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Ontology Name Visibility Terms Notes Reviews Projects Format Version Uploaded Contact Description categories groups
Cell Behavior Ontology (CBO) Public 241 0 0 7 OWL 1.0.0 04/17/2013 James P. Sluka Description: The Cell Behavior Ontology (CBO) describes multi-cell computational models. In particular to describe both the existential behaviors of cells (spatiality, growth, movement, adhesion, death, ...) and computational models of those behaviors.
Categories : Biological Process , Cell , All Organisms 		5060 5065 5073
Drosophila Development Ontology (FB-DV) Public 132 0 0 5 OBO unknown 02/15/2011 David Osumi-Sutherland Description: A structured controlled vocabulary of the development of Drosophila melanogaster.
Categories : Animal Development , Development 		2818 2803
NMR-instrument specific component of metabolomics investigations (NMR) Public 479 1 0 7 OWL 13.10.2006 11/19/2010 Daniel Schober Description: Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation.
Categories :
Medical Subject Headings (MESH) Public 229,698 0 1 12 RRF 2012_2011_09_09 02/02/2012 Stuart Nelson, M.D. Description: Medical Subject Headings (MeSH);National Library of Medicine; 2011
Categories : Health 		5058 ,UMLS,
Electrocardiography Ontology (ECG) Public 1,117 0 0 9 OWL 1.0 04/30/2013 Raimond L. Winslow, PhD & Stephen Granite Description: The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms.
Categories : Biomedical Resources 		5059
Protein modification (MOD) Public 1,338 0 0 4 OBO See Remote Site 03/03/2010 Psi-mod Administrators 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.
Categories : 		,PSI,
PRotein Ontology (PR) Public 35,470 0 0 8 OBO 34.0. 04/29/2013 Darren Natale Description: PRO provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp).
Categories : 		,OBO Foundry,
Mouse Adult Gross Anatomy Ontology (MA) Public 3,020 0 0 9 OBO unknown 03/15/2013 Terry Hayamizu Description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus).
Categories : Mouse Anatomy , Anatomy , Animal Gross Anatomy , Gross Anatomy 		2817 2810 2812 2811
Tick gross anatomy (TADS) Public 628 0 0 5 OBO 1.21 05/06/2013 Daniel Sonenshine Description: The anatomy of the Tick, Families: Ixodidae, Argassidae
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy 		2810 2812 2811
Ontology for Biomedical Investigations (OBI) Public 3,689 4 1 24 OWL 2012-07-01 07/16/2012 Bjoern Peters Description: OBI is an ontology of investigations, the protocols and instrumentation used, the material used, the data generated and the types of analysis performed on it.

To import,
Latest version (2012-07-01, OBI Summer 2012 release): http://purl.obolibrary.org/obo/obi.owl

Latest release notes at http://purl.obolibrary.org/obo/obi/release-notes.html

Note: BFO 2.0 pre-Graz release (not official release version) was used in this release.
Categories : Experimental Conditions 		2805 ,CTSA,
SNP-Ontology (SNPO) Public 2,256 0 0 4 OWL 1.6 full 01/15/2009 Adrien Coulet Description: SNP-Ontology is a domain ontology that provides a formal representation (OWL-DL) of genomic variations. Despite its name, SNP-Ontology, is not limited to the representation of SNPs but it encompasses genomic variations in a broader meaning. SNP-Ontology is general enough to enable the representation of variations observed in genome of various species. Latest versions of SNP-Ontology include the representation of haplotype and of CNV. The unambiguous representation of genomic variations provided by SNP-Ontology enables to integrate heterogeneous data related to genomic variations. To achieve this goal SNP-Ontology enables (1) to represent one variation in accordance with various ways that exist for describing it, (2) to represent the equivalence between two distinct descriptions of one variation, and (3) to represent correspondence between a genomic variation and its outcome at the transcriptome and proteome levels.
Categories : Genomic and Proteomic 		2806
African Traditional Medicine Ontology (ATMO) Public 223 2 3 4 OBO 1.101 06/28/2009 Ghislain Atemezing Description: African Traditional Medicine Ontology (ATMO) describes the actors' function (healer, fetishist or soothsayer); the different types of proposed process treatment, the symptom's roles and the disease consideration.
Categories : Health 		5058
BioTop Ontology (BT) Public 389 0 0 5 OWL Last modificationApr 24, 2012 by Stefan Schulz 04/24/2012 Stefan Schulz Description: A top-domain ontology that provides definitions for the foundational entities of biomedicine as a basic vocabulary to unambiguously describe facts in this domain.
Categories : Upper Level Ontology 		5075
Spatial Ontology (BSPO) Public 133 0 0 6 OBO unknown 05/17/2013 Chris Mungall Description: A small ontology for anatomical spatial references, such as dorsal, ventral, axis, and so forth.
Categories : Anatomy 		2810
GeoSpecies Ontology (GEOSPECIES) Public 0 0 0 3 OWL 2009-05-04 05/06/2009 Peter J. DeVries Description: This ontology was designed to help integrate species concepts with species occurrences, gene sequences, images, references and geographical information. See also Taxonconcept.org
Categories : Other 		2801
Chemical Entities of Biological Interest Ontology (CHEBI) Public 40,599 2 1 14 OBO 104 06/11/2013 Janna Hastings Description: A structured classification of chemical compounds of biological relevance.
Categories : Chemical 		2802 ,OBO Foundry,
Loggerhead Nesting Ontology (LHN) Public 308 0 0 4 OBO 13:01:2004 11/19/2010 Peter Midford 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.
Categories :
Mobile Genetic Element Ontology (MEGO) Public 368 0 0 3 OBO 1_8 05/14/2009 Ariane Toussaint Description: MeGO is a Gene Ontology under construction dedicated to the functions of mobile genetic elements. The terms defined in MeGO are used to annotate phage and plasmid protein families in ACLAME.
Categories : Biological Process , Gene Product 		5060 2820
Pseudogene (pseudo) Public 23 0 0 4 OBO 0.1 11/18/2008 Gerstein Lab Description:
Categories :
C. elegans Development Vocabulary (WB-LS) Public 89 0 0 4 OBO unknown 06/12/2013 Worm_development Administrators Description: A structured controlled vocabulary of the development of Caenorhabditis elegans.
Categories : Animal Development , Development 		2818 2803
Gene Ontology (GO) Public 39,464 0 1 58 OBO 2013-06-15 06/15/2013 Go Helpdesk Description: Provides structured controlled vocabularies for the annotation of gene products with respect to their molecular function, cellular component, and biological role. The Gene Ontology consists of three Vocabularies.
Categories : Genomic and Proteomic 		2806 ,CTSA,OBO Foundry,UMLS,caBIG,
Family Health History Ontology (FHHO) Public 238 0 0 5 OWL 1.0 05/10/2009 Jane Peace Description: The FHHO facilitates representing the family health histories of persons related by biological and/or social family relationships (e.g. step, adoptive) who share genetic, behavioral, and/or environmental risk factors for disease. SWRL rules are included to compute 3 generations of biological relationships based on parentage and family history findings based on personal health findings.
Categories : Health 		5058
Plant Anatomy (PO_PAE) Public 1,294 0 0 8 OBO Version #18, July 2012 07/15/2012 Pankaj Jaiswal Description: REPLACED BY: Plant Ontology (PO). A controlled vocabulary of plant morphological and anatomical structures representing organs, tissues, cell types, and their biological relationships based on spatial and developmental organization. Note that this has been subsumed into the PO. This file is created by filtering plant_ontology_assert_basic.obo to contain only terms from the plant anatomical entity branch of the PO. For more information, please see: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/
Categories : Plant , Plant Anatomy 		5063 2816
Ontology for Genetic Interval (OGI) Public 204 0 0 4 OWL 2.0 03/29/2013 Yu Lin Description: Using BFO as its framwork, OGI formalized the genomic element by defining an upper class 'genetic interval'. The definition of 'genetic interval' is "the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.
Categories : Genomic and Proteomic 		2806
Experimental Factor Ontology (EFO) Public 13,338 4 0 8 OWL 2.36 05/15/2013 James Malone Description: The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental variables in the Gene Expression Atlas, EBI. The ontology has been developed to increase the richness of the annotations that are currently made in the ArrayExpress repository, to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology describes cross-product classes from reference ontologies in area such as disease, cell line, cell type and anatomy. Contact James Malone for info: malone@ebi.ac.uk
Categories : Biological Process , Experimental Conditions 		5060 2805
Ontology of Physics for Biology (OPB.properties) Public 678 2 0 6 OWL 0.960 07/13/2012 Daniel L. Cook Description: The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.
Categories : Biological Process , Phenotype , Biomedical Resources , Physicochemical , Chemical 		5060 2807 5059 2822 2802
Sample processing and separation techniques (SEP) Public 194 0 0 6 OBO 1.070708 02/28/2009 SEP developers 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.
Categories : 		,PSI,
MedlinePlus Health Topics (MEDLINEPLUS) Public 970 0 0 3 RRF 20080614 07/31/2009 Ms. Naomi Miller Description: MedlinePlus Health Topics;National Library of Medicine;June 14, 2008;Bethesda, MD
Categories : Health 		5058 ,UMLS,
BRENDA Tissue and Enzyme Source Ontology (BTO) Public 5,444 1 0 5 OBO unknown 05/07/2013 BrendaTissue Administrators 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.
Categories :
Minimal Anatomical Terminology (MAT) Public 461 1 0 4 OBO 1.1 07/05/2009 EMAP Administrators Description: Minimal set of terms for anatomy
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy 		2810 2812 2811
Common Anatomy Reference Ontology (CARO) Public 50 0 0 5 OBO unknown 12/14/2011 Melissa Haendel 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)
Categories : Anatomy 		2810
Neural ElectroMagnetic Ontology (NEMO) Public 1,817 2 0 6 OWL v2.99 05/23/2013 Gwen Frishkoff Description: Neural ElectroMagnetic Ontology (NEMO) describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters). Working (unstable), Release (stable), and Old (archival) versions of NEMO can be found on sourceforge: http://sourceforge.net/projects/nemoontologies/.
Categories : Biological Process , Human , Anatomy , Experimental Conditions , Imaging 		5060 5062 2810 2805 5057
Physico-chemical process (REX) Public 552 0 0 4 OBO unknown 02/15/2011 Chebi Administrators 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.
Categories : Physicochemical 		2822
Fly Taxonomy (FB-SP) Public 6,599 0 0 5 OBO unknown 02/15/2011 Evidence_code Administrators Description: The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.
Categories : Taxonomic Classification 		2808
Biomedical Informatics Research Network Project Lexicon (BIRNLEX) Public 3,580 0 0 7 OWL 1.3.1 03/24/2008 William Bug Description: The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design.
Categories : Anatomy , Imaging 		2810 5057
Ontology of Clinical Research (OCRe) (OCRe) Public 385 7 0 5 OWL Revision 265 05/31/2013 Ida Sim Description: OCRe is an ontology designed to support systematic description of, and interoperable queries on, human studies and study elements.
Categories : Biomedical Resources 		5059 ,CTSA,
Teleost Anatomy Ontology (TAO) Public 3,371 2 0 5 OBO 2012-08-10 08/17/2012 Wasila Dahdul Description: TAO is a multispecies anatomy ontology for teleost fishes. Originally seeded from ZFA, but intended to cover terms relevant to other taxa.
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy , Fish Anatomy 		2810 2812 2811 2813
Hymenoptera Anatomy Ontology (HAO) Public 2,040 0 0 3 OWL 2012-11-28 11/28/2012 HAO developers Description: A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, sawflies and ants)
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy 		2810 2812 2811
Mosquito Gross Anatomy Ontology (TGMA) Public 1,864 0 0 5 OBO unknown 09/15/2011 C. Louis Description: A structured controlled vocabulary of the anatomy of mosquitoes.
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy 		2810 2812 2811
Bleeding History Phenotype Ontology (BHO) Public 543 0 0 4 OWL 0.4 12/22/2010 Shamim Mollah Description: An application ontology devoted to the standardized recording of phenotypic data related to hemorrhagic disorders.
Categories : Phenotype 		2807 ,CTSA,
Biomedical Resource Ontology (BRO) Public 486 73 1 8 OWL 3.2.1 08/31/2010 Trish Whetzel, Csongor Nyulas, Natasha Noy Description: A controlled terminology of resources, which is used to improve the sensitivity and specificity of web searches.
Categories : Biomedical Resources 		5059 ,CTSA,
Human Phenotype Ontology (HP) Public 10,132 0 0 12 OBO unknown 06/14/2013 Peter Robinson Description: The Human Phenotype Ontology is being developed to provide a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. Our goal is to provide resource for the computational analysis of the human phenome, with a current focus on monogenic diseases listed in the Online Mendelian Inheritance in Man (OMIM) database, for which annotations are also provided.
Categories : Human , Phenotype 		5062 2807
Biological Imaging Methods (FBbi) Public 624 0 0 6 OBO unknown 06/09/2011 Chris Woodcock Description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.
Categories : Experimental Conditions , Imaging 		2805 5057
Human Developmental Anatomy Ontology, abstract version 1 (EHDAA) Public 2,314 0 0 5 OBO unknown 02/15/2011 EMAP Administrators 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.
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy , Human Developmental Anatomy 		2810 2812 2811 2814
Systems Biology (SBO) Public 557 0 0 6 OBO 19:04:2011 20:42 05/03/2011 Nicolas Le Novere Description: The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. The ontology consists of six orthogonal vocabularies defining: the roles of reaction participants (eg. "substrate"), quantitative parameters (eg. "Michaelis constant"), a precise classification of mathematical expressions that describe the system (eg. "mass action rate law"), the modeling framework used (eg. "logical framework"), and a branch each to describe entity (eg. "macromolecule") and interaction (eg. "process") types, and a branch to define the different types of metadata that may be present within a model. SBO terms can be used to introduce a layer of semantic information into the standard description of a model, or to annotate the results of biochemical experiments in order to facilitate their efficient reuse. SBO is an Open Biomedical Ontologies (OBO) candidate ontology, and is free for use. More information about SBO can be found from the project FAQ, at http://www.ebi.ac.uk/sbo/ SBO is a project of the BioModels.net effort and is developed through community collaboration.
Categories : Vocabularies 		2809
Zebrafish anatomy and development (ZFA) Public 2,845 2 0 6 OBO unknown 04/12/2013 ZFIN administrators Description: A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio).
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy , Fish Anatomy 		2810 2812 2811 2813 ,OBO Foundry,
Plant Trait Ontology (TO) Public 1,311 0 0 6 OBO unknown 06/18/2013 Pankaj Jaiswal Description: A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part.
Categories : Plant , Phenotype 		5063 2807
Logical Observation Identifier Names and Codes (LOINC) Public 171,399 0 0 7 UMLS 236 06/08/2012 Ms. Kathy Mercer, LOINC Developer Description: Logical Observation Identifier Names and Codes (LOINC);Version 2.26;January 2, 2009
Categories : Health 		5058 ,UMLS,caBIG,
Gene Regulation Ontology (GRO) Public 511 0 0 6 OWL 0.5 10/11/2010 Vivian Lee Description: The Gene Regulation Ontology (GRO) 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.
Categories : Genomic and Proteomic 		2806
Phenotypic quality (PATO) Public 2,378 0 0 12 OBO unknown 05/21/2013 George Gkoutos 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.
Categories : 		,OBO Foundry,
Teleost taxonomy (TTO) Public 38,705 0 0 5 OBO unknown 07/19/2012 Peter Midford 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.
Categories : Taxonomic Classification 		2808
C. elegans Gross Anatomy Vocabulary (WB-BT) Public 7,203 0 0 4 OBO 2013-04-17 04/17/2013 Raymond Lee Description: A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy 		2810 2812 2811
Maize Gross Anatomy Ontology (ZEA) Public 179 0 0 7 OBO 1.2 04/12/2012 Leszek Vincent
Categories : Plant Anatomy 		2816
Cereal Plant Development Ontology (GRO-CPD) Public 235 0 0 6 OBO 1.6 08/24/2007 Plant Ontology Administrators Description: A structured controlled vocabulary for describing cereal plant development and growth stages. Please note that this ontology has now been superseded by the Plant Ontology.
Categories : Plant Development , Plant , Development 		2819 5063 2803
Physician Data Query (PDQ) Public 9,648 0 0 3 RRF 2010_08_10 12/20/2010 Volker Englisch Description: Physician Data Query (PDQ) Terminology is part of NCI's comprehensive cancer information database, which contains expert summaries on a wide range of cancer topics, a listing of some 30,000 cancer clinical trials from around the world, a directory of genetics services professionals, the NCI Dictionary of Cancer Terms, and the NCI Drug Dictionary.
Categories : Health 		5058 ,UMLS,
Ontology for Parasite LifeCycle (OPL) Public 359 0 0 4 OWL 2012-09-07 09/19/2012 Priti Parikh Description: The Ontology for Parasite LifeCycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.
Categories : Vocabularies , Phenotype , Development 		2809 2807 2803
Plant environmental conditions (EO) Public 500 1 0 7 OBO 1.6 02/15/2011 Pankaj Jaiswal Description: A structured controlled vocabulary for the representation of plant environmental conditions.
Categories : Phenotype 		2807
Sequence types and features (SO) Public 2,151 0 0 19 OBO unknown 11/01/2012 So Administrators 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.
Categories : Genomic and Proteomic 		2806
Proteomics Pipeline Infrastructure for CPTAC (CPTAC) Public 19 0 0 4 OWL alpha 1.1 05/20/2009 Fan Zhang Description: a basic ontology which describes the proteomics pipeline infrastructure for CPTAC project
Categories : Genomic and Proteomic 		2806
National Drug File (NDFRT) Public 45,757 0 0 4 RRF 2011_09_06 03/21/2012 Michael J. Lincoln MD Description: National Drug File - Reference Terminology Public Inferred Edition, 2008_03_11
Categories : Health 		5058 ,UMLS,
Computer-Based Patient Record Ontology (CPRO) Public 135 0 0 4 OWL Last modification: July 31th, 2011 Chimezie Ogbuji 04/24/2013 Chimezie Ogbuji Description: A uniform core set of data elements (whose formal semantics are captured in OWL) for use in a Computer-Based Patient Record (CPR)
Categories : Health 		5058
Protein Ontology [by Sidhu] (pro-ont) Public 42 0 1 4 OWL 2.0 05/18/2009 Dr. Amandeep S. Sidhu Description: Protein Ontology defines the basic concepts and relationships in the proteomics domain and the rules for combining data and information sources using these concepts and relationships. This helps us in obtaining complete protein information from diverse protein sources through Protein Ontology. Concepts are data descriptors for proteomics data and the relationships are used to link these concepts throughout the ontology. The Protein Ontology has (1) a hierarchical classification of concepts, from general to specific; (2) a list of properties related to each concept; (3) a set of relationships linking concepts in the ontology in more complicated ways than implied by the hierarchy, promoting their reuse; and (4) a set of algebraic operators for integrating diverse protein data sources and querying protein ontology instances. Protein Ontology describes sequence, structure, and functionality of proteins using concepts of Entry (Identification of Proteins), Structure (Three Dimensional Atomic Structure of Protein), StructuralDomains (Secondary Structures of Proteins), FunctionalDomains (First Functional Domain Classification Model for Proteins), ChemicalBonds (Chemical Bonds in Protein Structure) and Constraints (like Gene Defects that affect Protein Structure). There is no existing methodology that integrates protein data in so much detail.
Categories : Genomic and Proteomic , Protein 		2806 2821
Coding Symbols for a Thesaurus of Adverse Reaction Terms (COSTART) Public 1,641 0 0 3 RRF 1995 07/31/2009 U.S. Food and Drug Administration Center for Drug Evaluation and Research Description: Coding Symbols for Thesaurus of Adverse Reaction Terms (COSTART). 5th ed. Rockville (MD). COSTART is used for coding, filing, and retrieving post-marketing adverse drug and biologic experience reports. COSTART is organized in body system and pathophysiology hierarchies, as well as a separate fetal/neonatal category of less than 20 terms. COSTART has been superseded by the Medical Dictionary for Regulatory Activities (MedDRA) Terminology. For more information about MedDRA in the Metathesaurus, see the MedDRA source synopsis. COSTART was last updated in the Metathesaurus in 1999.
Categories : Health 		5058 ,UMLS,
Breast Cancer Grading Ontology (BCGO) Public 129 0 0 4 OWL 1.5 05/24/2011 Alexandra Bulzan Description: assigns a grade to a tumor starting from the 3 criteria of the NGS
Categories : Biological Process 		5060
International Classification of Primary Care (ICPC) Public 747 0 0 3 RRF 1993 07/31/2009 Henk Lamberts, University of Amsterdam Description: The International Classification of Primary Care (ICPC). Denmark: World Organisation of Family Doctors, 1993.
Categories : Health 		5058 ,UMLS,
Suggested Ontology for Pharmacogenomics (SOPHARM) Public 44,806 0 0 4 OWL 2.1.2 02/06/2009 Adrien Coulet Description: SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. SO-Pharm articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables to represent pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables to represent patient and more largely panel included in trials, and populations. SO-Pharm enables the representation of measured items on this patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains.
Categories : Genomic and Proteomic 		2806
SNOMED Clinical Terms (SNOMEDCT) Public 395,036 2 1 18 UMLS 2011_07_31 02/13/2012 Vivian A. Auld Description: SNOMED Clinical Terms
Categories : Health 		5058 ,UMLS,caBIG,
Human Developmental Anatomy Ontology, timed version (EHDA) Public 8,340 0 0 4 OBO unknown 02/15/2011 EMAP Administrators 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.
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy , Human Developmental Anatomy 		2810 2812 2811 2814
Physico-chemical methods and properties (FIX) Public 1,163 0 0 4 OBO unknown 12/14/2010 Kirill Degtyarenko 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.
Categories :
Symptom Ontology (SYMP) Public 936 0 0 6 OWL unknown 06/03/2013 Lynn Schriml Description: The symptom ontology was designed around the guiding concept of a symptom being: "A perceived change in function, sensation or appearance reported by a patient indicative of a disease". Understanding the close relationship of Signs and Symptoms, where Signs are the objective observation of an illness, the Symptom Ontology will work to broaden it's scope to capture and document in a more robust manor these two sets of terms. Understanding that at times, the same term may be both a Sign and a Symptom
Categories :
Xenopus anatomy and development (XAO) Public 1,285 0 0 5 OBO 2012-12-21 12/21/2012 Virgilio Ponferrada Description: A structured controlled vocabulary of the anatomy and development of the African clawed frog (Xenopus laevis).
Categories : 		,OBO Foundry,
OBO relationship types (OBO_REL) Public 0 0 0 21 OBO unknown 05/05/2011 Chris Mungall Description: Defines core relations used in all OBO ontologies. Obsolete. Replaced with RO.
Categories :
Dermatology Lexicon (DERMLEX) Public 6,104 0 0 4 OWL 1.0 04/17/2009 Naomi Levinthal Description: Version 1.0 of the American Academy of Dermatology's DermLex: The Dermatology Lexicon, a standardized terminology of dermatologic diagnoses, therapies, procedures, and laboratory tests.
Categories : Health 		5058
Malaria Ontology (IDOMAL) Public 2,595 2 0 3 OBO 1.2.9 05/29/2013 Pantelis Topalis Description: An application ontology for malaria extending the infectious disease ontology (IDO).
Categories : Biological Process , Human , Phenotype , Health , Other 		5060 5062 2807 5058 2801
Parasite Experiment Ontology (PEO) Public 143 0 0 3 OWL 1.0 06/20/2011 Priti Parikh Description: The Parasite Experiment Ontology (PEO) models provenance metadata associated with experiment protocols used in parasite research. The PEO extends the upper-level Provenir ontology (http://knoesis.wright.edu/provenir/provenir.owl) to represent parasite domain-specific provenance terms. The PEO (v 1.0) includes Proteome, Microarray, Gene Knockout, and Strain Creation experiment terms along with other terms that are used in pathway.
Categories :
Amphibian Taxonomy (ATO) Public 6,135 0 0 3 OBO See Remote Site 11/02/2009 AmphiAnat list Description: A taxonomy of Amphibia
Categories : Taxonomic Classification 		2808
Medaka Fish Anatomy and Development Ontology (MFO) Public 4,358 0 0 4 OBO unknown 06/09/2011 Medaka_ontology Administrators Description: A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy , Fish Anatomy 		2810 2812 2811 2813
WHO Adverse Reaction Terminology (WHO) Public 1,724 0 0 3 RRF 1997 07/31/2009 WHO Collaborating Centre for International Drug Monitoring Description: WHO Adverse Reaction Terminology, 1997
Categories : Health 		5058 ,UMLS,WHO-FIC,
Mouse Gross Anatomy and Development Ontology (EMAP) Public 13,731 0 0 5 OBO unknown 02/15/2011 EMAP Administrators Description: A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).
Categories : Mouse Anatomy , Anatomy , Animal Gross Anatomy , Gross Anatomy 		2817 2810 2812 2811
Drosophila Gross Anatomy Ontology (FB-BT) Public 8,064 0 0 6 OBO 1.23 04/16/2013 David Osumi-Sutherland Description: A structured controlled vocabulary of the anatomy of Drosophila melanogaster.
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy 		2810 2812 2811
Amphibian Gross Anatomy Ontology (AAO) Public 1,603 0 0 6 OBO unknown 07/22/2011 David Blackburn Description: A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon.
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy 		2810 2812 2811
Habronattus Courtship Ontology (HC) Summary Only 0 0 0 4 PROTEGE unknown 01/06/2012 Peter Midford 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.
Categories :
BioPortal Metadata Ontology (BP-METADATA) Public 27 0 0 4 OWL 0.9.3 06/18/2010 Natasha Noy Description: This ontology represents the structure that BioPortal uses to represent all of its metadata (ontology details, mappings, notes, reviews, views)
Categories : Other 		2801
Plant Structure Development Stage (PO_PSDS) Public 315 0 0 8 OBO Version #18, July 2012 07/15/2012 Plant Ontology Administrators Description: REPLACED BY: Plant Ontology (PO). A controlled vocabulary of growth and developmental stages in various plants. Note that this has been subsumed into the Plant Ontology (PO). This file is created by filtering plant_ontology_assert_basic.obo to contain only terms from the plant structure development stage branch of the PO. For more information, please see: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/
Categories : Plant Development , Plant , Development 		2819 5063 2803
NCBI organismal classification (NCBITaxon) Public 847,760 0 1 14 OWL 1.2 07/11/2012 NCBI information Description: The NCBITaxon ontology is an automatic translation of the NCBI taxonomy (a taxonomic classification of living organisms and associated artifacts) database into obo/owl.
Categories : Taxonomic Classification 		2808 ,UMLS,
Ontology of homology and related concepts in biology (HOM) Public 66 0 0 4 OBO 1.4 01/04/2010 Julien Roux Description: This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.
Categories : Anatomy , Molecule , Development , Other , All Organisms 		2810 5069 2803 2801 5073
Fungal Gross Anatomy Ontology (FAO) Public 90 0 0 4 OBO unknown 04/08/2013 Fungal_anatomy Administrators Description: A structured controlled vocabulary for the anatomy of fungi.
Categories : Anatomy , Gross Anatomy , Microbial Anatomy 		2810 2811 2815
Adult Mouse Brain Ontology (Allen Brain Atlas) (ABA-AMB) Public 913 0 1 6 OWL 1.0 08/08/2009 Allen Institute for Brain Science Description: Allen Brain Atlas P56 Mouse Ontology
Categories : Mouse Anatomy 		2817
C. elegans Phenotype Vocabulary (WB-PHENOTYPE) Public 2,142 0 0 4 OBO unknown 05/29/2013 Gary Schindelman Description: A structured controlled vocabulary of Caenorhabditis elegans phenotypes
Categories : Phenotype 		2807
Environment Ontology (ENVO) Public 1,639 1 0 9 OBO releases/2013-06-14 06/15/2013 Envo Administrators Description: Ontology of environmental features and habitats
Categories : 		,BIS,
Galen Ontology (GALEN) Public 23,141 0 0 4 OWL 1.1 01/16/2007 Julian Seidenberg Description: A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.
Categories : Other 		2801
Basic Formal Ontology (BFO) Public 39 0 1 21 OWL 1.1 07/24/2009 Barry Smith Description: BFO grows out of a philosophical orientation which overlaps with that of DOLCE and SUMO. Unlike these, however, it is narrowly focused on the task of providing a genuine upper ontology which can be used in support of domain ontologies developed for scientific research, as for example in biomedicine within the framework of the OBO Foundry. Thus BFO does not contain physical, chemical, biological or other terms which would properly fall within the special sciences domains.
Categories : Upper Level Ontology 		5075
Lipid Ontology (LIPRO) Public 715 0 0 4 OWL unknown 08/06/2010 Christipher Baker Description: Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied. The ontology describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define membership requirements for sub classes of lipid according to appropriate functional groups.
Categories :
Multiple Alignment Ontology (MAO) Public 166 0 0 4 OBO unknown 12/14/2010 Julie Thompson Description: An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment.
Categories :
Cancer Research and Management ACGT Master Ontology (ACGT-MO) Public 1,813 0 0 4 OWL 1.1 03/17/2010 Mathias Brochhausen Description: The intention of the ACGT Master Ontology (MO) is to represent the domain of cancer research and management in a computationally tractable manner.
Categories : Health 		5058
Epoch Clinical Trial Ontology (CTONT) Public 112 0 0 4 OWL 0.9 03/20/2007 Ravi Shankar, Stanford Medical Informatics
Categories : Experimental Conditions 		2805
Units of measurement (UO) Public 322 0 1 8 OBO unknown 04/18/2013 George Gkoutos Description: Metrical units for use in conjunction with PATO
Categories :
Ontology for disease genetic investigation (ODGI) Public 384 0 0 4 OWL 1.0 01/30/2013 Yu Lin Description: It is the ontology used to model the scientific investigation, especially Genome-Wide Association Study (GWAS), to find out genetic susceptibility factor to disease, such as Diabetes. It models the genetic varaints, polymorphisms, statistical measurement, populations and other elements that are essential to determine a genetic susceptibility factor in GWAS study. It must be used with other two ontologies, in the case of Diabetes, :Ontology of Geographical Region (OGR) and Ontology of Glucose Metabolism Disorder (OGMD) .
Categories : Experimental Conditions 		2805
Spider Ontology (SPD) Public 579 2 0 4 OBO 0.9.8 11/24/2011 Martin Ramirez 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).
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy 		2810 2812 2811
FlyBase Controlled Vocabulary (FB-CV) Public 821 0 0 4 OBO 1.23 04/03/2012 Evidence_code Administrators 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.
Categories : Vocabularies 		2809
Online Mendelian Inheritance in Man (OMIM) Public 71,139 0 0 5 RRF 2012_05_02 03/05/2013 Jan Willis, NLM Description: Online Mendelian Inheritance in Man, OMIM (TM). McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine
Categories : Health 		5058 ,UMLS,
Skin Physiology Ontology (SPO) Public 339 0 0 5 OWL 2.0 09/18/2008 Tariq Abdulla Description:
Categories : Biological Process 		5060
Cardiac Electrophysiology Ontology (EP) Public 79,481 0 0 6 OWL 1.0 04/27/2009 Raimond L. Winslow, PhD Description: The Cardiac Electrophysiology Ontology contains terms describing single-channel electrophysiological experiments and data obtained using voltage-clamp, current clamp and fluorescence imaging techniques applied at the cell level and multi-channel fluorescence imaging techniques applied at the cell, tissue and whole heart levels.
Categories : Experimental Conditions 		2805
Comparative Data Analysis Ontology (CDAO) Public 143 0 0 5 OWL unknown 02/05/2013 Jim Balhoff Description: A formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science
Categories : Experimental Conditions 		2805
Vaccine Ontology (VO) Public 4,639 3 0 7 OWL Vision Release; 1.0.711 06/14/2013 Yongqunh He Description: A biomedical ontology in the vaccine domain
Categories : Health , Immunology , All Organisms 		5058 5074 5073
Major Histocompatibility Complex Ontology (MHC) Public 6,718 0 0 4 OWL 1.0.1 04/15/2009 David S. DeLuca Description: The MaHCO contains terms necessary for describing and categorizing concepts related to MHC, in general, and for a number of model species, and also for humans.
Categories : Genomic and Proteomic 		2806
Ascomycete Phenotype Ontology (APO) Public 331 0 0 4 OBO unknown 05/02/2013 Maria Costanza Description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi
Categories : Phenotype 		2807
Proteomics data and process provenance (ProPreO) Public 398 0 0 4 OWL 1.1 03/05/2009 Satya S. Sahoo Description: A comprehensive proteomics data and process provenance ontology.
Categories :
Mass Spectrometry Ontology (MS) Public 4,895 0 0 6 OBO 3.50.0 05/31/2013 PSI-MS Administrators Description: A structured controlled vocabulary for the annotation of mass spectrometry experiments. Developed by the HUPO Proteomics Standards Initiative.
Categories : 		,PSI,
Protein-protein interaction (MI) Public 960 0 0 5 OBO 1.52 02/28/2009 Psi-mi Administrators Description: A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Developed by the HUPO Proteomics Standards Initiative.
Categories : 		,PSI,
Situation-Based Access Control (SitBAC) Public 176 0 0 5 OWL 1.3 02/21/2011 Mor Peleg Description: Context-based healthcare access-control policies
Categories : Other 		2801
Dictyostelium Discoideum Anatomy Ontology (DDANAT) Public 131 0 0 4 OBO unknown 01/22/2013 Rex Chisholm Description: A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum.
Categories : Anatomy , Gross Anatomy , Microbial Anatomy 		2810 2811 2815
Subcellular Anatomy Ontology (SAO) (SAO) Public 821 0 0 5 OWL 1.2.5 09/17/2007 Maryann Martone Description: SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules.
Categories : Anatomy 		2810
Ontology of Geographical Region (OGR) Public 39 0 0 4 OWL 1.1 05/19/2009 Yu Lin Description: This OWL ontology classified the geograhical regions related vocabularies extracted from UMLS. It used with other ontologies to represent the genetic susceptibility factors of diabetes.
Categories : Vocabularies 		2809
Rat Strain Ontology (RS) Public 3,434 1 0 5 OBO 4.13 06/17/2013 Rajni Nigam Description: This ontology defines the hierarchical display of the different rat strains as derived from the parental strains
Categories :
International Classification of Diseases, Version 9 - Clinical Modification (ICD9CM) Public 22,400 0 1 8 RRF 2012 04/06/2012 Patricia Brooks Description: The ICD is the international standard diagnostic classification for all general epidemiological, many health management purposes and clinical use.
Categories : 		,UMLS,WHO-FIC,
Cell Line Ontology (CLO) Public 37,405 0 0 4 OWL 2.1.44 06/18/2013 Sirarat Sarntivijai Description: The Cell Line Ontology (CLO) is a community-based ontology in domain of biological cell lines with a focus on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications.
Categories : Biological Process , Vocabularies , Taxonomic Classification , Cell , Phenotype , Anatomy , Experimental Conditions , Biomedical Resources , All Organisms 		5060 2809 2808 5065 2807 2810 2805 5059 5073
Human Disease Ontology (DOID) Public 8,683 5 0 9 OBO unknown 05/28/2013 Lynn Schriml Description: Creating a comprehensive hierarchical controlled vocabulary for human disease representation.
Categories :
Pathogen transmission (TRANS) Public 28 0 0 5 OBO unknown 12/14/2010 Human_disease Administrators 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.
Categories :
Neuroscience Information Framework Standard ontology (nif) Public 90,064 2 0 8 OWL 2.9.1 - January 23, 2012 01/30/2013 Fahim Imam Description: NIF Standard ontology (NIFSTD) is a core component of Neuroscience Information Framework (NIF) project (http://neuinfo.org), a semantically enhanced portal for accessing and integrating neuroscience data, tools and information. NIFSTD includes a set of modular ontologies that provide a comprehensive collection of terminologies to describe neuroscience data and resources.
Categories : Biological Process , Cell , Cellular anatomy , Anatomy , Subcellular , Subcellular anatomy , Molecule , All Organisms , Other , Neurological Disorder , Neurologic Disease , Dysfunction 		5060 5065 5066 2810 5067 5068 5069 5073 2801 5072 5071 5070
Mammalian Phenotype Ontology (MP) Public 9,440 0 0 7 OBO unknown 05/25/2013 JAX phenotype list Description: The Mammalian Phenotype Ontology is under development as a community effort to provide standard terms for annotating mammalian phenotypic data.
Categories : Phenotype 		2807
Microarray and Gene Expression Data Ontology (MO) Public 233 0 0 8 OWL 1.3.1.1 05/21/2009 Chris Stoeckert Description: Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1.
Categories : Experimental Conditions 		2805
Pathway ontology (PW) Public 1,356 1 0 5 OBO 5.2 06/07/2013 Victoria Petri Description: The goal of the Pathway Ontology is to cover all types of biological pathways, including altered and disease pathways, and to capture the relationships between them within the hierarchical structure of a Directed Acyclic Graph (DAG). The five nodes of the ontology are: classic metabolic, regulatory, signaling, drug and disease pathways. An extensive survey of the review literature along with searches of existing pathway databases have been used to choose terms and their position within the tree. The ontology is continually expanding along with the development of Pathway and Disease Portals at RGD. Mapping of pathways in other databases to terms in PW as synonyms further increased the content of the ontology. It also provided the means to bring in annotations made by these databases and link to their sites via automatic pipelines built at RGD. The ontology allows for the standardized annotation of rat as well as human and mouse genes to pathway terms. It also serves as a vehicle to connect between genes and ontology reports, between reports and interactive pathway diagrams, between pathways that directly connect to one another within a diagram or between pathways that in some fashion are globally related in pathway suites and suite networks. Metabolic, regulatory or signaling pathway terms have associated terms for the altered version of the pathway and the level at which the alteration(s) may occur. Proteins with mutations known to affect a particular pathway can be annotated to the normal and altered version(s) of the pathway and to a disease pathway, if known. Both the provision of terms for the altered versions of pathways and the representation of disease pathway diagrams as a collection of altered pathways are unique to the PW ontology and RGD's pathway data. The Pathway ontology is distributed under the terms of the Creative Commons Attribution license version 3.0 Unported (CC BY 3.0), see http://creativecommons.org/licenses/by/3.0 for details.
Categories : Biological Process 		5060
Amino Acid Ontology (AMINO-ACID) Public 46 0 0 6 OWL 1.2 (inferred) 07/02/2010 Nick Drummond, Georgina Moulton, Robert Stevens, Phil Lord Description: An ontology of amino acids and their properties. Inferred version.
Categories : Other 		2801
Evidence Codes Ontology (ECO) Public 297 8 0 7 OBO releases/2013-04-04 04/04/2013 Marcus Chibucos Description: A rich ontology for experimental and other evidence statements.
Categories : Other 		2801
Yeast phenotypes (YPO) Public 299 0 0 4 OBO unknown 09/30/2011 Mike Cherry Description: A structured controlled vocabulary for the phenotypes of budding yeast.
Categories : Phenotype 		2807
Cereal Plant Gross Anatomy Ontology (GRO-CPGA) Public 1,294 0 0 6 OBO unknown 07/12/2012 Plant Ontology Administrators Description: A structured controlled vocabulary for the anatomy of Gramineae. Please note that this ontology has now been superseded by the Plant Ontology.
Categories :
Cell Ontology (CL) Public 4,564 0 0 11 OBO releases/2013-06-03 06/03/2013 Alex Diehl 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 it covers cell types from prokaryotes to mammals. However, it excludes plant cell types, which are covered by PO. See the website http://cellontology.org for more details.
Categories : Cell , Anatomy 		5065 2810
Mosquito Insecticide Resistance Ontology (MIRO) Public 4,362 0 0 5 OBO 2.0.00 02/09/2013 C. Louis Description: Application ontology for entities related to insecticide resistance in mosquitos
Categories : Phenotype 		2807
Ontology of Glucose Metabolism Disorder (OGMD) Public 132 0 1 4 OBO 1.0 04/12/2011 Yu Lin Description: Including the disease names. phenotypes and their classifications involved in Glucose Metabolism Disorder, Diabetes. (OBO and OWL format are available in sourceforge.)
Categories : Human 		5062
RadLex (RID) Public 39,976 79 0 9 PROTEGE 3.8 02/19/2013 Radiological Society of North America Description: RadLex is a controlled terminology for radiology-a single unified source of radiology terms for radiology practice, education, and research. For license information see : http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/radlex_public_license_version_1-0-1.pdf
Categories : 		,caBIG,
NanoParticle Ontology (NPO) Public 1,903 3 0 6 OWL 2011-12-08 (yyyy-mm-dd) 08/17/2012 Nathan Baker Description: An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.
Categories : Chemical 		2802 ,caBIG,
Foundational Model of Anatomy (FMA) Public 83,281 0 1 15 OWL 3.1 09/14/2010 Onard Mejino Description: FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. The description of how this OWL version was generated is in "Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy" by N. F. Noy, J. L. Mejino, C. Rosse, M. A. Musen: http://bmir.stanford.edu/publications/view.php/pushing_the_envelope_challenges_in_a_frame_based_representation_of_human_anatomy
Categories : Anatomy 		2810 ,UMLS,
Mouse Pathology Ontology (MPATH) Public 888 0 0 4 OBO unknown 04/18/2013 Mouse_pathology Administrators Description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes
Categories : Phenotype 		2807
Infectious Disease Ontology (IDO) Public 508 0 0 9 OWL 2010-12-02 08/31/2011 Lindsay Cowell Description: The IDO ontologies are designed as a set of interoperable ontologies that will together provide coverage of the infectious disease domain. At the core of the set is a general Infectious Disease Ontology (IDO-Core) of entities relevant to both biomedical and clinical aspects of most infectious diseases. Sub-domain specific extensions of IDO-Core complete the set providing ontology coverage of entities relevant to specific pathogens or diseases.

To import,
Latest version: http://purl.obolibrary.org/obo/ido.owl
This version (2010-12-02): http://purl.obolibrary.org/obo/ido/2010-12-02/ido.owl
Previous versions:
2010-05-26 http://purl.obolibrary.org/obo/ido/2010-05-26/ido.owl
2009-08-14 http://purl.obolibrary.org/obo/ido/2009-08-14/ido.owl


Latest release notes at http://infectiousdiseaseontology.org/page/Download
Please note: The ontology metrics displayed by BioPortal do not distinguish IDO-developed terms from terms imported from other ontologies.
Categories : Health , All Organisms 		5058 5073
NCI Thesaurus (NCIt) Public 98,232 16 1 18 OWL 13.05d 06/10/2013 NCICB Support Description: A vocabulary for clinical care, translational and basic research, and public information and administrative activities.
Categories : 		,UMLS,caBIG,
NIF Dysfunction (NIF_Dysfunction) Public 11,403 0 0 3 OWL 1.5 (December, 2012) 01/22/2013 Fahim Imam Description: This ontology contains the former BIRNLex-Disease, version 1.3.2. -- The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. It is built using the organizational framework provided by the foundational Basic Formal Ontology (BFO). It uses an abstract biomedical layer on top of that - OBO-UBO which has been constructed as a proposal to the OBO Foundry. This is meant to support creating a sharable view of core biomedical objects such as biomaterial_entity, and organismal_entity that all biomedical ontologies are likely to need and want to use with the same intended meaning. The BIRNLex biomaterial entities have already been factored to separately maintained ontology - BIRNLexBiomaterialEntity.owl which this BIRNLex-Main.owl file imports. The Ontology of Biomedical Investigation (OBI) is also imported and forms the foundation for the formal description of all experiment-related artifacts. The BIRNLex will serve as the basis for construction of a formal ontology for the multiscale investigation of neurological disease.
Categories :
Information Artifact Ontology (IAO) Public 173 0 0 13 OWL 2012-09-20 09/20/2012 Alan Ruttenberg Description: The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI consortium.

To import

Latest released version: http://purl.obolibrary.org/obo/iao.owl

Other versions

Developer (live) version: http://purl.obolibrary.org/obo/iao/dev/iao.owl

Ontology metadata properties and classes only: http://purl.obolibrary.org/obo/iao/dev/iao.owl

Dated versions

Please note: The ontology metrics displayed by BioPortal do not distinguish IAO-developed terms from terms imported from other ontologies.

Tracker: http://purl.obolibrary.org/obo/iao/tracker
Discussion group: http://groups.google.com/group/information-ontology
Categories : Biomedical Resources , Imaging , Other

5059 5057 2801
Syndromic Surveillance Ontology (SSO) Public 175 0 0 3 OWL 1.0 09/18/2009 Anya Okhmatovskaia, David L Buckeridge Description: The SSO encodes agreement among experts about how Emergency Department (ED) chief complaints are grouped into syndromes of public health importance (consensus definitions).
Categories : Taxonomic Classification , Biomedical Resources 		2808 5059
Gazetteer Ontology (GAZ) Public 40,151 0 0 6 OBO $Revision: 1.512 $ 05/29/2013 Michael Ashburner Description: Gazetteer
Categories :
Ontology of Language Disorder in Autism (LDA) Public 36 0 0 3 OWL 12-15-2008 09/28/2009 Hari Cohly Description: We present the short review of language terms used in the domain of autism and populate them into ontology available for consultation and sharing. The language terms were obtained via text mining and automatic retrieval of terms from the corpus of PubMed abstracts.
Categories : Health 		5058
International Classification for Nursing Practice (ICNP) Public 3,290 0 0 3 OWL 2011 05/19/2011 Amy Coenen Description: International Classification for Nursing Practice
Categories : Taxonomic Classification 		2808 ,WHO-FIC,
NIF Cell (NIF_Cell) Public 2,766 0 0 3 OWL v.1.7 - May 2, 2012 12/10/2012 Fahim Imam Description: Cell types from NIFSTD
Categories :
Uber anatomy ontology (UBERON) Public 8,736 1 0 4 OBO releases/2013-05-26 05/27/2013 Chris Mungall Description: Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.
Categories :
Terminology for the Description of Dynamics (TEDDY) Public 161 0 0 2 OWL rel-2011-08-30 (inferred) 08/30/2011 Christian Knuepfer Description: The TErminology for the Description of DYnamics (TEDDY) project aims to provide an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.
Categories : Other 		2801
PKO_Re (PKO) Public 768 0 0 2 OWL 1.1 11/25/2009 Shreyas Karnik Description: Testing
Categories :
Kinetic Simulation Algorithm Ontology (KISAO) Public 238 0 1 3 OWL 2.3.4 01/28/2013 BioModels.net team Description: The Kinetic Simulation Algorithm Ontology aims at providing support in unambiguously referring to simulation algorithms when describing a simulation experiment. It describes and classifies existing algorithms and their inter-relationships through the algorithm characteristics and parameters.
Categories : Other 		2801
International Classification of Functioning, Disability and Health (ICF) Public 1,594 0 0 2 OWL 1.0.2 05/08/2012 The World Health Organization Description: The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. These domains are classified from body, individual and societal perspectives by means of two lists: a list of body functions and structure, and a list of domains of activity and participation. Since an individual's functioning and disability occurs in a context, the ICF also includes a list of environmental factors.

Source: http://www.who.int/classifications/icf/en/
Categories : Human , Vocabularies , Health 		5062 2809 5058 ,WHO-FIC,
Software Ontology (SWO) Public 3,668 1 0 4 OWL 0.4 04/25/2013 James Malone Description: The Software Ontology (SWO) has the scope of describing types of software used in Bioinformatics. The SWO covers areas such as the software type, the manufacturer of the software, the input and output data types and the uses (i.e. objectives) the software can be put to. The SWO intends to use BFO as an upper level ontolgoy and subclasses types from the Ontology of Biomedical Investigations. Contact James Malone for info: malone@ebi.ac.uk
Categories :
Ontology for General Medical Science (OGMS) Public 132 0 0 4 OWL 2011-09-20 09/20/2011 Albert Goldfain Description: The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. See http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
Categories : 		,CTSA,
Common Terminology Criteria for Adverse Events (CTCAE) Public 3,874 4 2 2 OWL 4.03 08/04/2011 CTCAE Help Description: A coding system for reporting adverse events that occur in the course of cancer therapy. It was derived from the Common Toxicity Criteria (CTC) v2.0 and is maintained by the Cancer Therapy Evaluation Program (CTEP) at the National Cancer Institution (NCI).
Categories :
Influenza Ontology (FLU) Public 733 0 0 3 OWL 0.9.0 01/06/2012 Burke Squires Description: Starting in the fall of 2007, a collaborative group of influenza researchers have established an influenza ontology. The influenza ontology is an application ontology. Consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS)
Categories :
Terminological and ontological Knowledge resources (TOK) Public 192 0 0 1 OWL 0.2.1 05/19/2010 Nizar ghoula Description: An Ontology describing Resources having different formats. This Ontology can be used to annotate and describe Terminological, Ontological Knowledge resources.
Categories : Taxonomic Classification 		2808
Taxonomic rank vocabulary (TAXRANK) Public 59 0 0 2 OBO unknown 12/14/2010 Peter Midford Description: A vocabulary of taxonomic ranks intended to replace the sets of rank terms found in the Teleost Taxonomy Ontology, the OBO translation of the NCBI taxonomy and similar OBO taxonomy ontologies. It provides terms for taxonomic ranks drawn from both the NCBI taxonomy database and from a rank vocabulary developed for the TDWG biodiversity information standards group. Cross references to appearances of each term in each source are provided. Consistent with its intended use as a vocabulary of labels, there is no relation specifying an ordering of the rank terms.
Categories :
Medical Dictionary for Regulatory Activities (MEDDRA) Public 69,389 0 0 3 RRF 12.0 02/04/2010 MSSO Help Desk Description: Medical Dictionary for Regulatory Activities Terminology (MedDRA)
Categories : Health 		5058 ,UMLS,caBIG,
RxNORM (RXNORM) Public 242,979 0 0 7 UMLS 11AB_120305F 11/14/2012 Stuart Nelson Description: RxNorm Vocabulary
Categories : Health 		5058 ,UMLS,
National Drug Data File (NDDF) Public 26,866 0 0 2 RRF 2009_08_07 02/04/2010 First DataBank Customer Support Description: National Drug Data File Plus Source Vocabulary
Categories : Health 		5058 ,UMLS,
International Classification of Diseases, Version 10 - Procedure Coding System (ICD10PCS) Public 177,782 0 0 2 RRF 2011 09/29/2011 Pat Brooks Description: ICD-10-PCS, 2009
Categories : Health 		5058 ,UMLS,
Master Drug Data Base Clinical Drugs (MDDB) Public 12,467 0 0 2 RRF 2009_08_05 02/04/2010 Karen Eckert Description: Master Drug Data Base, 2009_08_05
Categories : Health 		5058 ,UMLS,
Read Codes, Clinical Terms Version 3 (CTV3) (RCD) Public 201,333 0 0 3 RRF 1999 02/05/2010 NHS Information Authority Loughborough Description: Clinical Terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre
Categories : 		,UMLS,
Nursing Interventions Classification (NIC) (NIC) Summary Only 0 0 0 2 RRF 2005 02/05/2010 Center for Nursing Classification & Clinical Effectiveness Description: Nursing Interventions Classification (NIC)
Categories : Health 		5058 ,UMLS,
International Classification of Primary Care - 2 PLUS (ICPC2P) Public 8,319 0 0 2 RRF 2005 02/05/2010 Prof Helena Britt Description: ICPC-2 PLUS
Categories : Health 		5058 ,UMLS,
Artificial Intelligence Rheumatology Consultant System Ontology (AI-RHEUM) Public 681 0 0 2 RRF 1993 02/05/2010 May Cheh Description: AI/RHEUM is used for the diagnosis of rheumatologic diseases. AI/RHEUM contains findings, such as clinical signs, symptoms, laboratory test results, radiologic observations, tissue biopsy results, and intermediate diagnosis hypotheses. Findings and hypotheses, which include definitions, are used to reach diagnostic conclusions with definite, probable, or possible certainty. AI/RHEUM is used by clinicians and informatics researchers.
Categories : Health 		5058 ,UMLS,
Breast Tissue Cell Lines Ontology (MCBCC) Public 385 0 0 3 OWL 2.0 07/29/2010 Dr. Arathi Raghunath Description: Contains a comprehensive list of cell lines derived from breast tissue, both normal and pathological. The ontology in built in OWL with cross relation to classes- genetic variation, pathological condition, genes, chemicals and drugs. The relations built enable semantic query across different classes
Categories : Cell 		5065
General Formal Ontology (GFO) Public 45 0 0 2 OWL 1.0 03/02/2010 Heinrich Herre Description: The General Formal Ontology (GFO) is a top-level ontology integrating objects and processes.
Categories : All Organisms , Upper Level Ontology 		5073 5075
General Formal Ontology: Biology (GFO-BIO) Public 170 0 0 2 OWL 1.1 03/02/2010 Robert Hoehndorf Description: GFO-Bio is a biological core ontology built on the General Formal Ontology.
Categories : Animal Development , Biological Process , Mouse Anatomy , Human , Plant Development , Plant , Cell , Phenotype , Cellular anatomy , Anatomy , Subcellular , Subcellular anatomy , Development , Animal Gross Anatomy , Molecule , Protein , Gross Anatomy , Gene Product , Chemical , Human Developmental Anatomy , All Organisms , Plant Anatomy 		2818 5060 2817 5062 2819 5063 5065 2807 5066 2810 5067 5068 2803 2812 5069 2821 2811 2820 2802 2814 5073 2816
Chemical Information Ontology (CHEMINF) Public 641 0 0 6 OWL 1.0 05/20/2013 Janna Hastings Description: Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.
Categories :
Health Level Seven Reference Implementation Model, Version 3 (HL7) Public 7,500 0 1 7 OWL 2011ab 04/05/2012 Methodology and Modelling Committee Description: This version is the first update to Normative RIM, Release 3. It is based on changes approved in Harmonization in November 2010. This release of the RIM is bound to HL7 Abstract Data Types Release 2.
Categories : Health 		5058
Translational Medicine Ontology (TMO) Public 300 0 0 2 OWL 1.0.2 04/23/2012 TMO task in W3C's HCLS IG Description: This project focuses on the development of a high level patient-centric ontology for the pharmaceutical industry. The ontology should enable silos in discovery research, hypothesis management, experimental studies, compounds, formulation, drug development, market size, competitive data, population data, etc. to be brought together. This would enable scientists to answer new questions, and to answer existing scientific questions more quickly. This will help pharmaceutical companies to model patient-centric information, which is essential for the tailoring of drugs, and for early detection of compounds that may have sub-optimal safety profiles. The ontology should link to existing publicly available domain ontologies.
Categories : Health , All Organisms 		5058 5073
International Classification of External Causes of Injuries (ICECI) Public 2,230 0 0 2 OWL Original Source: 1.2; OWL version 1.02 05/07/2010 Samson Tu Description: The International Classification of External Causes of Injury (ICECI) is a system of classifications to enable systematic description of how injuries occur. It is designed especially to assist injury prevention. The ICECI was originally designed for use in settings in which information is recorded in a way that allows statistical reporting--for example, injury surveillance based on collection of information about cases attending a sample of hospital emergency departments. It has also been found useful for other purposes. For example, it has been used as a reference classification during revision of another classification, to record risk-factor exposure of children in a cohort study, as the basis for special-purpose classifications and in a growing number of other ways.
Categories :
Body System Terms from ICD11 (ICD11-BODYSYSTEM) Public 29 0 0 3 OWL 1.0 04/15/2010 Samson Tu Description: This is a set of body-system terms used in the ICD 11 revision
Categories : Anatomy 		2810
SysMO-JERM (JERM) Public 253 0 0 4 OWL 1.6Alpha 05/17/2013 Katy Wolstencroft Description: an ontology to describe the entities and relationships in the SEEK database, a Systems Biology environment for the sharing and exchange of data and models. The SysMO-SEEK database contains the work of the SysMO consortium (Systems Biology of Micro-Organisms) https://seek.sysmo-db.org/
Categories : Biological Process , Experimental Conditions , Biomedical Resources , Other 		5060 2805 5059 2801
Ontology of Adverse Events (OAE) Public 2,543 0 0 2 OWL Vision Release; 1.1.110 05/15/2013 Yongqun "Oliver" He Description: The Ontology of Adverse Events (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. AEO is a community-based ontology. Its development follows the OBO Foundry principles.
Categories : Health 		5058
Immunogenetics Ontology (IMGT-ONT) Public 289 0 0 2 OWL 1.0.1 01/25/2012 Véronique Giudicelli, Patrice Duroux, Professor Marie-Paule Lefranc Description: IMGT-ONTOLOGY is the first ontology for immunogenetics and immunoinformatics. It provides a semantic specification of the terms to be used in immunogenetics and immunoinformatics and manages the related knowledge, thus allowing the standardization for immunogenetics data from genome, proteome, genetics, two-dimensional (2D) and three-dimensional (3D) structures. IMGT-ONTOLOGY manages the knowledge through diverse facets relying on seven axioms, "IDENTIFICATION", "CLASSIFICATION", "DESCRIPTION", "NUMEROTATION", "LOCALIZATION", "ORIENTATION" and "OBTENTION". These axioms postulate that any object, any process and any relation can be identified, classified, described, numbered, localized and orientated, and the way it is obtained can be characterized. The axioms constitute the Formal IMGT-ONTOLOGY, also designated as IMGT-Kaleidoscope. As the same axioms can be used to generate concepts for multi-scale level approaches, the Formal IMGT-ONTOLOGY represents a paradigm for system biology ontologies, which need to identify, to classify, to describe, to number, to localize and to orientate objects, processes and relations at the molecule, cell, tissue, organ, organism or population levels. IMGT®, the international ImMunoGeneTics information system®, has been built on IMGT-ONTOLOGY. The version 1.0.1 of IMGT-ONTOLOGY, edited with Protégé (v4.2.0), includes the concepts of IDENTIFICATION which are "ChainType", "Classtype", "ConfigurationType", "EntityType", "FormatType", "FunctionalityType", "GeneType", "LevelChainType", "LocationType", "MolecularComponent", "MoleculeType", "MoleculeUnit", "StructureType", and "TaxonRank".
Categories : Immunology 		5074
Tissue Microarray Ontology (TMA) Public 7 0 0 2 OWL 1.0.0 05/07/2010 Chuck Borromeo Description: Tissue microarrays (TMA) are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential. The Resource Description Framework (RDF) provides a flexible method to represent knowledge in triples, which take the form Subject-Predicate-Object. All data resources are described using Uniform Resource Identifiers (URI), which are global in scope. We present an OWL (Web Ontology Language) schema that expands upon the TMA data exchange specification to address this issue and assist in data sharing and integration.
Categories : Experimental Conditions , Biomedical Resources , Other 		2805 5059 2801
PMA 2010 (pma) Public 2,082 0 0 2 OWL 0.9.1 10/18/2010 Jim Martin Description: The Portfolio Management Application (PMA) is a system for tracking grants and producing reports - Users can access grant data through a query interface and a variety of pre-defined forms and reports
Categories : Human , Health 		5062 5058
Embrace Data and Methods Ontology (EDAM) Public 2,746 0 2 7 OWL 1.2 12/14/2012 Jon Ison Description: EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. The applications of EDAM are within organising tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web.
Categories : Other 		2801
RNA ontology (RNAO) Public 240 0 0 3 OWL r113 07/01/2010 Colin Batchelor Description: The central aim of the RNA Ontology Consortium (ROC) is to develop an ontology to capture all aspects of RNA - from primary sequence to alignments, secondary and tertiary structure from base pairing and base stacking to sophisticated motifs.
Categories : All Organisms 		5073
Neomark Oral Cancer-Centred Ontology (NeoMarkOntology) Public 56 0 0 2 OWL 3.1 05/21/2010 Marta Ortega Description: Ontology that describes the medical information necessary for early detection of the oral cancer reoccurrence extracted from the NeoMark Project.
Categories : Health 		5058
Current Procedural Terminology (CPT) Public 9,442 0 0 2 RRF 2010AA 05/26/2010 Dorith Brown Description: Current Procedural Terminology
Categories : Health 		5058 ,UMLS,
Ontology for MicroRNA Target Prediction (OMIT) Public 375 0 0 3 OWL 1.1.1 10/26/2012 Jingshan Huang Description: The purpose of the OMIT ontology is to facilitate the identification and characterization of important roles microRNAs (miRNAs) played in human cancer. To be more specific, it aims to assist cancer biologists in unraveling important roles of miRNAs in human cancer.
Categories : Biological Process , Human , Cell , Molecule , Protein , Gene Product 		5060 5062 5065 5069 2821 2820
Gene Ontology Extension (GO-EXT) Public 34,400 0 0 3 OBO 2.0 06/24/2011 Gene Ontology Consortium Description: Gene Ontology Extension
Categories : 		,OBO Foundry,UMLS,caBIG,
Cell Cycle Ontology (CCO) Public 106,397 0 0 4 OBO 2.01 11/20/2012 Vladimir Mironov Description: An application ontology integrating knowledge about the eukaryotic cell cycle.
Categories : Biological Process , Arabadopsis , Human , Yeast , Protein 		5060 5061 5062 5064 2821
International Classification for Patient Safety (ICPS) Public 397 0 0 2 OWL 2.0 02/06/2012 Oscar Corcho Description: Ontology network about Patient Safety Incident. This work has been carried out by the Ontological Engineering Group, using sources from the University of Saint Etienne and the Australian Patient Safety Foundation, and supported by the World Health Organisation under the International Classification for Patient Safety programme.
Categories : Health 		5058
Metathesaurus Current-Procedural-Terminology Hierarchical Terms (MTHCH) Public 1,033 0 0 3 RRF 2010 06/28/2010 Jan Willis Description: Metathesaurus CPT Hierarchical Terms
Categories : Health 		5058 ,UMLS,
Interaction Network Ontology (INO) Public 1,122 0 0 2 OWL Vision Release; 1.0.37 02/22/2013 Yongqun "Oliver" He Description: The Interaction Network Ontology (INO) is an ontology in the domain of interaction network. INO aims to standardize interaction network annotation, integrate various interaction network data, and support computer-assisted reasoning. It is aimed to represent general interactions (e.g., molecular interactions) and interaction networks (e.g., Bayesian network). INO was initiated by supporting literature mining related to interactions and interaction networks. INO aligns with BFO. INO is a community-based ontology, and its development follows the OBO Foundry principles.
Categories : Biological Process , All Organisms 		5060 5073
International Classification of Diseases, Version 10 (ICD10) Public 12,318 0 0 5 RRF 1998 07/21/2010 World Health Organization Description: International Statistical Classification of Diseases and Related Health Problems (ICD-10). 10th rev. Geneva
Categories : 		,UMLS,WHO-FIC,caBIG,
Human Developmental Anatomy Ontology, abstract version 2 (EHDAA2) Public 2,734 0 0 3 OBO unknown 04/24/2013 EMAP Administrators 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.
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy , Human Developmental Anatomy 		2810 2812 2811 2814
Leukocyte Surface Marker Ontology (LSM) Public 469 0 0 2 OBO unknown 07/16/2011 Terry Meehan Description: An ontology of CD markers for lymphocyte classification in the cell ontology, and other categories of surface and secreted proteins useful for discriminating between lymphocyte subsets by flow cytometry, ELISPOT, ELISA and other assays typically used for phenotypic identification of individual lymphocytes or lymphocyte populations have been included.
Categories :
Neural Motor Recovery Ontology (NeuMORE) Public 33 0 0 2 OWL 0.1 08/11/2010 Jingshan Huang Description: Neural Functional Motor Recovery Ontology
Categories :
BioPAX Ontology (BP) Public 68 0 0 3 OWL Level3 v1.0 07/29/2010 Dr Emek Demir Description: The BioPAX ontology (www.biopax.org) is a standard language for formally representing biological pathways. BioPAX Level 3 supports the representation of metabolic pathways, signal transduction pathways, protein-protein interaction networks, gene regulatory networks and genetic interactions.
Categories : Biological Process 		5060
Santa Barbara Coastal Observation Ontology (oboe-sbc) Public 448 0 0 3 OWL 0.1 08/12/2010 Ben Leinfelder Description: Extensible Observation Ontology for the Santa Barbara Coastal Long Term Ecological Research project (SBC-LTER). OBOE SBC extends core concepts defined in the OBOE suite that are particular to the Santa Barbara Coastal Long Term Ecological Research project's data collection activities. These include specific measurement protocols, sites, etc. This is mean as a case study ontology for the Semtools project.
Categories : Other 		2801
Extensible Observation Ontology (OBOE) Public 26 0 0 3 OWL 1.0 08/12/2010 Ben Leinfelder Description: The Extensible Observation Ontology (OBOE) is a suite of OWL-DL ontologies for modeling and representing scientific observations. The OBOE model is designed as a generic data model with a number of constructs for defining observational data. Key features of OBOE include its ability to represent a wide range of measurement types, a mechanism for specifying measurement context, and the ability to associate the type of entity (e.g., sample, organism, etc.) being measured. OBOE is being used and developed within the Semtools project for describing a wide variety of ecological data stored within the Knowledge Network for Biodiversity (KNB) as well as extensions for ontology-based data annotation and discovery within the MetaCat software infrastructure.
Categories : Other 		2801
Computer Retrieval of Information on Scientific Projects Thesaurus (CRISP) Public 8,912 0 0 2 RRF 2006 08/27/2010 Anita Ghebeles Description: Computer Retrieval of Information on Scientific Projects (CRISP)
Categories : Health 		5058 ,UMLS,
Veterans Health Administration National Drug File (VANDF) Public 28,926 0 0 2 RRF 2010_01_25 09/01/2010 Michael Lincoln Description: NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes.
Categories : Health 		5058 ,UMLS,
Human Genome Organization Gene Symbols (HUGO) Public 32,917 0 0 6 OWL July2010 12/21/2010 Dr. Elspeth Bruford Description: Human Genome Organisation (HUGO) Gene Nomenclature Committee at the European Bioinformatics Institute approves a gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database.
Categories : Health 		5058
Healthcare Common Procedure Coding System (HCPCS) Public 5,660 0 0 3 RRF 2010 09/01/2010 Cynthia Hake Description: Healthcare Common Procedure Coding System
Categories : Health 		5058 ,UMLS,
Animal Natural History and Life History (ADW) Public 360 0 0 2 OWL 10/11/04 08/31/2010 Animal Diversity Web technical staff Description: An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.
Categories : Anatomy 		2810
SemanticScience Integrated Ontology (SIO) Public 1,395 0 0 5 OWL 0.9.21 05/22/2013 Michel Dumontier Description: The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. It provides vocabulary for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.
Categories : Biological Process , Vocabularies , Taxonomic Classification , Yeast , Phenotype , Cell , Genomic and Proteomic , Cellular anatomy , Subcellular , Physicochemical , Biomedical Resources , Subcellular anatomy , Protein , Molecule , Gene Product , Chemical , All Organisms 		5060 2809 2808 5064 2807 5065 2806 5066 5067 2822 5059 5068 2821 5069 2820 2802 5073
BioAssay Ontology (BAO) Public 1,298 0 0 9 OWL 1.6.2 12/12/2012 Stephan Schurer Description: The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 1000 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc.). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation.
Categories : Biological Process , Vocabularies , Cell , Subcellular , Physicochemical , Molecule , Protein , Chemical , Other 		5060 2809 5065 5067 2822 5069 2821 2802 2801
apollo-akesios (apollo) Public 3 0 0 1 OWL 0.1 09/30/2010 Jeremy Espino Description: A controlled vocabulary for public health models
Categories :
Terminology of Anatomy of Human Histology (TAHH) Summary Only 0 0 0 2 OBO unknown 09/30/2010 Pierre Sprumont Description:
Categories :
Terminology of Anatomy of Human Embryology (TAHE) Summary Only 0 0 0 2 OBO unknown 09/30/2010 Pierre Sprumont Description:
Categories :
Brucellosis Ontology (IDOBRU) Public 1,699 0 0 2 OWL Arbor version; 1.1.52 02/22/2013 Yongqunh "Oliver" He Description: Brucellosis Ontology is a biomedical ontology in the domain of zoonotic disease brucellosis that is caused by Brucella, a facultative intracellular baterium.
Categories : Health 		5058
Role Ontology (RoleO) Public 673 0 0 3 OWL 1.0.6 10/23/2010 Oliver He Description: The Role Ontology (RoleO) is a ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles.
Categories :
Neural-Immune Gene Ontology (NIGO) Public 4,835 0 0 2 OBO v1 10/28/2010 Eitan Rubin Description: The Neural-Immune Gene Ontology (NIGO) is a subset of GO directed for neurological and immunological systems. NIGO was created by clipping those GO terms that are not associated to any gene in human, rat and mouse, and by clipping terms not found to be relevant to the neural and/or immune domains.
Categories : Biological Process , Human , Other 		5060 5062 2801
Ontology for Drug Discovery Investigations (DDI) Public 164 0 0 3 OWL $Revision$ 04/21/2013 Larisa Soldatova; Da Qi (ddq@aber.ac.uk) Description: The goal of DDI project is to develop an ontology for the description of drug discovery investigations. DDI aims to follow to the OBO (Open Biomedical Ontologies) Foundry principles, uses relations laid down in the OBO Relation Ontology, and be compliant with Ontology for biomedical investigations (OBI).
Categories :
Cell Line Ontology [by Mahadevan] (MCCL) Public 811 0 0 3 OWL 1.0 10/28/2010 Usha Mahadevan Description: Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive of machine-interpretable definitions of basic concepts in the domain and relations among them. The need for ontologies that provide a systematic arrangement of available data and allow cross talk across various related domains is gaining momentum. In this backdrop, we have developed a comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format.
Categories : Cell , Anatomy , Health , Protein 		5065 2810 5058 2821
Crop Ontology (CO) Summary Only 0 0 0 4 OBO 2.0.2 11/08/2010 Rosemary Shrestha; Elizabeth Arnaud Description: This ontology includes crop-specific trait ontologies for several economically important plants like rice, wheat, maize, potato, musa, chickpea and sorghum along with other important domains for crop research such as germplasm, passport, trait measurement scales, experimental design factors etc.
Categories : Plant , Phenotype 		5063 2807
Wheat trait (CO_Wheat) Public 176 0 0 2 OBO 08.11.2010 11/09/2010 Rosemary Shrestha; Elizabeth Arnaud Description: This ontology defines traits of the International Wheat Information System (IWIS) database and wheat descriptor.
Categories : Plant , Phenotype 		5063 2807 ,CGIAR,
PHArmacogenomic RElationships Ontology (PHARE) Public 228 0 0 2 OWL 110114 01/14/2011 Adrien Coulet Description: The PHArmacogenomic RElationships Ontology (or PHARE) proposes concepts and roles to represent relationships of pharmacogenomics interest.
Categories : Biological Process , Human , Phenotype , Health , Chemical , Gene Product 		5060 5062 2807 5058 2802 2820
Reproductive trait and phenotype ontology (REPO) Public 95 0 0 2 OWL 1.1 10/12/2011 Wageningen UR Livestock Research Description: Ontology for livestock reproductive traits and phenotypes
Categories : Phenotype 		2807
International Classification of Diseases, Version 10 - Clinical Modfication (ICD10CM) Public 91,590 0 0 2 RRF 2011_01 09/29/2011 Patricia Brooks Description: International Classification of Diseases, 10th Edition, Clinical Modification, 2011_01
Categories : Health 		5058 ,UMLS,caBIG,
Vertebrate Skeletal Anatomy Ontology (VSAO) Public 314 0 0 2 OBO 2012-11-06 11/06/2012 Wasila Dahdul Description: VSAO is an anatomy ontology covering the vertebrate skeletal system. VSAO integrates terms for skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system.
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy , Fish Anatomy 		2810 2812 2811 2813
Cognitive Paradigm Ontology (COGPO) Public 355 0 0 4 OWL 1.0 12/16/2010 Jessica Turner Description: This ontology is used to describe the experimental conditions within cognitive/behavioral experiments, primarily in humans.
Categories : Human , Experimental Conditions , Imaging 		5062 2805 5057
Ontology of Medically Related Social Entities (OMRSE) Public 127 0 0 2 OWL 2012-06-24 03/28/2013 Bill Hogan Description: This ontology covers the domain of social entities that are related to health care, such as demographic information (social entities for recording gender (but not sex) and marital status, for example) and the roles of various individuals and organizations (patient, hospital,etc.)
Categories :
Pharmacovigilance Ontology (PVOnto) Public 33 0 0 2 OWL 0.1 01/17/2011 Jingshan Huang, huang@usouthal.edu; Jun (Luke) Huan Description: A pharmacovigilance ontology to connect known facts on drugs, disease, ADEs, and their molecular mechanisms.
Categories :
Anatomical Entity Ontology (AEO) Public 250 0 0 3 OBO unknown 06/01/2012 EMAP Administrators Description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology, to about 200 classes using the is_a relationship; it thus provides a detailed type classification for tissues. The new classes were chosen for their use in categorizing the major vertebrate and invertebrate anatomy ontologies at a granularity adequate for tissues of a single cell type. The ontology should be useful in increasing the amount of knowledge in anatomy ontologies, facilitating annotation and enabling interoperability across anatomy ontologies
Categories : Anatomy 		2810
Host Pathogen Interactions Ontology (HPIO) Public 281 0 0 2 OWL 1.0 02/08/2011 Wageningen UR Livestock Research Description: Ontology for host pathogen interactions in farmed animals
Categories : Health 		5058
Traditional Medicine Constitution Value Set (TM-CONST) Public 20 0 0 2 OWL 1.0 01/31/2011 Tania Tudorache Description: The value set for the Constitution property of the International Classification of Traditional Medicine (ICTM).
Categories : Human 		5062
Traditional Medicine Other Factors Value Set (TM-OTHER-FACTORS) Public 12 0 0 2 OWL 1.0 01/31/2011 Tania Tudorache Description: The value set for the Other Factors property of the International Classification of Traditional Medicine (ICTM).
Categories : Human 		5062
Traditional Medicine Signs and Symptoms Value Set (TM-SIGNS-AND-SYMPTS) Public 325 0 0 2 OWL 1.0 01/31/2011 Tania Tudorache Description: The value set for the Signs and Symptoms property of the International Classification of Traditional Medicine (ICTM).
Categories :
Traditional Medicine Meridian Value Sets (TM-MER) Public 20 0 0 2 OWL 1.0 02/01/2011 Tania Tudorache Description: The meridian value set used in the International Classification of Traditional Medicine.
Categories :
vertebrate Homologous Organ Groups (vHOG) Public 1,185 0 0 3 OBO unknown 12/06/2012 Bgee team Description: vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 "historical homology". Each mapping has been manually reviewed, and we provide confidence codes and references when available.
Categories : Animal Development , Mouse Anatomy , Human , Anatomy , Animal Gross Anatomy , Gross Anatomy , Human Developmental Anatomy , Fish Anatomy 		2818 2817 5062 2810 2812 2811 2814 2813
Exposure Ontology (EXO) Public 81 0 0 2 OBO 1 01/19/2012 Carolyn Mattingly Description: Exposure Ontology. A draft ontology for exposure science.
Categories :
Adverse Event Reporting Ontology (AERO) Public 391 1 0 3 OWL unknown 04/29/2013 Melanie Courtot Description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events.
Categories : Health , Biomedical Resources 		5058 5059
Health Indicator Codes (HLTHINDICES) Public 538 0 0 3 OWL 0.1 02/18/2011 Ketty Mobed Description: Standardized health outcome and health determinant indicators as maintained by the CDC National Center for Health Statistics
Categories : Human , Vocabularies , Health , Other 		5062 2809 5058 2801 ,CTSA,CTSA-HOM,
Clusters of Orthologous Groups Analysis Ontology (CAO) Public 204 0 0 3 OWL 1.4 10/13/2011 Asiyah Yu Lin Description: CAO ontology is designed for supporting the COG enrichment study by using Fisher's exact test
Categories : Gene Product 		2820
Clinical Measurement Ontology (CMO) Public 1,628 0 0 4 OBO 2.4 06/17/2013 Mary Shimoyama Description: The Clinical Measurement Ontology is designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs
Categories :
Measurement Method Ontology (MMO) Public 393 0 0 4 OBO 2.2 06/17/2013 Mary Shimoyama Description: The Measurement Method Ontology is designed to represent the variety of methods used to make qualitative and quantitative clincial and phenotype measurements both in the clinic and with model organisms.
Categories : Phenotype 		2807
Experimental Conditions Ontology (XCO) Public 303 0 0 7 OBO 2.2 06/17/2013 Mary Shimoyama Description: The Experimental Conditions Ontology is designed to represent the conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.
Categories : Phenotype , Experimental Conditions 		2807 2805
Orphanet Ontology of Rare Diseases (OntoOrpha) Public 12,829 0 0 2 OWL lite_2012-10-02 10/22/2012 Ferdinand Dhombres Description: OntoOrpha is an ontology of Rare Diseases that includes clinical signs (phenotypes) and genes. The full Orphanet nomenclature (labels, synonyms) is provided in six languages with external references annotations (ICD, OMIM, HGNC, Genatlas, Swissprot). This version now includes epidemiology data related to rare diseases in Europe (class of prevalence, average age of onset, average age at death) extracted from the literature.
Part of an ongoing research project, this ontology is developed to support editorial procedures of Orphanet knowledge bases and services. Current alpha version is under active development. The version provided on bioportal contains only the main english labels. A version on the ontology with the full nomenclature of rare diseases (labels and synonyms in 6 languages based on skos annotations) is available on demand.

Creative Commons : Attribution - Non Commercial - No Derivs
OntoOrpha is available under Creative Commons license ''Attribution-Non-Commercial-No Derivative Works 3.0''
Categories : Human , Vocabularies , Taxonomic Classification , Phenotype , Health , Biomedical Resources , Protein 		5062 2809 2808 2807 5058 5059 2821
Plant Ontology (PO) Public 1,644 1 0 6 OBO Release #19 12/31/2012 Pankaj Jaiswal Description: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plants.
Categories : Plant Development , Plant , Plant Anatomy 		2819 5063 2816
Ontology of General Purpose Datatypes (OntoDT) Public 143 0 0 3 OWL 1.0 05/31/2012 Pance Panov Description: This ontology contains entities such as: datatype, datatype generator, datatype qualiy and others giving the possibility to represent arbitrary complex datatypes. This is an important fact for a general data mining ontology that wants to represent and query over modelling algorithms for mining structured data. The ontology was first developed under the OntoDM (Ontology of Data Mining is available at http://kt.ijs.si/panovp/OntoDM) ontology, but for generality and reuse purpose it was decided to export it as a separate ontology. Additionaly, the OntoDT ontology is based on and ISO/IEC 11404 (http://www.iso.org/iso/catalogue_detail.htm?csnumber=39479) standard and can be reused used independently by any domain ontology that requires representation and reasoning about general purpose datatypes.
Categories :
Bone Dysplasia Ontology (BDO) Public 13,918 0 0 4 OWL 1.5 02/09/2012 Tudor Groza Description: The Bone Dysplasia ontology provides a comprehensive and formal representation of the different domain concepts involved in documenting the full complexity of the skeletal dysplasia domain. It captures and combines the genetic features that discriminate the bone dysplasias with the multitude of phenotypic characteristics manifested by patients and required to be taken into account in order to support the diagnosis process.
Categories : Human , Health 		5062 5058
Interaction Ontology (IXNO) Public 53 0 0 2 OBO 1 04/21/2011 Carolyn Mattingly Description: The Interaction ontology (IxnO) was developed to enable curation of chemical-gene and chemical-protein interactions for the Comparative Toxicogenomics Database (CTD). CTD is a freely available resource that aims to promote understanding and novel hypothesis development about the effects of the environment on human health.
Categories : Other 		2801
Systems Chemical Biology/Chemogenomics (Chem2Bio2OWL) Public 104 0 0 2 OWL unknown 09/23/2012 Bin Chen, Ying Ding, David Wild Description: Ontology for Systems Chemical Biology and Chemogenomics
Categories : Biological Process , Biomedical Resources , Molecule , Protein , Chemical 		5060 5059 5069 2821 2802
Phylogenetic Ontology (PhylOnt) Public 147 0 0 2 OWL ver8 03/11/2013 maryam panahiazar Description: Ontology for Phylogenetic Analysis
Categories : Other 		2801
Neuro Behavior Ontology (NBO) Public 813 5 0 2 OBO 2012-07-09 02/19/2013 George Gkoutos Description: The Neurobehavior Ontology (NBO) consists of two main components, an ontology of behavioral processes and an ontology of behavioral phenotypes. The behavioral process branch of NBO contains a classification of behavior processes complementing and extending GO’s process ontology. The behavior phenotype branch of NBO consists of a classification of both normal and abnormal behavioral characteristics of organisms
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Enzyme Mechanism Ontology (EMO) Public 259 0 0 2 OWL 1.1 03/02/2012 Jules Jacobsen Description: The Enzyme Mechanism Ontology (EMO) was created to describe the active components of the enzyme's reactions (cofactors, amino acid residues and cognate ligands) and their roles in the reaction. EMO builds upon this by formalizing key concepts, and the relationships between them, necessary to define enzymes and their functions. This describes not only the general features of an enzyme, including the EC number (catalytic activity), 3D structure and cellular locations, but also allows for the detailed annotation of the mechanism. This mechanistic detail can be either at a gross level (overall reaction only), or the more detailed granularity of the steps and components required to effect the overall chemical transformation.
Categories : Biological Process , Physicochemical , Protein , Chemical 		5060 2822 2821 2802
Web-Service Interaction Ontology (WSIO) Public 30 0 0 4 OBO beta1 03/14/2013 Matus Kalas Description: Web Service Interaction Ontology (WSIO) enables automated interaction with more complex Web services that are typical for example within life sciences. WSIO is however independent of the application domain and relevant for both SOAP and REST Web services, and for batch execution engines in general. If the interaction scenario with a Web service is nontrivial (and incorporates session handling), annotation with WSIO concepts will enable automatic generation of client programs, scripts, or interactive applications with a graphical user interface. WSIO also enables automation of different ways of data transfer and data un-/compression or en-/decoding. We strongly discourage providers from developing complex interaction and data-transfer/compression scenarios, however when needed, WSIO may enable smooth automated interaction with them. Future versions will support more interaction scenarios. WSIO aims to serve also as a means to standardise the complex interaction scenarios primarily within both SOAP and REST Web services, and secondarily to apply also to batch execution infrastructure in general.
Categories : Other 		2801
Cognitive Atlas Ontology (COGAT) Public 1,698 0 0 4 OWL 0.3 04/03/2012 Russell Poldrack Description: The Cognitive Atlas is a collaborative knowledge building project that aims to develop an ontology that characterizes the state of current thought in cognitive science. It defines a set of mental concepts along with a set of mental tasks, and the measurement relations between those classes.
Categories : Human , Vocabularies , Phenotype 		5062 2809 2807
Ontology of Core Data Mining Entities (OntoDM-core) Public 746 0 0 3 OWL 1.0R 04/06/2012 Pance Panov Description: OntoDM is a generic ontology for the domain of data mining. The ontology includes the information processing processes that occur in the domain of data mining, participants in the processes and their specifications. OntoDM is highly transferable and extendable due to its adherence to accepted standards, and compliance with existing ontology resources. The generality in scope allows wide number of applications of the ontology, such as semantic annotation of data mining scenarios, ontology based support for QSARs, etc.
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Epilepsy Ontology (EPILONT) Public 137 0 0 3 OWL V1 07/18/2011 Antonio Dourado Description: Ontology about the epilepsy domain and epileptic seizures. Based on the diagnosis proposed by the International League Against Epilepsy (ILAE).
Categories : Human , Vocabularies , Health , Biomedical Resources , Development , Neurological Disorder , Neurologic Disease 		5062 2809 5058 5059 2803 5072 5071
Pediatric Terminology (PedTerm) Public 1,771 0 0 3 OWL Version 2.0 01/25/2013 Ranjana Srivastava Description: Terms associated with pediatrics, representing information related to child health and development from pre-birth through 21 years of age; contributed by the National Institute of Child Health and Human Development.
Categories : Human , Health 		5062 5058
Units Ontology (UnitsOntology) Public 63 0 0 3 OWL 1.0 07/27/2011 Sivaram Arabandi Description: A small ontology for the units of measurement developed during the development of the Sleep Domain Ontology (SDO). It supports the use of SDO within the PhysioMIMI application.
Categories : Other 		2801
Sleep Domain Ontology (SDO) Public 1,381 0 0 2 OWL Last modification: Feb. 11, 2013 Sivaram Arabandi 02/11/2013 Sivaram Arabandi Description: An application ontology for the domain of Sleep Medicine.
Categories : Human , Phenotype , Health , Neurological Disorder , Neurologic Disease 		5062 2807 5058 5072 5071
PharmGKB-in-OWL (pharmgkb-owl) Summary Only 0 0 0 2 OWL 1.0 08/05/2011 Robert Hoehndorf Description: PharmGKB represented in OWL and linked to related ontologies.
Categories : Phenotype , Health , Physicochemical , Molecule , Chemical , All Organisms , Other , Dysfunction 		2807 5058 2822 5069 2802 5073 2801 5070
PhenomeBLAST ontology (phenomeblast-owl) Summary Only 0 0 0 2 OWL 2.0 10/19/2012 Robert Hoehndorf Description: A cross-species phenotype and anatomy ontology resulting from combining available anatomy and phenotype ontologies and their definitions. The ontology includes phenotype definitions for yeast, mouse, fish, worm, fly and human phenotypes and diseases.
Categories : Biological Process , Mouse Anatomy , Human , Phenotype , Anatomy , Gross Anatomy , All Organisms , Other , Fish Anatomy , Dysfunction 		5060 2817 5062 2807 2810 2811 5073 2801 2813 5070
Quadrupedal Gait (CAMRQ) Summary Only 0 0 0 1 OWL 08/20/2011 Süleyman Gülsüner Description: CEREBELLAR ATAXIA AND MENTAL RETARDATION WITH OR WITHOUT QUADRUPEDAL LOCOMOTION. OMIM: 224050, 610185, 613227
Categories : Human , Phenotype , Neurological Disorder 		5062 2807 5072
Vertebrate Trait Ontology (VT) Public 3,305 0 0 1 OBO 3.16 06/04/2013 Jim Reecy Description: The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.
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Student Health Record (SHR) Public 343 0 0 2 OWL unknown 09/29/2011 Dr.Gholamreza Ghayour, Hassan Shojaee Description: The goal of SHR project is to develop an ontology for the description of student health records. Student health records are created for entering college students in order to provide better health services will be formed. This file contains various sections such as history of disease, family history of disease, public examinations and ... .
Categories :
Emotion Ontology (MFOEM) Public 855 0 0 2 OWL beta 2013-03-25 03/25/2013 Janna Hastings Description: An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings, designed to support interdisciplinary research by providing unified annotations. The ontology is a domain specialisation of the broader Mental Functioning Ontology.
Categories : Other 		2801
Quantitative Imaging Biomarker Ontology (QIBO) Public 616 0 0 1 OWL unknown 10/06/2011 David Paik Description: An ontology that describes various concepts in quantitative imaging biomarkers.
Categories : Imaging 		5057
The Drug Interaction Knowledge Base (dikb-evidence) Public 124 0 0 3 OWL The Dug Interaction Knowledge Base ontology. This version is essentially the original version from 2007 with a change to the base IRI to use a PURL 02/09/2013 Richard D Boyce Description: An evidence taxonomy for pharmacologic studies that, when combined with a set of inclusion criteria, enable drug experts to specify what their confidence in a drug mechanism assertion would be if it were supported by a specific set of evidence. Boyce R, Collins C, Horn J, Kalet I. Computing with evidence Part I: A drug-mechanism evidence taxonomy oriented toward confidence assignment. J Biomed Inform. 2009 Dec;42(6):979-89. Epub 2009 May 10. PubMed PMID: 19435613; PubMed Central PMCID: PMC2783801.
Categories : Vocabularies 		2809
Randomized Controlled Trials (RCT) Ontology (RCTOntology) Public 186 0 0 1 OWL 2.0 10/14/2011 Amrapali Zaveri Description: We developed and evaluated an ontology specifically for Randomized Controlled Trials in order to facilitate the production of systematic reviews and metaanalysis.
Categories : Biomedical Resources 		5059
Neomark Oral Cancer Ontology (NeoMark) Public 324 0 0 1 OWL 4.1 11/11/2011 Dario Salvi Description: Ontology that describes the medical information necessary for early detection of the oral cancer reoccurrence extracted from the NeoMark Project.
Categories : Human , Genomic and Proteomic , Anatomy , Health 		5062 2806 2810 5058
Fission Yeast Phenotype Ontology (FYPO) Public 4,612 0 0 1 OBO 2013-06-17 06/17/2013 Midori Harris Description: FYPO is a formal ontology of phenotypes observed in fission yeast. FYPO is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the new online fission yeast resource (www.pombaes.org). Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions.
Categories : Phenotype 		2807
Synapse Ontology (SYN) Public 14,462 0 0 1 OWL .3 01/07/2013 Sage Bionetworks Description: The controlled vocabulary used for various entity properties in the Synapse platform.
Categories :
VIVO (vivo) Public 164 0 0 4 OWL 1.5 07/16/2012 Stella Mitchell Description: The VIVO ontology represents researchers in the context of their experience, outputs, interests, accomplishments, and associated institutions.
Categories : Other 		2801 ,CTSA,
Minimal Information about any Sequence Controlled Vocabularies (MIXSCV) Public 519 0 0 1 OBO 1 01/31/2012 Doug Wendel Description: Controlled vocabularies for the MIxS family of metadata checklists. See http://gensc.org/gc_wiki/index.php/MIxS for details on the MIxS checklists.
Categories :
Mental Functioning Ontology (MF) Public 666 1 0 1 OWL alpha 2012-11-03 02/24/2013 Janna Hastings Description: The Mental Functioning Ontology is an ontology for mental functioning, including mental processes such as cognition and traits such as intelligence, and related diseases and disorders. It is developed in the context of the Ontology for General Medical Science and the Basic Formal Ontology. The project is being developed in collaboration between the University of Geneva, Switzerland, and the University at Buffalo, USA. The project is being developed with full involvement of all relevant communities, following best practices laid out by the OBO Foundry. Efforts are currently underway to align with related projects including the Behaviour Ontology, the Cognitive Atlas, the Cognitive Paradigm Ontology and the Neural Electro Magnetic Ontologies.
Categories :
Computational Neuroscience Ontology (CNO) Public 394 5 0 1 OWL version 0.5 02/21/2013 Yann Le Franc Description: CNO is a controlled vocabulary of terms used in Computational Neurosciences to describe models of the nervous system. This first release of CNO is an alpha version and should be further aligned with other ontologies accessible on Bioportal and should be made compliant with the OBO foundry recommendations. This work is licensed under the Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. If you have any comments, questions or suggestions, please contact Yann Le Franc at ylefranc(at)gmail.com.
Categories : Vocabularies 		2809
Natural Products Ontology (NatPrO) Public 9,460 0 0 1 OWL unknown 02/08/2012 Riza Theresa Batista-Navarro Description: An ontology for describing biological activities of natural products.
Categories :
Ontology of Experimental Variables and Values (OoEVV) Public 47 0 0 1 OWL 0.0.4 07/18/2012 Gully Burns Description: The ontology of experimental variables and values provides a lightweight representation of (a) the variables used to measure experimental properties and (b) the measurement scales that form the complex data types supporting that data. Many different variables measure the same thing, here we use a lightweight representation driven by a small number of classes and a large number of variables to focus only on providing a vocabulary of variables that may be extended for consolidation to standardized variables for specific things and functions to map between values from different measurements scales. We use the base ontology description to provide a very lightweight representation of the basic elements of an experimental design and we use views to instantiate it for specific domains.
Categories : Vocabularies 		2809
Content Archive Resource Exchange Lexicon (CARELEX) Public 322 0 0 2 OWL 1.02 06/10/2013 Zack Schmidt Description: Categories and terms used to classify content (documents, images, etc) in electronic content repositories for life science / BioPharma. Initial version contains content model for use with clinical trial electronic Trial Master Files or eTMF archives. A Content model contains content classification categories (classes) and metadata properties (data properties). Data properties should be assigned to each Content Type. Information is available at CareLex.org. Recent changes include: addition of electronic signature support, medical imaging classifications.
Categories : Vocabularies 		2809
Metagenome and Microbes Environmental Ontology (MEO) Public 176 0 0 1 OWL Version 0.3 03/13/2013 MicrobeDB.jp Project Team Description: An Ontology for organismal habitats (especially focused on microbes)
Categories : Other 		2801
Non Randomized Controlled Trials Ontology (NonRCTOntology) Public 155 0 0 1 OWL 2.0 02/24/2012 Amrapali Zaveri Description: We built an ontology to help the systematic review and meta-analysis process of non randomized clinical trials.
Categories :
Diagnostic Ontology (DIAGONT) Public 96 0 0 1 OWL 2.0 02/27/2012 Amrapali Zaveri Description: We built a computational diagnostic ontology containing 91 elements, including classes and sub-classes, which are required to conduct SR-MA (Systematic Review - Meta Analysis) for diagnostic studies, that will assist in standardized reporting of diagnostic articles. We also report high percentage of agreement among five observers as a result of the inter-observer agreement that we conducted among them to tag 13 articles using the diagnostic ontology. Moreover, we extend our existing repository CERR-N (Center of Excellence in Research Reporting in Neurosurgery) to include diagnostic studies.
Categories :
Physical Medicine and Rehabilitation (PMR) Public 137 0 0 1 OWL 1.5 03/06/2012 Laia Subirats Description: Knowledge representation related to computer-based decision support in rehabilitation; concepts and relationships in the rehabilitation domain, integrating clinical practice, the ICD (specifically its 11th revision), the clinical investigator record ontology, the ICF and SNOMED CT.
Categories : Health 		5058
Eagle-I Research Resource Ontology (ERO) Public 3,906 1 0 2 OWL 2013-05-06 05/06/2013 Carlo Torniai Description: This ontology models research resources such instruments. protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/).
Categories : Biomedical Resources 		5059
OWL Version of MeSH (RH-MESH) Public 286,380 1 0 2 OWL 2012 03/26/2012 Robert Hoehndorf Description: Medical Subjects Headings Thesaurus 2012, OWL version. This is an OWL representation of MeSH so that it can be integrated with other ontologies represented in OWL. It contains all terms that are in MeSH and in the MeSH concept tree. Concepts in the MeSH concept tree are merged with MeSH term ids.
Categories : Human , Vocabularies , Phenotype , Health , Dysfunction 		5062 2809 2807 5058 5070
Cell Phenotype Ontology (CPO) Public 136,005 0 0 2 OWL unknown 04/18/2012 Robert Hoehndorf Description: An ontology of cellular phenotype. Primarily focused on cell physiology phenotypes.
Categories : Cell , Phenotype , Physicochemical , All Organisms 		5065 2807 2822 5073
BioModels Ontology (BIOMODELS) Public 187,519 0 0 1 OWL 21 04/03/2012 Robert Hoehndorf Description: OWL Representation of the models in the BioModels repository.
Categories : Biological Process , Biomedical Resources , All Organisms 		5060 5059 5073
Cerebrotendinous Xanthomatosis Ontology (CTX) Public 477 0 0 1 OWL vtemp2 04/30/2013 Maria Taboada Description: The ontology represents CTX phenotypes, genetic variants, and bidirectional relationships between them though a patient model. The CTX ontology was build reusing the Human Phenotype Ontology (HPO) and the Snomed ct ontologies. A set of temporal clinical manifestations are semantically annotated with a domain phenotype ontology and registered with a time-stamped value.
Categories : Phenotype 		2807
SoyOntology (SOY) Public 1,835 0 0 1 OBO unknown 04/30/2013 Rex Nelson Description: Growth, trait and development ontology for soybean
Categories : Plant 		5063
Solanaceae Phenotype Ontology (SPTO) Public 396 0 0 1 OBO unknown 11/05/2012 Naama Menda Description: Solanaceae crop phenotypes and traits, developed in collaboration with the research community, especially for breeder traits of agronomic importance.
Categories :
Cancer Chemoprevention Ontology (CANCO) Public 126 0 0 2 OWL 0.3 05/01/2013 Dimitris Zeginis Description: The Cancer Chemoprevention Ontology constitutes a vocabulary that is able to describe and semantically interconnect the different paradigms of the cancer chemoprevention domain.
Categories : Experimental Conditions , Health , Biomedical Resources , Molecule 		2805 5058 5059 5069
Quantities, Units, Dimensions and Types (QUDT) Licensed 195 0 0 2 OWL $Id: OSG_qudt-(v1.1).ttl 4989 2011-06-01 21:56:40Z RalphHodgson $ 02/11/2013 Ralph Hodgson Description: The QUDT, or 'Quantity, Unit, Dimension and Type' collection of ontologies define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems. The goal of the QUDT ontology is to provide a unified model of, measurable quantities, units for measuring different kinds of quantities, the numerical values of quantities in different units of measure and the data structures and data types used to store and manipulate these objects in software. This OWL schema is a foundation for a basic treatment of units.
Categories : Other 		2801
Time Event Ontology (TEO) Public 589 0 0 1 OWL 1.0.8 04/27/2012 Cui Tao Description: The Time Event Ontology (TEO) is an ontology for representing events, time, and their relationships.
Categories : Other 		2801
Medical Diagnostic Categories - Diagnosis Related Groups (MDCDRG) Public 791 0 0 0 OWL 1.2 08/08/2012 Ketty Mobed Description: Ontology of Medical Diagnostic Categories-Diagnosis Related Groups
Categories : Human , Health , Biomedical Resources , Other 		5062 5058 5059 2801 ,CTSA-HOM,
uni-ece (uni-ece) Public 179 0 0 0 OWL unknown 05/10/2012 fatemehyb Description: implement ece college
Categories :
Phenotype Fragment Ontology (PFO) Public 20 0 0 1 OWL 2.0 08/05/2012 Tudor Groza Description: The Phenotype Fragment Ontology provides a formal entity/quality representation for fine-grained human phenotype.
Categories : Human , Phenotype 		5062 2807
Darwin Core Terms (DWC) Public 0 0 0 2 OWL 2013-04-02 04/24/2013 John Wieczorek (DwC coordinator), John Deck, Dag Endresen Description: The Darwin Core is body of standards used for biodiversity information resources. This vocabulary provides a flat list of Darwin Core terms intended as a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts). Darwin Core is intended to facilitate the sharing of information about biological diversity by providing reference definitions, examples, and commentaries. The Darwin Core is primarily based on taxa, their occurrence in nature as documented by observations, specimens, and samples, and related information.
See also the Darwin Core project page: http://bioportal.bioontology.org/projects/168.
The Darwin Core terms cause parse error here in BioPortal. We are exploring the cause of this parse error. The Darwin Core terms are described as a flat list of terms. The RDF resource can be seen as a minimal however valid OWL full ontology.
Categories : Taxonomic Classification , All Organisms 		2808 5073 ,BIS,
BOOK (BO) Public 74 0 0 1 OWL unknown 05/27/2012 yanpingli Description: BOOK
Categories :
Ontology of Data Mining Investigations (OntoDM-KDD) Public 263 0 0 1 OWL 1.0 06/06/2012 Pance Panov Description: OntoDM-KDD is an ontology for representing data mining investigations. Its goal is to allow the representation of knowledge discovery processes and be general enough to represent the data mining investigations. The ontology is based on the CRISP-DM process methodology.
Categories :
PhenX Terms (PhenX) Public 369 0 0 2 OWL 0.9 03/04/2013 PhenX Admin Description: Standard measures related to complex diseases, phenotypic traits and environmental exposures
Categories : Phenotype 		2807
SANOU (OntoMA) Public 622 0 0 1 OWL Version 1.1 Date: 11-2011 06/25/2012 SANOU MARTIN Description: Common concepts for communication between traditional medicine and western medicine
Categories :
Cell Culture Ontology (CCONT) Public 5,516 0 0 1 OWL 1.1 07/11/2012 Matthias Ganzinger Description: CCONT is an ontology for the formal representation of cell lines and their correspnding culture conditions.
Categories : Biological Process , Vocabularies , Experimental Conditions 		5060 2809 2805
RAPID Phenotype Ontology (RPO) Public 1,544 0 0 3 OWL 1.0 08/13/2012 Dr. Sujatha Mohan Description: RAPID phenotype ontology presents controlled vocabulary of ontology class structures and entities of observed phenotypic terms for primary immunodeficiency diseases (PIDs) that facilitate global sharing and free exchange of PID data with users’ communities
Categories : Human , Phenotype , Immunology 		5062 2807 5074
Bioinformatics Web Service Ontology (OBIWS) Public 227 0 0 1 OWL Release v1.1 12/18/2012 jie zheng Description: The Bioinformatics Web Services ontology (OBIws) is an ontology that extends the Ontology for Biomedical Investigations (OBI) to build an Ontology that supports consistent annotation of Bioinformatics Web services.
Categories : Other 		2801
Vital Sign Ontology (VSO) Public 137 0 0 1 OWL 2012-04-25 07/23/2012 Albert Goldfain Description: The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.
Categories : Health 		5058
NIF-Subcellular (NIF-Subcell) Public 2,797 0 0 1 OWL 1.3 (May 2012) 07/27/2012 Fahim Imam Description: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl
Categories :
Immune Disorder Ontology (IMMDIS) Public 1,413 0 0 1 OBO unknown 07/31/2012 Richard Scheuermann Description: The Immune Disorder Ontology was generated as part of the Bioinformatics Integration Support Contract (BISC) funded by the Division of Allergy, Immunology and Transplantation (DAIT) within NIAID. The ontology is based on the National Library of Medicine (NLM) Medical Subject Headings; National Cancer Institute Thesaurus; International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM); ICD-10; and other open source public databases.

Lineage(s)

A class may be related to its superclass through a true is_a relationship (e.g., Polymyositis is a Dermatomyositis, which is an Autoimmune_Disease, which is an Immune_Disorder). Based on description logic, a class inherits all the Relationships (Object Properties) and Datatype Properties (if any) assigned to its superclass. In a few occasions, a class may have more than one superclass and belongs to more than one lineage.

Annotations

Specific information may be available about a class, including Preferred_Name, DEFINITION, Synonym, etc. The following provides more detail on annotation information presented:
DEFINITION: A human-readable definition is provided for each class in the ontology and the displayed format is Owner|Definition (Source).
FULL_SYN: Synonym of a class in the ontology with type (PT: preferred term, SY: synonym) and source of this synonym indicated. Synonym|Type of Synonym|Source of Synonym is the format displayed.
ICD-10_Code: Code of International Classification of Diseases and Related Health Problems, 10th revision. ICD-10 is a detailed description of known diseases and injuries. It is published by the World Health Organization (WHO) and is used worldwide for mortality statistics.
ICD-9_Code: Code of International Classification of Diseases and Related Health Problems, 9th revision.
Class Name: Class_Name is used as a unique identifier by Protege-OWL, the environment where this ontology is being developed and therefore has to be OWL-compliant. Class_Name is composed of a string only made of digits, letters, underscores, and hyphens. A Class_Name cannot start with a digit.
Preferred_Name: A human-friendly and commonly used name in plain English.
Synonym: Synonym of a class in plain English, including those in plural form or British spelling. In contrast to FULL_SYN, no type nor source of synonym is indicated. Synonym is human-friendly and not OWL-compliant. A class may have multiple synonyms.
UMLS_CUI: Concept Unique Identifier in Unified Medical Language System that is produced and distributed by NLM. There are three UMLS Knowledge Sources: the Metathesaurus, the Semantic Network, and SPECIALIST Lexicon. The purpose of UMLS is to facilitate the development of computer systems that behave as if they "understand" the meaning of the language of biomedicine and health.

Relationships (Object Properties)

Relationships are properties by which one class is related to another class in the ontology. For example, "Population_Group" (a class) has_susceptibility_to_disease (a relationship) "Immune_Disorder" (a class). This box may be empty if no relationship has been used for modeling.

Datatype Properties

Datatype Properties are properties by which a class is related to a datatype. This box may be empty if no datatype property has been used for modeling.
Categories : Human , Health , Immunology 		5062 5058 5074
Informed Consent Permission Ontology (CONSENT-ONT) Public 288 0 0 1 OWL Alpha, version 2. 01/16/2013 01/27/2013 Maria Adela Grando Description: The aim of this ontology is to capture permissions given by subjects consenting to participate in a research study. Has been developed within the iDASH project.
Categories :
PROV-O (prov-o) Public 0 0 0 3 OWL unknown 06/18/2013 Timothy Lebo Description: The PROV Ontology (PROV-O) expresses the PROV Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes, properties, and restrictions that can be used to represent and interchange provenance information generated in different systems and under different contexts. It can also be specialized to create new classes and properties to model provenance information for different applications and domains.
Categories :
Ontology for Newborn Screening Follow-up and Translational Research (ONSTR) Public 1,850 0 0 1 OWL 0.3 05/02/2013 Rani Singh, Prabhu Shankar, Snezana Nikolic Description: Ontology for Newborn Screening Follow-up and Translational Research (ONSTR) is an application ontology covering the domain of newborn screening, follow-up and translational research pertaining to patients diagnosed with inheritable and congenital diseases mainly identified through newborn dried blood spot screening. ONSTR is a central component of the project Newborn Screening Follow-up Data Integration Collaborative (NBSDC). ONSTR uses the Basic Formal Ontology v2 (BFO2, v2012-07-20) as top-level ontology and extends the classes imported from OBO Foundry ontologies and candidate ontologies. For latest release notes please see: http://onstr.googlecode.com/svn/tags/currentRelease/2013-05-02/ NBSDC project page: https://nbsdc.org (under construction).
Categories : Biological Process , Human , Phenotype , Health , Development , Dysfunction 		5060 5062 2807 5058 2803 5070
MicroRNA Ontology (MIRNAO) Public 662 0 0 1 OWL 1.5 05/03/2013 Vicky Dritsou Description: An application ontology for microRNAs.
Categories : Other 		2801
The Biomedical Research Integrated Domain Group (BRIDG) model (BRIDG) Public 319 0 0 1 OWL 3.2 09/04/2012 Cecil Lynch Description: The Biomedical Research Integrated Domain Group (BRIDG) Model is a collaborative effort engaging stakeholders from the Clinical Data Interchange Standards Consortium (CDISC), the HL7 Regulated Clinical Research Information Management Technical Committee (RCRIM TC), the National Cancer Institute (NCI) and its Cancer Biomedical Informatics Grid (caBIG®), and the US Food and Drug Administration (FDA). The BRIDG model is an instance of a Domain Analysis Model (DAM). The goal of the BRIDG Model is to produce a shared view of the dynamic and static semantics for the domain of protocol-driven research and its associated regulatory artifacts. This domain of interest is further defined as: Protocol-driven research and its associated regulatory artifacts: i.e. the data, organization, resources, rules, and processes involved in the formal assessment of the utility, impact, or other pharmacological, physiological, or psychological effects of a drug, procedure, process, or device on a human, animal, or other subject or substance plus all associated regulatory artifacts required for or derived from this effort, including data specifically associated with post-marketing adverse event reporting. This OWL version of the BRIDG model is create by the National Cancer Institute (NCI). Source repository: https://ncisvn.nci.nih.gov/WebSVN/listing.php?repname=bridg-model&path=%2Ftrunk%2FModel+-+OWL%2F&
Categories : Health 		5058
Gene Expression Ontology (GEXO) Public 89,733 0 0 0 OBO 1.01 11/17/2012 Vladimir Mironov Description: An application ontology for the domain of gene expression. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations.
Categories : Biological Process , Human , Genomic and Proteomic , Protein , Gene Product 		5060 5062 2806 2821 2820
Regulation of Gene Expression Ontolology (ReXO) Public 77,609 0 0 1 OBO 1.01 11/17/2012 Vladimir Mironov Description: An application ontology for the domain of gene expression regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations.
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Neglected Tropical Disease Ontology (NTDO) (NTDO) Public 525 0 0 1 OWL Rev. 368 09/12/2012 Filipe Santana Description: The Neglected Tropical Disease Ontology (NTDO) aims at representing classes and relations to a specific set of diseases which persist in exactly the physical, psychosocial and economic situation of the poorest, most marginalized populations of the developing world, the Neglected Tropical Diseases (NTD). The current focus of NTDO is related to the transmission of vector-borne diseases and how they are related to the death. NTDO is based on BioTop (main classes and relations) and GFO (Time Representation) and represented in Description Logics (DL). NTDO includes information about the proper disease, its causative agent (when available), dispositions, and the geographic location the disease happens. In addition, NTDO includes a generic attempt to identify the process which leads a person to death, due to NTDs or other diseases. NTDO was built with a rich set of axioms and the intended usage is related to Health Surveillance of NTD-related morbidity and mortality cases.
Categories : Biological Process , Human , Health , Other 		5060 5062 5058 2801
Ontological Knowledge Base Model for Cystic Fibrosis (ONTOKBCF) Public 408 0 0 3 OWL 1301 01/16/2013 Xia Jing Description: OntoKBCF is an ontological knowledge base model for cystic fibrosis. There are molecular genetic information (i.e. gene mutations) and health information included in OntoKBCF. The purposes of OntoKBCF include management of molecular genetic information and health information and embedding OntoKBCF into EHR settings.
Categories : Phenotype , Health , Biomedical Resources , Gene Product 		2807 5058 5059 2820
Semantic Web for Earth and Environment Technology (SWEET) Public 4,527 0 0 1 OWL 2.3 09/24/2012 ESIP Description: The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology de-veloped at the NASA Jet Propulsion Laboratory that currently contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level con-cepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research). SWEET is now officially under the governance of the ESIP foundation.
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Variation Ontology (VariO) Public 378 0 0 1 OBO 2013-06-14 06/14/2013 Mauno Vihinen Description: Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations.
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Regulation of Transcription Ontolology (ReTO) Public 70,221 0 0 0 OBO 1.01 11/17/2012 Vladimir Mironov Description: An application ontology for the domain of gene transcription regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations.
Categories : Biological Process 		5060
Glycomics Ontology (GLYCO) Public 235 0 0 1 OWL 4.6.0.0 10/29/2012 Will York Description: The GlycO ontology provides an up-to-date knowledge base of experimentally verified glycan structures. Glycan (oligosaccharide or polysaccharide) structures are represented as trees of monosaccharide residues. Linkage to proteins and lipids is supported as well. Insertion of a new glycan is controlled by curation process that includes matching the new glycan against a canonical glyco-tree (a highly branched representation for a family of glycans).
Categories : Biomedical Resources , Molecule , Protein , Chemical , Other 		5059 5069 2821 2802 2801
Dengue Fever Ontology (IDODEN) Public 5,003 0 0 0 OWL 0.05 05/14/2013 Elvira Mitraka Description: An ontology for dengue fever.
Categories : Human , Health , Other 		5062 5058 2801
XEML Environment Ontology (XeO) Public 144 0 0 1 OBO 1.6 04/03/2013 Jan Hummel Description: XeO has been created to help plant scientists in documenting and sharing metadata describing the abiotic environment.
Categories : Other 		2801
ThomCan: Upper-level Cancer Ontology (ThomCan) Public 56 0 0 0 OBO unknown 11/20/2012 Andre Stander Description: Providing an upper-level ontology for cancer.
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Genomic Clinical Decision Support Ontology (GENE-CDS) Public 2,265 0 0 0 OWL 0.8.0 11/21/2012 Matthias Samwald Description: The Genomic CDS ontology aims to unify several functionalities in a single resource, being: * A knowledge base for clinical pharmacogenomics/pharmacogenetics that can be used for question-answering (e.g., which SNPs are associated with this drug?) * A rule base for clinical decision support (e.g., inferring that a patient with a specific set of SNPs requires a lowered dose of warfarin and generating a CDS message that can be viewed by clinicians) * A tool for checking data consistency (e.g., highlighting which allele definitions in PharmGKB are overlapping, or which clinical decision support rules are matching the same group of patients)
Categories : Human , Genomic and Proteomic , Health 		5062 2806 5058
Mouse Experimental Design Ontology (MEDO) Public 83 0 0 0 OWL 1.0 11/22/2012 Helen Parkinson Description: A representation of experimental design for high-throughput mouse analysis pipelines.
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OntoPneumo (OntoPneumo) Public 1,153 0 0 0 OWL 0.1 12/04/2012 Jean Charlet Description: Ontology of pneumology (french version). The ONTOPNEUMO ontology was developped by Audrey Baneyx, under the direction of Jean Charlet about knowledge engineering expertise and by François-Xavier Blanc in collaboration with Bruno Housset about medical expertise. The OWL compliant ONTOPNEUMO ontology is available under Creative Commons license “Attribution-Non-Commercial-No Derivative Works 2.0 UK”. Details of this license are accessible at : http://creativecommons.org/licenses/ by-nc-nd/2.0/uk/.
Categories : Human , Health 		5062 5058
Fanconi Anemia Ontology (IFAR) Public 2,797 1 0 1 OWL 1.2 01/10/2013 Erica Sanborn Description: An application ontology devoted to the standardized recording of data related to Fanconi Anemia (FA). This ontology was created using an OWL file provided by Dr. Ada Hamish (and Francois Schiettecatte) at the Centers for Mendelian Genetics, with their permission. Their original ontology can be found at: http://phenodb.net/help/features. Modifications were made using HPO, OMIM, NCI, and SNOMED. Novel classes pertaining to FA were added and defined as appropriate.
Categories : Other 		2801
Top-Menelas (Top-Menelas) Public 524 0 0 0 OWL 1.0 01/14/2013 Jean Charlet Description: The two main goals MENELAS contributes to are to (i) Provide better account of and better access to medical information through natural languages in order to help physicians in their daily practice, and to (ii) Enhance European cooperation by multilingual access to standardised medical nomenclatures. The major achievements of MENELAS are the realisation of its two functional systems: (i) The Document Indexing System encodes free text PDSs into both an internal representation (a set of Conceptual Graphs) and international nomenclature codes (ICD-9-CM). Instances of the Document Indexing System have been realised for French, English and Dutch ; (ii) The Consultation System allows users to access the information contained in PDSs previously indexed by the Document Indexing System. The test domain for the project was coronary diseases. The existing prototype shows promising results for information retrieval from natural language PDSs and for automatically encoding PDSs into an existing classification such as ICD-9-CM. A set of components, tools, knowledge bases and methods has also been produced by the project. These include language-independent ontology and models for the domain of coronary diseases; conceptual description of the relevant ICD-9-CM codes. This ontology includes a top-ontology, a top-domain ontology and a domain ontology (Coronay diseases surgery). The menelas-top ontology here is the part of the whole ontology without any reference to medical domain.
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Anatomic Pathology Lexicon (PATHLEX) Public 1,785 0 0 0 OWL 1.2 01/22/2013 Christel Daniel Description: PathLex, a comprehensive lexicon—a unified language of anatomic pathology terms—for standardized indexing and retrieval of anatomic pathology information resources.
Categories : Vocabularies , Taxonomic Classification , Anatomy , Health 		2809 2808 2810 5058
Semantically-integrated human physiome (SemPhysKB-Human) Public 5,937 0 0 0 OWL 0.0.1 02/18/2013 Maxwell Neal Description: Ontological representation of human physiological models collected from various public repositories.
Categories : Biological Process , Phenotype , Anatomy , Physicochemical 		5060 2807 2810 2822
Biological Collections Ontology (BCO) Public 80 0 0 0 OWL unknown 06/17/2013 bco-discuss list Description: The biological collection ontology includes consideration of the distinctions between individuals, organisms, voucher specimens, lots, and samples the relations between these entities, and processes governing the creation and use of "samples". Within scope as well are properties including collector, location, time, storage environment, containers, institution, and collection identifiers.
Categories : All Organisms 		5073 ,BIS,
Human Interaction Network Ontology (HINO) Public 37,331 0 0 0 OWL Vision Release: 1.0.38 02/22/2013 Yongqun "Oliver" He Description: The Human Interaction Network Ontology (HINO) is an INO extension for the domain of human interaction networks. It has currently incoporated Reactome reactions and pathways. Like INO, HINO aligns with BFO. HINO is developed by following the OBO Foundry principles.
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Porifera Ontology (PORO) Public 644 0 0 0 OWL unknown 02/25/2013 Bob Thacker Description: An ontology covering the anatomy of Porifera (sponges)
Categories : Phenotype , Anatomy 		2807 2810
Animal Trait Ontology for Livestock (ATOL) Public 1,938 0 0 1 OBO v5_210113 03/11/2013 Léa Joret Description: An ontology of livestock animal traits dedicated to the production
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Image and Data Quality Assessment Ontology (IDQA) Public 180 0 0 0 OWL v32 03/11/2013 Thomas Schrader Description: Image and Data Quality Assessment for scientific data management
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Ontology of Physical Exercises (OPE) Public 633 0 0 0 OWL 0.0.1 03/21/2013 Juan-Carlos Foust Description: The Ontology of Physical Exercises (OPE) provides a reference for describing an exercise in terms of functional movements, engaged musculoskeletal system parts, related equipment or monitoring devices, intended health outcomes, as well as target ailments for which the exercise might be employed as a treatment or preventative measure.
Categories : Human , Anatomy , Health , Other 		5062 2810 5058 2801
Taxonomy for rehabilitation of knee conditions (TRAK) Public 1,292 0 0 0 OBO unknown 04/23/2013 Irena Spasic Description: TRAK (Taxonomy for RehAbilitation of Knee conditions) is an ontology that formally models information relevant for the rehabilitation of knee conditions. TRAK provides the framework that can be used to collect coded data in sufficient detail to support epidemiologic studies so that the most effective treatment components can be identified, new interventions developed and the quality of future randomized control trials improved to incorporate a control intervention that is well defined and reflects clinical practice.
Categories : Biomedical Resources 		5059
Ontology for Genetic Susceptibility Factor (OGSF) Public 384 0 0 0 OWL 0.7 06/16/2013 Yu Lin Description: Ontology for Genetic Susceptibility Factor (OGSF) is an application ontology to model/represent the notion of genetic susceptibility to a specific disease or an adverse event or a pathological biological process. It is developed using BFO2.0's framwork. The ontology is under the domain of genetic epidemiology.
Categories : Human , Genomic and Proteomic , Health 		5062 2806 5058
Minimal Information about any Sequence Ontology (MIXS) Public 7 0 0 0 OWL unknown 04/10/2013 John Deck Description: An RDF representation of the MIxS Family of Checklists
Categories : 		,BIS,
G Protein-Coupled Receptor BioAssays Ontology (BAO-GPCR) Public 891 0 0 1 OWL 1.0 06/17/2013 Stephan Schurer Description: The G protein-coupled receptors (GPCRs) ontology (http://www.bioassayontology.org/bao_gpcr) describes pharmacology, biochemistry and physiology of these important and therapeutically promising class of academic and pharmaceutical research targets. Incorporation and comparison of various small molecule screening data sets, such as those deposited in PubChem, ChEMBL, KEGG, PDSP, and/or IUPHAR databases, requires a formalized electronic organization system. In order to bridge the gap between the overflow of HTS data and the bottleneck of integrated analysis tools, herein, we provide the first comprehensive GPCR ontology. The development and utility of GPCR ontology was based on previously developed BioAssay Ontology (BAO). The GPCR ontology contains information about biochemical, pharmacological, and functional properties of individual GPCRs as well as GPCR-selective ligands inclusive of their HTS screening results and other records. This provides the first all-inclusive GPCR ontology with all available data to model the relationship between the GPCR binding sites and their physiologic and pharmacologic role in physiology via small molecule chemical structures. We developed this system using emerging semantic technologies, by leveraging existing and descriptive domain level ontologies.
Categories : Biological Process , Vocabularies , Subcellular , Physicochemical , Molecule , Protein , Chemical , Other 		5060 2809 5067 2822 5069 2821 2802 2801
Computer Assisted Brain Injury Rehabilitation Ontology (CABRO) Public 59 0 0 0 OWL 0.5 03/29/2013 Dimitrios Zikos Description: a web ontology for the semantic representation of the computer assisted brain trauma rehabilitation domain. This is a novel and emerging domain, since it employs the use of robotic devices, adaptation software and machine learning to facilitate interactive, adaptive and personalized rehabilitation care, patient monitoring and assisted living.
Categories : Human , Health , Biomedical Resources , Neurological Disorder , Neurologic Disease , Dysfunction 		5062 5058 5059 5072 5071 5070
Tribolium Ontology (TrOn) Public 965 0 0 2 OBO unknown 05/20/2013 Jürgen Dönitz, Daniela Grossmann Description: TrOn is an ontology about the anatomical structures of the red flour beetle Tribolium castaneum in the developmental stages larva, pupa and adult.
Categories : Anatomy , Development 		2810 2803
Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy (MTHMST) Public 1,699 0 0 0 RRF 01/01/2001 04/03/2013 Jan Willis, NLM Description: Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy. Bethesda, MD: National Library of Medicine, 2001.
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Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy, French Translation (MTHMSTFRE) Public 1,700 0 0 0 RRF 2001 04/03/2013 Jan Willis, NLM Description: Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy, French Translation, 2001
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Genome Component Ontology (GCO) Public 4 0 0 0 OWL 0.2 05/22/2013 Zuotian Tatum Description: The Genome Component Ontology is intended to define the abstract division of the total genetic information of an organism by its physical separation into different components, thereby providing a high level reference point to which more specific descriptions of the characteristics of these components can be linked.
Categories : Genomic and Proteomic , Biomedical Resources 		2806 5059
Lowongan Kerja Terbaru 2013 (career) Summary Only 0 0 0 0 OWL 04/25/2013 duakerja Description: Lowongan Kerja, Lowongan Kerja Terbaru 2013, Lowongan Bank, Lowongan BUMN, Lowongan CPNS 2013, Lowongan Pertamina, Lowongan Telkom, Lowongan Kereta Api, Lowongan Astra, Lowongan Guru, Lowongan SMA sederajat
Categories : Anatomy 		2810
Synthetic Biology Open Language Visual (SBOLv) Public 22 0 0 0 OWL unknown 04/26/2013 Jacqueline Quinn Description: Synthetic Biology Open Language Visual (SBOLv) is an ontology to represent standardized graphical notation for synthetic biology.
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Ontology of Vaccine Adverse Events (OVAE) Public 835 0 0 0 OWL Vision Release: 1.0.28 06/17/2013 Oliver He Description: The Ontology of Vaccine Adverse Events (OVAE) is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the Ontology of Adverse Events (OAE) and the Vaccine Ontology (VO). OVAE is aimed to represent and analyze various vaccine-specific adverse events.
Categories : Human , Phenotype , Health , Immunology 		5062 2807 5058 5074
Eligibility Feature Hierarchy (ELIG) Public 29 0 0 0 OWL v. 1.0 05/07/2013 Mary Regina Boland Description: We derived a set of 1,437 eligibility features that were organized into a feature hierarchy using 80 breast cancer trials.
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SNOMED International, 1998 (SNMI) Public 112,688 0 0 0 LEXGRID 1998 05/23/2013 Jill Rosenthal Description: Cote, Roger A., editor. Systematized Nomenclature of Human and Veterinary Medicine: SNOMED International. Northfield (IL): College of American Pathologists; Schaumburg (IL): American Veterinary Medical Association, Version 3.5, 1998.
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Congenital Heart Defects Wiki Ontology (CHDWIKI) Public 511 0 0 0 OWL 1.1 06/03/2013 Charalampos Moschopoulos Description: An ontology that describes the CHDWiki data.
Categories : Human 		5062
Biodiversity Ontology (BOF) Public 188 0 0 0 OWL unknown 05/23/2013 Franco Description: An ontology of biodiversity of INPA
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Vertebrate Taxonomy Ontology (VTO) Public 107,063 0 0 1 OWL unknown 05/31/2013 James Balhoff Description: The Vertebrate Taxonomy Ontology includes both extinct and extant vertebrates, aiming to provide one comprehensive hierarchy. The hierarchy backbone for extant taxa is based on the NCBI taxonomy. Since the NCBI taxonomy only includes species associated with archived genetic data, to complement this, we also incorporate taxonomic information across the vertebrates from the Paleobiology Database (PaleoDB). The Teleost Taxonomy Ontology (TTO) and AmphibiaWeb (AWeb) are incorporated to provide a more authoritative hierarchy and a richer set of names for specific taxonomic groups.
Categories : Taxonomic Classification 		2808
Pathogenic Disease Ontology (PDO) Public 272 0 0 0 OWL Version 0.1 05/30/2013 MicrobeDB.jp Project Team Description: An ontology for describing both infectious disease caused by bacteria and the disease that is related to bacterial infection.
Categories : Health 		5058
Clinical Signs and Symptoms Ontology (CSSO) Public 277 0 0 0 OWL Version 0.1 05/30/2013 MicrobeDB.jp Project Team Description: An ontology for describing clinical signs and symptoms.
Categories : Health 		5058
Research Network and Patient Registry Inventory Ontology (RNPRIO) Public 79 0 0 0 OWL 1.0 06/07/2013 Seena Farzaneh Description: Ontology for Inventories of Clinical Data Research Networks, Patient-Powered Research Networks, and Patient Registries
Categories : Biomedical Resources 		5059