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Informed Consent Ontology ICO Public 376 0 0 0 OWL Arbor version; 1.0.50 07/08/2014 "Asiyah" Yu Lin Yongqun Oliver He Description: The Informed Consent Ontology (ICO) is a biomedical ontology in the domain of informed consent and informed consent. ICO aims to standardize informed consent process, integrate various related data, and support computer-assisted reasoning. http://data.bioontology.org/categories/Health
GeoSpecies Ontology GEOSPECIES Public 0 0 0 0 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 http://data.bioontology.org/categories/Other
Time Event Ontology TEO Public 653 0 0 0 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. http://data.bioontology.org/categories/Other
Translational Medicine Ontology TMO Public 300 0 0 0 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. http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/categories/Health
Regional Healthcare System Interoperability and Information Exchange Measurement Ontology HEIO Public 123 0 0 0 OWL Version 1.11 06/30/2014 Lingkai Zhu Josephine McMurray Description: The purpose of this ontology is to develop a model for regional healthcare system interoperability and information exchange quantification (measured by the electronic health information exchange (eHIE) indicator). The eHIE is hypothesized as a leading measure of regional healthcare system integration. A publication associated with this ontology is currently under review. http://data.bioontology.org/categories/Other
Infectious Disease Ontology IDO Public 506 0 0 6 OWL 2014-08-01 08/04/2014 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.
http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/categories/Health
FlyBase Controlled Vocabulary FB-CV Public 848 0 0 1 OBO 2014-03-28 06/11/2014 Marta Costa 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. This ontology includes the Drosophila phenotype ontology (DPO), provided here together with FBcv for legacy purposes.
http://data.bioontology.org/categories/Vocabularies
Neuroscience Information Framework (NIF) Dysfunction Ontlogy NIFDYS Public 2,750 0 0 0 OWL 1.5 (December, 2012) 08/05/2013 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.
Bilingual Ontology of Alzheimer's Disease and Related Diseases ONTOAD Public 5,899 0 0 0 OWL 1.0 12/02/2013 Khadim Dramé Description: OntoAD is a bilingual (English-French) domain ontology for modeling knowledge about Alzheimer's Disease and Related Syndromes. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Dysfunction http://data.bioontology.org/categories/Neurologic_Disease http://data.bioontology.org/categories/Neurological_Disorder http://data.bioontology.org/categories/Human
Tissue Microarray Ontology TMA Public 7 0 0 0 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. http://data.bioontology.org/categories/Experimental_Conditions http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Other
HIVOntologymain.owl HIVO004 Public 539 0 9 1 OWL 009 09/12/2014 Hanfei Bao Description: In the processes that HIV causes in the development of AIDS, there are thousands of micromechanisims in molecular world involved. They include the combinations and decompositions of substances, the participations of the forces and energies of the molecules and atoms and their groups, the spatial movement and the effects of the spatial barriers or passages, the biologic effects of molecular distributions, sequnces or patterns and even the steric configurations. All of them constitute the variety of sophisticated pictures such as molecular trains, trees, loops or circles or feedbacks, oscillatings or fluctuations and forked roads (uncertainty points), and the huge and dymanic networks, at last. The author believes that HIV and AIDS ontologies are able to help know and understand the knowledge semantic networks better. Toward this end, HIV ontology will make the granularity of the elements (or entities) and relations (or object properties) detailed enough and develop a set of AIDS clinic ontology and calculation ontologies as the powerful assistant bases. The knowledge in ontology is expressed by the form of The Resource Description Framework (RDF), known as the “triple” ( “Thing1(URI) --relation(URI) -- Thing2(URI)”. Therefore ontology is mainly the computer readable and understandable knowledge resources. Ontology is esentially an ever-continuing work, the initial version of HIV ontology (HIVOnt006.owl) is published here. The is the main part of a set of ontologies on HIV and AIDS, a work being designed and developed underway. http://data.bioontology.org/categories/Immunology http://data.bioontology.org/categories/Taxonomic_Classification http://data.bioontology.org/categories/Molecule http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Dysfunction http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Subcellular http://data.bioontology.org/categories/Protein
Semanticscience Integrated Ontology SIO Public 1,414 0 0 3 OWL 1.0.10 06/13/2014 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. http://data.bioontology.org/categories/Yeast http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/categories/Cellular_anatomy_ http://data.bioontology.org/categories/Taxonomic_Classification http://data.bioontology.org/categories/Molecule http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Genomic_and_Proteomic http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Subcellular http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Subcellular_anatomy http://data.bioontology.org/categories/Chemical http://data.bioontology.org/categories/Cell http://data.bioontology.org/categories/Protein http://data.bioontology.org/categories/Gene_Product http://data.bioontology.org/categories/Vocabularies http://data.bioontology.org/categories/Physicochemical
Protein Modification Ontology PSIMOD Public 2,001 0 0 0 OBO 1.013.0 06/17/2014 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. http://data.bioontology.org/groups/PSI
Resource of Asian Primary Immunodeficiency Diseases (RAPID) Phenotype Ontology RPO Public 1,544 0 0 1 OWL Version 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 http://data.bioontology.org/categories/Immunology http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Human
Biomedical Informatics Research Network Project Lexicon BIRNLEX Public 3,580 0 0 4 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. http://data.bioontology.org/categories/Imaging http://data.bioontology.org/categories/Anatomy
Pathway Ontology PW Public 1,556 0 0 1 OBO 6.6 09/12/2014 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. http://data.bioontology.org/categories/Biological_Process
Ontology for Genetic Susceptibility Factor OGSF Public 0 0 0 0 OWL 0.7 08/10/2013 Asiyah 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. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Genomic_and_Proteomic http://data.bioontology.org/categories/Human
Open Biological and Biomedical Ontologies Relationship Types OBOREL Public 0 0 0 17 OBO unknown 05/05/2011 Chris Mungall Description: Defines core relations used in all OBO ontologies. Obsolete. Replaced with RO.
PhenomeBLAST Ontology PHENOMEBLAST Summary Only 0 0 0 1 OWL 2 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. http://data.bioontology.org/categories/Mouse_Anatomy http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/categories/Fish_Anatomy http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Dysfunction http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Other http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Human
Ontology for Parasite LifeCycle OPL Public 359 0 0 0 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. http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Development http://data.bioontology.org/categories/Vocabularies
BioPortal Metadata Ontology BP-METADATA Public 31 0 0 0 OWL 0.9.5 08/21/2013 Natasha Noy Description: This ontology represents the structure that BioPortal uses to represent all of its metadata (ontology details, mappings, notes, reviews, views) http://data.bioontology.org/categories/Other
EDDA Study Design Terminology EDDA Public 169 0 0 0 OWL version: 1.2.05 07/01/2014 Tanja Bekhuis Description: EDDA Study Design Terminology. Evidence in Documents, Discovery, and Analysis (EDDA) Group. Tanja Bekhuis (PI); Eugene Tseytlin and Kevin Mitchell (Developers); Ashleigh Faith (Taxonomist). Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pennsylvania, USA. This work was made possible by the US National Library of Medicine, National Institutes of Health, grant no. R00LM010943. For details, see: Bekhuis T, Demner-Fushman D, Crowley RS. Comparative effectiveness research designs: an analysis of terms and coverage in Medical Subject Headings (MeSH) and Emtree. JMLA: J Med Libr Assoc. 2013 Apr;101(2):92-100. doi:10.3163/1536-5050.101.2.004. PubMed PMID: 23646024; PubMed Central PMCID: PMC3634392. The terminology appearing in JMLA has been enriched with terms from MeSH, and Emtree, the controlled vocabularies for MEDLINE and Embase, respectively. Variants include American and British spellings and some inverted terms. Disclaimer: The EDDA Study Design Terminology is not an ontology. It is a set of terms that we have found useful for our machine learning experiments. http://data.bioontology.org/categories/Experimental_Conditions http://data.bioontology.org/categories/Vocabularies
test_onto TESTONTO Public 5 0 0 0 OWL 03/26/2014 Willy WOLFF Description: Test onto
KB_Bio_101 AURA Public 27,396 0 0 0 OWL 1.0 01/21/2014 Vinay Chaudhri Description: KB_Bio_101 is the ontology of the AURA + Inquire project @ SRI International, Menlo Park. This work is owned by Vulcan Inc. and is licensed for use under the Creative Commons Attribution-NonCommerical-ShareAlike 3.0 license (http://creativecommons.org/licenses/by-nc-sa/3.0/). Vulcan Inc., June 2013
General Formal Ontology for Biology GFO-BIO Public 167 0 0 0 OWL 1.1 03/02/2010 Robert Hoehndorf Description: GFO-Bio is a biological core ontology built on the General Formal Ontology. http://data.bioontology.org/categories/Mouse_Anatomy http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/categories/Cellular_anatomy_ http://data.bioontology.org/categories/Molecule http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Subcellular http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Human_Developmental_Anatomy http://data.bioontology.org/categories/Plant_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Plant http://data.bioontology.org/categories/Human http://data.bioontology.org/categories/Subcellular_anatomy http://data.bioontology.org/categories/Chemical http://data.bioontology.org/categories/Cell http://data.bioontology.org/categories/Development http://data.bioontology.org/categories/Protein http://data.bioontology.org/categories/Animal_Gross_Anatomy http://data.bioontology.org/categories/Gene_Product http://data.bioontology.org/categories/Plant_Development http://data.bioontology.org/categories/Animal_Development
Family Health History Ontology FHHO Public 238 0 0 1 OWL 1 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. http://data.bioontology.org/categories/Health
Ontology of Data Mining Investigations ONTODM-KDD Public 263 0 0 1 OWL 0.1 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.
Ontology for General Medical Science OGMS Public 125 0 0 3 OWL 2014-06-20 06/20/2014 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 http://data.bioontology.org/groups/CTSA
Biomedical Resource Ontology BRO Public 488 73 1 4 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. http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/groups/CTSA
Psychology Ontology APAONTO Public 8,947 0 0 0 OWL 4 07/29/2014 alexander garcia Ian Galloway Description: APA thesaurus . Flat ontology file http://data.bioontology.org/categories/Biomedical_Resources
Plant Trait Ontology PTO Public 1,331 0 0 3 OBO unknown 09/17/2014 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. http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Plant
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.
Cognitive Atlas Ontology COGAT Public 1,702 0 0 3 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. http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Human http://data.bioontology.org/categories/Vocabularies
Health Level Seven Reference Implementation Model, Version 3 HL7 Public 7,500 0 1 3 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. http://data.bioontology.org/categories/Health
Cognitive Paradigm Ontology COGPO Public 355 0 0 2 OWL 1 12/16/2010 Jessica Turner Description: This ontology is used to describe the experimental conditions within cognitive/behavioral experiments, primarily in humans. http://data.bioontology.org/categories/Imaging http://data.bioontology.org/categories/Experimental_Conditions http://data.bioontology.org/categories/Human
Amphibian Gross Anatomy Ontology AAO Public 1,603 0 0 2 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. http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Animal_Gross_Anatomy
Upper-Level Cancer Ontology CANONT Public 56 0 0 0 OBO unknown 11/20/2012 Andre Stander Description: Providing an upper-level ontology for cancer.
Cell Culture Ontology CCONT Public 15,390 0 0 0 OWL 1.1 07/23/2014 Matthias Ganzinger Description: CCONT is an ontology for the formal representation of cell lines and their correspnding culture conditions. http://data.bioontology.org/categories/Experimental_Conditions http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Vocabularies
Ontological Knowledge Base Model for Cystic Fibrosis ONTOKBCF Public 408 0 0 2 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. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Gene_Product
Epilepsy Ontology EPILONT Public 137 0 0 1 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). http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Neurologic_Disease http://data.bioontology.org/categories/Neurological_Disorder http://data.bioontology.org/categories/Human http://data.bioontology.org/categories/Development http://data.bioontology.org/categories/Vocabularies
Experimental Factor Ontology EFO Public 15,181 4 0 6 OWL 2.52 09/17/2014 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 http://data.bioontology.org/categories/Experimental_Conditions http://data.bioontology.org/categories/Biological_Process
Traditional Medicine Other Factors Value Set TM-OTHER-FACTORS Public 12 0 0 0 OWL 1 01/31/2011 Tania Tudorache Description: The value set for the Other Factors property of the International Classification of Traditional Medicine (ICTM). http://data.bioontology.org/categories/Human
RegenBase ontology RB Public 407 0 0 0 OWL 1.0 09/02/2014 Alison Callahan Description: The RegenBase ontology describes biological entities and processes studied in spinal cord injury (SCI) research. http://data.bioontology.org/categories/Health
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) http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Genomic_and_Proteomic http://data.bioontology.org/categories/Human
International Classification of Functioning, Disability and Health ICF Public 1,595 0 0 1 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/
http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Human http://data.bioontology.org/categories/Vocabularies http://data.bioontology.org/groups/WHO-FIC
Loggerhead Nesting Ontology LHN Public 308 0 0 0 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.
Parasite Experiment Ontology PEO Public 142 0 0 0 OWL 1 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.
Variation Ontology VARIO Public 384 0 0 0 OBO 2014-01-16 01/16/2014 Mauno Vihinen Description: Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations.
Ontology of Glucose Metabolism Disorder OGMD Public 134 0 0 0 OBO 1 10/07/2013 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.) OWL file is downloadable as the different view here. http://data.bioontology.org/categories/Human
Ontology of Clinical Research OCRE Public 388 7 0 1 OWL Revision 315 06/21/2013 Ida Sim Description: OCRe is an ontology designed to support systematic description of, and interoperable queries on, human studies and study elements. http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/groups/CTSA
Traditional Medicine Signs and Symptoms Value Set TM-SIGNS-AND-SYMPTS Public 325 0 0 0 OWL 1 01/31/2011 Tania Tudorache Description: The value set for the Signs and Symptoms property of the International Classification of Traditional Medicine (ICTM).
Fire Ontology FIRE Public 53 0 0 0 OWL 0.8 02/24/2014 Adriano Souza Description: The ontology of Fire was created in order to represent the set of concepts about the fire occurring in natural vegetation, its characteristics, causes and effects, with focus on Cerrado vegetation domain. The fire plays a determinant role on the structure and composition of Cerrado physiognomies.
Neglected Tropical Disease Ontology NTDO Public 525 0 0 0 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. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Other http://data.bioontology.org/categories/Human
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). http://data.bioontology.org/categories/Molecule http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Other http://data.bioontology.org/categories/Chemical http://data.bioontology.org/categories/Protein
Randomized Controlled Trials Ontology RCTONT Public 186 0 0 0 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. http://data.bioontology.org/categories/Biomedical_Resources
Ontology of Physics for Biology OPB Public 678 2 0 2 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. http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Chemical http://data.bioontology.org/categories/Physicochemical
Plant Anatomy PAE Public 1,356 0 0 4 OBO Release #20 08/21/2013 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.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/ http://data.bioontology.org/categories/Plant_Anatomy http://data.bioontology.org/categories/Plant
HIV ontology HIV Public 0 0 0 0 OBO 1.31 05/02/2014 Martin Schiller Description: The HIV ontology encompasses all knowledge about HIV http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/categories/Taxonomic_Classification http://data.bioontology.org/categories/Molecule http://data.bioontology.org/categories/Genomic_and_Proteomic http://data.bioontology.org/categories/Other http://data.bioontology.org/categories/Subcellular http://data.bioontology.org/categories/Human http://data.bioontology.org/categories/Microbial_Anatomy http://data.bioontology.org/categories/Protein
Spider Ontology SPD Public 661 2 0 0 OBO 0.9.9 01/13/2014 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). http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Animal_Gross_Anatomy
Cancer Chemoprevention Ontology CANCO Public 126 0 0 1 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. http://data.bioontology.org/categories/Experimental_Conditions http://data.bioontology.org/categories/Molecule http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Biomedical_Resources
Ontology of Medically Related Social Entities OMRSE Public 127 0 0 0 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.)
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. http://data.bioontology.org/categories/Biomedical_Resources
Ontology for Drug Discovery Investigations DDI Public 164 0 0 1 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).
Medical Dictionary for Regulatory Activities MEDDRA Public 65,369 0 0 3 UMLS 2014AA 05/28/2014 MSSO Help Desk Description: Medical Dictionary for Regulatory Activities Terminology (MedDRA) http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/caBIG http://data.bioontology.org/groups/UMLS
Situation-Based Access Control Ontology SITBAC Public 176 0 0 1 OWL 1.3 02/21/2011 Mor Peleg Description: Context-based healthcare access-control policies http://data.bioontology.org/categories/Other
Physico-Chemical Process REX Public 552 0 0 0 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. http://data.bioontology.org/categories/Physicochemical
NMR-Instrument Component of Metabolomics Investigations Ontology NMR Public 715 0 0 3 OWL 1.0.0 03/11/2014 nmrML list Daniel Schober Description: This is the new msi-sanctioned nmr CV, created within the COSMOS EU project, to support the nmrML data standard for nuclear magnetic resonance data in metabolomics with meaningful raw data descriptors.
suicideo SuicidO Public 198 0 0 1 OWL 1 07/03/2013 Alexander Garcia Description: Ontology for Suicidology http://data.bioontology.org/categories/Health
Menelas Project Top-Level Ontology TOP-MENELAS Public 458 0 0 0 OWL 1.1 07/15/2013 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.
Comparative Data Analysis Ontology CDAO Public 143 0 0 1 OWL $Revision$ 08/20/2013 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 http://data.bioontology.org/categories/Experimental_Conditions
Biologie Hors Nomenclature BHN Public 2,534 0 0 0 OWL 3.2 11/19/2013 Description: L'activité innovante de biologie et d'anatomo-pathologie réalisée notamment dans les Centres Hospitalo-Universitaires est habituellement appelée "activité hors nomenclature" (BHN pour la biologie hors nomenclature et PHN pour l'anatomo-pathologie hors nomenclature). Ce caractère "hors nomenclature" signifie que l'assurance maladie n'a pas encore intégré ces actes dans la Nomenclature des Actes de Biologie Médicale (NABM) ou la Nomenclature Générale des Actes Professionnels (NGAP). http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Vocabularies
Mosquito Gross Anatomy Ontology TGMA Public 1,864 0 0 1 OBO unknown 09/15/2011 C. Louis Description: A structured controlled vocabulary of the anatomy of mosquitoes. http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Animal_Gross_Anatomy
Radiation Oncology Ontology ROO Public 0 0 0 0 OWL 0.1 09/09/2014 Andre Dekker Description: The Radiation Oncology Ontology aims to cover the radiation oncology domain with a strong focus on re-using existing ontologies. http://data.bioontology.org/categories/Imaging http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Human http://data.bioontology.org/categories/Development http://data.bioontology.org/categories/Vocabularies
Interaction Ontology IXNO Public 53 0 0 0 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. http://data.bioontology.org/categories/Other
National Drug Data File NDDF Public 26,911 0 0 1 UMLS 2014AA 05/28/2014 First DataBank Customer Support Description: National Drug Data File Plus Source Vocabulary http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
Influenza Ontology FLU Public 0 0 0 1 OWL 06/06/2014 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)
Metagenome and Microbes Environmental Ontology MEO Public 783 0 0 0 OWL Version 0.7 02/01/2014 MicrobeDB.jp Project Team Description: An Ontology for organismal habitats (especially focused on microbes) http://data.bioontology.org/categories/Other
International Classification of Diseases, Version 9 - Clinical Modification ICD9CM Public 22,534 0 1 3 UMLS 2014AA 05/28/2014 Patricia Brooks Description: The ICD is the international standard diagnostic classification for all general epidemiological, many health management purposes and clinical use. http://data.bioontology.org/groups/WHO-FIC http://data.bioontology.org/groups/UMLS
Cerrado concepts and plant community dynamics CCON Public 85 0 0 0 OWL 0.9.3 01/29/2014 Adriano Souza Description: The ontology of Cerrado wood plant dynamics was created in order to represent the set of concepts about the dynamics, that is, changes over time of the wood vegetation structure, of Cerrado. Ccon describes the main parameters used to measure the changes, such as mortality rate and recruitment rate.
International Classification for Nursing Practice ICNP Public 3,894 0 0 0 OWL 2011 06/25/2013 Amy Coenen Description: International Classification for Nursing Practice http://data.bioontology.org/categories/Taxonomic_Classification http://data.bioontology.org/groups/WHO-FIC
Protein Ontology PR Public 83,656 0 0 5 OBO 41.0. 06/12/2014 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). http://data.bioontology.org/groups/OBO_Foundry
BioModels Ontology BIOMODELS Public 187,519 0 0 0 OWL 21 04/03/2012 Robert Hoehndorf Description: OWL Representation of the models in the BioModels repository. http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Biological_Process
Bone Dysplasia Ontology BDO Public 13,816 0 0 2 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. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Human
G Protein-Coupled Receptor BioAssays Ontology BAO-GPCR Public 903 0 0 1 OWL 1.1 10/28/2013 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. http://data.bioontology.org/categories/Molecule http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Other http://data.bioontology.org/categories/Subcellular http://data.bioontology.org/categories/Chemical http://data.bioontology.org/categories/Protein http://data.bioontology.org/categories/Vocabularies http://data.bioontology.org/categories/Physicochemical
National Institutes of Health Stroke Scale Ontology NIHSS Public 18 0 0 0 OWL 2014/01 08/28/2014 Petr Vcelak Description: Domain ontology for National Institutes of Health Stroke Scale (NIHSS). Scores range from 0-42. Patients are given more points for greater deficiencies. A score of 0 indicates that the test is normal. http://data.bioontology.org/categories/Neurologic_Disease
Bioinformatics Web Service Ontology OBIWS Public 227 0 0 3 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. http://data.bioontology.org/categories/Other
Minimal Anatomical Terminology MAT Public 461 0 0 0 OBO 1.1 07/05/2009 EMAP Administrators Description: Minimal set of terms for anatomy http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Animal_Gross_Anatomy
Minimal Standard Terminology of Digestive Endoscopy, French MSTDE-FRE Public 1,832 0 0 0 UMLS 2014AA 05/28/2014 NLM Customer Service Description: Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy, French Translation, 2001
Traditional Medicine Constitution Value Set TM-CONST Public 20 0 0 0 OWL 1 01/31/2011 Tania Tudorache Description: The value set for the Constitution property of the International Classification of Traditional Medicine (ICTM). http://data.bioontology.org/categories/Human
Physical Medicine and Rehabilitation PMR Public 137 0 0 0 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. http://data.bioontology.org/categories/Health
Surgical Secondary Events SSE Public 243 0 0 0 OWL 1.1 07/17/2013 Mindy Sovel Description: Memorial Sloan-Kettering Cancer Center Surgical Secondary Events Ontology (Adverse Events) http://data.bioontology.org/categories/Health
Chemical Entities of Biological Interest Ontology CHEBI Public 52,784 2 0 11 OBO 119 09/01/2014 Janna Hastings Description: A structured classification of chemical compounds of biological relevance. http://data.bioontology.org/categories/Chemical http://data.bioontology.org/groups/OBO_Foundry
Fungal Gross Anatomy Ontology FAO Public 90 0 0 0 OBO unknown 02/07/2014 Saccharomyces Genome Database Description: A structured controlled vocabulary for the anatomy of fungi. http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Microbial_Anatomy
Quantities, Units, Dimensions, and Types Ontology QUDT Public 204 0 0 1 OWL $Id: OSG_qudt-(v1.1).ttl 4989 2011-06-01 21:56:40Z RalphHodgson $ 08/11/2013 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. http://data.bioontology.org/categories/Other
Ontology of Core Data Mining Entities ONTODM-CORE Public 768 0 0 1 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.
RNRMU RNRMU Public 2,310 0 0 0 OWL 0.1 07/04/2014 Olga Gennady Bogopolskiy Description: The terms of RNRMU http://data.bioontology.org/categories/Development
Biological Collections Ontology BCO Public 135 0 0 0 OWL 2014-03-29 05/28/2014 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. http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/groups/BIS
Measurement Method Ontology MMO Public 558 0 0 1 OBO 2.20 06/13/2014 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. http://data.bioontology.org/categories/Phenotype
Tick Gross Anatomy Ontology TADS Public 628 0 0 1 OBO 1.21 05/06/2013 Daniel Sonenshine Description: The anatomy of the Tick, Families: Ixodidae, Argassidae http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Animal_Gross_Anatomy
DICOM Controlled Terminology DCM Public 3,005 0 0 0 OWL 2013_draft20140223 07/23/2014 David Clunie Description: DICOM Controlled Terminology (PS3.16 2013 Annex D) http://data.bioontology.org/categories/Imaging
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. http://data.bioontology.org/categories/Taxonomic_Classification http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Vocabularies
Xenopus Anatomy and Development Ontology XAO Public 1,342 0 0 1 OBO 2013-10-09 11/21/2013 Erik Segerdell Description: A structured, controlled vocabulary of the anatomy and development of the African clawed frogs (Xenopus laevis and tropicalis). http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Development http://data.bioontology.org/groups/OBO_Foundry
Eagle-I Research Resource Ontology ERO Public 3,948 0 0 2 OWL 2013-08-02 08/05/2013 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/). http://data.bioontology.org/categories/Biomedical_Resources
C. elegans Phenotype Vocabulary WB-PHENOTYPE Public 2,195 0 0 0 OBO unknown 09/17/2014 Gary Schindelman Description: A structured controlled vocabulary of Caenorhabditis elegans phenotypes http://data.bioontology.org/categories/Phenotype
EDAM bioinformatics operations, data types, formats, identifiers and topics EDAM Public 2,824 2 0 5 OWL 1.3 02/18/2014 Matúš Kalaš 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. http://data.bioontology.org/categories/Other
Computational Neuroscience Ontology CNO Public 395 5 0 0 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. http://data.bioontology.org/categories/Vocabularies
Autism Spectrum Disorder Phenotype Ontology ASDPTO Public 284 0 0 0 OWL 1 01/21/2014 Alexa T McCray Description: Autism Spectrum Disorder Phenotype Ontology encapsulates the Autism Spectrum Disorder behavioral phenotype, informed by the standard ASD assessment instruments and the currently known characteristics of this disorder. http://www.ncbi.nlm.nih.gov/pubmed/24163114 http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Neurological_Disorder http://data.bioontology.org/categories/Human
Microbial Typing Ontology TYPON Public 4,838 0 0 1 OWL 20140910 09/16/2014 PHYLOViZ Team TYPON Team Description: TyPon provides a comprehensive description of the existing microbial typing methods for the identification of bacterial Isolates and their classification. Such a description constitutes an universal format for the exchange of information on the microbial typing field, providing a vehicle for the integration of the numerous disparate online databases. In its current version, TyPon describes most used microbial typing methods but it is, and always will be, a work in progress given the constant advances in the microbial typing field.
Chemical Information Ontology CHEMINF Public 723 0 0 5 OWL 1.0 08/14/2014 Janna Hastings Description: Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.
General Formal Ontology GFO Public 44 0 0 0 OWL Version 1.0 ($Revision: 1.13 $) 03/02/2010 Heinrich Herre Description: The General Formal Ontology (GFO) is a top-level ontology integrating objects and processes. http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/categories/Upper_Level_Ontology
Biological Imaging Methods Ontology FBbi Public 624 0 0 3 OBO unknown 11/05/2013 Chris Woodcock Description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. http://data.bioontology.org/categories/Imaging http://data.bioontology.org/categories/Experimental_Conditions
Rat Strain Ontology RS Public 3,795 0 0 3 OBO 5.23 07/22/2014 Rajni Nigam Description: This ontology defines the hierarchical display of the different rat strains as derived from the parental strains
Human Disease Ontology DOID Public 8,757 5 0 4 OBO unknown 09/17/2014 Lynn Schriml Description: Creating a comprehensive hierarchical controlled vocabulary for human disease representation. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Neurologic_Disease http://data.bioontology.org/categories/Neurological_Disorder http://data.bioontology.org/categories/Human
Clusters of Orthologous Groups (COG) Analysis Ontology CAO Public 204 0 0 1 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 http://data.bioontology.org/categories/Gene_Product
Human Developmental Anatomy Ontology, timed version EHDA Public 8,340 0 0 0 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. http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Human_Developmental_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Animal_Gross_Anatomy
Congenital Heart Defects Ontology CHD Public 511 0 0 0 OWL 1.1 06/03/2013 Charalampos Moschopoulos Description: An ontology that describes the Congenital Heart Defects data. http://data.bioontology.org/categories/Human
NGS ontology NGSONTO Public 85 0 0 0 OWL 0.7 07/02/2014 mickael silva Description: The NGSOnto ontology aims at capturing the workflow of all the processes involved in a Next Generation Sequencing, in order to ensure the reproducibility of the entire process, through the use of a controled and specific vocabulary.
Minimal Information about any Sequence (MIxS) Controlled Vocabularies MIXSCV Public 519 0 0 0 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.
Ontology of Adverse Events OAE Public 2,820 0 0 0 OWL Vision Release; 1.1.147 08/04/2014 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. http://data.bioontology.org/categories/Health
International Classification of Primary Care - 2 PLUS ICPC2P Public 7,543 0 0 0 UMLS 2014AA 05/28/2014 Prof Helena Britt Description: ICPC-2 PLUS http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
Reference Sequence Annotation RSA Public 10 0 0 0 OWL 0.6 01/31/2014 Zuotian Tatum Description: An ontology for sequence annotations and how to preserve them with reference sequences. http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Genomic_and_Proteomic
PharmGKB Ontology PHARMGKB Summary Only 0 0 0 1 OWL 1 08/05/2011 Robert Hoehndorf Description: PharmGKB represented in OWL and linked to related ontologies. http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/categories/Molecule http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Dysfunction http://data.bioontology.org/categories/Other http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Chemical http://data.bioontology.org/categories/Physicochemical
Pharmacogenomic Relationships Ontology PHARE Public 228 0 0 0 OWL Developed by the Helix Group, Department of Genetics, Stanford University, and by the Orpailleur Group, LORIA - INRIA Nancy. 01/14/2011 Adrien Coulet Description: The PHArmacogenomic RElationships Ontology (or PHARE) proposes concepts and roles to represent relationships of pharmacogenomics interest. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Human http://data.bioontology.org/categories/Chemical http://data.bioontology.org/categories/Gene_Product
XEML Environment Ontology XEO Public 144 0 0 1 OBO 1.6 06/25/2014 Kenny Billiau Description: XeO has been created to help plant scientists in documenting and sharing metadata describing the abiotic environment. http://data.bioontology.org/categories/Other
Robert Hoehndorf Version of MeSH RH-MESH Public 305,349 0 0 2 OWL 2014 04/21/2014 Robert Hoehndorf Description: Medical Subjects Headings Thesaurus 2014, Modified 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, including the pharmacological actions (represented as subclass relations). Concepts in the MeSH concept tree are merged with MeSH term ids.

--------------------------

Note that, while this ontology is composed of MeSH terms, it does not correspond directly to UMLS MeSH. In particular, a single term in UMLS MeSH often results in multiple classes in this ontology. For example, in MeSH there is a single term with the label "Heart". The internal code (unique identifier) for this term is A07.541. In this ontology there are two entirely different terms, both of which have the label "Heart". The codes for these terms are A07.541 and D006321.

http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Dysfunction http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Human http://data.bioontology.org/categories/Vocabularies
Tribolium Ontology TRON Public 965 0 0 1 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. http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Development
Cereal Plant Gross Anatomy Ontology GRO-CPGA Public 1,356 0 0 2 OBO unknown 08/20/2013 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.
Human Genome Organization Gene Symbols HUGO Public 32,917 0 0 2 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. http://data.bioontology.org/categories/Health
Amino Acid Ontology AMINO-ACID Public 46 0 0 2 OWL classified 07/02/2010 Nick Drummond, Georgina Moulton, Robert Stevens, Phil Lord Description: An ontology of amino acids and their properties. Inferred version. http://data.bioontology.org/categories/Other
Solanaceae Phenotype Ontology SPTO Public 396 0 0 0 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.
World Health Organization (WHO) Adverse Reaction Terminology WHO-ART Public 0 0 0 1 UMLS 2014AA 05/28/2014 WHO Collaborating Centre for International Drug Monitoring Description: WHO Adverse Reaction Terminology, 1997 http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/WHO-FIC http://data.bioontology.org/groups/UMLS
Bleeding History Phenotype Ontology BHO Public 543 0 0 0 OWL 0.4 12/22/2010 Shamim Mollah Description: An application ontology devoted to the standardized recording of phenotypic data related to hemorrhagic disorders. http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/groups/CTSA
Mammalian Phenotype Ontology MP Public 10,760 0 0 5 OBO releases/2014-09-11 09/17/2014 JAX phenotype list Description: The Mammalian Phenotype Ontology is under development as a community effort to provide standard terms for annotating mammalian phenotypic data. http://data.bioontology.org/categories/Phenotype
BioPAX Ontology of Biological Pathways BP Public 68 0 0 1 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. http://data.bioontology.org/categories/Biological_Process
Microbial Culture Collection Vocabulary MCCV Public 16 0 0 0 OWL Version 0.94 beta 02/17/2014 Shuichi Kawashima Description: Structured controlled vocabulary for describing meta information of microbial calture collection maintained in biological research centers http://data.bioontology.org/categories/Other
National Cancer Institute Thesaurus NCIT Public 0 16 1 14 OWL 14.08d 09/17/2014 NCICB Support Description: A vocabulary for clinical care, translational and basic research, and public information and administrative activities. http://data.bioontology.org/groups/caBIG http://data.bioontology.org/groups/UMLS
Artificial Intelligence Rheumatology Consultant System Ontology AI-RHEUM Public 814 0 0 0 UMLS 2014AA 05/28/2014 NLM Customer Service 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. http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
Master Drug Data Base Clinical Drugs MDDB Public 13,446 0 0 0 UMLS 2014AA 05/28/2014 Karen Eckert Description: Master Drug Data Base, 2009_08_05 http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
Coding Symbols for a Thesaurus of Adverse Reaction Terms COSTART Public 1,713 0 0 0 UMLS 2014AA 05/28/2014 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. http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
Skin Physiology Ontology SPO Public 339 0 0 1 OWL 2 09/18/2008 Tariq Abdulla http://data.bioontology.org/categories/Biological_Process
Microarray and Gene Expression Data Ontology MO Public 233 0 0 3 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. http://data.bioontology.org/categories/Experimental_Conditions
Non-Randomized Controlled Trials Ontology NONRCTO Public 155 0 0 0 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.
Medical image simulation OntoVIP Public 3,144 0 0 1 OWL v1 07/11/2013 Bernard Gibaud Description: The OntoVIP ontology was developed in the context of the Virtual Imaging Platform project (VIP), a french project supported by ANR (ANR-09-COSI-03 grant) aiming at sharing medical image simulation resources. This ontology describes the content of the models used in medical image simulation. This ontology can be used to annotate such models in order to highlight the different entities that are present in the 3D scene to be imaged, i.e. anatomical structures, pathological structures, foreign bodies, contrast agents etc. The model allows also to associate to these entities information about their physical qualities, which are used in the medical image simulation process (to mimick physical phenomena involved in CT, MR, US and PET imaging). This ontology partly relies on the OntoNeuroLOG ontology (ONL-DP ONL-MR-DA), as well as PATO, RadLex, FMA and ChEBI. http://data.bioontology.org/categories/Imaging
Alzheimer's disease ontology ADO Public 1,564 0 0 1 OWL 1.1.1 07/23/2013 Ashutosh Malhotra Description: ADO is a first attempt to develop an open, public ontology representing relevant knowledge on Alzheimer’s disease. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Neurologic_Disease http://data.bioontology.org/categories/Neurological_Disorder http://data.bioontology.org/categories/Human
Regulation of Gene Expression Ontolology REXO Public 77,610 0 0 0 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.
Bone and Cartilage Tissue Engineering Ontology BCTEO Public 253 0 0 0 OBO releases/2013-08 06/18/2014 Federica Viti / Alessandro Orro Description: Ontology that describes the field of Tissue Engineering for what concerns bone and cartilage tissues.
Dengue Fever Ontology IDODEN Public 0 0 0 0 OWL 1.00 09/18/2014 Elvira Mitraka Description: An ontology for dengue fever. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Other http://data.bioontology.org/categories/Human
Logical Observation Identifier Names and Codes LOINC Public 162,372 0 0 5 UMLS 2014AA 05/28/2014 LOINC Support Description: Logical Observation Identifier Names and Codes (LOINC) http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/caBIG http://data.bioontology.org/groups/UMLS
Ontology for Genetic Disease Investigations OGDI Public 384 0 0 0 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) . http://data.bioontology.org/categories/Experimental_Conditions
Diabetes phenotypes ontology (ALPHA VERSION) DPO Public 583 0 0 0 OWL alpha_01 07/14/2014 Jon Ison Description: An ontology of phenotypes associated with type II diabetes (!! ALPHA VERSION !!) http://data.bioontology.org/categories/Phenotype
Pseudogene pseudo Public 23 0 0 0 OBO 0.1 11/18/2008 Gerstein Lab
Mouse Pathology Ontology MPATH Public 888 0 0 1 OBO unknown 08/12/2013 Mouse_pathology Administrators Description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes http://data.bioontology.org/categories/Phenotype
Human Physiology Simulation Ontology HUPSON Public 2,919 0 0 0 OWL 1.1.1 04/07/2014 Michaela Guendel Description: Large biomedical simulation initiatives, such as the Virtual Physiological Human (VPH), are substantially dependent on controlled vocabularies to facilitate the exchange of information, of data and of models. Hindering these initiatives is a lack of a comprehensive ontology that covers the essential concepts of the simulation domain. We propose a first version of a newly constructed ontology, HuPSON, as a basis for shared semantics and interoperability of simulations, of models, of algorithms and of other resources in this domain. The ontology is based on the Basic Formal Ontology, and adheres to the MIREOT principles. http://data.bioontology.org/categories/Health
Immunogenetics Ontology IMGT-ONTOLOGY Public 1,412 0 0 1 OWL 1.0.2 07/17/2013 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 1.0.2 of IMGT-ONTOLOGY includes the concepts of IDENTIFICATION and the concepts of CLASSIFICATION. http://data.bioontology.org/categories/Immunology
Immune Disorder Ontology IMMDIS Public 0 0 0 0 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.
http://data.bioontology.org/categories/Immunology http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Human
Ontology for MicroRNA Target Prediction OMIT Public 2,338 0 0 1 OBO OBO 4.0-12122013-2338 12/20/2013 Jingshan Huang Description: The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). OMIT has reused and extended a set of well-established concepts from existing bio-ontologies, e.g., Gene Ontology, Sequence Ontology, Protein Ontology, NCBI Organism Taxonomy, Human Disease Ontology, Foundational Model of Anatomy, and so forth. http://data.bioontology.org/categories/Molecule http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Human http://data.bioontology.org/categories/Cell http://data.bioontology.org/categories/Protein http://data.bioontology.org/categories/Gene_Product
Medical Subject Headings MESH Public 245,887 0 1 12 UMLS 2014AA 07/07/2014 NLM Customer Service Description: Medical Subject Headings (MeSH);National Library of Medicine; 2011 http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
Biological Observation Matrix Ontology BIOMO Public 1,426 0 0 1 OWL 0.0.1 07/29/2014 Mikel Egaña Aranguren Description: The BIOMO ontology maps the HDF5 based BIOM format (http://biom-format.org/) to OWL, offering a method to convert a BIOM file to RDF and therefore publish it as Linked Data http://data.bioontology.org/categories/Other
RNA Ontology RNAO Public 240 0 0 1 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. http://data.bioontology.org/categories/All_Organisms
Vaccine Ontology VO Public 4,709 3 0 3 OWL Vision Release; 1.0.755 08/17/2014 Yongqunh He Description: A biomedical ontology in the vaccine domain http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/categories/Immunology http://data.bioontology.org/categories/Health
Semantic DICOM Ontology SEDI Public 19 0 0 0 OWL 0.4 07/29/2014 Detlef Grittner Description: An ontology for DICOM as used in the SeDI project.
Cell Line Ontology CLO Public 41,747 0 0 2 OWL 2.1.59 02/21/2014 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. http://data.bioontology.org/categories/Experimental_Conditions http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/categories/Taxonomic_Classification http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Cell http://data.bioontology.org/categories/Vocabularies
Cell Line Ontology [by Mahadevan] MCCL Public 5,474 0 0 1 OWL 2 08/04/2014 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. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Cell http://data.bioontology.org/categories/Protein
Ontology of Geographical Region OGR Public 39 0 0 0 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. http://data.bioontology.org/categories/Vocabularies
Zebrafish Anatomy and Development Ontology ZFA Public 2,983 2 0 4 OBO unknown 09/17/2014 ZFIN administrators Description: A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio). http://data.bioontology.org/categories/Fish_Anatomy http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Animal_Gross_Anatomy http://data.bioontology.org/groups/OBO_Foundry
Healthcare Common Procedure Coding System HCPCS Public 5,721 0 0 2 UMLS 2014AA 05/28/2014 Cynthia Hake Description: Healthcare Common Procedure Coding System http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
International Classification of Diseases, Version 10 - Clinical Modification ICD10CM Public 92,174 0 0 1 UMLS 2014AA 05/28/2014 Patricia Brooks Description: International Classification of Diseases, 10th Edition, Clinical Modification, 2011_01 http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/caBIG http://data.bioontology.org/groups/UMLS
Physico-Chemical Methods and Properties FIX Public 1,163 0 0 0 OBO 1.2 02/11/2014 Chebi Administrators 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.
Drosophila Development Ontology FB-DV Public 207 0 0 2 OBO 2014-07-29 07/29/2014 Marta Costa Description: A structured controlled vocabulary of the development of Drosophila melanogaster. http://data.bioontology.org/categories/Development http://data.bioontology.org/categories/Animal_Development
Hymenoptera Anatomy Ontology HAO Public 2,276 0 0 0 OWL unknown 10/28/2013 HAO developers Description: A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, sawflies and ants) http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Animal_Gross_Anatomy
International Classification of Diseases, Version 10 - Procedure Coding System ICD10PCS Public 178,325 0 0 0 UMLS 2014AA 05/28/2014 Pat Brooks Description: ICD-10-PCS, 2009 http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
Plant Structure Development Stage PSDS Public 333 0 0 4 OBO Release #20 08/21/2013 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.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/ http://data.bioontology.org/categories/Plant http://data.bioontology.org/categories/Development http://data.bioontology.org/categories/Plant_Development
Lipid Ontology LIPRO Public 309 0 0 0 OWL See Remote Site 02/11/2014 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.
Clinical Measurement Ontology CMO Public 2,533 0 0 1 OBO 2.31 08/12/2014 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
Ontology of Vaccine Adverse Events OVAE Public 817 0 0 0 OWL Vision Release: 1.0.30 08/14/2013 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. http://data.bioontology.org/categories/Immunology http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Human
Metagenome Sample Vocabulary MSV Public 1 0 0 0 OWL Version 0.11 02/01/2014 MicrobeDB.jp Project Team Description: An ontology for metagenome sample metadata. This ontology mainly defines predicates. http://data.bioontology.org/categories/Other
International Classification of Diseases, Version 10 ICD10 Public 12,451 0 0 2 UMLS 2014AA 05/28/2014 World Health Organization Description: International Statistical Classification of Diseases and Related Health Problems (ICD-10). 10th rev. Geneva http://data.bioontology.org/groups/WHO-FIC http://data.bioontology.org/groups/caBIG http://data.bioontology.org/groups/UMLS
Environment Ontology ENVO Public 1,690 0 0 7 OBO releases/2014-09-16 09/17/2014 Envo Administrators Description: Ontology of environmental features and habitats http://data.bioontology.org/groups/BIS
RxNORM RXNORM Public 119,543 0 0 4 UMLS 2014AA 05/28/2014 NLM Customer Service Description: RxNorm Vocabulary http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
Computer Retrieval of Information on Scientific Projects Thesaurus CRISP Public 9,045 0 0 0 UMLS 2014AA 05/28/2014 Anita Ghebeles Description: Computer Retrieval of Information on Scientific Projects (CRISP) http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
BRENDA Tissue and Enzyme Source Ontology BTO Public 5,660 0 0 2 OBO unknown 06/10/2014 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.
Gene Regulation Ontology GRO Public 506 0 0 2 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. http://data.bioontology.org/categories/Genomic_and_Proteomic
Malaria Ontology IDOMAL Public 2,690 2 0 0 OBO 1.3.7 04/11/2014 Pantelis Topalis Description: An application ontology for malaria extending the infectious disease ontology (IDO).
Cell Ontology CL Public 5,901 0 0 8 OBO releases/2014-07-08 07/08/2014 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. http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Cell
Teleost Taxonomy Ontology TTO Public 38,705 0 0 1 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. http://data.bioontology.org/categories/Taxonomic_Classification
CPTAC Proteomics Pipeline Infrastructure Ontology CPTAC Public 19 0 0 0 OWL alpha 1.1 05/20/2009 Fan Zhang Description: a basic ontology which describes the proteomics pipeline infrastructure for CPTAC project http://data.bioontology.org/categories/Genomic_and_Proteomic
Human Interaction Network Ontology HINO Public 37,745 0 0 0 OWL Vision Release: 1.0.69 06/27/2014 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.
Taxonomic Rank Vocabulary TAXRANK Public 59 0 0 0 OBO unknown 01/30/2014 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.
Vertebrate Homologous Organ Group Ontology VHOG Public 1,185 0 0 1 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. http://data.bioontology.org/categories/Mouse_Anatomy http://data.bioontology.org/categories/Fish_Anatomy http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Human_Developmental_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Human http://data.bioontology.org/categories/Animal_Gross_Anatomy http://data.bioontology.org/categories/Animal_Development
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. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Dysfunction http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Neurologic_Disease http://data.bioontology.org/categories/Neurological_Disorder http://data.bioontology.org/categories/Human
Web-Service Interaction Ontology WSIO Public 31 0 0 4 OBO beta2 06/19/2014 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. http://data.bioontology.org/categories/Other
Disease core ontology applied to Rare Diseases HRDO Public 13,539 0 0 1 OWL V2 02/07/2014 Ferdinand Dhombres Description: This resource was designed during a PhD in medical informatics (funded by INSERM, 2010-2012). Its components are (i) a core ontology consistent with a metamodel (disorders and groups of disorders, genes, clinical signs and their relations) and (ii) an instantiation of this metamodel with Orphanet Data (available on http://orphadata.org). Research experiments demonstrated (i) efficient classifications generation based on SPARQL Construct, (ii) perspectives in semantic audit of a knowledge base, (iii) semantic comparison with OMIM (www.omim.org) using proximity measurements and (iv) opened perspectives in knowledge sharing (LORD, http://lord.bndmr.fr). Current production services of Orphanet developed ORDO, released in 2014, an ontology synchronized with their production database. This ontology is now available on Bioportal. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Human
Phenotypic Quality Ontology PATO Public 2,457 0 0 11 OBO unknown 08/15/2014 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. http://data.bioontology.org/groups/OBO_Foundry
Common Terminology Criteria for Adverse Events CTCAE Public 3,874 4 2 1 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).
Ascomycete Phenotype Ontology APO Public 340 0 0 0 OBO unknown 06/30/2014 Saccharomyces Genome Database Description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi http://data.bioontology.org/categories/Phenotype
National Center for Biotechnology Information (NCBI) Organismal Classification NCBITAXON Public 821,506 0 0 11 UMLS 2014AA 08/28/2014 NCBI information Description: The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. http://data.bioontology.org/categories/Taxonomic_Classification http://data.bioontology.org/groups/UMLS
Protein-Protein Interaction Ontology PPIO Public 5,123 0 0 1 OBO 3.67.1 09/17/2014 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. http://data.bioontology.org/groups/PSI
Neuroscience Information Framework (NIF) Subcellular Ontology NIFSUBCELL Public 2,800 0 0 0 OWL 1.3 (May 2012) 07/27/2012 Fahim Imam Description: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl
Minimal Standard Terminology of Digestive Endoscopy MSTDE Public 1,832 0 0 0 UMLS 2014AA 05/28/2014 NLM Customer Service Description: Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy. Bethesda, MD: National Library of Medicine, 2001.
Systematized Nomenclature of Medicine - Clinical Terms SNOMEDCT Public 300,542 2 1 20 UMLS 2014AA 02/21/2014 NLM Customer Service Description: SNOMED Clinical Terms http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/caBIG http://data.bioontology.org/groups/UMLS
Ontology of General Purpose Datatypes ONTODT Public 143 0 0 1 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.
Neuroscience Information Framework (NIF) Standard Ontology NIFSTD Public 108,426 2 0 5 OWL 2.9.6.1 - September 3, 2013 09/03/2013 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. http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/categories/Cellular_anatomy_ http://data.bioontology.org/categories/Molecule http://data.bioontology.org/categories/Dysfunction http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Other http://data.bioontology.org/categories/Subcellular http://data.bioontology.org/categories/Neurologic_Disease http://data.bioontology.org/categories/Neurological_Disorder http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Subcellular_anatomy http://data.bioontology.org/categories/Cell
Soy Ontology SOY Public 1,835 0 0 0 OBO unknown 04/30/2013 Rex Nelson Description: Growth, trait and development ontology for soybean http://data.bioontology.org/categories/Plant
Ontology of Language Disorder in Autism LDA Public 36 0 0 0 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. http://data.bioontology.org/categories/Health
Neural Motor Recovery Ontology NEUMORE Public 33 0 0 0 OWL 0.1 08/11/2010 Jingshan Huang Description: Neural Functional Motor Recovery Ontology
Software Ontology SWO Public 3,775 0 0 4 OWL 0.4 12/05/2013 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 http://data.bioontology.org/categories/Experimental_Conditions http://data.bioontology.org/categories/Biomedical_Resources
Ontology of Biological and Clinical Statistics OBCS Public 628 0 0 0 OWL Version: 1.0.28 05/08/2014 Yongqun (Oliver) He Jie Zheng Description: The Ontology of Biological and Clinical Statistics (OBCS) is a biomedical ontology in the domain of biological and clinical statistics. OBCS is primarily targeted for statistical representation in the fields in biological, biomedical, and clinical domains. OBCS uses the Basic Formal Ontology (BFO) as the upper level ontology. OBCS imports all biostatistics related terms in the Ontology for Biomedical Investigations (OBI) including all logical axioms. http://data.bioontology.org/categories/Other
Mobile Genetic Element Ontology MEGO Public 374 0 0 0 OBO 2_1 06/27/2013 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. http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Gene_Product
MicroRNA Ontology MIRNAO Public 676 0 0 0 OWL 1.7 12/10/2013 Vicky Dritsou Description: An application ontology for microRNAs. http://data.bioontology.org/categories/Other
Fly Taxonomy FB-SP Public 6,599 0 0 2 OBO unknown 06/20/2013 Evidence_code Administrators Description: The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. http://data.bioontology.org/categories/Taxonomic_Classification
Radiology Lexicon RADLEX Public 45,753 48 0 8 OWL 3.11 02/19/2014 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 Converted to use OWL format submissions http://data.bioontology.org/groups/caBIG
Image and Data Quality Assessment Ontology IDQA Public 259 0 0 2 OBO v50 12/05/2013 Thomas Schrader Description: Image and Data Quality Assessment for scientific data management http://data.bioontology.org/categories/Imaging
Galen Ontology GALEN Public 23,141 0 0 0 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. http://data.bioontology.org/categories/Other
NHS Quality Indicators NHSQI2009 Summary Only 0 0 0 0 PROTEGE 06/28/2013 Pam Description: This ontology seeks to organise a 2009 set of over 200 NHS quality indicators from different sources. Relationships between indicators, a basic set of inclusion/exclusion criteria, clinical pathway, clinical code and purpose (per 1992 Institute of Medicine, originally intended to categorise clinical guidelines) are identifies and made searchable. http://data.bioontology.org/categories/Health
Ontology of Genes and Genomes OGG Public 69,688 0 0 0 OWL Vision Release: 1.0.58 09/01/2014 Oliver He Description: OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. http://data.bioontology.org/categories/Genomic_and_Proteomic http://data.bioontology.org/categories/Gene_Product
Biomedical Research Integrated Domain Group Model BRIDG Public 325 0 0 0 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& http://data.bioontology.org/categories/Health
Body System Terms from ICD11 ICD11-BODYSYSTEM Public 29 0 0 1 OWL 1 04/15/2010 Samson Tu Description: This is a set of body-system terms used in the ICD 11 revision http://data.bioontology.org/categories/Anatomy
VIVO Ontology for Researcher Discovery VIVO Public 224 0 0 2 OWL version 1.1 07/16/2012 Stella Mitchell Description: The VIVO ontology represents researchers in the context of their experience, outputs, interests, accomplishments, and associated institutions. http://data.bioontology.org/categories/Other http://data.bioontology.org/groups/CTSA
Adverse Event Reporting Ontology AERO Public 407 0 0 4 OWL unknown 09/12/2013 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. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Biomedical_Resources
Systems Biology Ontology SBO Public 609 0 0 2 OBO 09:01:2014 09/17/2014 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. http://data.bioontology.org/categories/Vocabularies
Human Developmental Anatomy Ontology, abstract version 1 EHDAA Public 2,314 0 0 1 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. http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Human_Developmental_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Animal_Gross_Anatomy
Cell Cycle Ontology CCO Public 264,019 0 0 2 OBO 2.10 06/26/2014 Vladimir Mironov Description: An application ontology integrating knowledge about the eukaryotic cell cycle. http://data.bioontology.org/categories/Yeast http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Arabadopsis http://data.bioontology.org/categories/Human http://data.bioontology.org/categories/Protein
Gazetteer GAZ Public 518,196 0 0 4 OBO $Revision: 1.512 $ 09/17/2014 Michael Ashburner Description: Gazetteer
Vertebrate Trait Ontology VT Public 0 0 0 0 OBO 4.11 09/05/2014 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.
Maize Gross Anatomy Ontology ZEA Public 179 0 0 3 OBO 1.2 04/12/2012 Leszek Vincent http://data.bioontology.org/categories/Plant_Anatomy
Ontology for Genetic Interval OGI Public 204 0 0 0 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. http://data.bioontology.org/categories/Genomic_and_Proteomic
Crop Ontology CO Summary Only 0 0 0 3 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. http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Plant
International Classification of External Causes of Injuries ICECI Public 2,231 0 0 0 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.
Ontology of Pneumology 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/. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Human
Provenance Ontology PROVO Public 30 0 0 2 OWL Recommendation version 2013-04-30 08/16/2013 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.
Read Codes, Clinical Terms Version 3 (CTV3) RCD Public 140,071 0 0 1 UMLS 2014AA 05/28/2014 NHS Information Authority Loughborough Description: Clinical Terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre http://data.bioontology.org/groups/UMLS
Units of Measurement Ontology UO Public 331 0 0 5 OBO unknown 04/21/2014 George Gkoutos Description: Metrical units for use in conjunction with PATO
Parkinson's Disease Ontology PDON Public 631 0 0 0 OWL 1.0 08/18/2014 Dr. Erfan Younesi Description: Here, we introduce the Parkinson’s disease ontology (PDO) as a comprehensive semantic framework covering the whole breadth of the Parkinson’s knowledge domain. This ontology with a subclass-based taxonomic hierarchy not only covers the broad spectrum of major biomedical concepts from molecular to clinical features of the disease, but also the different views on disease features held by molecular biologists, clinicians and drug developers.
Breast Cancer Grading Ontology BCGO Public 129 0 0 1 OWL 1.5 05/24/2011 Alexandra Bulzan Description: assigns a grade to a tumor starting from the 3 criteria of the NGS http://data.bioontology.org/categories/Biological_Process
Neomark Oral Cancer Ontology, version 3 NEOMARK3 Public 55 0 0 0 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. http://data.bioontology.org/categories/Health
Brucellosis Ontology IDOBRU Public 2,029 0 0 0 OWL Arbor version; 1.2.29 09/17/2014 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. http://data.bioontology.org/categories/Health
Breast Tissue Cell Lines Ontology MCBCC Public 385 0 0 1 OWL 2 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 http://data.bioontology.org/categories/Cell
Role Ontology ROLEO Public 673 0 0 1 OWL Vision Release; 1.0.11 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.
Magnetic Resonance Dataset Acquisition Ontology ONL-MR-DA Public 701 0 0 2 OWL V1 07/09/2013 Bernard Gibaud Description: This ontology is a module of the OntoNeuroLOG ontology, developed in the context of the NeuroLOG project, a french project supported by ANR (ANR-06-TLOG-024 grant) aiming at integrating distributed heterogeneous resources in neuroimaging. If covers the domain of Magnetic Resonance Imaging (MRI) dataset acquisition, i.e. MRI protocols, and MRI sequence parameters. In particular, it includes a multi-axial classification of MR sequences. http://data.bioontology.org/categories/Imaging
Dermatology Lexicon DERMLEX Public 6,106 0 0 0 OWL 1 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. http://data.bioontology.org/categories/Health
InterNano Nanomanufacturing Taxonomy InterNano Public 278 0 0 2 OWL 1.2 09/17/2014 InterNano Description: The InterNano Taxonomy is a unique, custom-built terminology to describe the nanomanufacturing enterprise. This project is supported by the National Science Foundation CMMI-1025020 http://data.bioontology.org/categories/Chemical
Semantic Types Ontology STY Public 133 0 0 0 UMLS 2014AA 08/06/2014 bioportal Description: Fixed hierarchy.
BioTop Ontology BT Public 389 0 0 1 OWL Last modification Apr 24, 2012 by Stefan Schulz 05/20/2014 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. http://data.bioontology.org/categories/Upper_Level_Ontology
Ontology of Alternative Medicine, French ONTOMA Public 435 0 0 0 OWL Version 1.1 Date: 11-2011 06/25/2012 SANOU MARTIN Description: Common concepts for communication between traditional medicine and western medicine. (In French)
Mouse Gross Anatomy and Development Ontology EMAP Public 13,731 0 0 2 OBO unknown 02/15/2011 EMAP Administrators Description: A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). http://data.bioontology.org/categories/Mouse_Anatomy http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Animal_Gross_Anatomy
Cigarette Smoke Exposure Ontology CSEO Public 20,085 0 0 0 OWL 1.0 07/10/2014 Dr. Sam Ansari Description: The CSEO has potential to become a widely used standard within the academic and industrial community. Mainly because of the emerging need of systems toxicology to controlled vocabularies and also the lack of suitable ontologies for this domain, the CSEO prepares the ground for integrative systems-based research in the exposure science. http://data.bioontology.org/categories/Health
Mass Spectrometry Ontology MS Public 5,123 0 0 2 OBO 3.67.1 09/17/2014 PSI-MS Administrators Description: A structured controlled vocabulary for the annotation of mass spectrometry experiments. Developed by the HUPO Proteomics Standards Initiative (PSI). http://data.bioontology.org/groups/PSI
Drug Interaction Knowledge Base Ontology DIKB Public 124 0 0 2 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. http://data.bioontology.org/categories/Vocabularies
Fission Yeast Phenotype Ontology FYPO Public 7,069 0 0 0 OBO releases/2014-09-01 09/17/2014 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. http://data.bioontology.org/categories/Phenotype
Cellular microscopy phenotype ontology CMPO Public 299 0 0 0 OWL 1.3 04/15/2014 Simon Jupp Description: The Cellular Microscopy Phenotype Ontology (CMPO) is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is an application ontology developed in OWL that contains precomposed phenotypes descriptions that are defined using the Gene Ontology (GO) and the Phenotype Trait Ontology (PATO). http://data.bioontology.org/categories/Cellular_anatomy_ http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Cell
Student Health Record Ontology SHR Public 343 0 0 1 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 ... .
Ontology for Newborn Screening Follow-up and Translational Research ONSTR Public 0 0 0 0 OWL 0.4 09/04/2014 Rani Singh, 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). http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Dysfunction http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Human http://data.bioontology.org/categories/Development
Mental Functioning Ontology MF Public 692 0 0 0 OWL beta 2013-11-05 11/05/2013 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.
Genomic Feature and Variation Ontology GFVO Public 92 0 0 1 OWL 0.9.44 09/01/2014 Joachim Baran Description: The Genomic Feature and Variation Ontology (GFVO) is modeled to represent genomic data using the Resource Description Format (RDF). It is captures the contents of data files that adhere to the Generic Feature Format Version 3 (GFF3, http://www.sequenceontology.org/resources/gff3.html), the General Transfer Format (GTF, http://mblab.wustl.edu/GTF22.html), the Genome Variation Format Version 1 (GVF, http://www.sequenceontology.org/resources/gvf.html), and the Variant Call Format (VCF, http://vcftools.sourceforge.net/specs.html). The creation of the ontology was inspired by previous work of Robert Hoehndorf on RDF2OWL (http://code.google.com/p/rdf2owl). NOTE: GFVO in BioPortal is a simplified version without ontology imports and having class/property equivalences removed. The full ontology is available at: http://www.biointerchange.org/gfvo http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Genomic_and_Proteomic http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Human http://data.bioontology.org/categories/Gene_Product
Experimental Conditions Ontology XCO Public 461 0 0 4 OBO 4.5 06/27/2014 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. http://data.bioontology.org/categories/Experimental_Conditions http://data.bioontology.org/categories/Phenotype
Vertebrate Taxonomy Ontology VTO Public 107,087 0 0 1 OWL unknown 05/14/2014 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. http://data.bioontology.org/categories/Taxonomic_Classification
C. elegans Gross Anatomy Vocabulary WB-BT Public 7,214 0 0 0 OBO 2014-05-26 09/17/2014 Raymond Lee Description: A structured controlled vocabulary of the anatomy of Caenorhabditis elegans. http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Animal_Gross_Anatomy
Portfolio Management Application PMA Public 2,082 0 0 0 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 http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Human
Synthetic Biology Open Language Visual Ontology SBOL Public 41 0 0 0 OBO unknown 07/18/2013 Jacqueline Quinn Description: Synthetic Biology Open Language Visual (SBOLv) is an ontology to represent standardized graphical notation for synthetic biology. http://data.bioontology.org/categories/Other
Subcellular Anatomy Ontology SAO Public 821 0 0 1 OWL Version 1.2 09/17/2007 Maryann Martone Description: SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules. http://data.bioontology.org/categories/Anatomy
Neural ElectroMagnetic Ontology NEMO Public 1,851 2 0 3 OWL v3.10 10/21/2013 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/. http://data.bioontology.org/categories/Imaging http://data.bioontology.org/categories/Experimental_Conditions http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Human
Pathogen Transmission Ontology PTRANS Public 28 0 0 1 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.
Common Anatomy Reference Ontology CARO Public 50 0 0 1 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) http://data.bioontology.org/categories/Anatomy
Units Ontology UNITSONT Public 63 0 0 1 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. http://data.bioontology.org/categories/Other
Neomark Oral Cancer Ontology, version 4 NEOMARK4 Public 324 0 0 0 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. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Genomic_and_Proteomic http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Human
Neural-Immune Gene Ontology NIGO Public 4,835 0 0 0 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. http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Other http://data.bioontology.org/categories/Human
Santa Barbara Coastal Observation Ontology OBOE-SBC Public 630 1 0 1 OWL Version 1.0 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. http://data.bioontology.org/categories/Other
Ortholog Ontology ORTHO Public 19 0 0 0 OWL 2014-07-30 08/05/2014 Hirokazu Chiba Description: Ortholog Ontology (OrthO) http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/categories/Genomic_and_Proteomic http://data.bioontology.org/categories/Gene_Product
Reproductive Trait and Phenotype Ontology REPO Public 95 0 0 0 OWL 1.1 10/12/2011 Wageningen UR Livestock Research Description: Ontology for livestock reproductive traits and phenotypes http://data.bioontology.org/categories/Phenotype
Flora Phenotype Ontology FLOPO Public 25,407 0 0 0 OWL 0.4 04/06/2014 Robert Hoehndorf Claus Weiland Thomas Hamann George Gosline Quentin Groom Description: This is a draft of the Flora Phenotype Ontology. The original version was developed at the pro-iBiosphere Hackathon in Leiden. This is the pre-classified version of the ontology; the original OWL file is at http://jagannath.pdn.cam.ac.uk/plant/flopo-unclassified.owl The Flora Phenotype Ontology is generated from the Flora Malesiana, Flora Gabon, Flora of Central Africa, and a collection of Kew's African Floras. Every class in the ontology has at least one taxon annotation. The (draft) taxon annotation are available at http://jagannath.pdn.cam.ac.uk/plant/flora/clean-rerun/ http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Plant
Botryllus schlosseri anatomy and development ontology BSAO Public 92 0 0 0 OBO Version 1 08/29/2013 Delphine DAUGA Description: The first ontology describing the anatomy and the development of Botryllus schlosseri. Working group : Lucia Manni, Fabio Gasparini, Kohji Hotta, Katherine J. Ishizuka J, Lorenzo Ricci, Stefano Tiozzo, Ayelet Voskoboynik, Delphine Dauga http://data.bioontology.org/categories/Anatomy
Vital Sign Ontology VSO Public 177 0 0 0 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. http://data.bioontology.org/categories/Health
Habronattus Courtship Ontology HC Summary Only 0 0 0 0 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.
Online Mendelian Inheritance in Man OMIM Public 76,717 0 0 1 UMLS 2014AA 05/28/2014 NLM Customer Service 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 http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
Veterans Health Administration National Drug File VANDF Public 24,619 0 0 0 UMLS 2014AA 05/28/2014 Michael Lincoln Description: NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes. http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
Interaction Network Ontology INO Public 426 0 0 0 OWL Vision Release; 1.0.78 08/15/2014 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. http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/categories/Biological_Process
Mathematical Modelling Ontology MAMO Public 76 0 0 0 OWL 2014-06-28 06/27/2014 mamo-ontology-discuss Description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. http://data.bioontology.org/categories/Other
Clinical Signs and Symptoms Ontology CSSO Public 296 0 0 0 OWL Version 0.5 08/20/2014 MicrobeDB.jp Project Team Description: An ontology for describing clinical signs and symptoms. http://data.bioontology.org/categories/Health
Cardiac Electrophysiology Ontology EP Public 82,019 0 0 2 OWL 1 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. http://data.bioontology.org/categories/Experimental_Conditions
Syndromic Surveillance Ontology SSO Public 176 0 0 0 OWL 1 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). http://data.bioontology.org/categories/Taxonomic_Classification http://data.bioontology.org/categories/Biomedical_Resources
Amphibian Taxonomy Ontology ATO Public 6,135 0 0 1 OBO See Remote Site 11/02/2009 AmphiAnat list Description: A taxonomy of Amphibia http://data.bioontology.org/categories/Taxonomic_Classification
Uber Anatomy Ontology UBERON Public 13,043 0 0 4 OWL releases/2014-06-15 08/29/2014 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. http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Anatomy
Emotion Ontology MFOEM Public 901 0 0 1 OWL beta 2013-07-23 10/07/2013 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. http://data.bioontology.org/categories/Other
Cancer Research and Management ACGT Master Ontology ACGT-MO Public 1,769 0 0 0 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. http://data.bioontology.org/categories/Health
Terminological and Ontological Knowledge Resources Ontology TOK Public 192 0 0 0 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. http://data.bioontology.org/categories/Taxonomic_Classification
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 http://data.bioontology.org/groups/BIS
Medaka Fish Anatomy and Development Ontology MFO Public 4,358 0 0 0 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. http://data.bioontology.org/categories/Fish_Anatomy http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Animal_Gross_Anatomy
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.
Statistics Ontology STATO Public 608 0 0 1 OWL 1.2 06/13/2014 Alejandra Gonzalez-Beltran STATO mailing list Philippe Rocca-Serra Description: STATO is a general-purpose STATistics Ontology. Its aim is to provide coverage for processes such as statistical tests, their conditions of applications, and information needed or resulting from statistical methods, such as probability distributions, variable, spread and variation metrics. STATO also covers aspects of experimental design and description of plots and graphical representations commonly used to provide visual cues of data distribution or layout and to assist review of the results. http://data.bioontology.org/categories/Experimental_Conditions http://data.bioontology.org/categories/Biomedical_Resources
Chemical Methods Ontology CHMO Public 2,866 0 0 0 OBO releases/2014-09-16 09/17/2014 Colin Batchelor Description: CMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI). http://data.bioontology.org/categories/Chemical
Evidence Codes Ontology ECO Public 575 8 0 3 OBO releases/2014-06-26 06/26/2014 Marcus Chibucos Description: A rich ontology for experimental and other evidence statements. http://data.bioontology.org/categories/Other
Pathogenic Disease Ontology PDO Public 322 0 0 0 OWL Version 0.4 08/17/2014 MicrobeDB.jp Project Team Description: An ontology for describing both human infectious diseases caused by microbes and the diseases that is related to microbial infection. http://data.bioontology.org/categories/Health
Diagnosis Ontology of Clinical Care Classification DOCCC Public 204 0 0 0 OWL 20131004 10/03/2013 Description: Diagnosis Ontology of Clinical Care Classification (CCC) http://data.bioontology.org/categories/Health
Current Procedural Terminology CPT Public 13,083 0 0 0 UMLS 2014AA 05/28/2014 Dorith Brown Description: Current Procedural Terminology http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
Dataset processing ONL-DP Public 540 0 0 2 OWL V1 07/09/2013 Bernard Gibaud Description: This ontology is a module of the OntoNeuroLOG ontology, developed in the context of the NeuroLOG project, a french project supported by ANR (ANR-06-TLOG-024 grant) aiming at integrating distributed heterogeous resources in neuroimaging. If covers the domain of Datasets and the processing of datasets. It includes a detailed taxonomy of datasets in the area of neuroimaging (and especially MR imaging) as well as a taxonomy of medical image processing. http://data.bioontology.org/categories/Imaging
Sage Bionetworks Synapse Ontology SYN Public 14,462 0 0 0 OWL .3 01/07/2013 Sage Bionetworks Description: The controlled vocabulary used for various entity properties in the Synapse platform.
Sample Processing and Separation Techniques Ontology SEP Public 194 0 0 2 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. http://data.bioontology.org/groups/PSI
Human Developmental Anatomy Ontology, abstract version 2 EHDAA2 Public 2,734 0 0 2 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. http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Human_Developmental_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Animal_Gross_Anatomy
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 http://data.bioontology.org/categories/Anatomy
Enzyme Reaction Ontology for annotating Partial Information of chemical transformation PIERO Public 27 0 0 0 OWL 06/24/2014 Masaaki Kotera Description: Enzyme Reaction Ontology for annotating Partial Information of chemical transformation
Orphanet Rare Disease Ontology ORDO Public 12,009 0 0 0 OWL 1.4 07/15/2014 Ana Rath Description: The Orphanet Rare Disease ontology (ORDO) is jointly developed by Orphanet and the EBI to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It derived from the Orphanet database (www.orpha.net ) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, SNOMED CT, UMLS, MedDRA),databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10). The ontology will be maintained by Orphanet and further populated with new data. Orphanet classifications can be browsed in the OLS view. The Orphanet Rare Disease Ontology is updated monthly and follows the OBO guidelines on deprecation of terms. It constitutes the official ontology of rare diseases produced and maintained by Orphanet (INSERM, US14). http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Human
Regulation of Transcription Ontology RETO Public 70,222 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. http://data.bioontology.org/categories/Biological_Process
Information Artifact Ontology IAO Public 173 0 0 11 OWL $Revision: 80 $ 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

http://data.bioontology.org/categories/Imaging http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Other
Animal Natural History and Life History Ontology ADW Public 362 0 0 0 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. http://data.bioontology.org/categories/Anatomy
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. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Other http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Human
Kinetic Simulation Algorithm Ontology KISAO Public 241 0 1 1 OWL 2.3.6 04/25/2014 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. http://data.bioontology.org/categories/Other
NanoParticle Ontology NPO Public 1,903 3 0 3 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. http://data.bioontology.org/categories/Chemical http://data.bioontology.org/groups/caBIG
Pharmacovigilance Ontology PVONTO Public 33 0 0 0 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.
Human Phenotype Ontology HP Public 10,593 0 0 9 OBO unknown 06/25/2014 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. http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Human
Cerebrotendinous Xanthomatosis Ontology CTX Public 477 0 0 0 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. http://data.bioontology.org/categories/Phenotype
Name Reaction Ontology RXNO Public 746 0 0 0 OBO rxno/releases/2014-04-24/rxno.owl 09/17/2014 Colin Batchelor Description: RXNO, the name reaction ontology, connects organic name reactions such as the Diels-Alder cyclization and the Cannizzaro reaction to their roles in an organic synthesis. http://data.bioontology.org/categories/Chemical
Spatial Ontology BSPO Public 133 0 0 3 OBO unknown 05/17/2013 Chris Mungall Description: A small ontology for anatomical spatial references, such as dorsal, ventral, axis, and so forth. http://data.bioontology.org/categories/Anatomy
Allen Brain Atlas (ABA) Adult Mouse Brain Ontology ABA-AMB Public 913 0 0 4 OWL 1 08/08/2009 Allen Institute for Brain Science Description: Allen Brain Atlas P56 Mouse Ontology http://data.bioontology.org/categories/Mouse_Anatomy
Mosquito Insecticide Resistance Ontology MIRO Public 4,408 0 0 1 OBO 2.0.00 05/08/2014 C. Louis Description: Application ontology for entities related to insecticide resistance in mosquitos http://data.bioontology.org/categories/Phenotype
Bionutrition Ontology BNO Public 100 0 0 1 OWL 0.2 08/15/2013 Cameron Coffran, Diane Meehan, Andrea Ronning Description: The Bionutrition Ontology relates concepts and terminologies used for human nutrition in a clinical and biomedical setting. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Human
Cereal Plant Development Ontology GRO-CPD Public 235 0 0 2 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. http://data.bioontology.org/categories/Plant http://data.bioontology.org/categories/Development http://data.bioontology.org/categories/Plant_Development
Traditional Medicine Meridian Value Sets TM-MER Public 20 0 0 0 OWL 1 02/01/2011 Tania Tudorache Description: The meridian value set used in the International Classification of Traditional Medicine.
Wheat Trait Ontology CO-WHEAT Public 176 0 0 0 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. http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Plant http://data.bioontology.org/groups/CGIAR
Nursing Interventions Classification NIC Summary Only 0 0 0 0 UMLS 2013AB 09/25/2013 Center for Nursing Classification & Clinical Effectiveness Description: Nursing Interventions Classification (NIC) http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
Diagnostic Ontology DIAGONT Public 96 0 0 0 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.
Semantic Web for Earth and Environment Technology Ontology SWEET Public 4,549 0 0 0 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.
Single-Nucleotide Polymorphism (SNP) Ontology SNPO Public 2,207 0 0 0 OWL TODO: Take into account alternative splicing. 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. http://data.bioontology.org/categories/Genomic_and_Proteomic
Epoch Clinical Trial Ontology CTONT Public 41 0 0 0 OWL
Version 0.97
Date 3/2/2007

03/20/2007 Ravi Shankar, Stanford Medical Informatics http://data.bioontology.org/categories/Experimental_Conditions
African Traditional Medicine Ontology ATMO Public 223 2 0 2 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. http://data.bioontology.org/categories/Health
Porifera Ontology PORO Public 747 0 0 0 OWL unknown 07/19/2014 Bob Thacker Description: An ontology covering the anatomy of Porifera (sponges) http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Anatomy
Foundational Model of Anatomy FMA Public 83,319 0 0 12 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 http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/groups/UMLS
Symptom Ontology SYMP Public 936 0 0 1 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
Cell Behavior Ontology CBO Public 241 0 0 3 OWL 1.0.1 06/02/2014 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. http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Cell
NeuroMorpho.Org species ontology NMOSP Public 1,340 0 0 0 OBO 1.0 04/22/2014 Sridevi Polavaram Description: The NeuroMorpho.Org species ontology adopts and integrates relevant portions of available taxonomies “as needed” based on the species and strain terms represented in the current release of NeuroMorpho.Org (72 terms as of the 5.7 release) and any future additions. When a NeuroMorpho.Org term is mapped with an external resource, its entire lineage (ancestors and descendants) is added to the NeuroMorpho.Org species ontology. The resulting 1,340 terms of this initial version of the ontology come for 65% from the NCBI taxonomy (24 NeuroMorpho.Org species/strain terms mapped), 30% from the Rat Gene Database (1 term mapped), and altogether 5% from NIFSTD (7 terms mapped), MeSH (2 terms mapped), ITIS (1 term mapped), and custom-added concepts (41 terms mapped, largely mouse strains from Jackson Labs). http://data.bioontology.org/categories/All_Organisms
Terminology for the Description of Dynamics TEDDY Public 167 0 0 0 OWL rel-2014-04-24 (inferred) 04/25/2014 BioModels.net team 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. http://data.bioontology.org/categories/Other
Content Archive Resource Exchange Lexicon CARELEX Public 322 0 0 1 OWL 1.02 06/10/2013 Jennifer Alpert Palchak Description: Contains controlled vocabulary terms from National Cancer Institute used to classify clinical trial electronic content (documents, images, etc). A Content model contains content classification categories (classes) and metadata properties (data properties). Data properties should be assigned to each Content Type. This model has been published as part of the new OASIS eTMF Standard, a draft specification available at: http://oasis-open.org/committees/etmf. CareLex is a non-profit organization formed to promote eClinical application and content interoperability for the life sciences and healthcare industries. For more info go to www.CareLex.Org http://data.bioontology.org/categories/Vocabularies
Host Pathogen Interactions Ontology HPIO Public 281 0 0 0 OWL 1 02/08/2011 Wageningen UR Livestock Research Description: Ontology for host pathogen interactions in farmed animals http://data.bioontology.org/categories/Health
BioAssay Ontology BAO Public 3,336 0 0 7 OWL 2.0 04/25/2014 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. http://data.bioontology.org/categories/Molecule http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Other http://data.bioontology.org/categories/Subcellular http://data.bioontology.org/categories/Chemical http://data.bioontology.org/categories/Cell http://data.bioontology.org/categories/Protein http://data.bioontology.org/categories/Vocabularies http://data.bioontology.org/categories/Physicochemical
Mouse Adult Gross Anatomy Ontology MA Public 3,229 0 0 6 OBO unknown 07/15/2014 Terry Hayamizu Description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus). http://data.bioontology.org/categories/Mouse_Anatomy http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Animal_Gross_Anatomy
Research Network and Patient Registry Inventory Ontology RNPRIO Public 79 0 0 0 OWL 1 06/07/2013 Seena Farzaneh Description: Ontology for Inventories of Clinical Data Research Networks, Patient-Powered Research Networks, and Patient Registries http://data.bioontology.org/categories/Biomedical_Resources
Computer-Based Patient Record Ontology CPRO Public 135 0 0 0 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) http://data.bioontology.org/categories/Health
International Classification for Patient Safety ICPS Public 397 0 0 0 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. http://data.bioontology.org/categories/Health
suicideonto suicideo Public 289 0 0 1 OWL 2 08/25/2013 alexander garcia Description: ontology for suicidology http://data.bioontology.org/categories/Other
Neuroscience Information Framework (NIF) Cell Ontology NIFCELL Public 2,769 0 0 0 OWL v.1.10 - July 17, 2013 08/05/2013 Fahim Imam Description: Cell types from NIFSTD
Systems Chemical Biology and Chemogenomics Ontology CHEMBIO Public 104 0 0 0 OWL unknown 09/23/2012 Bin Chen, Ying Ding, David Wild Description: Ontology for Systems Chemical Biology and Chemogenomics http://data.bioontology.org/categories/Molecule http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Chemical http://data.bioontology.org/categories/Protein
An ontology for experimental actions EXACT Public 0 0 0 0 OWL 2 09/18/2014 Larisa Soldatova Description: EXACT aims to explicitly define the semantics of experimental protocols in order to ensure their reproducibility, and to support computer applications that assist biologists in the preparation, maintenance, submission and sharing of experimental protocols.
Teleost Anatomy Ontology TAO Public 3,371 2 0 1 OBO 2012-08-10 08/22/2013 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. http://data.bioontology.org/categories/Fish_Anatomy http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Animal_Gross_Anatomy
Vertebrate Skeletal Anatomy Ontology VSAO Public 314 0 0 0 OBO 2012-11-06 08/22/2013 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. http://data.bioontology.org/categories/Fish_Anatomy http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Animal_Gross_Anatomy
Beta Cell Genomics Ontology OBI_BCGO Public 1,672 0 0 1 OWL 2014-01-13 01/29/2014 Jie Zheng Description: Beta Cell Genomics Ontology (BCGO) is an application ontology built for the Beta Cell Genomics database (http://genomics.betacell.org/gbco/) aiming to support database annotation, complicated semantic queries, and automated cell type classification. The ontology is developed using Basic Formal Ontology (BFO) as upper ontology, Ontology for Biomedical Investigations (OBI) as ontology framework and integrated subsets of multiple OBO Foundry (candidate) ontologies. Current the BCGO contains 2383 classes including terms referencing to 24 various OBO Foundry ontologies including CL, CLO, UBERON, GO, PRO, UO, etc.
C. elegans Development Vocabulary WB-LS Public 658 0 0 0 OBO unknown 08/04/2014 Worm_development Administrators Description: A structured controlled vocabulary of the development of Caenorhabditis elegans. http://data.bioontology.org/categories/Development http://data.bioontology.org/categories/Animal_Development
Dispedia Core Ontology DCO Public 48 0 0 1 OWL 0.7.0.0002 08/13/2014 Romy Elze Description: Dispedia Core Ontology is a schema for information brokering and knowledge management in the complex field of rare diseases. On the one hand, the Dispedia schema uses semantic technologies to describe patients affected by rare diseases, and on the other hand, to record expertise concerning these particular diseases in machine-processable form. In addition to the differentiated attribution of facts to the individual need for information, Dispedia enables information brokering which adjusts to the type of recipient, its character as well as its personal attitude. The schema was initially geared to an exemplified disease, Amyotrophe Lateralsclerose (ALS). http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Other http://data.bioontology.org/categories/Human http://data.bioontology.org/categories/Vocabularies
Proteomics Data and Process Provenance Ontology PROPREO Public 398 0 0 0 OWL 1.1 03/05/2009 Satya S. Sahoo Description: A comprehensive proteomics data and process provenance ontology.
Population and Community Ontology PCO Public 1,545 0 0 0 OWL 2013-10-03 05/23/2014 Description: The Population and Community Ontology (PCO) models material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. The PCO is complient with the Basic Formal Ontology (BFO) and is designed to be compatible with other OBO Foundry ontologies. http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/categories/Other
Suggested Ontology for Pharmacogenomics SOPHARM Public 44,952 0 0 0 OWL Author: Adrien Coulet Version: SO-Pharm 2.1 Release: 01/15/2009 Contact: adrien dot coulet at loria dot fr University of Nancy 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. http://data.bioontology.org/categories/Genomic_and_Proteomic
MedlinePlus Health Topics MEDLINEPLUS Public 2,109 0 0 1 UMLS 2014AA 05/28/2014 NLM Customer Service Description: MedlinePlus Health Topics;National Library of Medicine;June 14, 2008;Bethesda, MD http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
Ontology of Homology and Related Concepts in Biology HOM Public 66 0 0 1 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. http://data.bioontology.org/categories/All_Organisms http://data.bioontology.org/categories/Molecule http://data.bioontology.org/categories/Other http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Development
National Drug File - Reference Terminology NDFRT Public 44,365 0 0 1 UMLS 2014AA 05/28/2014 Michael J. Lincoln MD Description: National Drug File - Reference Terminology Public Inferred Edition, 2008_03_11 http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
Ontology of Experimental Variables and Values OOEVV Public 47 0 0 0 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. http://data.bioontology.org/categories/Vocabularies
Nursing Care Coordination Ontology NCCO Public 400 0 0 1 OWL 1.0 11/05/2013 Description: Nursing Care Coordination Ontology contains activities that nurses use while coordinating care among patients. http://data.bioontology.org/categories/Health
Phylogenetic Ontology PHYLONT Public 147 0 0 0 OWL ver8 03/11/2013 maryam panahiazar Description: Ontology for Phylogenetic Analysis http://data.bioontology.org/categories/Other
Gene Ontology Extension GO-EXT Public 34,400 0 0 1 OBO 2 06/24/2011 Gene Ontology Consortium Description: Gene Ontology Extension http://data.bioontology.org/groups/OBO_Foundry http://data.bioontology.org/groups/caBIG http://data.bioontology.org/groups/UMLS
Quantitative Imaging Biomarker Ontology QIBO Public 618 0 0 0 OWL unknown 10/06/2011 David Paik Description: An ontology that describes various concepts in quantitative imaging biomarkers. http://data.bioontology.org/categories/Imaging
Sequence Types and Features Ontology SO Public 2,021 0 0 17 OWL unknown 01/29/2014 SO Administrators Description: SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ http://data.bioontology.org/categories/Genomic_and_Proteomic
Ontology for Biomedical Investigations OBI Public 2,799 4 0 22 OWL 2014-08-18 08/25/2014 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: 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.
http://data.bioontology.org/categories/Experimental_Conditions http://data.bioontology.org/groups/OBO_Foundry
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. http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Genomic_and_Proteomic
Physician Data Query PDQ Public 7,877 0 0 0 UMLS 2014AA 05/28/2014 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. http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
Drosophila Gross Anatomy Ontology FB-BT Public 8,934 0 0 3 OBO 2014-05-26 06/11/2014 Marta Costa Description: A structured controlled vocabulary of the anatomy of Drosophila melanogaster. http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Animal_Gross_Anatomy
Fanconi Anemia Ontology IFAR Public 4,530 0 0 1 OWL 3 02/18/2014 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. http://data.bioontology.org/categories/Other
Gene Ontology GO Public 41,694 0 1 57 OBO releases/2014-08-30 09/17/2014 http://data.bioontology.org/categories/Genomic_and_Proteomic http://data.bioontology.org/groups/OBO_Foundry http://data.bioontology.org/groups/caBIG http://data.bioontology.org/groups/CTSA http://data.bioontology.org/groups/UMLS
Basic Formal Ontology BFO Public 39 0 0 20 OWL 1.1.1 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. http://data.bioontology.org/categories/Upper_Level_Ontology
Major Histocompatibility Complex Ontology MHC Public 7,928 0 0 0 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. http://data.bioontology.org/categories/Genomic_and_Proteomic
The Drug Ontology DRON Public 0 0 0 0 OWL 07/10/2014 William Hogan Description: An ontology of drugs. DrOn contains content developed by the National LIbrary of Medicine in RxNorm. In creating DrOn, we have used RxNorm content only with SAB = RXNORM. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Human
Mental State Assessment ONL-MSA Public 768 0 0 1 OWL v1 07/09/2013 Bernard Gibaud Description: This ontology is a module of the OntoNeuroLOG ontology, developed in the context of the NeuroLOG project, a french project supported by ANR (ANR-06-TLOG-024 grant) aiming at integrating distributed heterogeous resources in neuroimaging. This MSA ontology module covers the field of mental state assessments, i.e. instruments, instrument variables, assessments, and resulting scores. It includes a generic domain core ontology, that provides a general model of such entities and a general taxonomy of behavioural, neurosychological and neuroclinical instruments, that can be easily extended to model any particular kind of instrument. It also includes such extensions for 8 relatively standard instruments, namely: (1) the Beck-depression-inventory-(BDI-II), (2) the Expanded-Disability-Status-Scale, (3) the Controlled-oral-word-association-test, (4) the Free-and-Cued-Selective-Reminding-Test-with-Immediate-Recall-16-item-version-(The-Gröber-and-Buschke-test), (5) the Mini-Mental-State, (6) the Stroop-color-and-word-test, (7) the Trail-making-test-(TMT), (8) the Wechsler-Adult-Intelligence-Scale-third-edition, (9) the Clinical-Dementia-Rating-scale, (10) the Category-verbal-fluency, (11) the Rey-Osterrieth-Complex-Figure-Test-(CFT). http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Neurological_Disorder http://data.bioontology.org/categories/Human
Biodiversity Ontology BOF Public 188 0 0 0 OWL 1.2 07/11/2013 Franco Description: An ontology of biodiversity of INPA
Sleep Domain Ontology SDO Public 1,381 0 0 0 OWL Last modification: Feb. 11, 2013 Sivaram Arabandi 02/11/2013 Sivaram Arabandi Description: An application ontology for the domain of Sleep Medicine. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Neurologic_Disease http://data.bioontology.org/categories/Neurological_Disorder http://data.bioontology.org/categories/Human
Natural Products Ontology NATPRO Public 9,462 0 0 0 OWL unknown 02/08/2012 Riza Theresa Batista-Navarro Description: An ontology for describing biological activities of natural products.
International Classification of Primary Care ICPC Public 880 0 0 0 UMLS 2014AA 05/28/2014 Henk Lamberts, University of Amsterdam Description: The International Classification of Primary Care (ICPC). Denmark: World Organisation of Family Doctors, 1993. http://data.bioontology.org/categories/Health http://data.bioontology.org/groups/UMLS
Neuro Behavior Ontology NBO Public 1,098 6 0 0 OBO 2012-07-09 07/04/2014 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
Pediatric Terminology PEDTERM Public 1,771 0 0 1 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. http://data.bioontology.org/categories/Health http://data.bioontology.org/categories/Human
Dictyostelium Discoideum Anatomy Ontology DDANAT Public 131 0 0 0 OBO 1.19 01/22/2013 Rex Chisholm Description: A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum. http://data.bioontology.org/categories/Gross_Anatomy http://data.bioontology.org/categories/Anatomy http://data.bioontology.org/categories/Microbial_Anatomy
SysMO JERM Ontology of Systems Biology for Micro-Organisms JERM Public 253 0 0 2 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/ http://data.bioontology.org/categories/Experimental_Conditions http://data.bioontology.org/categories/Biomedical_Resources http://data.bioontology.org/categories/Biological_Process http://data.bioontology.org/categories/Other
Plant Environmental Conditions PECO Public 561 0 0 3 OBO March 2014 06/04/2014 Pankaj Jaiswal Description: The Plant Environment Ontology describes the treatments,growing conditions, and/or study types used in various types of plant biology experiments. The subjects of the studies may also include in vitro plant structures (PO:0000004). A plant treatment is the most specific,and may be a component of a plant growing condition, and the plant study type. The broadest classes are the plant study types where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own and it may also involve instances of biotic and abiotic treatments and different growing conditions. http://data.bioontology.org/categories/Experimental_Conditions http://data.bioontology.org/categories/Phenotype http://data.bioontology.org/categories/Plant
Human Dermatological Disease Ontology DERMO Public 3,425 0 0 0 OBO 1.17 07/17/2013 Paul Schofield Description: Ontology of human dermatologic disease http://data.bioontology.org/categories/Biomedical_Resources
PhenX Phenotypic Terms PHENX Public 369 0 0 0 OWL 0.9 03/04/2013 PhenX Admin Description: Standard measures related to complex diseases, phenotypic traits and environmental exposures http://data.bioontology.org/categories/Phenotype
Systematized Nomenclature of Medicine, International Version SNMI Public 109,156 0 0 0 UMLS 2014AA 05/28/2014 IHTSDO 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.
Electrocardiography Ontology ECG Public 1,123 0 0 5 OWL 1 09/12/2014 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. http://data.bioontology.org/categories/Biomedical_Resources
Plant Ontology PO Public 1,691 0 0 5 OBO Version # 20 08/20/2013 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. http://data.bioontology.org/categories/Plant_Anatomy http://data.bioontology.org/categories/Plant http://data.bioontology.org/categories/Plant_Development http://data.bioontology.org/groups/OBO_Foundry