id adult_mouse_anatomy title Mouse adult gross anatomy namespace MA foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo source ftp://ftp.informatics.jax.org/pub/reports/adult_mouse_anatomy.obo home Mouse Anatomy Dictionary|http://www.informatics.jax.org/searches/AMA_form.shtml documentation contact Anatomy at JAX anatomy informatics.jax.org format obo description A structured controlled vocabulary of the adult anatomy of the mouse (Mus). domain anatomy subtypes_of CARO:0000000 patho_type canonical granularity organismal relevant_organism NCBITaxon:10088|Mus id amphibian_anatomy title Amphibian gross anatomy namespace AAO foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/amphibian/amphibian_anatomy.obo source home www.amphibanat.org documentation contact AmphiAnat mailing list sbhdbe mst.edu format obo description A structured controlled vocabulary of the anatomy of Amphibians. domain anatomy subtypes_of CARO:0000000 patho_type canonical granularity organismal relevant_organism NCBITaxon:8292|Amphibia id animalhist title Animal natural history and life history namespace ADW foundry No status Inactive download source http://animaldiversity.ummz.umich.edu/site/about/technology/ADW_ontology_protege.zip/view.html home Animal Diversity Web|http://www.animaldiversity.org documentation ADW Technology|http://animaldiversity.ummz.umich.edu/site/about/technology/index.html contact Animal Diversity Web technical staff adw_geeks umich.edu format protege description An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities. is_obsolete true id quality title Phenotypic quality namespace PATO foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo source home PATO wiki|http://www.bioontology.org/wiki/index.php/PATO:Main_Page documentation contact George Gkoutos obo-phenotype lists.sourceforge.net format obo description Phenotypic qualities (properties). This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested. domain phenotype subtypes_of bfo:DependentContinuant patho_type all granularity all relevant_organism all id biological_process title Biological process namespace GO foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology_edit.obo source ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo home www.geneontology.org|http://www.geneontology.org documentation Gene Ontology documentation|http://www.geneontology.org/GO.doc.shtml contact Gene Ontology go geneontology.org format obo description Provides structured controlled vocabularies for the annotation of gene products with respect to their biological role. One of the three vocabularies of the Gene Ontology. relevant_organism all subtypes_of bfo:Occurrent patho_type canonical domain biological process granularity molecular,cellular,organismal,multi-organismal id brenda title BRENDA tissue / enzyme source namespace BTO foundry No status Active download source http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO home BRENDA enzyme database|http://www.brenda-enzymes.info documentation BRENDA ontology help|http://www.brenda-enzymes.info contact BRENDA tissue ontology curators marion.gremse uni-koeln.de format obo description A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. domain anatomy id caro title Common Anatomy Reference Ontology namespace CARO foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro.obo source home CARO Wiki|http://www.bioontology.org/wiki/index.php/CARO:Main_Page documentation contact Melissa Haendel obo-anatomy lists.sourceforge.net format obo description The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO will be described in Anatomy Ontologies for Bioinformatics: Principles and Practice Albert Burger, Duncan Davidson and Richard Baldock (Editors) relevant_organism all subtypes_of bfo:IndependentContinuant domain anatomy patho_type canonical granularity organismal id spatial title Spatial Ontology namespace BSPO foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/spatial.obo source home CARO Wiki|http://www.bioontology.org/wiki/index.php/CARO:Main_Page documentation contact Chris Mungall obo-anatomy lists.sourceforge.net format obo description A small ontology for anatomical spatiol references, such as dorsal, ventral, axis, and so forth. relevant_organism all subtypes_of bfo:DependentContinuant domain anatomy patho_type canonical granularity organismal id spider_anatomy title Spider Ontology namespace SPD foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/spider/spider_comparative_biology.obo source http://research.amnh.org/atol/files/Content/SVsManual/files/Spider_homologues.obo home Phylogeny of Spiders|http://research.amnh.org/atol/files/ documentation Spider Standard Views|http://research.amnh.org/atol/files/Content/SVsManual/ contact Martin Ramirez ramirez macn.gov.ar format obo description An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). domain anatomy subtypes_of CARO:0000000 patho_type canonical granularity organismal relevant_organism NCBITaxon:34643|cobweb weavers id cell title Cell type namespace CL foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo source home Cell Type Ontology home|http://lists.sourceforge.net/lists/listinfo/obo-cell-type documentation contact Oliver Hofmann obo-cell-type lists.sourceforge.net format obo description The Cell Ontology is designed as a structured controlled vocabulary for cell types. This ontology was constructed for use by the model organism and other bioinformatics databases, where there is a need for a controlled vocabulary of cell types. This ontology is not organism specific; indeed it includes cell types from prokaryotes to mammals, including plants and fungi. A full description of the Cell Ontology can be found in Bard, Rhee and Ashburner. 2005. An Ontology for Cell Types. relevant_organism all subtypes_of bfo:IndependentContinuant domain anatomy patho_type canonical granularity cellular id cellular_component title Cellular component namespace GO foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology_edit.obo source ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo home www.geneontology.org|http://www.geneontology.org documentation Gene Ontology documentation|http://www.geneontology.org/GO.doc.shtml contact Gene Ontology go geneontology.org format obo description Provides structured controlled vocabularies for the annotation of gene products with respect to their cellular location. One of the three vocabularies of the Gene Ontology. relevant_organism all subtypes_of bfo:IndependentContinuant domain anatomy patho_type canonical granularity sub-cellular id chebi title Chemical entities of biological interest namespace CHEBI foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo source ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo home ChEBI home|http://www.ebi.ac.uk/chebi documentation ChEBI user manual|http://www.ebi.ac.uk/chebi/init.do?toolBarForward=userManual contact ChEBI help chebi-help ebi.ac.uk format obo description A structured classification of chemical compounds of biological relevance. subtypes_of bfo:IndependentContinuant relevant_organism all subtypes_of bfo:IndependentContinuant domain biochemistry patho_type canonical granularity molecular id cob title Protein covalent bond namespace RESID foundry No status Active home RESID Info|http://www.ebi.ac.uk/RESID/ download source ftp://ftp.ebi.ac.uk/pub/databases/RESID/RESIDUES.XML documentation contact John Garavelli john.garavelli ebi.ac.uk format XML description For the description of covalent bonds in proteins. domain proteins id dictyostelium_discoideum_anatomy title Dictyostelium discoideum anatomy namespace DDANAT foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/microbial_gross_anatomy/dictyostelium/dictyostelium_anatomy.obo source home Dictybase|http://dictybase.org/ documentation contact Rex Chisholm dictybase northwestern.edu format obo description A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum. relevant_organism NCBITaxon:44689|Dictyostelium discoideum subtypes_of CARO:0000000 patho_type canonical granularity organismal,cellular domain anatomy id disease_ontology title Human disease namespace DOID foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/human_disease.obo source http://diseaseontology.svn.sourceforge.net/viewvc/*checkout*/diseaseontology/trunk/HumanDO.obo home Disease Ontology|http://diseaseontology.sourceforge.net/ documentation Disease Ontology|http://diseaseontology.sourceforge.net/ contact discussion list diseaseontology-discussion lists.sourceforge.net format obo description Creating a comprehensive hierarchical controlled vocabulary for human disease representation. relevant_organism NCBITaxon:9606|Homo sapiens subtypes_of bfo:DependentContinuant patho_type pathological granularity organismal,cellular domain health id infectious_disease_ontology title Infectious disease namespace IDO foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/infectious_disease.obo source http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_10.08.07.obo home Infectious Disease Ontology|http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology documentation contact Lindsay Cowell ido duke.edu format obo description relevant_organism NCBITaxon:9606|Homo sapiens subtypes_of bfo:DependentContinuant patho_type pathological granularity organismal,cellular domain health id disease_ontology title Human disease namespace DOID foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/human_disease.obo source http://diseaseontology.svn.sourceforge.net/viewvc/*checkout*/diseaseontology/trunk/HumanDO.obo home Disease Ontology|http://diseaseontology.sourceforge.net/ documentation Disease Ontology|http://diseaseontology.sourceforge.net/ contact discussion list diseaseontology-discussion lists.sourceforge.net format obo description Creating a comprehensive hierarchical controlled vocabulary for human disease representation. relevant_organism NCBITaxon:9606|Homo sapiens subtypes_of bfo:DependentContinuant patho_type pathological granularity organismal,cellular domain health id emap title Mouse gross anatomy and development namespace EMAP foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/EMAP.obo source home GeneX|http://genex.hgu.mrc.ac.uk/ documentation contact Jonathan Bard J.Bard ed.ac.uk format obo description A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). domain anatomy subtypes_of CARO:0000000 patho_type canonical granularity organismal relevant_organism NCBITaxon:10088|Mus id envo title Environment Ontology namespace ENVO foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/environmental/envo.obo source home EnvO|http://environmentontology.org/ documentation http://www.envoc.org contact Norman Morrison obo-envo lists.sourceforge.net format obo description Ontology of environmental features and habitats relevant_organism all subtypes_of bfo:IndependentContinuant patho_type all granularity molecular,cellular,organismal,multi-organismal domain environment id event title Event (INOH pathway ontology) namespace IEV foundry No status Active download source Event Ontology Download|http://www.inoh.org/ontologies/EventOntology.obo home The INOH Pathway Database|http://www.inoh.org documentation INOH Ontologies|http://www.inoh.org/info/ontologies/ contact INOH curators curator inoh.org format obo description A structured controlled vocabulary of pathway centric biological processes. This ontology is a INOH pathway annotation ontology, one of a set of ontologies intended to be used in pathway data annotation to ease data integration. This ontology is used to annotate biological processes, pathways, sub-pathways in the INOH pathway data.
INOH is part of the BioPAX working group. domain biological process id evidence_code title Evidence codes namespace ECO foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/evidence_code.obo source home documentation contact Sue Rhee evidence genome.stanford.edu format obo description A rich ontology for experimental and other evidence statements. relevant_organism all subtypes_of bfo:DependentContinuant patho_type canonical domain experiments granularity molecular,cellular,organismal,multi-organismal id evoc title eVOC (Expressed Sequence Annotation for Humans) namespace EV foundry No status Active download source http://www.evocontology.org/uploads/Main/evoc_v2.7_obo.tar.gz home eVoc|http://www.evocontology.org/ documentation contact eVOC mailing list evoc sanbi.ac.za format obo description Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment. domain experiments id fix title Physico-chemical methods and properties namespace FIX foundry No status Inactive download source http://www.ebi.ac.uk/~kirill/FIX/fix.obo home documentation contact Kirill Degtyarenko chebi-help ebi.ac.uk format obo description FIX consists of two ontologies: methods and properties (but not objects, which are subject of the chemical ontology). The methods are applied to study the properties. id fly_anatomy title Drosophila gross anatomy namespace FBbt foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fly/fly_anatomy.obo source home FlyBase|http://www.flybase.org/ documentation contact David Osumi-Sutherland obo-anatomy lists.sourceforge.net format obo description A structured controlled vocabulary of the anatomy of Drosophila melanogaster. relevant_organism NCBITaxon:7227|Drosophila subtypes_of CARO:0000000 patho_type canonical domain anatomy granularity organismal id fly_development title Drosophila development namespace FBdv foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/developmental/animal_development/fly/fly_development.obo source home FlyBase|http://www.flybase.org/ documentation contact David Osumi-Sutherland obo-anatomy lists.sourceforge.net format obo description A structured controlled vocabulary of the development of Drosophila melanogaster. relevant_organism NCBITaxon:7227|Drosophila subtypes_of bfo:Occurent patho_type canonical domain anatomy granularity organismal id fly_taxonomy title Fly taxonomy namespace FBsp foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/fly_taxonomy.obo source home FlyBase|http://www.flybase.org/ documentation contact Michael Ashburner ma11 gen.cam.ac.uk format obo description The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. relevant_organism NCBITaxon:7227|Drosophila subtypes_of bfo:IndependentContinuant patho_type canonical domain taxonomy granularity organismal id flybase_vocab title FlyBase Controlled Vocabulary namespace FBcv foundry No status Inactive download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/vocabularies/flybase_controlled_vocabulary.obo source home FlyBase|http://www.flybase.org/ documentation FlyBase Reference Manual|http://flybase.bio.indiana.edu/.data/docs/refman/refman-G.html#G.2 contact Michael Ashburner ma11 gen.cam.ac.uk format obo description A structured controlled vocabulary used for various aspects of annotation by FlyBase.
This ontology is maintained by FlyBase for various aspects of annotation not covered, or not yet covered, by other OBO ontologies. If and when community ontologies are available for the domains here covered FlyBase will use them. is_obsolete true id fma_lite title Foundational Model of Anatomy (subset) namespace FMA foundry Yes status Production and review download http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo source home FMA|http://sig.biostr.washington.edu/projects/fm/index.html documentation contact OBO Anatomy obo-anatomy lists.sourceforge.net format obo description Obo format translation of the FMA, omitting all relationships other than is_a, part_of and has_part. Future versions of fma_obo will include more relationships relevant_organism NCBITaxon:9606|Homo sapiens subtypes_of CARO:0000000 patho_type canonical domain anatomy granularity organismal id fungal_anatomy title Fungal gross anatomy namespace FAO foundry Yes status Quiescent download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/microbial_gross_anatomy/fungi/fungal_anatomy.obo source home fungal gross anatomy|http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/ documentation description|http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/#description contact Maria Costanzo maria genome.stanford.edu format obo description A structured controlled vocabulary for the anatomy of fungi. relevant_organism NCBITaxon:4751|Fungal subtypes_of CARO:0000000 patho_type canonical domain anatomy granularity organismal id gene_regulation title Gene Regulation Ontology namespace BOOTStrep foundry No status Active download source http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO_v0.2_20Dec2007.owl home http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html documentation contact Vivian Lee vlee ebi.ac.uk format owl description The BOOTStrep Ontology is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. GRO is intended to represent common knowledge about gene regulation in a formal way rather than representing extremely fine-grained classes as can be found in ontologies such as the Gene Ontology (GO) (created for data base annotation purposes) and various relevant databases. The main purpose of the ontology is to support NLP applications. It has a particular focus on the relations between processes and the molecules (participants) involved. The basic structure of the GRO is a direct acyclic graph (DAG) with ontology classes as nodes and is-a relations between classes as edges. The taxonomic backbone is further enriched by several semantic relation types (part-of, from-species, participates-in with the two sub-relations agent-of and patient-of). domain genomic id habronattus_courtship title Habronattus courtship namespace foundry No status Inactive download source protege source|http://www.mesquiteproject.org/ontology/Habronattus/Protege_source/ home Mesquite Project Habronattus Index|http://www.mesquiteproject.org/ontology/Habronattus/index.html documentation Ontologies For Ethology|http://www.mesquiteproject.org/ontology/ contact Peter Midford peteremidford yahoo.com format protege description A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms. An ontology for courtship behavior of the spider Habronattus californicus. is_obsolete true id human-dev-anat-abstract title Human developmental anatomy, abstract version namespace EHDAA foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-abstract.obo source home GeneX|http://genex.hgu.mrc.ac.uk/ documentation contact Jonathan Bard J.Bard ed.ac.uk format obo description A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release. relevant_organism NCBITaxon:9606|Homo sapiens subtypes_of CARO:0000000 patho_type canonical domain anatomy granularity organismal id human-dev-anat-staged title Human developmental anatomy, timed version namespace EHDA foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-staged.obo source home GeneX|http://genex.hgu.mrc.ac.uk/ documentation contact Jonathan Bard J.Bard ed.ac.uk format obo description A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once. relevant_organism NCBITaxon:9606|Homo sapiens subtypes_of bfo:Occurent patho_type canonical domain anatomy granularity organismal id image title Biological imaging methods namespace FBbi foundry No status Inactive download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/experimental_conditions/imaging_methods/image.obo source home FlyBase|http://www.flybase.org/ documentation contact Kathy Matthews matthewk indiana.edu format obo description A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. domain experiments id interpro title Protein Domains namespace IPR foundry No status Active download source InterPro FTP directory|ftp://ftp.ebi.ac.uk/pub/databases/interpro/ home InterPro home page|http://www.ebi.ac.uk/interpro/index.html documentation InterPro documentation|http://www.ebi.ac.uk/interpro/documentation.html contact InterPro Help interhelp ebi.ac.uk format XML description A database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. domain proteins id loggerhead_nesting title Loggerhead nesting namespace foundry No status Inactive download source B8467OBO|http://www.mesquiteproject.org/ontology/OBO/B8467OBO home Mesquite Project Loggerhead Index|http://www.mesquiteproject.org/ontology/Loggerhead/index.html documentation Ontologies For Ethology|http://www.mesquiteproject.org/ontology/ contact Peter Midford peteremidford yahoo.com format obo description A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms. An ontology for Loggerhead sea turtle (Caretta caretta) nesting behavior, based on the published ethogram of Hailman and Elowson. is_obsolete true id mammalian_phenotype title Mammalian phenotype namespace MP foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mammalian_phenotype.obo source MPheno_OBO.ontology|ftp://ftp.informatics.jax.org/pub/reports/MPheno_OBO.ontology home Mammalian Phenotype Browser|http://www.informatics.jax.org/searches/MP_form.shtml documentation contact JAX phenotype list pheno informatics.jax.org format obo description The Mammalian Phenotype Ontology is under development as a community effort to provide standard terms for annotating mammalian phenotypic data. domain phenotype subtypes_of PATO:0000000,MA:0000000,GO:0000000 patho_type pathological granularity organismal relevant_organism NCBITaxon:10088|Mus id mao title Multiple alignment namespace RO foundry No status Inactive download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/mao.obo source home MAO Home|http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html documentation contact Julie Thompson julie.thompson igbmc.u-strasbg.fr format obo description An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment. is_obsolete true id medaka_anatomy_development title Medaka fish anatomy and development namespace MFO foundry Yes status Quiescent download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/medaka_ontology.obo source home documentation contact Thorsten Henrich Thorsten.Henrich embl-heidelberg.de format obo description A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes. domain anatomy relevant_organism NCBITaxon:8089|Oryzias subtypes_of CARO:0000000 patho_type canonical granularity organismal id mged title Microarray experimental conditions namespace MO foundry No status Active download source http://mged.sourceforge.net/ontologies/MGEDOntology.owl home MGED ontology|http://mged.sourceforge.net/ontologies/MGEDontology.php documentation MGED downloads|http://mged.sourceforge.net/software/downloads.php contact MGED mged-ontologies lists.sourceforge.net format owl description Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. domain experiments id molecular_function title Molecular function namespace GO foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology_edit.obo source ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo home www.geneontology.org|http://www.geneontology.org documentation Gene Ontology documentation|http://www.geneontology.org/GO.doc.shtml contact Gene Ontology go geneontology.org format obo description Provides structured controlled vocabularies for the annotation of gene products with respect to their molecular function. One of the three vocabularies of the Gene Ontology. relevant_organism all subtypes_of bfo:DependentContinuant patho_type canonical domain biological function granularity molecular,cellular,organismal,multi-organismal id molecule_role title Molecule role (INOH Protein name/family name ontology) namespace IMR foundry No status Active download source molecule_role.obo|http://www.inoh.org/ontologies/MoleculeRoleOntology.obo home The INOH Pathway Database|http://www.inoh.org documentation INOH Ontologies|http://www.inoh.org/info/ontologies/ contact INOH curators curator inoh.org format obo description A structured controlled vocabulary of concrete protein names and generic (abstract) protein names. This ontology is a INOH pathway annotation ontology, one of a set of ontologies intended to be used in pathway data annotation to ease data integration. This ontology is used to annotate protein names, protein family names, generic/concrete protein names in the INOH pathway data.
INOH is part of the BioPAX working group. domain proteins id mosquito_anatomy title Mosquito gross anatomy namespace TGMA foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mosquito_anatomy.obo source http://www.anobase.org/anatomy/mosquito_anatomy.obo home AnoBase / Vectorbase|http://www.anobase.org documentation contact C. Louis louis imbb.forth.gr format obo description A structured controlled vocabulary of the anatomy of mosquitoes. domain anatomy relevant_organism NCBITaxon:44484|Anopheles subtypes_of CARO:0000000 patho_type canonical granularity organismal id mosquito_insecticide_resistance title Mosquito insecticide resistance namespace MIRO foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mosquito_insecticide_resistance.obo source source http://www.anobase.org/miro/miro_release.obo home AnoBase / Vectorbase|http://www.anobase.org documentation contact C. Louis louis imbb.forth.gr format obo description Application ontology for entities related to insecticide resistance in mosquitos domain environment relevant_organism NCBITaxon:44484|Anopheles subtypes_of bfo:DependentContinuant patho_type canonical granularity organismal id mouse_pathology title Mouse pathology namespace MPATH foundry Yes status Quiescent download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mouse_pathology/mouse_pathology.obo source home Pathbase|http://www.pathbase.net documentation contact Paul Schofield PS mole.bio.cam.ac.uk format obo description A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes domain health relevant_organism NCBITaxon:10088|Mus subtypes_of bfo:DependentContinuant patho_type pathological granularity organismal,cellular id ncbi_taxonomy title NCBI organismal classification namespace NCBITaxon foundry No status Active download source taxonomy.dat|ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat home NCBI Taxonomy home page|http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ documentation contact NCBI information info ncbi.nlm.nih.gov format plain text description A taxonomic classification of living organisms and associated artifacts for their controlled description within the context of databases. domain taxonomy id ncithesaurus title NCI Thesaurus namespace NCIt foundry No status Active download source EVS ftp site|ftp://ftp1.nci.nih.gov/pub/cacore/EVS/ home NCI Enterprise Vocabulary Services|http://ncicb.nci.nih.gov/core/EVS documentation NCI Terminology Browser|http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do contact NCICB Support ncicb pop.nci.nih.gov format owl description The NCI Thesaurus is an ontology-like vocabulary that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities; anatomy; agents, drugs and chemicals; genes and gene products and so on. In certain areas, like cancer diseases and combination chemotherapies, it provides the most granular and consistent terminology available. It combines terminology from numerous cancer research related domains, and provides a way to integrate or link these kinds of information together through semantic relationships. The Thesaurus currently contains over 34,000 concepts, structured into 20 taxonomic trees. The NCI Thesaurus provides concept history tables to record changes in the vocabulary over time as the science changes. Within NCI, the Thesaurus is used to provide terminology support to the Institutes public Web portal, http://cancer.gov, numerous portals supporting consortia and other communities of researchers, and is used in the caCORE as the semantic base for metadata and objects that form the infrastructure upon which the NCICB portals are built (see http://ncicb.nci.nih.gov). It is published under an open content license in a number of formats including OWL. domain health id newt title UniProt taxonomy namespace NEWT foundry No status Active download source Organism identification code list|ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt home NEWT index|http://www.ebi.ac.uk/newt documentation NEWT taxonomy help|http://www.ebi.ac.uk/newt/taxonomyhelp contact Sandrine Pilbout sandrine.pilbout isb-sib.ch format plain text description A taxonomic classification of living organisms and associated artifacts for their controlled description within the context of databases. NEWT integrates taxonomy data compiled in the NCBI database and data specific to the Swiss-Prot protein knowledgebase. domain taxonomy id nmr title NMR-instrument specific component of metabolomics investigations namespace NMR foundry No status Inactive download source https://msi-workgroups.svn.sourceforge.net/svnroot/msi-workgroups/ontology/NMR.owl home Metabolomics Standards Initiative - Ontology Working Group (MSI-OWG)|http://msi-ontology.sourceforge.net/ documentation NMR.owlDocument.doc|http://msi-ontology.sourceforge.net/ontology/NMR.owlDocument.doc contact Daniel Schober via MSI OWG mailing list msi-workgroups-ontology lists.sourceforge.net format owl description Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation. domain experiments id obi title Ontology for biomedical investigations namespace OBI foundry Yes status Discussion and review download source http://purl.obofoundry.org/obo/obi.owl home OBI Home|http://obi.sourceforge.net/index.php documentation OBI Ontology Information|http://obi.sourceforge.net/ontologyInformation/ contact OBI Developers obi-devel lists.sourceforge.net format owl description OBI models the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. This project was formerly titled the Functional Genomics Investigation Ontology (FuGO) project. domain experiments relevant_organism all subtypes_of bfo patho_type canonical granularity molecular,cellular,organismal,multi-organismal id pathway title Pathway ontology namespace PW foundry No status Active download source pathway.obo|ftp://rgd.mcw.edu/pub/data_release/pathway.obo home RGD ontology browser and viewer|http://rgd.mcw.edu/tools/ontology/ont_search.cgi documentation PW_Introduction.doc|ftp://rgd.mcw.edu/pub/data_release/PW_Introduction.doc contact Victoria Petri vpetri mcw.edu format obo description The Pathway Ontology is a controlled vocabulary for pathways that provides standard terms for the annotation of gene products. The Pathway Ontology is under development at Rat Genome Database. domain biological process id plant_environment title Plant environmental conditions namespace EO foundry No status Inactive download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/environment/environment_ontology.obo source home Gramene|http://www.gramene.org documentation Gramene Ontology website|http://www.gramene.org/plant_ontology/index.html#eo contact Pankaj Jaiswal pj37 cornell.edu format obo description A structured controlled vocabulary for the representation of plant environmental conditions. domain environment id plant_trait title Cereal plant trait namespace TO foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/plant_traits/plant_trait.obo source http://brebiou.cshl.edu/viewcvs/Poc/ontology/collaborators_ontology/gramene/traits/trait.obo home Gramene Ontology database website|http://www.gramene.org/plant_ontology/ documentation Gramene Ontology database|http://www.gramene.org/plant_ontology/index.html#to contact Gramene curators gramene gramene.org format obo description A controlled vocabulary of describe phenotypic traits in cereal plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature cereal plant. domain phenotype id plasmodium_life_cycle title Plasmodium life cycle namespace PLO foundry No status Inactive download source http://www.sanger.ac.uk/Users/mb4/PLO/PLO_ontology.txt definitions http://www.sanger.ac.uk/Users/mb4/PLO/PLO_defs.shtml home Parasite Life Cycle Ontology|http://www.sanger.ac.uk/Users/mb4/PLO/ documentation contact Matt Berriman mb4 sanger.ac.uk format go description A structured controlled vocabulary for the life cycle of the malaria parasite Plasmodium. relevant_organism NCBITaxon:5820|Drosophila domain anatomy id po_anatomy title Plant structure namespace PO foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/plant_gross_anatomy/plant/po_anatomy.obo source http://brebiou.cshl.edu/viewcvs/Poc/ontology/OBO_format/po_anatomy.obo home Plant Ontology Consortium|http://www.plantontology.org documentation Plant Ontology database|http://www.plantontology.org/docs/docs.html contact Plant Ontology Consortium developers po-dev plantontology.org format obo description A controlled vocabulary of plant morphological and anatomical structures representing organs, tissues, cell types, and their biological relationships based on spatial and developmental organization.
The plant ontologies, which includes both the plant structure and growth and development stages can be downloaded as a single file in OBO format. domain anatomy relevant_organism NCBITaxon:33090|Viridiplantae subtypes_of CARO:0000000 patho_type canonical granularity organismal id po_temporal title Plant growth and developmental stage namespace PO foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/developmental/plant_development/plant/po_temporal.obo source http://brebiou.cshl.edu/viewcvs/Poc/ontology/OBO_format/po_temporal.obo home Plant Ontology Consortium|http://www.plantontology.org documentation Plant Ontology database|http://www.plantontology.org/docs/docs.html contact Plant Ontology Consortium developers po-dev plantontology.org format obo description A controlled vocabulary of growth and developmental stages in various plants.
The plant ontologies, which includes both the plant structure and growth and development stages can be downloaded as a single file in OBO format. domain anatomy relevant_organism NCBITaxon:33090|Viridiplantae subtypes_of bfo:Occurent patho_type canonical granularity organismal id protein title protein ontology namespace PRO foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/pro.obo source pro.obo|ftp://ftp.pir.georgetown.edu/databases/ontology/pro_obo/pro.obo home Protein Ontology|http://pir.georgetown.edu/pro/ documentation PRO README|ftp://ftp.pir.georgetown.edu/databases/ontology/pro_obo/pro_readme.txt contact Darren Natale dan5 georgetown.edu format obo description PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes (ontology for ProEvo), to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies publication http://www.biomedcentral.com/content/pdf/1471-2105-8-S9-S1.pdf wiki https://pir5.georgetown.edu/wiki/PRO domain proteins relevant_organism all subtypes_of bfo:IndependentContinuant patho_type canonical granularity molecular id provenance title Proteomics data and process provenance namespace ProPreO foundry No status Active download source http://lsdis.cs.uga.edu/projects/glycomics/propreo/ProPreO-060506.owl home ProPreO Ontology home|http://lsdis.cs.uga.edu/projects/glycomics/propreo/ documentation ProPreO Ontology home|http://lsdis.cs.uga.edu/projects/glycomics/propreo/ contact Satya S. Sahoo satya30 uga.edu format owl description A comprehensive proteomics data and process provenance ontology. domain proteins id psi-mi title Protein-protein interaction namespace MI foundry Yes status Discussion and review download source http://psidev.sourceforge.net/mi/psi-mi.obo home Proteomics Standards Initiative for Molecular Interaction|http://psidev.sf.net documentation PSI documentation|http://psidev.sourceforge.net/mi/xml/doc/user/index.html contact Henning Hermjakob Henning.Hermjakob ebi.ac.uk format obo description A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Developed by the HUPO Proteomics Standards Initiative. domain experiments relevant_organism all subtypes_of bfo:IndependentContinuant patho_type canonical granularity molecular id psi-mod title Protein modification namespace MOD foundry Yes status Discussion and review download source http://psidev.sourceforge.net/mod/data/PSI-MOD.obo home Proteomic Standard Initiative for Protein Modification|http://psidev.sourceforge.net/mod/ documentation Proteomic Standard Initiative for Protein Modification|http://psidev.sourceforge.net/mod/ contact Luisa Montecchi luisa ebi.ac.uk format obo description PSI-MOD is an ontology consisting of terms that describe protein chemical modifications, logically linked by an is_a relationship in such a way as to form a direct acyclic graph (DAG). The PSI-MOD ontology has more than 45 top-level nodes, and provides alternative hierarchical paths for classifying protein modifications either by the molecular structure of the modification, or by the amino acid residue that is modified. domain proteins relevant_organism all subtypes_of bfo:IndependentContinuant patho_type canonical granularity molecular id relationship title OBO relationship types namespace OBO_REL foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo source home OBO Relation Ontology|http://www.obofoundry.org/ro documentation contact Chris Mungall obo-relations lists.sourceforge.net format obo description Defines core relations used in all OBO ontologies. domain all relevant_organism all subtypes_of bfo patho_type canonical granularity all id rex title Physico-chemical process namespace REX foundry No status Active download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/physicochemical/rex.obo source http://www.ebi.ac.uk/~kirill/REX/rex.obo home REX directory|http://www.ebi.ac.uk/~kirill/REX/ documentation contact Kirill Degtyarenko chebi-help ebi.ac.uk format obo description REX is an ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. REX includes both microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes. Some biochemical processes from Gene Ontology (GO Biological process) can be described as instances of REX. id sao title Subcellular anatomy ontology namespace SAO foundry Yes status Production and review download source http://ccdb.ucsd.edu/SAO/1.2/SAO.owl home http://ccdb.ucsd.edu/CCDBWebSite/sao.html documentation contact Bill Bug wbug ncmir.ucsd.edu format owl description We have developed the Subcellular Anatomy Ontology for the Nervous System (SAO) to provide a formal ontology to describe structures from the dimensional range known as the “mesoscale,” encompassing cellular and subcellular structure, supracellular domains, and macromolecules. The SAO describes the parts of neurons and glia and how these parts come together to define supracellular structures such as synapses and neuropil (Fong et al., submitted). Molecular specializations of each compartment and cell type are identified. The SAO was designed with the goal of providing a means to annotate cellular and subcellular data obtained from light and electron microscopy, including assigning macromolecules to their approporiate subcellular domains. The SAO thus provides a bridge between ontologies that describe molecular species and those concerned with more gross anatomical scales. Because it is intended to integrate into ontological efforts at these other scales, particular care was taken to construct the ontology in a way that supports such integration. relevant_organism NCBITaxon:9606|Homo sapiens subtypes_of bfo:IndependentContinuant domain anatomy patho_type canonical granularity sub-cellular id sep title Sample processing and separation techniques namespace SEP foundry No status Inactive download source https://psidev.svn.sourceforge.net/svnroot/psidev/psi/sepcv/trunk/sep.obo home SEP Ontology|http://psidev.info/index.php?q=node/312 documentation SEP Ontology documentation|http://psidev.info/index.php?q=node/312 contact SEP developers via the PSI and MSI mailing lists psidev-gps-dev lists.sourceforge.net format obo description A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments, such as, and including, gel electrophoresis, column chromatography, capillary electrophoresis, centrifugation and so on. Developed jointly by the HUPO Proteomics Standards Initiative and The Metabolomics Standards Initiative. domain provenance is_obsolete true id sequence title Sequence types and features namespace SO foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo source http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo home SO home|http://song.sourceforge.net/ documentation contact SONG developers song-devel lists.sourceforge.net format obo description The Sequence Ontology provides a structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases. SOFA is a minimal version of SO for use in data exchange. domain biological sequence relevant_organism all subtypes_of bfo patho_type all granularity molecular id systems_biology title Systems Biology namespace SBO foundry Yes status Discussion and review download source http://www.ebi.ac.uk/sbo/docs/exports/SBO_OBO.obo alternate_download http://www.ebi.ac.uk/sbo/docs/exports/SBO_OWL.owl home SBO : Systems Biology Ontology home|http://www.ebi.ac.uk/sbo/ documentation contact Nicolas Le Novère lenov ebi.ac.uk format owl description The Systems Biology Ontology aims to strictly index and define terms used in quantitative biochemistry. The ontology is made up of four orthogonal vocabularies. A controlled vocabulary defines the roles of reaction participants, such as "substrate", "catalyst", etc. A taxonomy orders the quantitative parameters used in biochemistry such as "Michaelis constant", but also "first-order forward rate constant". A precise classification of rate laws defines them, such as "first-order reversible mass action kinetics". Each term contains a precise mathematical expression stored as a MathML lambda function. Finally, a list of simulation frameworks, such as "discrete" or "continuous" precises the validity of a rate-law. The Systems Biology Ontology can be used to increase the semantic content of quantitative models. SBO vocabularies can also be used to annotate results of biochemical experiments in order to facilitate their efficient reuse. relevant_organism all subtypes_of bfo:IndependentContinuant domain biochemistry patho_type canonical granularity molecular id pharmacogenomics title Suggested Ontology for Pharmacogenomics namespace SOPHARM foundry Yes status Discussion and review download source http://purl.oclc.org/NET/loria/sopharm/owl/sopharm home SO-Pharm description|http://www.loria.fr/~coulet/sopharm2.0_description.php documentation SO-Pharm documentation|http://www.loria.fr/~coulet/ontology/sopharm/version2.0/owlDoc/index.html contact Adrien Coulet Adrien.Coulet loria.fr format owl description SO-Pharm is a formal ontology that represent domain knowledge in pharmacogenomics. To achieve this goal SO-Pharm articulates ontologies from sub domains of phamacogenomics (i.e. genotype, phenotype, drug, trial representations). SO-Pharm enables to support knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. domain health relevant_organism NCBITaxon:9606|Homo sapiens subtypes_of bfo patho_type pathological granularity molecular,cellular,organismal,multi-organismal id teleost_anatomy title Teleost anatomy and development namespace TAO foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/teleost_anatomy.obo source home PhenoScape|https://www.nescent.org/phenoscape/Main_Page documentation contact obo-teleost obo-teleost-discuss lists.sourceforge.net format obo description Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa relevant_organism NCBITaxon:32443|Teleostei subtypes_of bfo:IndependentContinuant patho_type canonical domain anatomy granularity organismal xrefs_to zebrafish_anatomy id teleost_taxonomy title Teleost taxonomy namespace TTO foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/teleost_taxonomy.obo source home PhenoScape|https://www.nescent.org/phenoscape/Main_Page documentation contact Peter Midford peteremidford yahoo.com format obo description The Teleost taxonomy ontology is being used to facilitate annotation of phenotypes, particularly for taxa that are not covered by NCBI because no submissions of molecular data have been made. Taxonomy ontologies can also be valuable in annotating legacy data, where authors make phenotype or ecological assertions (e.g., host-parasite associations) that refer to groups that are reorganized or no longer recognized. The taxonomy ontology serves as the source of taxa for our project's use for identifying evolutionary changes that match the phenotype of a zebrafish mutant. relevant_organism NCBITaxon:32443|Teleostei subtypes_of bfo:IndependentContinuant patho_type canonical domain taxonomy granularity organismal id transmission title Pathogen transmission namespace TRANS foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/transmission_process.obo source http://gemina.cvs.sourceforge.net/*checkout*/gemina/Gemina/ontologies/transmission_process.obo home Disease Ontology|http://diseaseontology.sourceforge.net/ documentation contact Lynn Schriml diseaseontology-discussion lists.sourceforge.net format obo description This vocabulary describes a process that is the means of how a pathogen is transmitted from one host, reservoir, or source to another host. This transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles. relevant_organism NCBITaxon:9606|Homo sapiens subtypes_of patho_type canonical granularity organismal,cellular domain health id cereal_anatomy title Cereal plant gross anatomy namespace GRO foundry No status Inactive download source http://brebiou.cshl.edu/viewcvs/Poc/ontology/OBO_format/po_anatomy.obo home Gramene Ontology database website|http://www.gramene.org/plant_ontology/ documentation Gramene Ontology database|http://www.gramene.org/plant_ontology/index.html#po contact Gramene curators gramene gramene.org format obo description A structured controlled vocabulary for the anatomy of Graminae. Please note that this ontology has now been superseded by the plant anatomy ontology. domain anatomy is_obsolete true consider po_anatomy id temporal_gramene title Cereal plant development namespace GRO foundry No status Inactive download source http://brebiou.cshl.edu/viewcvs/Poc/ontology/collaborators_ontology/gramene/temporal_gramene.obo home Gramene Ontology database website|http://www.gramene.org/plant_ontology/ documentation Gramene Ontology database|http://www.gramene.org/plant_ontology/index.html#po contact Gramene curators gramene gramene.org format obo description A structured controlled vocabulary for expressing cereal plant development and growth stages. is_obsolete true consider po_temporal id tick_anatomy title Tick gross anatomy namespace TADS foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/tick_anatomy.obo source http://www.anobase.org/anatomy/tick_anatomy.obo home AnoBase / VectorBase|http://www.anobase.org documentation contact Daniel Sonenshine dsonensh odu.edu format obo description The anatomy of the Tick, Families: Ixodidae, Argassidae domain anatomy relevant_organism NCBITaxon:6939|Ixodidae subtypes_of CARO:0000000 patho_type canonical granularity organismal id unit title Units of measurement namespace UO foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo source home PATO wiki|http://www.bioontology.org/wiki/index.php/PATO:Main_Page documentation contact OBO Unit list obo-unit lists.sourceforge.net format obo description Metrical units for use in conjunction with PATO relevant_organism all subtypes_of bfo:DependentContinuant patho_type canonical domain phenotype granularity molecular,cellular,organismal,multi-organismal id worm_anatomy title C. elegans gross anatomy namespace WBbt foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/worm/worm_anatomy/WBbt.obo source http://brebiou.cshl.edu/viewcvs/*checkout*/Wao/WBbt.obo home Wormbase|http://www.wormbase.org/ documentation contact Raymond Lee raymond caltech.edu format obo description A structured controlled vocabulary of the anatomy of Caenorhabditis elegans. relevant_organism NCBITaxon:6237|Caenorhabditis subtypes_of bfo:IndependentContinuant patho_type canonical domain anatomy granularity organismal id worm_development title C. elegans development namespace WBls foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/developmental/animal_development/worm/worm_development.obo source http://tazendra.caltech.edu/~azurebrd/var/work/phenote/worm_development.obo home WormBase|http://www.wormbase.org/ documentation contact Wen J. Chen wchen its.caltech.edu format obo description A structured controlled vocabulary of the development of Caenorhabditis elegans. domain anatomy relevant_organism NCBITaxon:6237|Caenorhabditis subtypes_of bfo:Occurent patho_type canonical granularity organismal id worm_phenotype title C. elegans phenotype namespace WBPhenotype foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype.obo source http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi home WormBase|http://www.wormbase.org/ documentation contact Gary Schindelman garys caltech.edu format obo description A structured controlled vocabulary of Caenorhabditis elegans phenotypes domain phenotype relevant_organism NCBITaxon:6237|Caenorhabditis subtypes_of bfo:DependentContinuant patho_type pathological granularity organismal id xenopus_anatomy title Xenopus anatomy and development namespace XAO foundry Yes status Discussion and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/frog/xenopus_anatomy.obo source ftp://ftp.xenbase.org/pub/XenopusAnatomyOntology/xenopus_anatomy.obo home Xenbase Atlas|http://www.xenbase.org/anatomy/atlas.do documentation contact Erik Segerdell esegerde ucalgary.ca format obo description A structured controlled vocabulary of the anatomy and development of the African clawed frog (Xenopus laevis). relevant_organism NCBITaxon:8353|Xenopus subtypes_of bfo:IndependentContinuant patho_type canonical domain anatomy granularity organismal id zea_mays_anatomy title Maize gross anatomy namespace ZEA foundry No status Inactive source http://brebiou.cshl.edu/viewcvs/Poc/ontology/collaborators_ontology/maizegdb/Zea_mays_anatomy_ontology.txt definitions http://brebiou.cshl.edu/viewcvs/Poc/ontology/collaborators_ontology/maizegdb/Zea_mays_anatomy_ontology_definitions.txt home Maizemap|http://www.maizemap.org/ documentation contact Leszek Vincent Leszek missouri.edu format obo description A structured controlled vocabulary for the anatomy of Zea mays. relevant_organism NCBITaxon:4575|Zea subtypes_of bfo:IndependentContinuant patho_type canonical domain anatomy granularity organismal is_obsolete true id zebrafish_anatomy title Zebrafish anatomy and development namespace ZFA foundry Yes status Production and review download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/zebrafish_anatomy.obo source prerelease_download http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/preversion.zfish.obo home ZFIN Summary|http://zfin.org/zf_info/anatomy/dict/sum.html documentation contact ZFIN administrators zfinadmin zfin.org format obo description A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio). relevant_organism NCBITaxon:7954|Danio subtypes_of bfo:IndependentContinuant patho_type canonical domain anatomy granularity organismal