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The Vocabulary Knowledge Center (VKC) and the National Cancer Institute's Center for Biomedical Informatics and Information Technology (NCI CBIIT) in cooperation with the National Cancer Research Institute (NCRI, U.K.) and the National Center for Biomedical Ontologies (NCBO, U.S.) are undertaking a study on controlled terminologies, their use, and the data stored and served about them.

Each organization has such information and serves it to the community in varying ways in support of the fact that standards are fundamental in building research software. The goal of the study is to determine common ground that, when implemented, could serve the community better overall. The study will strive to find consistency in the approach that will better serve the research community and avoid confusion about controlled terminologies.

The Ontology Representation Working Group has organized itself on the Ontology Representation WG pages of the NCI wiki. Feedback is always welcome.

Click the text in the header to sort the column.

Terminology

NCI EVS hosted

caBIG® Approved

Description of Terminology

FAQ Link

Download

Gene Ontology (GO)

Yes

Yes

Provides a controlled vocabulary to describe gene and gene product attributes in any organism.

Gene Ontology FAQ

OBO

Logical Observation Identifiers Names and Codes (LOINC) Terminology

Yes

Yes

Facilitates the exchange and pooling of clinical results for clinical care, outcomes management, and research by providing a set of universal codes and names to identify laboratory and other clinical observations.

LOINC FAQ

RRF

NCI Thesaurus (NCIt)

Yes

Yes

An ontology-like vocabulary that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities; anatomy; agents, drugs and chemicals; genes and gene products and so on. In certain areas, like cancer diseases and combination chemotherapies, it provides the most granular and consistent terminology available

NCIt FAQ

OWL

Radiology Lexicon (RadLex) (RID)

Yes

Yes

A Lexicon for Uniform Indexing and Retrieval of Radiology Information Resources

Radlex FAQ

Protege

Systematized Nomenclature of Medicine (SNOMED) Clinical Terms (SNOMED CT)

Yes

Yes

One of a suite of designated data standards for use in the electronic exchange of clinical health information. It is considered to be the most comprehensive, multilingual clinical healthcare terminology in the world.

SNOMED CT FAQ

RRF

African Traditional Medicine Ontology (ATMO)

No

Unknown

Describes the actors' function (healer, fetishist or soothsayer); the different types of proposed process treatment, the symptom's roles and the disease consideration.

ATMO FAQ

OBOF

Amphibian Gross Anatomy Ontology (AmphibAnat)

No

Unknown

A structured controlled vocabulary of the anatomy of Amphibians.

AmphibAnat FAQ

OBOF

Biological Imaging Methods Vocabulary (FBbi)

No

Unknown

Covers sample preparation, visualization and imaging methods.

FBbi FAQ

OBOF

Biomedical Grid Terminology (BiomedGT) (Retired) (BiomedGT)

Retired

Retired

An open, collaboratively developed terminology for translational research.

Retired

Retired

BioPortal Metadata (BPMetadata)

No

Unknown

Represents the structure that BioPortal will use to represent all of its metadata (ontology details, mappings, notes, reviews, views)

BPMetadata FAQ

OWL

BioTop Ontology (biotop)

No

Unknown

A top-domain ontology that provides definitions for the foundational entities of biomedicine as a basic vocabulary to unambiguously describe facts in this domain.

biotop FAQ

OWL

BIRNLex Terminology (birnlex)

No

Unknown

Provides entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design.

BIRNlex FAQ

OWL

Bleeding History (Phenotype) Ontology (BHO)

No

Unknown

An application ontology devoted to the standardized recording of phenotypic data related to hemorrhagic disorders.

BHO FAQ

Protege

BRENDA tissue and enzyme source vocabulary (BTO)

No

Unknown

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.

BTO FAQ

OBOF

C. elegans development vocabulary (WBls)

No

Unknown

A structured controlled vocabulary of the development of Caenorhabditis elegans.

WBIs FAQ

OBOF

C. elegans gross anatomy vocabulary (WBbt)

No

Unknown

A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.

WBbt FAQ

OBOF

C. elegans phenotype vocabulary (WBPhenotype)

No

Unknown

A structured controlled vocabulary of Caenorhabditis elegans phenotypes

WBPhenotype FAQ

OBOF

Cardiac Electrophysiology Ontology (EP)

No

Unknown

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.

EP FAQ

OWL

Cell Behavior Ontology (CBO)

No

Unknown

Designed as a structured controlled vocabulary for what cells do. This ontology is a draft and independent of cell type.

CBO FAQ

PROTEGE

Cell Cycle (A. thaliana) Ontology (CCO)

No

Unknown

An ontology that integrates and manages knowledge about the cell cycle components and regulatory aspects of A. thaliana.

CCO FAQ

OBOF

Cell Cycle (H. sapiens) Ontology (CCO)

No

Unknown

An ontology that integrates and manages knowledge about the cell cycle components and regulatory aspects of H. sapiens.

CC H. Sapiens FAQ

OBOF

Cell Cycle (S. cerevisiae) Ontology (CCO)

No

Unknown

An ontology that integrates and manages knowledge about the cell cycle components and regulatory aspects of S. cerevisiae.

CC S. cerevisiae FAQ

OBOF

Cell Cycle (S. pombe) Ontology (CCO)

No

Unknown

An ontology that integrates and manages knowledge about the cell cycle components and regulatory aspects of S. pombe.

CC S. pombe FAQ

OBOF

Cell Type Ontology (CL)

No

Unknown

Designed as a structured controlled vocabulary for cell types. This ontology is not organism specific; indeed it includes cell types from prokaryotes to mammals, including plants and fungi.

CL FAQ

OBOF

Cereal Plant Development Vocabulary (GRO)

No

Unknown

A structured controlled vocabulary for expressing cereal plant development and growth stages.

GRO FAQ

OBOF

Cereal Plant Trait Vocabulary (TO)

No

Unknown

A controlled vocabulary to describe each trait as a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature individual.

TO FAQ

OBOF

Chemical Entities of Biological Interest Dictionary (CHEBI)

Yes

Unknown

A structured classification of chemical compounds of biological relevance.

CHEBI FAQ

OBOF

Common Anatomy Reference Ontology (CARO)

No

Unknown

Facilitates interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies

CARO FAQ

OBOF

Common Terminology Criteria for Adverse Events (CTCAE)

Yes

Unknown

A list of adverse event (AE) terms commonly encountered in oncology. Each AE term is defined and accompanied by a grading scale that indicates the severity of the AE. In the new CTCAE v4.0, the AE terms are organized by the System Organ Classes (SOCs) defined by the Medical Dictionary for Regulatory Activities (MedDRA). CTCAE has been developed from the earlier vocabulary known as CTC (Common Toxicity Criteria).

CTCAE FAQ

OWL

Comparative Data Analysis Ontology (CDAO)

No

Unknown

An ontology intended to provide a common ontological framework for evolutionary analysis regardless of the type of data involved.

CDAO FAQ

OWL

Dendritic Cell Ontology (DC_CL)

No

Unknown

Representation of types of dendritic cell. Note that the domain of this ontology is wholly subsumed by the domain of the Cell ontology (CL).

DC_CL FAQ

OBOF

DermLex Terminology (DermLex)

No

Unknown

Version 0.1 of the American Academy of Dermatology's lexicon, DermLex

DermLex FAQ

OWL

Dictyostelium Discoideum Anatomy Vocabulary (DDANAT)

No

Unknown

A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum.

DDANAT FAQ

OBOF

Drosophila Development Vocabulary (FBdv)

No

Unknown

A structured controlled vocabulary of the development of Drosophila melanogaster.

FBdv FAQ

OBOF

Drosophila Gross Anatomy Vocabulary (FBbt)

No

Unknown

A structured controlled vocabulary of the anatomy of Drosophila melanogaster.

FBbt FAQ

OBOF

Electrocardiography Ontology (ECG)

No

Unknown

A Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms.

ECG FAQ

OWL

Environment Ontology (ENVO)

No

Unknown

Ontology of environmental features and habitats

ENVO FAQ

OBOF

Event (INOH pathway ontology) (IEV)

No

Unknown

A structured controlled vocabulary of pathway centric biological processes. This ontology is a INOH pathway annotation ontology, one of a set of ontologies intended to be used in pathway data annotation to ease data integration. This ontology is used to annotate biological processes, pathways, sub-pathways in the INOH pathway data.INOH is part of the BioPAX working group.

IEV FAQ

OBOF

Evidence Codes Ontology (ECO)

No

Unknown

A rich ontology for experimental and other evidence statements.

ECO FAQ

OBOF

Expressed Sequence Annotation for Humans Vocabularies (EV)

No

Unknown

Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment.

EV FAQ

OBOF

Experimental Factor Ontology (EFO)

No

Unknown

An application focused ontology modelling the experimental factors in ArrayExpress. 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 methodology employed in the development of EFO involves construction of mappings to multiple existing domain specific ontologies, such as the Disease Ontology and Cell Type Ontology. This is achieved using a combination of automated and manual curation steps and the use of a phonetic matching algorithm. The ontology is evaluated with use cases from the ArrayExpress repository.

EFO FAQ

OBOF

Family Health History Ontology (FHHO)

No

Unknown

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.

FHHO FAQ

OBOF

Fly Taxonomy (FBsp)

No

Unknown

The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.

FBsp FAQ

OBOF

FlyBase Controlled Vocabulary (FBcv)

No

Unknown

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.

FBcv FAQ

OBOF

Foundational Model of Anatomy Ontology (FMA)

No

Unknown

The Foundational Model of Anatomy Ontology (FMA) is an evolving computer-based knowledge source for biomedical informatics; it is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. Its ontological framework can be applied and extended to all other species

FMA FAQ

Frames

Fungal Gross Anatomy Vocabulary (FAO)

No

Unknown

A structured controlled vocabulary for the anatomy of fungi.

FAO FAQ

OBOF

Gene Regulation Ontology (BOOTStrep)

No

Unknown

A conceptual model for the domain of gene regulation.

BOOTStrep FAQ

OBOF

Health Level 7 (HL7)

Yes

Unknown

Terminology to populate messages for clinical and administrative data within the health care arena.

HL7 FAQ

XML

Human Disease Vocabulary (DOID)

No

Unknown

A comprehensive hierarchical controlled vocabulary for human disease representation

DOID FAQ

OBOF

HUGO Gene Nomenclature Committee Ontology (HGNC)

Yes

Unknown

Approved gene names and symbols from the Human Genome Organisation (HUGO) Gene Nomenclature Committee (HGNC) at the European Bioinformatics Institute. Each symbol is unique and each gene is only given one approved gene symbol(short-form abbreviation) for each known human gene. This facilitates electronic data exchange and retrieval.

HGNC FAQ

Text
RRF

Human Phenotype Ontology (HP)

No

Unknown

Provides 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.

HP FAQ

OBOF

International Classification of Diseases Ninth Revision Clinical Modification (ICD-9-CM)

Yes

Yes

Used to code and classify morbidity data from inpatient and outpatient records, physician offices, and most National Center for Health Statistics (NCHS) surveys. ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States.

ICD-9-CM FAQ

Text
RRF

International Classification of Diseases Tenth Revision (ICD-10)

Yes

Yes

Used to code and classify mortality data for reporting to the World Health Organization (WHO)

ICD-10 FAQ

Text
RRF

International Classification of Diseases Tenth Revision Clinical Modification (ICD-10-CM)

Yes

Yes

Scheduled to replace ICD-9-CM for coding and classifying morbidity data withing the United States.

ICD-10-CM FAQ

Text
RRF

Maize Gross Anatomy Vocabulary (ZEA)

No

Unknown

A structured controlled vocabulary for the anatomy of Zea mays.

ZEA FAQ

OBOF

Mammalian Phenotype Ontology (MP)

No

Unknown

A community effort to provide standard terms for annotating mammalian phenotypic data.

MP FAQ

OBOF

Mass Spectrometry Vocabulary (MS)

No

Unknown

A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry. Developed by the HUPO Proteomics Standards Initiative.

MS FAQ

OBOF

Medaka Fish Anatomy and Development Vocabulary (MFO)

No

Unknown

A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.

MFO FAQ

OBOF

Medical Dictionary for Regulatory Activities Terminology (MedDRA)

Yes

Yes

A pragmatic, medically valid terminology with an emphasis on ease of use for data entry, retrieval, analysis, and display, as well as a suitable balance between sensitivity and specificity within the regulatory environment. MedDRA terminology applies to all phases of drug development, excluding animal toxicology. It also applies to the health effects and malfunction of devices.

MedDRA FAQ

RRF

Microarray and Gene Expression Data Ontology (MGED)

Yes

Unknown

An ontology for describing samples used in microarray experiments.

MGED FAQ

OWL

Microarray Experimental Conditions Terminology (MO)

No

Unknown

Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1.

MO FAQ

OWL

Mosquito Gross Anatomy Terminology (TGMA)

No

Unknown

A structured controlled vocabulary of the anatomy of mosquitoes.

TGMA FAQ

OBOF

Mosquito Insecticide Resistance Ontology (MIRO)

No

Unknown

Application ontology for entities related to insecticide resistance in mosquitos

MIRO FAQ

OBOF

Mouse Adult Gross Anatomy Terminology (MA)

Yes

Unknown

A structured controlled vocabulary of the adult anatomy of the mouse (Mus).

MA FAQ

OBOF

Mouse Gross Anatomy and Development Terminology (EMAP)

No

Unknown

A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).

EMAP FAQ

OBOF

Mouse Pathology Terminology (MPATH)

No

Unknown

A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes

MPATH FAQ

OBOF

Multiple Alignment Terminology (MAO)

No

Unknown

A joint effort to define community standards for data retrieval and exchange in the fields of DNA/RNA alignment, protein sequence and protein structure alignment.

MAO FAQ

OBOF

NanoParticle Ontology (NPO)

Yes

Unknown

An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.

NPO FAQ

OBOF

National Drug File - Reference Terminology (NDF-RT)

Yes

Unknown

Developed for the Veterans Administration as a reference standard for medications to support a variety of clinical, administrative and analytical purposes.

NDF-RT FAQ

OWL

NCI Metathesaurus Terminology (NCIm)

Yes

Unknown

Modeled after the same RRF structure used for the UMLS Metathesaurus. While the table structures are the same, there are differences in the data that is contained in the NCI Metathesaurus vs the UMLS Metathesaurus.

NCIm FAQ

RRF

NIFSTD Ontology (NIFSTD)

No

Unknown

Composed of a collection of OWL modules with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, organism, function and dysfunction.

NIFSTD FAQ

OWL

OBO Relationship Types for Ontologies (OBO_REL)

No

Unknown

Defines core relations used in all OBO ontologies.

OBO_REL FAQ

OBOF

Ontology for Biomedical Investigations (OBI)

Yes

Unknown

Models the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it.

OBI FAQ

OWL

Ontology of Clinical Research (OCRe)

No

Unknown

An ontology designed to support systematic description of, and interoperable queries on, human studies and study elements.

OCRe FAQ

OWL

Ontology of Physics for Biology (OPB)

No

Unknown

A reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (i.e., multiscale; e.g., molecules to organisms) and multiple physical domains (i.e., multidomain; e.g.,fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.

OPB FAQ

OWL

Parasite Life Cycle Ontology (PLO)

No

Unknown

Models the life cycle stage details of Trypanosoma cruzi and two related kinetoplastids, Trypanosoma brucei and Leishmania major. In addition to life cycle stages, the ontology also models necessary contextual details such as host information, vector information, strain and anatomical location. All the entities in the ontology are linked to each other by explicitly modeled named relationships.

PLO FAQ

OWL

Pathogen Transmission Terminology (TRANS)

No

Unknown

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.

TRANS FAQ

OBO

Pathway Ontology (PW)

No

Unknown

A controlled vocabulary for pathways that provides standard terms for the annotation of gene products.

PW FAQ

OBOF

Phenotypic Quality Ontology (PATO)

No

Unknown

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.

PATO FAQ

OBOF

Physician Data Query Terminology (PDQ)

Yes

Unknown

Part of NCI's comprehensive cancer database, which contains expert summaries on a wide range of cancer topics.

PDQ FAQ

Data Query PDQ

Physico-chemical Methods and Properties Ontologies (FIX)

No

Unknown

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.

FIX FAQ

OBOF

Plant Environmental Conditions Terminology (EO)

No

Unknown

Represents a controlled vocabulary to describe different types of supplemental environments that have been reported in the experimental profiles of gene expression and phenotype (mutant and QTL) studies on cereal plants.

EO FAQ

OBOF

Plant Growth and Developmental Stage Terminology (PO)

No

Unknown

A controlled vocabulary of growth and developmental stages in various plants.

PO Growth FAQ

OBOF

Plant Structure Terminology (PO)

No

Unknown

A controlled vocabulary of plant morphological and anatomical structures representing organs, tissues, cell types, and their biological relationships based on spatial and developmental organization.

PO Structure FAQ

OBOF

Protein Modification Ontology (MOD)

No

Unknown

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.

MOD FAQ

OBOF

PRotein Ontology (PRO)

No

Unknown

Designed to describe the relationships of proteins and protein evolutionary classes (ontology for ProEvo), to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies

PRO FAQ

OBOF

Protein-Protein Interaction Terminology (MI)

No

Unknown

A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Developed by the HUPO Proteomics Standards Initiative.

MI FAQ

OBOF

Proteomics Data and Process Provenance Ontology (ProPreO)

No

Unknown

A comprehensive proteomics data and process provenance ontology.

ProPreO FAQ

OWL

Rat Strain Ontology (RS)

No

Unknown

Defines the hierarchical display of the different rat strains as derived from the parental strains

RS FAQ

OBOF

Sample Processing and Separation Techniques Terminology (SEP)

No

Unknown

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.

SEP FAQ

OBOF

Sequence Ontology (SO)

No

Unknown

A set of terms and relationships used to describe the features and attributes of biological sequence. SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process.

SO FAQ

OBOF

SNP-Ontology (SNPO)

No

Unknown

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.

SNPO FAQ

OWL

Spatial Ontology (BSPO)

No

Unknown

A small ontology for anatomical spatial references, such as dorsal, ventral, axis, and so forth.

BSPO FAQ

OBOF

Spider Ontology (SPD)

No

Unknown

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).

SPD FAQ

OBOF

Subcellular Anatomy Ontology (SAO)

No

Unknown

Describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules.

SAO FAQ

OWL

Suggested Ontology for Pharmacogenomics (SOPHARM)

No

Unknown

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.

SOPHARM FAQ

OWL

Systems Biology Ontology (SBO)

No

Unknown

A terminology for indexing and defining terms used in quantitative biochemistry. The ontology is made up of four orthogonal vocabularies.

SBO FAQ

OBOF

Teleost Anatomy and Development Ontology (TAO)

No

Unknown

Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa

TAO FAQ

OBOF

Teleost Taxonomy (TTO)

No

Unknown

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.

TTO FAQ

OBOF

Tick Gross Anatomy Terminology (TADS)

No

Unknown

The anatomy of the Tick, Families: Ixodidae, Argassidae.

TADS FAQ

OBOF

Uber Anatomy Ontology (UBERON)

No

Unknown

A multi-species anatomy ontology created to facilitate comparison of phenotypes across multiple species. Uberon is generated semi-automatically from the union of existing species-centric anatomy ontologies.

UBERON FAQ

OBOF

UMLS Semantic Network Terminology (UMLS)

Yes

Unknown

One of three UMLS Knowledge Sources developed as part of the Unified Medical Language System (UMLS) project. The network provides a consistent categorization of all concepts represented in the UMLS Metathesaurus.

UMLS FAQ

RRF

Units of Measurement Terminology (UO)

No

Unknown

Metrical units for use in conjunction with PATO

UO FAQ

OBOF

Vaccine Ontology (VO)

No

Unknown

Vaccines play a central role in preventing infectious diseases and improving public health. To standardize vaccine annotation, integrate varied vaccine types for comprehensive data analysis, and support automated reasoning, the community-based Vaccine Ontology (VO) has been developed. VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. Currently VO covers varied vaccine related aspects with an emphasis on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines.

VO FAQ

OWL

Xenopus Anatomy and Development Terminology (XAO)

No

Unknown

A structured controlled vocabulary of the anatomy and development of the African clawed frog (Xenopus laevis).

XAO FAQ

OBOF

Yeast Phenotypes Terminology (YPO)

No

Unknown

A structured controlled vocabulary for the phenotypes of budding yeast.

YPO FAQ

OBOF

Zebrafish Terminology (ZFA)

Yes

Unknown

A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio).

ZFA FAQ

OBO

 

 

Page: African Traditional Medicine Ontology Page: Amphibian Gross Anatomy Ontology Page: Biological Imaging Methods Vocabulary Page: Biomedical Grid Terminology (BiomedGT) (Retired) Page: BioPortal Metadata Page: BioTop Ontology Page: BIRNLex Terminology Page: Bleeding History (Phenotype) Ontology Page: BRENDA tissue and enzyme source vocabulary Page: C. elegans development vocabulary Page: C. elegans gross anatomy vocabulary Page: C. elegans phenotype vocabulary Page: Cardiac Electrophysiology Ontology Page: Cell Behavior Ontology Page: Cell Cycle (A. thaliana) Ontology Page: Cell Cycle (H. sapiens) Ontology Page: Cell Cycle (S. cerevisiae) Ontology Page: Cell Cycle (S. pombe) Ontology Page: Cell Type Ontology Page: Cereal Plant Development Vocabulary Page: Cereal Plant Trait Vocabulary Page: Chemical Entities of Biological Interest Dictionary Page: Common Anatomy Reference Ontology Page: Common Terminology Criteria for Adverse Events Page: Comparative Data Analysis Ontology Page: Dendritic Cell Ontology Page: DermLex Terminology Page: Dictyostelium Discoideum Anatomy Vocabulary Page: Drosophila Development Vocabulary Page: Drosophila Gross Anatomy Vocabulary Page: Electrocardiography Ontology Page: Environment Ontology Page: Event (INOH pathway ontology) Page: Evidence Codes Ontology Page: Experimental Factor Ontology Page: Expressed Sequence Annotation for Humans Vocabularies Page: Family Health History Ontology Page: FlyBase Controlled Vocabulary Page: Fly Taxonomy Page: Foundational Model of Anatomy Ontology Page: Fungal Gross Anatomy Vocabulary Page: Gene Ontology Page: Gene Regulation Ontology Page: HUGO Gene Nomenclature Committee Ontology Page: Human Disease Vocabulary Page: Human Phenotype Ontology Page: International Classification of Diseases Ninth Revision Clinical Modification Page: International Classification of Diseases Tenth Revision Page: International Classification of Diseases Tenth Revision Clinical Modification Page: Logical Observation Identifiers Names and Codes (LOINC) Terminology Page: Maize Gross Anatomy Vocabulary Page: Mammalian Phenotype Ontology Page: Mass Spectrometry Vocabulary Page: Medaka Fish Anatomy and Development Vocabulary Page: Medical Dictionary for Regulatory Activities Terminology Page: Microarray and Gene Expression Data Ontology Page: Microarray Experimental Conditions Terminology Page: Mosquito Gross Anatomy Terminology Page: Mosquito Insecticide Resistance Ontology Page: Mouse Adult Gross Anatomy Terminology Page: Mouse Gross Anatomy and Development Terminology Page: Mouse Pathology Terminology Page: Multiple Alignment Terminology Page: NanoParticle Ontology Page: National Drug File - Reference Terminology Page: NCI Metathesaurus Terminology Page: NCI Thesaurus Terminology Page: NIFSTD Ontology Page: OBO Relationship Types for Ontologies Page: Ontology for Biomedical Investigations Page: Ontology of Clinical Research Page: Ontology of Physics for Biology Page: Parasite Life Cycle Ontology Page: Pathogen Transmission Terminology Page: Pathway Ontology Page: Phenotypic Quality Ontology Page: Physician Data Query Terminology Page: Physico-chemical Methods and Properties Ontologies Page: Plant Environmental Conditions Terminology Page: Plant Growth and Developmental Stage Terminology Page: Plant Structure Terminology Page: Protein Modification Ontology Page: PRotein Ontology Page: Protein-Protein Interaction Terminology Page: Proteomics Data and Process Provenance Ontology Page: Radiology Lexicon (RadLex) Page: Rat Strain Ontology Page: RxNorm Page: Sample Processing and Separation Techniques Terminology Page: Sequence Ontology Page: SNOMED Clinical Terms Page: SNP-Ontology Page: Spatial Ontology Page: Spider Ontology Page: Subcellular Anatomy Ontology Page: Suggested Ontology for Pharmacogenomics Page: Systems Biology Ontology Page: Teleost Anatomy and Development Ontology Page: Teleost Taxonomy Page: Tick Gross Anatomy Terminology Page: Uber Anatomy Ontology Page: UMLS Semantic Network Terminology Page: Units of Measurement Terminology Page: Vaccine Ontology Page: Xenopus Anatomy and Development Terminology Page: Yeast Phenotypes Terminology Page: Zebrafish Terminology