Access all ontologies that are available in BioPortal: You can filter this list by category to display ontologies relevant for a certain domain (try selecting "Anatomy or Experimental Conditions" in the "Filter by category" menu below). You can also filter ontologies that belong to a certain group such as ontologies from the OBO Foundry, or ontologies from the Cancer Biomedical Informatics Grid (caBIG). Subscribe to the BioPortal RSS feed to receive alerts for submissions of new ontologies, new versions of ontologies, new notes, and new projects. You can subscribe to feeds for a specific ontology at the individual ontology page. Add a new biomedical ontology to BioPortal using the Submit New Ontology link.


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Ontology Name Format Version Author Uploaded On Group Description categories groups Status
Cell Behavior Ontology
(CBO) 		OWL 0.0 Benjamin Zaitlen 05/05/2009 Description: The Cell Behavior Ontology is designed as a structured controlled vocabulary for what cells do. This ontology is a draft and independent of cell type.
Explore
Drosophila development
(FBdv) 		OBO Format 1.17 Http://obo Administrators 08/26/2010 Description: A structured controlled vocabulary of the development of Drosophila melanogaster.
Categories : Animal Development , Development 		2818 2803 Explore
NMR-instrument specific component of metabolomics investigations
(NMR) 		OWL See Remote Site Https://svn Administrators 04/13/2009 Description: Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation.
Categories : Other 		2801
Medical Subject Headings
(MSH) 		RRF 2010_2009_08_17 Stuart Nelson, M.D. 01/08/2010
UMLS
 Description: Medical Subject Headings (MeSH);National Library of Medicine;Februrary, 2009;Bethesda, MD;ENG
Categories : Health 		5058 UMLS Explore
Electrocardiography Ontology
(ECG) 		OWL 0.1.7 Raimond L. Winslow, PhD & Stephen Granite 06/15/2010 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 Explore
Protein modification
(MOD) 		OBO Format See Remote Site Psi-mod Administrators 03/03/2010
PSI
 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.
PSI Explore
PRotein Ontology (PRO)
(PRO) 		OBO Format 1.27 Darren Natale 08/20/2010
OBO Foundry
 Description: PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes (ontology for ProEvo), to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies
Categories : Genomic and Proteomic 		2806 OBO Foundry Explore
Mouse adult gross anatomy
(MA) 		OBO Format 1.205 Anatomy JAX 08/26/2010
OBO Foundry
 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 OBO Foundry Explore
Tick gross anatomy
(TADS) 		OBO Format 1.2 Http://www Administrators 08/26/2010 Description: The anatomy of the Tick, Families: Ixodidae, Argassidae
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy 		2810 2812 2811 Explore
Ontology for Biomedical Investigations
(OBI) 		OWL 2009-11-06 Philly (aka version 1.0) Release Candidate OBI Consortium 11/10/2009 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. Access the current version of OBI at http://purl.obolibrary.org/obo/obi.owl and view release notes at http://purl.obolibrary.org/obo/obi/release-notes.html
Categories : Experimental Conditions 		2805 Explore
SNP-Ontology
(SNPO) 		OWL 1.6 Adrien Coulet 01/15/2009 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 Explore
African Traditional Medicine
(ATMO) 		OBO Format 1.101 Ghislain Atemezing 06/28/2009 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 Explore
BioTop OWL dev Stefan Schulz 11/29/2009 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 : Other 		2801 Explore
Spatial Ontology
(BSPO) 		OBO Format 1.18 Http://obo Administrators 08/26/2010 Description: A small ontology for anatomical spatiol references, such as dorsal, ventral, axis, and so forth.
Categories : Anatomy 		2810 Explore
GeoSpecies Ontology
(geospecies) 		OWL beta Peter J. DeVries 05/06/2009 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 Explore
Chemical entities of biological interest
(CHEBI) 		OBO Format 1.70 Chebi Administrators 08/26/2010
OBO Foundry
 Description: A structured classification of chemical compounds of biological relevance.
Categories : Chemical 		2802 OBO Foundry Explore
Loggerhead nesting OBO Format See Remote Site Http://www Administrators 04/13/2009 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 : Ethology 		2804
MeGO
(MeGO) 		OBO Format 1_8 Ariane Toussaint 05/14/2009 Description: bacteriophage and plasmid reproduction and maintenance processes
Categories : Gene Product , Biological Process 		2820 5060 Explore
Pseudogene OBO Format 0.1 Gerstein Lab 11/18/2008
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C. elegans development
(WBls) 		OBO Format 1.3 Worm_development Administrators 08/26/2010 Description: A structured controlled vocabulary of the development of Caenorhabditis elegans.
Categories : Animal Development , Development 		2818 2803 Explore
Gene Ontology
(GO) 		OBO Format 1.986 Gene Ontology 08/29/2010
UMLS
OBO Foundry
 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 UMLS , OBO Foundry Explore
Family Health History Ontology
(FHHO) 		OWL 1.0 Jane Peace 05/10/2009 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 Explore
Plant structure
(PO) 		OBO Format 819 Po_anatomy Administrators 05/03/2010 Description: A controlled vocabulary of plant morphological and anatomical structures representing organs, tissues, cell types, and their biological relationships based on spatial and developmental organization.
The plant ontologies, which includes both the plant structure and growth and development stages can be downloaded as a single file in OBO format.
Categories : Anatomy , Gross Anatomy , Plant Anatomy 		2810 2811 2816 Explore
Bilateria anatomy
(BILA) 		OBO Format Unknown Thorsten Heinrich 03/03/2010 Description: Anatomy of Bilateria.
Categories : Anatomy 		2810 Explore
Ontology for Genetic Interval
(OGI) 		OWL 0.15 Yu Lin 06/09/2009 Description: An ontology to describe the genetic interval, and the relations between genetic intervals.
Categories : Genomic and Proteomic 		2806 Explore
Experimental Factor Ontology
(EFO) 		OWL 124 James Malone 09/01/2010 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
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Ontology of Physics for Biology
(OPB) 		OWL 0.905 Daniel L. Cook 02/10/2010 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 		5060 Explore
Sample processing and separation techniques
(SEP) 		OBO Format 1.070708 Http://psidev Administrators 02/28/2009
PSI
 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.
PSI Explore
MedlinePlus Health Topics
(MEDLINEPLUS) 		RRF 20080614 Ms. Naomi Miller 07/31/2009
UMLS
 Description: MedlinePlus Health Topics;National Library of Medicine;June 14, 2008;Bethesda, MD
Categories : Health 		5058 UMLS Explore
BRENDA tissue / enzyme source
(BTO) 		OBO Format 1.3 BrendaTissue Administrators 09/18/2009 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.
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Minimal anatomical terminology
(MAT) 		OBO Format 1.1 EMAP Administrators 07/05/2009 Description: Minimal set of terms for anatomy
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy 		2810 2812 2811 Explore
Common Anatomy Reference Ontology
(CARO) 		OBO Format 1.5 Http://obo Administrators 08/26/2010 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 Explore
Neural ElectroMagnetic Ontologies
(NEMO) 		OWL 1.10 Gwen Frishkoff 07/30/2010 Description: Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).
Categories : Biological Process , Human , Anatomy , Experimental Conditions , Imaging 		5060 5062 2810 2805 5057 Explore
Physico-chemical process
(REX) 		OBO Format 1.13 Chebi Administrators 08/26/2010 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 Explore
Fly taxonomy
(FBsp) 		OBO Format 1.1 Evidence_code Administrators 08/26/2010 Description: The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.
Categories : Taxonomic Classification 		2808 Explore
BIRNLex
(birnlex) 		OWL 1.3.1 William Bug 03/24/2008 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 : Imaging , Anatomy 		5057 2810 Explore
Ontology of Clinical Research (OCRe)
(OCRe) 		OWL 0.95 Ida Sim 10/14/2009 Description: OCRe is an ontology designed to support systematic description of, and interoperable queries on, human studies and study elements.
Categories : Experimental Conditions 		2805 Explore
Teleost Anatomy Ontology
(TAO) 		OBO Format 1.179 Wasila Dahdul 08/27/2010 Description: Multispecies fish anatomy ontology. 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 Explore
Hymenoptera Anatomy Ontology
(HAO) 		OBO Format SVN Revision 2804 HAO developers 10/08/2009 Description: A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)
Categories : Anatomy 		2810 Explore
Mosquito gross anatomy
(TGMA) 		OBO Format 1.10 C. Louis 08/26/2010 Description: A structured controlled vocabulary of the anatomy of mosquitoes.
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy 		2810 2812 2811 Explore
Molecule role (INOH Protein name/family name ontology)
(IMR) 		OBO Format See Remote Site Event Administrators 04/13/2009 Description: A structured controlled vocabulary of concrete protein names and generic (abstract) protein names. This ontology is a INOH pathway annotation ontology, one of a set of ontologies intended to be used in pathway data annotation to ease data integration. This ontology is used to annotate protein names, protein family names, generic/concrete protein names in the INOH pathway data.
INOH is part of the BioPAX working group.
Bleeding History Phenotype
(BHO) 		OWL 0.3.1 Andreas Mauer 08/26/2009 Description: An application ontology devoted to the standardized recording of phenotypic data related to hemorrhagic disorders.
Categories : Phenotype 		2807 Explore
Biomedical Resource Ontology
(BRO) 		OWL 3.2.1 Trish Whetzel, Csongor Nyulas, Natasha Noy 08/31/2010 Description: A controlled terminology of resources, which is used to improve the sensitivity and specificity of web searches.
Categories : Biomedical Resources 		5059 Explore
Dendritic cell
(DC_CL) 		OBO Format 1.5 Lindsay Cowell 08/26/2010 Description: Representation of types of dendritic cell. Note that the domain of this ontology is wholly subsumed by the domain of the Cell ontology (CL).
Categories : Anatomy 		2810 Explore
Human Phenotype Ontology
(HP) 		OBO Format 1318 Peter N 08/25/2010 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.
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Biological imaging methods
(FBbi) 		OBO Format 1.4 Chris Woodcock 08/26/2010 Description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.
Categories : Experimental Conditions , Imaging 		2805 5057 Explore
Human developmental anatomy, abstract version
(EHDAA) 		OBO Format 1.3 EMAP Administrators 08/26/2010 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 Explore
Systems Biology
(SBO) 		OBO Format 1.0 Http://www Administrators 10/28/2009 Description: The Systems Biology Ontology aims to strictly index and define terms used in quantitative biochemistry. The ontology is made up of four orthogonal vocabularies. A controlled vocabulary defines the roles of reaction participants, such as "substrate", "catalyst", etc. A taxonomy orders the quantitative parameters used in biochemistry such as "Michaelis constant", but also "first-order forward rate constant". A precise classification of rate laws defines them, such as "first-order reversible mass action kinetics". Each term contains a precise mathematical expression stored as a MathML lambda function. Finally, a list of simulation frameworks, such as "discrete" or "continuous" precises the validity of a rate-law. The Systems Biology Ontology can be used to increase the semantic content of quantitative models. SBO vocabularies can also be used to annotate results of biochemical experiments in order to facilitate their efficient reuse.
Categories : Chemical 		2802 Explore
Zebrafish anatomy and development
(ZFA) 		OBO Format 1.29 ZFIN administrators 08/06/2010
OBO Foundry
 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 Explore
Cereal plant trait
(TO) 		OBO Format 1.349 Po_anatomy Administrators 08/29/2010 Description: A controlled vocabulary of describe phenotypic traits in cereal plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature cereal plant.
Categories : Phenotype 		2807 Explore
Logical Observation Identifier Names and Codes
(LNC) 		RRF 229 Ms. Kathy Mercer, LOINC Developer 08/12/2010
UMLS
 Description: Logical Observation Identifier Names and Codes (LOINC);Version 2.26;January 2, 2009
Categories : Health 		5058 UMLS Explore
Gene Regulation Ontology
(GRO) 		OWL 0.4 Vivian Lee 05/04/2009 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 Explore
Phenotypic quality
(PATO) 		OBO Format 1.256 Quality Administrators 09/01/2010
OBO Foundry
 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 : Phenotype 		2807 OBO Foundry Explore
Teleost taxonomy
(TTO) 		OBO Format 1.63 Http://www Administrators 08/24/2010 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 Explore
C. elegans gross anatomy
(WBbt) 		OBO Format 1.54 Http://brebiou Administrators 08/26/2010 Description: A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy 		2810 2812 2811 Explore
Maize gross anatomy
(ZEA) 		OBO Format See Remote Site Zea_mays_anatomy Administrators 01/30/2009 Description: A structured controlled vocabulary for the anatomy of Zea mays.
Categories : Plant Anatomy 		2816
Cereal plant development
(GRO) 		OBO Format 1.6 Gramene curators 08/24/2007 Description: A controlled vocabulary of describe phenotypic traits in cereal plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature cereal plant.
Categories : Plant Development , Development , Plant 		2819 2803 5063 Explore
Physician Data Query
(PDQ) 		RRF 2007_02 Margaret Haber 07/31/2009
UMLS
 Description: Physician Data Query. Bethesda (MD): National Cancer Institute, February 2007.
Categories : Health 		5058 UMLS Explore
Parasite Life Cycle
(PLO) 		OWL 0.10 Satya S. Sahoo, Brent Weatherly, Flora Logan 03/07/2009 Description: This ontology models the life cycle stage details of Trypanosoma cruzi and two related kinetoplastids, Trypanosoma brucei and Leishmania major. In addition to life cycle stages, the ontology also models necessary contextual details such as host information, vector information, strain and anatomical location. All the entities in the ontology are linked to each other by explicitly modeled named relationships.
Categories : Development 		2803 Explore
Plant environmental conditions
(EO) 		OBO Format 1.6 Pankaj Jaiswal 08/26/2010 Description: A structured controlled vocabulary for the representation of plant environmental conditions.
Categories : Phenotype 		2807 Explore
Sequence types and features
(SO) 		OBO Format 1.185 So Administrators 08/27/2010 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 Explore
Proteomics Pipeline Infrastructure for CPTAC
(CPTAC) 		OWL alpha 1.1 Fan Zhang 05/20/2009 Description: a basic ontology which describes the proteomics pipeline infrastructure for CPTAC project
Categories : Genomic and Proteomic 		2806 Explore
National Drug File
(NDFRT) 		RRF 2008_03_11 Steven H. Brown;MD 07/31/2009
UMLS
 Description: National Drug File - Reference Terminology Public Inferred Edition, 2008_03_11
Categories : Health 		5058 UMLS Explore
Computer-based Patient Record Ontology OWL 0.85 Chimezie Ogbuji 04/04/2009
Categories : Health 		5058 Explore
Protein Ontology OWL 2.0 Amandeep S. Sidhu 05/18/2009
Categories : Genomic and Proteomic , Protein 		2806 2821 Explore
COSTART
(CST) 		RRF 1995 U.S. Food and Drug Administration Center for Drug Evaluation and Research 07/31/2009
UMLS
 Description: Coding Symbols for Thesaurus of Adverse Reaction Terms (COSTART). 5th ed. Rockville (MD)
Categories : Health 		5058 UMLS Explore
Breast Cancer Grading Ontology
(BCGO) 		OWL 1.4 Emina Szocs 06/26/2009 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) 		RRF 1993 Henk Lamberts, University of Amsterdam 07/31/2009
UMLS
 Description: The International Classification of Primary Care (ICPC). Denmark: World Organisation of Family Doctors, 1993.
Categories : Health 		5058 UMLS Explore
Suggested Ontology for Pharmacogenomics
(SOPHARM) 		OWL 2.1.2 Adrien Coulet 02/06/2009 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 Explore
SNOMED Clinical Terms
(SNOMEDCT) 		RRF 2010_01_31 Vivian A. Auld 05/12/2010
UMLS
 Description: SNOMED Clinical Terms, 2010_01_31
Categories : Health 		5058 UMLS Explore
Human developmental anatomy, timed version
(EHDA) 		OBO Format 1.3 EMAP Administrators 08/26/2010 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 Explore
Physico-chemical methods and properties
(FIX) 		OBO Format See Remote Site Chebi Administrators 04/13/2009 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 : Chemical 		2802
Symptom Ontology
(SYMP) 		OBO Format unknown Lynn Schriml 08/06/2010 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
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Xenopus anatomy and development
(XAO) 		OBO Format 1.20 Xenbase Xenbase 08/26/2010
OBO Foundry
 Description: A structured controlled vocabulary of the anatomy and development of the African clawed frog (Xenopus laevis).
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy 		2810 2812 2811 OBO Foundry Explore
OBO relationship types
(OBO_REL) 		OBO Format 1.1 Chris Mungall 08/26/2010 Description: Defines core relations used in all OBO ontologies.
eVOC (Expressed Sequence Annotation for Humans)
(EV) 		OBO Format 2.9 Evoc Administrators 08/17/2010 Description: Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment.
Categories : Phenotype 		2807 Explore
DermLex: The Dermatology Lexicon
(DermLex) 		OWL 1.0 Naomi Levinthal 04/17/2009 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 Explore
Malaria Ontology
(IDOMAL) 		OBO Format 1.2 Pantelis Topalis 07/01/2010 Description: An application ontology for malaria extending the infectious disease ontology (IDO). Version 1.2 contains a major restructuring of "Anopheles breeding sites".
Categories : Biological Process , Human , Phenotype , Health , Other 		5060 5062 2807 5058 2801 Explore
Parasite Experiment Ontology
(PEO) 		OWL 0.20 Satya S. Sahoo, Brent Weatherly, Priti Parikh, Flora Logan 12/27/2009 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. This is second version of PEO and includes Proteome and Microarray experiment terms. These are in addition to Gene Knockout and Strain Creation experiment terms modeled in previous version of PEO.
Categories : Experimental Conditions 		2805 Explore
Amphibian taxonomy
(ATO) 		OBO Format See Remote Site AmphiAnat list 11/02/2009 Description: A taxonomy of Amphibia
Categories : Taxonomic Classification 		2808 Explore
Medaka fish anatomy and development
(MFO) 		OBO Format 1.1 Medaka_ontology Administrators 08/26/2010 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 Explore
WHO Adverse Reaction Terminology
(WHO) 		RRF 1997 WHO Collaborating Centre for International Drug Monitoring 07/31/2009
UMLS
 Description: WHO Adverse Reaction Terminology, 1997
Categories : Health 		5058 UMLS Explore
Event (INOH pathway ontology)
(IEV) 		OBO Format See Remote Site Event Administrators 04/13/2009 Description: A structured controlled vocabulary of pathway centric biological processes. This ontology is a INOH pathway annotation ontology, one of a set of ontologies intended to be used in pathway data annotation to ease data integration. This ontology is used to annotate biological processes, pathways, sub-pathways in the INOH pathway data.
INOH is part of the BioPAX working group.
Mouse gross anatomy and development
(EMAP) 		OBO Format 1.2 EMAP Administrators 08/26/2010 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 Explore
Drosophila gross anatomy
(FBbt) 		OBO Format 1.38 Http://obo Administrators 08/26/2010 Description: A structured controlled vocabulary of the anatomy of Drosophila melanogaster.
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy 		2810 2812 2811 Explore
Amphibian gross anatomy
(AAO) 		OBO Format 1.8 David Blackburn 08/26/2010 Description: A structured controlled vocabulary of the anatomy of Amphibians.
Categories : Anatomy , Animal Gross Anatomy , Gross Anatomy 		2810 2812 2811 Explore
Habronattus courtship PROTEGE See Remote Site Http://www Administrators 04/13/2009 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 : Other 		2801
BioPortal Metadata
(BPMetadata) 		OWL 0.9.3 Natasha Noy 06/18/2010 Description: This ontology represents the structure that BioPortal will use to represent all of its metadata (ontology details, mappings, notes, reviews, views)
Categories : Other 		2801 Explore
Plant growth and developmental stage
(PO) 		OBO Format 1.34 Po_anatomy Administrators 05/03/2010 Description: A controlled vocabulary of growth and developmental stages in various plants.
The plant ontologies, which includes both the plant structure and growth and development stages can be downloaded as a single file in OBO format.
Categories : Plant Development , Development 		2819 2803 Explore
NCBI organismal classification
(NCBITaxon) 		OBO Format 1.2 NCBI information 05/13/2009
UMLS
 Description: A taxonomic classification of living organisms and associated artifacts for their controlled description within the context of databases.
Categories : Taxonomic Classification 		2808 UMLS Explore
Ontology of homology and related concepts in biology
(HOM) 		OBO Format 1.4 Julien Roux 01/04/2010 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 Explore
Fungal gross anatomy
(FAO) 		OBO Format 1.4 Fungal_anatomy Administrators 08/26/2010 Description: A structured controlled vocabulary for the anatomy of fungi.
Categories : Anatomy , Gross Anatomy , Microbial Anatomy 		2810 2811 2815 Explore
ABA Adult Mouse Brain
(ABA) 		OWL 1.0 Allen Institute for Brain Science 08/08/2009 Description: Allen Brain Atlas P56 Mouse Ontology
Categories : Mouse Anatomy 		2817 Explore
C. elegans phenotype
(WBPhenotype) 		OBO Format 1.145 Http://tazendra Administrators 08/27/2010 Description: A structured controlled vocabulary of Caenorhabditis elegans phenotypes
Categories : Phenotype 		2807 Explore
Environment Ontology
(ENVO) 		OBO Format 1.53 Envo Administrators 08/26/2010 Description: Ontology of environmental features and habitats
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Galen OWL 1.1 01/16/2007
Categories : Other 		2801 Explore
Basic Formal Ontology
(BFO) 		OWL 1.1 07/24/2009 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 : Other 		2801 Explore
Lipid Ontology
(LiPrO) 		OWL unknown Christipher Baker 08/06/2010 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.
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Multiple alignment
(MAO) 		OBO Format 1.1 Mao Administrators 08/06/2010 Description: An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment.
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Cancer Research and Management ACGT Master Ontology OWL 1.1 Mathias Brochhausen 03/17/2010 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 Explore
Epoch Clinical Trial Ontologies
(ClinicalTrialOntology) 		OWL 0.9 Ravi Shankar, Stanford Medical Informatics 03/20/2007
Categories : Experimental Conditions 		2805 Explore
Units of measurement
(UO) 		OBO Format 1.29 Unit Administrators 09/01/2010 Description: Metrical units for use in conjunction with PATO
Categories : Phenotype 		2807 Explore
PhysicalFields
(Field) 		OWL v0.1 Marco Viceconti 08/13/2009
Categories : Physicochemical 		2822 Explore
Ontology for disease genetic investigation OWL 0.7.1 Yu Lin 05/18/2009 Description: The ontology for the original papers investigating the relations between genetic factors and disease.
Categories : Experimental Conditions 		2805 Explore
Spider Ontology
(SPD) 		OBO Format 1.19 Martin Ramirez 08/26/2010 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 Explore
FlyBase Controlled Vocabulary
(FBcv) 		OBO Format 1.18 Evidence_code Administrators 08/26/2010 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 Explore
Online Mendelian Inheritance in Man
(OMIM) 		RRF 2007_12_19 Jan Willis, NLM 07/31/2009
UMLS
 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 Explore
Skin Physiology Ontology
(SPO) 		OWL 2.0 Tariq Abdulla 09/18/2008
Categories : Biological Process 		5060 Parsing Error
Cardiac Electrophysiology Ontology
(EP) 		OWL 1.0 Raimond L. Winslow, PhD 04/27/2009 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 Explore
Comparative Data Analysis Ontology
(CDAO) 		OWL 1.26 Enrico Pontelli 09/22/2009 Description: An ontology intended to provide a common ontological framework for evolutionary analysis regardless of the type of data involved.
Categories : Experimental Conditions 		2805 Explore
Vaccine Ontology
(VO) 		OWL 435 Yongqunh He 08/30/2010 Description: A biomedical ontology in the vaccine domain
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MaHCO - An MHC Ontology
(MHC) 		OWL 1.0.1 David S. DeLuca 04/15/2009 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 Explore
Cell line ontology
(MCCL) 		OBO Format 1.0 Usha Mahadevan 07/21/2009 Description: Cell lines are key experimental models to understand protein interactions and signaling pathways. With a large pool of such data coming from different cell lines of different origin -of normal and -pathological tissues, proper analysis requires segregating data pertaining to specific cell lines. The project envisaged brings together hierarchical trees of organs, mammalian cell lines and diseases in one platform. Certain specific terms from Cell Type (CL) ontology, Foundational Model of Anatomy (FMA) and DOID ontologies are mapped for searchability. Ontology is developed in both OBO and OWL.
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Ascomycete phenotype ontology
(APO) 		OBO Format 1.15 SGD curators 08/26/2010 Description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi
Categories : Phenotype 		2807 Explore
Smoking Behavior Risk Ontology
(SBRO) 		OWL 1.0 Paul Thomas 08/30/2010 Description: An ontology representing a causal model of smoking behavior risk, including genetic and environmental components. It also includes concepts for describing smoking-related phenotypes.
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Proteomics data and process provenance
(ProPreO) 		OWL 1.1 Satya S. Sahoo 03/05/2009 Description: A comprehensive proteomics data and process provenance ontology.
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Mass spectrometry
(MS) 		OBO Format 1.139 PSI-MS Administrators 08/11/2010
PSI
 Description: A structured controlled vocabulary for the annotation of mass spectrometry experiments. Developed by the HUPO Proteomics Standards Initiative.
PSI Explore
Protein-protein interaction
(MI) 		OBO Format 1.52 Psi-mi Administrators 02/28/2009
PSI
 Description: A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Developed by the HUPO Proteomics Standards Initiative.
PSI Explore
Situation-Based Access Control
(SitBAC) 		OWL 1.2 Mor Peleg 05/01/2010 Description: Context-based healthcare access-control policies
Categories : Other 		2801 Explore
Dictyostelium discoideum anatomy
(DDANAT) 		OBO Format 1.10 Rex Chisholm 08/26/2010 Description: A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum.
Categories : Anatomy , Gross Anatomy , Microbial Anatomy 		2810 2811 2815 Explore
Subcellular Anatomy Ontology (SAO) OWL 1.2.5 Maryann Martone 09/17/2007 Description: SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules.
Categories : Anatomy 		2810 Explore
Ontology of Geographical Region OWL 1.1 Yu Lin 05/19/2009 Description: This OWL ontology classified the geograhical regions related vocabularies extracted from UMLS.
Categories : Vocabularies 		2809 Explore
Rat Strain Ontology
(RS) 		OBO Format 2.1 Rajni Nigam 06/22/2010 Description: This ontology defines the hierarchical display of the different rat strains as derived from the parental strains
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International Classification of Diseases
(ICD-9) 		LEXGRID 9 The World Health Organization 05/13/2009
WHO-FIC
UMLS
 Description: The ICD is the international standard diagnostic classification for all general epidemiological, many health management purposes and clinical use.
WHO-FIC , UMLS Explore
Cell Line Ontology
(CLO) 		OWL 1.0 Sirarat Sarntivijai 07/08/2009 Description: The Cell Line Knowledge Base is a public data warehouse for searching cell line data extracted from both ATCC and HyperCLDB. The knowledge base uses our Cell Line Ontology, created with the Protege ontology editing tool from the National Center for Biomedical Ontologies (NCBO) and merges concepts from other ontologies, including the Cell Type Ontology.
Categories : Vocabularies , Cell , All Organisms 		2809 5065 5073 Explore
Human disease
(DOID) 		OBO Format 1.258 Human_disease Administrators 08/28/2010 Description: Creating a comprehensive hierarchical controlled vocabulary for human disease representation.
Categories : Phenotype 		2807 Explore
Pathogen transmission
(TRANS) 		OBO Format 1.11 Human_disease Administrators 08/26/2010 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 : Phenotype 		2807 Explore
NIFSTD
(nif) 		OWL 1.9.5 Fahim Imam 08/13/2010 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 Explore
Mammalian phenotype
(MP) 		OBO Format 1.382 JAX list 08/29/2010 Description: The Mammalian Phenotype Ontology is under development as a community effort to provide standard terms for annotating mammalian phenotypic data.
Categories : Phenotype 		2807 Explore
MGED Ontology
(MO) 		OWL 1.3.1.1 MGED 05/21/2009
caBIG
 Description: Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1.
Categories : Experimental Conditions 		2805 caBIG Explore
Pathway ontology
(PW) 		OBO Format 1.060710 Victoria Petri 06/09/2010
Categories : Biological Process 		5060 Explore
Animal natural history and life history
(ADW) 		PROTEGE unknown Http://animaldiversity Administrators 08/31/2010 Description: An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.
Categories : Anatomy 		2810 Parsing Error
Gene Regulation Ontology
(BOOTStrep) 		OWL See Remote Site Vivian Lee 05/05/2009 Description: The BOOTStrep Ontology is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. GRO is intended to represent common knowledge about gene regulation in a formal way rather than representing extremely fine-grained classes as can be found in ontologies such as the Gene Ontology (GO) (created for data base annotation purposes) and various relevant databases. The main purpose of the ontology is to support NLP applications. It has a particular focus on the relations between processes and the molecules (participants) involved. The basic structure of the GRO is a direct acyclic graph (DAG) with ontology classes as nodes and is-a relations between classes as edges. The taxonomic backbone is further enriched by several semantic relation types (part-of, from-species, participates-in with the two sub-relations agent-of and patient-of).
Amino Acid
(amino-acid) 		OWL 1.2 (inferred) Nick Drummond, Georgina Moulton, Robert Stevens, Phil Lord 07/02/2010 Description: An ontology of amino acids and their properties. Inferred version.
Categories : Other 		2801 Explore
Basic Vertebrate Anatomy
(basic-vertebrate-gross-anatomy) 		OWL 1.1 01/16/2007 Description: A basic vertebrate anatomy derived mainly from FMA.
Categories : Gross Anatomy 		2811 Explore
Evidence codes
(ECO) 		OBO Format 1.21 Michelle Giglio 08/26/2010 Description: A rich ontology for experimental and other evidence statements.
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Yeast phenotypes
(YPO) 		OBO Format 1.20 Mike Cherry 08/26/2010 Description: A structured controlled vocabulary for the phenotypes of budding yeast.
Categories : Phenotype 		2807 Explore
Cereal plant gross anatomy
(GRO) 		OBO Format See Remote Site Po_anatomy Administrators 04/13/2009 Description: A structured controlled vocabulary for the anatomy of Graminae. Please note that this ontology has now been superseded by the plant anatomy ontology.
Categories : Plant , Anatomy , Plant Anatomy 		5063 2810 2816
Cell type
(CL) 		OBO Format 1.44 Alex Diehl 08/18/2010 Description: The Cell Ontology is designed as a structured controlled vocabulary for cell types. This ontology was constructed for use by the model organism and other bioinformatics databases, where there is a need for a controlled vocabulary of cell types. This ontology is not organism specific; indeed it includes cell types from prokaryotes to mammals, including plants and fungi. A full description of the Cell Ontology can be found in Bard, Rhee and Ashburner. 2005. An Ontology for Cell Types.
Categories : Anatomy 		2810 Explore
Mosquito insecticide resistance
(MIRO) 		OBO Format 1.911 C. Louis 08/29/2010 Description: Application ontology for entities related to insecticide resistance in mosquitos
Categories : Phenotype 		2807 Explore
Ontology of Glucose Metabolism Disorder OWL 1.2 Yu Lin 05/18/2009 Description: Including the disease names. phenotypes and their classifications involved in Glucose Metabolism Disorder
Categories : Phenotype , Health 		2807 5058 Explore
RadLex
(RID) 		PROTEGE 2.1 Radiological Society of North America 08/17/2010
caBIG
 Description: RadLex is a controlled terminology for radiology-a single unified source of radiology terms for radiology practice, education, and research. For liscence information see : http://www.rsna.org/RadLex/upload/radlex_public_license_version_1-0-1.pdf
Categories : Imaging 		5057 caBIG Explore
NanoParticle Ontology
(NPO) 		OWL 2010-07-30 (inferred) Nathan Baker 07/31/2010
caBIG
 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 Explore
Foundational Model of Anatomy
(FMA) 		OWL 3.0 Onard Mejino 05/12/2009
UMLS
 Description: FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy.
Categories : Anatomy 		2810 UMLS Explore
Mouse pathology
(MPATH) 		OBO Format 1.4 Mouse_pathology Administrators 08/26/2010 Description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes
Categories : Phenotype 		2807 Explore
Infectious disease
(IDO) 		OWL unknown Lindsay Cowell 08/19/2010
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NCI Thesaurus
(NCIt) 		OWL 10.03 NCICB Support 05/24/2010
caBIG
UMLS
 Description: A vocabulary for clinical care, translational and basic research, and public information and administrative activities.
caBIG , UMLS Explore
NIF Dysfunction
(NIF_Dysfunction) 		OWL See Remote Site Fahim Imam 09/10/2009 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.
Information Artifact Ontology
(IAO) 		OWL 2009-07-15 Alan Ruttenberg 09/18/2009 Description: The Information Artifact Ontology (IAO) is a new ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch.
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Syndromic Surveillance Ontology
(SSO) 		OWL 1.0 Anya Okhmatovskaia, David L Buckeridge 09/18/2009 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 Explore
MDSS Mo
(MO) 		OBO Format 1.0 09/25/2009 Description: Terms from our Decision Support System for Malaria (MDSS)
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Gazetteer
(GAZ) 		OBO Format 1.446 Michael Ashburner 09/28/2009 Description: Gazetteer
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Ontology of Language Disorder in Autism
(LDA) 		OWL Protege 3.4 Administrator 09/28/2009 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 Explore
Pilot Ontology
(POL) 		OWL 0.1 09/28/2009 Description: This a pilot ontology
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International Classification for Nursing Practice
(ICNP) 		OWL 2 Amy Coenen 10/21/2009 Description: International Classification for Nursing Practice
Categories : Taxonomic Classification 		2808 Explore
NIF Cell
(NIF_Cell) 		OWL See Remote Site Fahim Imam 10/21/2009 Description: Cell types from NIFSTD
Uber anatomy ontology
(UBERON) 		OBO Format 1.93 Http://obo Administrators 08/16/2010 Description: Uberon is a multi-species anatomy ontology created to facilitate comparison of phenotypes across multiple species, and for GO cross-products. Each uberon class is the superclass of all the classes stated as xrefs. The deployed version of uberon is generated from the editors version by stripping out external links and materializing inferred links via the oboedit reasoner.
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linkingkin2pep
(k2p) 		OWL 0.1 11/04/2009 Description: An ontology to try out the mapping capabilities of NCBO Bioportal
Categories : Protein , Cell 		2821 5065 Explore
Terminology for the Description of Dynamics
(TEDDY) 		OWL rel-2009-10-16 (inferred) Christian Knuepfer 12/07/2009 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 Explore
PKO_Re
(PKO) 		OWL 1.1 11/25/2009 Description: Testing
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Kinetic Simulation Algorithm Ontology
(KiSAO) 		OBO Format Sat Jan 24 18:58:35 2009 UTC Dagmar Waltemath 11/12/2009 Description: The KiSA Ontology covers the most important simulation algorithms and simulation methods used to simulate biological kinetic models and puts those algorithms and methods into relation. KiSAO aims at providing support in unambiguously referring to simulation algorithms when describing a simulation experiment. KiSAO is under continuous development. Please feel free to make suggestions for the improvement of the ontology's structure.
Categories : Other 		2801 Explore
International Classification of Functioning, Disability and Health (ICF)
(ICF) 		OWL 1.0 The World Health Organization 11/16/2009 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/
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Software Ontology
(SWO) 		OWL 102 James Malone 02/16/2010 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
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Ontology for General Medical Science
(OGMS) 		OWL See Remote Site Albert Goldfain 12/04/2009 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
Common Terminology Criteria for Adverse Events
(CTCAE) 		OWL 4.02 CTCAE Help 12/07/2009 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).
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Influenza Ontology
(FLU) 		OWL See Remote Site Burke Squires 01/12/2010
TOK_Ontology
(TOK) 		OWL 0.2.1 Nizar ghoula 05/19/2010 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 Explore
Taxonomic rank vocabulary
(TAXRANK) 		OBO Format 1.1 Http://www Administrators 08/06/2010 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.
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MedDRA
(MDR) 		RRF 12.0 Kate Studeman 02/04/2010
UMLS
 Description: Medical Dictionary for Regulatory Activities Terminology (MedDRA)
Categories : Health 		5058 UMLS Explore
RxNORM
(RXNORM) 		RRF 09AA_090908F Stuart Nelson 02/04/2010
UMLS
 Description: RxNorm Vocabulary
Categories : Health 		5058 UMLS
National Drug Data File
(NDDF) 		RRF 2009_08_07 First DataBank Customer Support 02/04/2010
UMLS
 Description: National Drug Data File Plus Source Vocabulary
Categories : Health 		5058 UMLS
ICD-10-PCS
(ICD10PCS) 		RRF 2009 Pat Brooks 02/04/2010
UMLS
 Description: ICD-10-PCS, 2009
Categories : Health 		5058 UMLS Explore
Master Drug Data Base
(MDDB) 		RRF 2009_08_05 Karen Eckert 02/04/2010
UMLS
 Description: Master Drug Data Base, 2009_08_05
Categories : Health 		5058 UMLS
Read Codes, Clinical Terms Version 3 (CTV3)
(RCD) 		RRF 1999 NHS Information Authority Loughborough 02/05/2010
UMLS
 Description: Clinical Terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre
UMLS Explore
Nursing Interventions Classification (NIC)
(NIC) 		RRF 2005 Center for Nursing Classification & Clinical Effectiveness 02/05/2010
UMLS
 Description: Nursing Interventions Classification (NIC)
Categories : Health 		5058 UMLS Explore
ICPC-2 PLUS
(ICPC2P) 		RRF 2005 Prof Helena Britt 02/05/2010
UMLS
 Description: ICPC-2 PLUS
Categories : Health 		5058 UMLS
AIR
(AIR) 		RRF 1993 May Cheh 02/05/2010
UMLS
 Description: AIR, AI/RHEUM, 1993
Categories : Health 		5058 UMLS Explore
Breast tissue cell lines
(MCBCC) 		OWL 2.0 Dr. Arathi Raghunath 07/29/2010 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 Explore
General Formal Ontology
(GFO) 		OWL 1.0 Heinrich Herre 03/02/2010 Description: The General Formal Ontology (GFO) is a top-level ontology integrating objects and processes.
Categories : Other , All Organisms 		2801 5073 Explore
General Formal Ontology: Biology
(GFO-Bio) 		OWL 1.1 Robert Hoehndorf 03/02/2010 Description: GFO-Bio is a biological core ontology built on the General Formal Ontology.
Categories : Animal Gross Anatomy , Subcellular anatomy , Mouse Anatomy , Cell , Gene Product , Gross Anatomy , Plant Anatomy , Molecule , Biological Process , Development , Human Developmental Anatomy , Protein , Anatomy , Plant , Animal Development , Phenotype , Subcellular , Chemical , All Organisms , Human , Cellular anatomy , Plant Development 		2812 5068 2817 5065 2820 2811 2816 5069 5060 2803 2814 2821 2810 5063 2818 2807 5067 2802 5073 5062 5066 2819 Explore
Chemical Information Ontology
(CHEMINF) 		OWL See Remote Site Cheminf discussion 03/08/2010 Description: Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.
Categories : Experimental Conditions , Physicochemical , Molecule , Chemical 		2805 2822 5069 2802
Health Level Seven
(HL7) 		LEXGRID 0230 Methodology and Modelling Committee 03/30/2010 Description: This version is the first update to Normative RIM, Release 2. It is based on changes approved in Harmonization in November 2009. This release of the RIM is bound to HL7 Abstract Data Types Release 2.
Categories : Health 		5058 Explore
Translational Medicine Ontology
(TMO) 		OWL r18 TMO task in W3C's HCLS IG 05/06/2010 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.
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International Classification of External Causes of Injuries
(ICECI) 		OWL Original Source: 1.2; OWL version 1.02 Samson Tu 05/07/2010 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.
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Body System
(bodysystem) 		OWL 1.0 Samson Tu 04/15/2010 Description: This is a set of body-system terms used in the ICD 11 revision
Categories : Anatomy 		2810 Explore
SysMO-JERM
(JERM) 		OWL 0.4Alpha Katy Wolstencroft 07/07/2010 Description: an ontology to describe the entities and relationships in SysMO-DB, a Systems Biology environment for the sharing and exchange of data and models. Version 0.4Alpha provides extensions to describe microarray data and map it to MGED
Categories : Experimental Conditions , Biomedical Resources , Other 		2805 5059 2801 Explore
Adverse Event Ontology
(AEO) 		OWL 1.0.11 Yongqun "Oliver" He 04/20/2010 Description: The Adverse Event Ontology (AEO) is a biomedical ontology in the domain of adverse event. AEO aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. AEO has been initiated and led by by Dr. Yongqun "Oliver" He at the University of Michigan Medical School. AEO is a community-based ontology, and its development follows the OBO Foundry principles. Vaccine adverse events are used as an initial testing use case.
Categories : Health 		5058 Explore
Platynereis stage ontology
(PD_ST) 		OBO Format 04.21.2010 Thorsten Heinrich 07/01/2010 Description: Developmental stages of Platynereis.
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IMGT-ONTOLOGY
(IMGT) 		OWL 1.0.0 Véronique Giudicelli, Patrice Duroux, Professor Marie-Paule Lefranc 04/22/2010 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 first version of IMGT-ONTOLOGY, edited with Protégé (v3.4.4), includes a part of the concepts of IDENTIFICATION which are "ConfigurationType", "EntityType", "FunctionalityType", "GeneType", "LocationType", "MolecularComponent", "MoleculeType", "MoleculeUnit", the "StructureType", and "TaxonRank".
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Tissue Microarray Ontology
(TMA) 		OWL 1.0.0 Chuck Borromeo 05/07/2010 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 Explore
PMA 2010
(pma) 		OWL 0.9 Jim Martin 05/22/2010
Categories : Human , Health 		5062 5058
EDAM
(EDAM) 		OBO Format beta08 Jon Ison 08/18/2010 Description: EDAM (EMBRACE Data and Methods) is an ontology for bioinformatics tools and data. It includes a set of defined terms with relationships between terms. EDAM provides a controlled vocabulary for description in semantic terms of things such as web services, XSD data schema, standalone tools, web servers, databases, data objects and file formats. The goal is for EDAM to describe, at a coarse level at least, all major bioinformatics tools and data currently in use. EDAM is being actively developed. The current "beta" version provides a starting point for service nomenclature and is intended primarily for testing and feedback.
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NCI Metathesaurus
(NCIM) 		RRF 201002D NCICB Support 05/12/2010
caBIG
 Description: NCI Metathesaurus
caBIG
RNA ontology
(RNAO) 		OWL r113 Colin Batchelor 07/01/2010 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 Explore
Neomark Oral Cancer-Centred Ontology
(NeoMark Ontology) 		OWL 3.1 Marta Ortega 05/21/2010 Description: Ontology that describes the medical information necessary for early detection of the oral cancer reoccurrence extracted from the NeoMark Project.
Categories : Health 		5058 Explore
Current Procedural Terminology
(CPT) 		RRF 2010AA Dorith Brown 05/26/2010
UMLS
 Description: Current Procedural Terminology
Categories : Health 		5058 UMLS
Ontology for MicroRNA Target Prediction
(OMIT) 		OWL 0.2 Jingshan Huang 06/30/2010 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 Explore
Gene Ontology Extension
(GO) 		OBO Format 1.0 Gene Ontology Consortium 06/14/2010
UMLS
OBO Foundry
 Description: Gene Ontology Extension
Categories : Genomic and Proteomic 		2806 UMLS , OBO Foundry Explore
Cell Cycle Ontology
(CCO) 		OBO Format 0.95 Vladimir Mironov 06/25/2010 Description: An application ontology integrating knowledge about the eukaryotic cell cycle.
Categories : Biological Process , Arabadopsis , Human , Yeast 		5060 5061 5062 5064 Explore
ICPS Network
(ICPS) 		OWL 2.0 Oscar Corcho 08/17/2010 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 Explore
Metathesaurus CPT Hierarchical Terms
(MTHCH) 		RRF 2010 Jan Willis 06/28/2010
UMLS
 Description: Metathesaurus CPT Hierarchical Terms
Categories : Health 		5058 UMLS Explore
Interaction Network Ontology
(INO) 		OWL 1.0.17 Yongqun "Oliver" He 08/24/2010 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 has been initiated and led by by Dr. Yongqun "Oliver" He at the University of Michigan Medical School. INO aligns with BFO. INO is a community-based ontology, and its development follows the OBO Foundry principles.
Categories : All Organisms 		5073 Explore
ICD10
(ICD10) 		RRF 1998 World Health Organization 07/21/2010
UMLS
 Description: International Statistical Classification of Diseases and Related Health Problems (ICD-10). 10th rev. Geneva
UMLS Explore
Human developmental anatomy, abstract version, v2
(EHDAA2) 		OBO Format 1.1 EMAP Administrators 08/26/2010 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 Explore
Leukocyte Surface Markers
(LSM) 		OBO Format unknown Terry Meehan 08/17/2010 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.
Neural Motor Recovery Ontology
(NeuMORE) 		OWL 0.1 Jingshan Huang 08/11/2010 Description: Neural Functional Motor Recovery Ontology
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BioPAX
(BP) 		OWL Level3 v1.0 Dr Emek Demir 07/29/2010 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 Explore
OBOE SBC
(oboe-sbc) 		OWL 0.1 Ben Leinfelder 08/12/2010 Description: OBOE Extension for SBC-LTER
Categories : Other 		2801 Explore
OBOE
(OBOE) 		OWL 1.0 Ben Leinfelder 08/12/2010 Description: Observational Modeling
Categories : Other 		2801 Explore
eVOC (Expressed Sequence Annotation for Humans)
(EV) 		OBO Format See Remote Site Evoc Administrators 08/18/2010 Description: Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment.
CRISP Thesaurus, 2006
(CSP) 		RRF 2006 Anita Ghebeles 08/27/2010 Description: Computer Retrieval of Information on Scientific Projects (CRISP)
Categories : Health 		5058 Explore
VANDF
(VANDF) 		RRF 2010_01_25 Michael Lincoln 09/01/2010 Description: Veterans Health Administration National Drug File
Categories : Health 		5058 Explore
HUGO
(HUGO) 		RRF 2009_04 Dr. Elspeth Bruford 09/01/2010 Description: HUGO Gene Nomenclature
Categories : Health 		5058 Explore
HCPCS
(HCPCS) 		RRF 2010 Cynthia Hake 09/01/2010 Description: Healthcare Common Procedure Coding System
Categories : Health 		5058 Explore
Animal natural history and life history
(ADW) 		PROTEGE See Remote Site Http://animaldiversity Administrators 09/01/2010 Description: An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.
The National Center for Biomedical Ontology is one of the National Centers for Biomedical Computing supported by the NIH Roadmap.
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Release 2.6 (released August 17, 2010)