb md5] -- tbl[64 kb md5] -- prolog[472 kb md5] -- obo.html[1105 kb md5] -- |
| spatial:Spatial Ontology | BSPO | obo_xml[73 kb md5] -- obo[38 kb md5] -- owl[175 kb md5] -- tbl[7 kb md5] -- prolog[71 kb md5] -- owl2[79 kb md5] -- xref[3 kb md5] -- |
| spider_anatomy:Spider Ontology | SPD | obo_xml[242 kb md5] -- obo[124 kb md5] -- owl[559 kb md5] -- tbl[56 kb md5] -- prolog[222 kb md5] -- owl2[257 kb md5] -- xref[10 kb md5] -- |
| systems_biology:Systems Biology | SBO | obo_xml[544 kb md5] -- obo[414 kb md5] -- owl[837 kb md5] -- tbl[343 kb md5] -- prolog[490 kb md5] -- owl2[549 kb md5] -- xref[13 kb md5] -- |
| taxonomic_rank:Taxonomic rank vocabulary | TAXRANK | Could not index: Source not available at specified URL as recognised format |
| teleost_anatomy:Teleost Anatomy Ontology | TAO | obo_xml[1371 kb md5] -- obo[751 kb md5] -- owl[3091 kb md5] -- tbl[356 kb md5] -- prolog[1408 kb md5] -- owl2[0 kb md5] -- xref[48 kb md5] -- |
| teleost_taxonomy:Teleost taxonomy | TTO | obo_xml[26534 kb md5] -- obo[10467 kb md5] -- owl[59207 kb md5] -- tbl[2430 kb md5] -- prolog[28462 kb md5] -- owl2[12517 kb md5] -- xref[2746 kb md5] -- |
| temporal_gramene:Cereal plant development | GRO | Could not index: Source not available at specified URL as recognised format |
| tick_anatomy:Tick gross anatomy | TADS | obo_xml[405 kb md5] -- obo[253 kb md5] -- owl[867 kb md5] -- tbl[142 kb md5] -- prolog[391 kb md5] -- owl2[421 kb md5] -- xref[19 kb md5] -- |
| transmission:Pathogen transmission | TRANS | obo_xml[17 kb md5] -- obo[10 kb md5] -- owl[35 kb md5] -- tbl[6 kb md5] -- prolog[14 kb md5] -- stats[0 kb md5] -- owl2[15 kb md5] -- xref[1 kb md5] -- |
| uberon:Uber anatomy ontology | UBERON | pro[0 kb md5] -- obo[29549 kb md5] -- obo_xml[0 kb md5] -- owl[33535 kb md5] -- prolog[0 kb md5] -- obo.html[0 kb md5] -- |
| unit:Units of measurement | UO | obo_xml[164 kb md5] -- obo[87 kb md5] -- owl[320 kb md5] -- tbl[38 kb md5] -- prolog[147 kb md5] -- owl2[130 kb md5] -- xref[6 kb md5] -- |
| vHOG:verteberate Homologous Organ Groups | vHOG | obo_xml[564 kb md5] -- obo[264 kb md5] -- owl[1313 kb md5] -- tbl[108 kb md5] -- prolog[545 kb md5] -- owl2[584 kb md5] -- xref[39 kb md5] -- |
| vaccine:Vaccine ontology | VO | owl[5693 kb md5] -- obo.html[0 kb md5] -- |
| vertebrate_anatomy:Vertebrate Musculoskeletal Anatomy Ontology | VAO | Could not index: Source not available at specified URL as recognised format |
| worm_anatomy:C. elegans gross anatomy | WBbt | obo_xml[3010 kb md5] -- obo[1366 kb md5] -- owl[7813 kb md5] -- tbl[487 kb md5] -- prolog[2793 kb md5] -- owl2[3587 kb md5] -- xref[151 kb md5] -- |
| worm_development:C. elegans development | WBls | Could not index: Source not available at specified URL as recognised format |
| worm_phenotype:C. elegans phenotype | WBPhenotype | obo_xml[1333 kb md5] -- obo[746 kb md5] -- owl[2900 kb md5] -- tbl[457 kb md5] -- prolog[1471 kb md5] -- owl2[1204 kb md5] -- xref[133 kb md5] -- |
| xenopus_anatomy:Xenopus anatomy and development | XAO | obo_xml[637 kb md5] -- obo[360 kb md5] -- owl[1458 kb md5] -- tbl[155 kb md5] -- prolog[567 kb md5] -- owl2[0 kb md5] -- xref[31 kb md5] -- |
| yeast_phenotype:Yeast phenotypes | YPO | obo_xml[125 kb md5] -- obo[75 kb md5] -- owl[287 kb md5] -- tbl[27 kb md5] -- prolog[159 kb md5] -- owl2[89 kb md5] -- xref[4 kb md5] -- |
| zea_mays_anatomy:Maize gross anatomy | ZEA | Could not index: Source not available at specified URL as recognised format |
| zebrafish_anatomy:Zebrafish anatomy and development | ZFA | obo_xml[2563 kb md5] -- obo[1292 kb md5] -- owl[6625 kb md5] -- tbl[411 kb md5] -- prolog[2224 kb md5] -- owl2[2644 kb md5] -- xref[230 kb md5] -- |
| zebrafish_anatomy_prerelease:Zebrafish anatomy and development PRERELEASE | ZFA | obo_xml[2563 kb md5] -- obo[1292 kb md5] -- owl[6625 kb md5] -- tbl[411 kb md5] -- prolog[2224 kb md5] -- owl2[2644 kb md5] -- xref[230 kb md5] -- |
Logical definitions (cross-products)
The following are supplementary to the above ontologies - they enhance existing ontologies with logical definitions (also known colloquially in the GO as cross-products). For more information, see Cross-Products. These files are generated using the Mappings Metadata File. The files listed below are manually vetted cross-products. For a full comprehensive list of automatically generated cross products, see the Obol web page.
Mappings
Links between terms across ontologies or databases. See Mappings page on the OBO Foundry wiki
| Ontology | ID Prefix | Files |
|---|---|---|
| caro_to_bfo:CARO to BFO is_a mappings | caro_to_bfo | obo_xml[2 kb md5] -- obo[1 kb md5] -- owl[6 kb md5] -- tbl[0 kb md5] -- prolog[1 kb md5] -- stats[0 kb md5] -- owl2[2 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| cog2go:cog2go mapping | COG2GO | obo_xml[17 kb md5] -- obo[6 kb md5] -- owl[36 kb md5] -- tbl[1 kb md5] -- prolog[6 kb md5] -- stats[0 kb md5] -- owl2[7 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| ec2go:ec2go mapping | EC2GO | obo_xml[535 kb md5] -- obo[166 kb md5] -- owl[1468 kb md5] -- tbl[52 kb md5] -- prolog[308 kb md5] -- owl2[275 kb md5] -- xref[93 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| egad2go:egad2go mapping | EGAD2GO | obo_xml[9 kb md5] -- obo[3 kb md5] -- owl[24 kb md5] -- tbl[0 kb md5] -- prolog[4 kb md5] -- stats[0 kb md5] -- owl2[4 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| genprotec2go:genprotec2go mapping | GENPROTECGO | obo_xml[48 kb md5] -- obo[20 kb md5] -- owl[102 kb md5] -- tbl[3 kb md5] -- prolog[21 kb md5] -- stats[0 kb md5] -- owl2[16 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| go_xrf_metadata:GO database cross-references metadata | GO_XRF_ABBS | obo_xml[286 kb md5] -- obo[142 kb md5] -- owl[255 kb md5] -- prolog[160 kb md5] -- owl2[45 kb md5] -- |
| hamap2go:hamap2go mapping | HAMAP2GO | obo_xml[562 kb md5] -- obo[183 kb md5] -- owl[1544 kb md5] -- tbl[54 kb md5] -- prolog[329 kb md5] -- owl2[78 kb md5] -- xref[108 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| interpro2go:interpro2go mapping | INTERPRO2GO | obo_xml[4760 kb md5] -- obo[2117 kb md5] -- owl[9329 kb md5] -- tbl[318 kb md5] -- prolog[4173 kb md5] -- owl2[13606 kb md5] -- xref[734 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| ma2ncit:Adult Mouse Anatomy to NCI thesauris | ma2ncit | imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| map_CL-EMAPA:CL to EMAPA mappings | CL-EMAPA | obo_xml[1625 kb md5] -- obo[874 kb md5] -- owl[3986 kb md5] -- tbl[293 kb md5] -- prolog[1736 kb md5] -- stats[0 kb md5] -- owl2[1929 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| metacyc2go:metacyc2go mapping | METACYC2GO | obo_xml[689 kb md5] -- obo[261 kb md5] -- owl[1861 kb md5] -- tbl[61 kb md5] -- prolog[426 kb md5] -- owl2[308 kb md5] -- xref[177 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| mips2go:mips2go mapping | MIPS2GO | obo_xml[179 kb md5] -- obo[77 kb md5] -- owl[372 kb md5] -- tbl[12 kb md5] -- prolog[82 kb md5] -- stats[0 kb md5] -- owl2[60 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| multifun2go:multifun2go mapping | MULTIFUN2GO | obo_xml[126 kb md5] -- obo[48 kb md5] -- owl[274 kb md5] -- tbl[9 kb md5] -- prolog[58 kb md5] -- stats[0 kb md5] -- owl2[42 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| oboInOwl:OBO metamodel | oboInOwl | obo_xml[13 kb md5] -- obo[6 kb md5] -- owl[29 kb md5] -- tbl[0 kb md5] -- prolog[12 kb md5] -- stats[0 kb md5] -- owl2[8 kb md5] -- |
| pfam2go:pfam2go mapping | PFAM2GO | obo_xml[1641 kb md5] -- obo[545 kb md5] -- owl[3708 kb md5] -- tbl[131 kb md5] -- prolog[1337 kb md5] -- owl2[802 kb md5] -- xref[243 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| prints2go:prints2go mapping | PRINTS2GO | obo_xml[744 kb md5] -- obo[259 kb md5] -- owl[1668 kb md5] -- tbl[58 kb md5] -- prolog[618 kb md5] -- owl2[316 kb md5] -- xref[116 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| prodom2go:prodom2go mapping | PRODOM2GO | obo_xml[150 kb md5] -- obo[54 kb md5] -- owl[334 kb md5] -- tbl[11 kb md5] -- prolog[126 kb md5] -- owl2[86 kb md5] -- xref[23 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| prosite2go:prosite2go mapping | PROSITE2GO | obo_xml[1195 kb md5] -- obo[423 kb md5] -- owl[2683 kb md5] -- tbl[92 kb md5] -- prolog[1006 kb md5] -- owl2[560 kb md5] -- xref[196 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| quality_bfo_bridge:PATO BFO constraints | PATO_BFO_BRIDGE | obo_xml[3 kb md5] -- obo[1 kb md5] -- owl[7 kb md5] -- tbl[0 kb md5] -- prolog[2 kb md5] -- stats[0 kb md5] -- owl2[2 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| reactome2go:reactome2go mapping | REACTOM2GO | obo_xml[3978 kb md5] -- obo[1415 kb md5] -- owl[10862 kb md5] -- tbl[366 kb md5] -- prolog[2401 kb md5] -- owl2[90 kb md5] -- xref[908 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| rfam2go:rfam2go mapping | RFAMGO | obo_xml[126 kb md5] -- obo[41 kb md5] -- owl[292 kb md5] -- tbl[10 kb md5] -- prolog[61 kb md5] -- stats[0 kb md5] -- owl2[5 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| ro_bfo_bridge1_1:RO BFO domain and range constraints | OBO_REL_BFO_BRIDGE | obo_xml[3 kb md5] -- obo[1 kb md5] -- owl[8 kb md5] -- prolog[3 kb md5] -- stats[0 kb md5] -- owl2[3 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| smart2go:smart2go mapping | SMART2GO | obo_xml[207 kb md5] -- obo[67 kb md5] -- owl[481 kb md5] -- tbl[16 kb md5] -- prolog[170 kb md5] -- owl2[118 kb md5] -- xref[32 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| spkw2go:spkw2go mapping | SPKW2GO | obo_xml[116 kb md5] -- obo[43 kb md5] -- owl[254 kb md5] -- tbl[8 kb md5] -- prolog[97 kb md5] -- owl2[143 kb md5] -- xref[17 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| tigr2go:tigr2go mapping | TIGR2GO | obo_xml[45 kb md5] -- obo[21 kb md5] -- owl[84 kb md5] -- tbl[2 kb md5] -- prolog[17 kb md5] -- stats[0 kb md5] -- owl2[14 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| tigrfams2go:tigrfams2go mapping | TIGRFAMS2GO | obo_xml[1017 kb md5] -- obo[469 kb md5] -- owl[2009 kb md5] -- tbl[65 kb md5] -- prolog[445 kb md5] -- stats[0 kb md5] -- owl2[115 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| uberon_anatomy_ontologies_bridge:is_a links to uberon terms | uberon_anatomy_ontologies_bridge | obo_xml[938 kb md5] -- obo[810 kb md5] -- owl[1999 kb md5] -- tbl[196 kb md5] -- prolog[852 kb md5] -- owl2[1980 kb md5] -- imports.obo[1 kb md5] -- imports.owl[1 kb md5] -- |
| um-bbd_enzymeid2go:um-bbd_enzymeid2go mapping | UMBBDENZYMEID2GO | obo_xml[15 kb md5] -- obo[5 kb md5] -- owl[46 kb md5] -- tbl[1 kb md5] -- prolog[9 kb md5] -- owl2[8 kb md5] -- xref[3 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| um-bbd_pathwayid2go:um-bbd_pathwayid2go mapping | UMBBDPATHWAYID2GO | obo_xml[17 kb md5] -- obo[6 kb md5] -- owl[52 kb md5] -- tbl[1 kb md5] -- prolog[10 kb md5] -- owl2[9 kb md5] -- xref[3 kb md5] -- imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
| vHOG_associations:vHOG_associations | vHOG_ASSOC | imports.obo[0 kb md5] -- imports.owl[0 kb md5] -- |
Formats
The following formats are generated. See below for caveats. All indexed ontologies can be downloaded en-masse for any one particular format, see download section below. The format metadata spec can be found Here
-
obo-- The Obo text format. If this is not the source format, this is generated using flat2obo (part of obo-edit)
-
obo_xml-- The Obo XML format. Generated using go-perl
-
go_ont-- The old deprecated go DAG format. Generated using go-perl
-
owl-- See W3 OWL page for details. Generated from obo-xml using oboxml_to_owl.xsl. See OboInOwl for details of mapping. All obo files converted to owl are made available using the http://purl.org/obo/ URI scheme; for example http://purl.org/obo/GO
-
chadoxml-- See Chado-XML pages. This format can be loaded into a Chado-schema database using a generic loader such as DBStag.
-
godb_prestore-- This format can be loaded into a GO DB schema database using a generic loader such as DBStag.
-
go_rdf-- GO RDF XML format. May soon be deprecated in favour of the OWL export.
-
tbl-- Simple table-based format
-
prolog-- Prolog database. Can be reasoned over using a prolog engine. See obol and blip.
-
owl-classified-by-pellet-- result of running the OWL through the peller classifier. Potentially includes missing subclasses
-
obo-classified-by-oboedit-- result of running the obo through the oboedit reasoner. Potentially includes missing is_a and relationship links. For best results, see the logical definitions files.
Reports
The following reports are generated from each of the ontologies that are indexable
-
validation_report-- reports redundant relationships between classes. This report will be extended to report inconsistences obtained by using a reasoning engine
-
error_report-- reports any syntax errors
-
stats-- Ontology statistics
Download
All the above are available for download on an ftp site:
Compressed tar files are available for the entire download matrix, and also on a per-format basis. No historic archive is maintained, beyond what is provided by the projects managing the individual ontologies
Metadata
Metadata derived from the above ontologies can be downloaded as an xml file here:
- obo-all/ontology_index.xml -- XML
- obo-all/ontology_index.rdf -- RDF
Statistics
Statistics on each indexable ontology is performed as part of the creation of this resource. Individual statistics files are available, per-ontology, above.
- stats.tbl -- tab delimited text
- stats.html -- DHTML table (click on columns to sort)
The tab-delimited version can be used with unix tools such as sort and grep, or imported into an application like Excel.
You can also download stats from previous versions in the archive
Alignment
You can download a basic all-vs-all text alignment of classes in the indexed OBO files above. This is based on text matching using names and synonyms.
This file is updated irregularly and may be out of sync with the above files
Browsing and querying
As yet there is no way to browse all the ontologies as a whole. In future we may provide this using a tool such as AmiGO.
Caveats
- This web page should be considered alpha. The contents may change in the future. The URL is not stable, and caution should be exercised when linking to it
- Not every obo ontology is indexed. Currently we index (deprecated) GO and Obo formatted files. There may be problems with GO formatted files. This is a deprecated format (note: everyone has now switched to obo or another suported format). Ontology maintainers should switch to Obo format.
- Many ontologies reside on sourceforge. Sometimes an ontology will not download correctly because of a sourceforge glitch. If this happens, the ontology will be omitted from the list above, or the ontology from the previous week will be used. Eventually we would like a more robust way of handling this
- Some ontologies such as evoc are supplied as a bundle of separate ontologies. Unfortunately, we do not yet index these. We also do not index ontologies that are not available as a simple one-file download from a URL
- We endeavour to produce this on a weekly basis. System problems may prevent us from doing this. The production of these files is automated, unexpected problems may occur. We hope to make this a more reliable process in the future
- This resource is derived automatically from information submitted to the obo site maintainers. This site is not a substitute for any data or formats made available by the individual ontology providers. The purpose of this site is to make available as much of OBO as possible in a uniform fashion for a variety of formats. For any serious analysis, you should perform the file format conversion yourself using the ontology provided directly by the ontology provider. See main OBO site for obtaining this information.
- The MeSH file should be treated with caution. The source mesh.obo file treats links in MeSH as is_a relations, which is incorrect. This means that the resulting OWL file uses owl:subClassOf, which is also incorrect
-
The NCBI Taxonomy transformation treats this resource
as an ontology of organism types. The taxonomic rank
(species, genus, order, family, phylum, etc)
is treated as a term property_value. These are
translated to annotationProperties in the owl
version. See note below on term property_values with oboedit.
Also note that due to the presence of {} characters in the NCBI Taxonomy you will need oboedit1.1 or oboedit1.100-beta12 or higher, due to a bug in previous versions.
-
In the Obo generated from OWL, owl
AnnotationProperties are converted into oboedit class
properties. You will need
OBO-Edit 1.003-beta1 to be able to load the ontology
without errors. A quick hack is also to simply run
grep -v ^property_value: in.obo > out.oboThis will also lose property values for instances, but these are not currently displayed in oboedit anyway. (will be visible in a future version) -
This page is semantic-web friendly! Try viewing it with Piggy Bank
How this site works
This site is generated using the tools available in the obo sourceforge cvs, under obo/website/utils