AcronymStatusNameDescription
AAO
eukaryotesanatomyAmphibians
ClassifiedAmphibian gross anatomy
A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon.
ABA-AMB
neurobiologyanatomyneurology'laboratory animal science''mouse clinic'Mouse
ClassifiedAllen Brain Atlas (ABA Adult Mouse Brain Ontology)
Allen Brain Atlas P56 Mouse Ontology.
ABD
ClassifiedAnthology of Biosurveillance Diseases
Our disease ontology provides information on infectious diseases, disease synonyms, transmission pathways, disease agents, affected populations and disease properties. Diseases have been grouped into syndromic disease categories, such that programmers can look through relevant categories, as well as at specific diseases. Organisms, linked to both agents and populations, are structured hierarchically, to provide multiple levels of organism resolution. In addition, both disease transmission and relevant disease properties are available to search. Disease properties include tags like 'notifiable diseases' and 'economic importance' to flag particular disease characteristics that may be of interest, but are not captured elsewhere.
ACGT-MO
oncology'preclinical and clinical studies'pathologyHuman
ClassifiedCancer Research and Management ACGT Master Ontology
The intention of the ACGT Master Ontology (MO) is to represent the domain of cancer research and management in a computationally tractable manner.
ADAR
neurologypsychiatryneurobiologypaediatricsHuman
ClassifiedAutism DSM-ADI-R ontology
ADMIN
'laboratory information management''information retrieval'medicineHuman
UnknownNurse Administrator
ADO
neurobiologypsychiatryneurologypathology'geriatric medicine'Human
ClassifiedAlzheimer's disease ontology
ADO is a first attempt to develop an open, public ontology representing relevant knowledge on Alzheimer’s disease.
ADW
ecologyinvertebratestaxonomy'developmental biology''evolutionary biology'vertebratesAnimalia
ClassifiedAnimal Natural History and Life History Ontology
An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.
AEO
anatomy'cell biology''structural biology'All life
ClassifiedAnatomical Entity Ontology
AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology
AERO
pathology'preclinical and clinical studies'pharmacologypharmacovigilenceHuman
ClassifiedAdverse Event Reporting Ontology
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
AI-RHEUM
'musculoskeletal medicine''medicine research and development''preclinical and clinical studies''medical imaging'Human
ClassifiedArtificial Intelligence Rheumatology Consultant System Ontology
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.
AIDS
Unloadableamatuer AIDS
ontology on HIV AND AIDS
ALLERGYDETECTOR
'allergy, clinical immunology and immunotherapeutics.'Human
ClassifiedAllergy Detector II
AMINO-ACID
'peptides and amino acids'biologyproteins'molecular biology'proteomicsinsdxmlHuman
ClassifiedAmino Acid Ontology
An ontology of amino acids and their properties. Inferred version.
ANCESTRO
genomics'population genetics''evolutionary biology''data deposition, annotation and curation'Human
ClassifiedAncestry Ontology
AO
ClassifiedAsthma Ontology
Asthma ontology
APACOMPUTER
'software engineering''data management'All life
ClassifiedComputer Cluster
APA Computer Cluster
APADISORDERS
psychiatryneurologyHuman
ClassifiedDisorders cluster
APA Disorders cluster, owls loaded from urls.
APAEDUCLUSTER
'data management'Human
ClassifiedEducational Cluster
APA Educational Cluster, URI based ontology load
APANEUROCLUSTER
neurobiologyneurologyanatomyphysiologypsychiatryHuman
ClassifiedAPA Neuro Cluster
APA Neuropsychology and Neurology Cluster
APAOCUEMPLOY
'data management'Human
ClassifiedAPA Occupational and Employment cluster
APA Occupational and Employment Cluster
APAONTO
psychiatryneurobiologyphysiologyneurologyHuman
ClassifiedPsychology Ontology
APA thesaurus . Flat ontology file
APASTATISTICAL
'statistics and probability''data management'All life
ClassifiedAPA Statistical Cluster
APA Statistical Cluster
APATANDT
'developmental biology'neurologyneurobiology'statistics and probability'Human
ClassifiedAPA Tests and Testing cluster
APA Tests and Testing Cluster
APATREATMENT
'complementary medicine'psychiatrypathologyHuman
ClassifiedAPA Treatment Cluster
APA Treatment Cluster
APO
fungiphenomics'laboratory animal science'Ascomycetes
ClassifiedAscomycete phenotype ontology
A structured controlled vocabulary for the phenotypes of Ascomycete fungi
ARD
UnknownAssociations of Relevant Diseases for Biosurveillance
ASDPTO
neurobiologyneurologypsychiatryphenomicspathologypaediatricsHuman
ClassifiedAutism Spectrum Disorder Phenotype Ontology
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
ATC
anatomy'medicinal chemistry'pharmacology'pharmacokinetics and pharmacodynamics'Human
ClassifiedAnatomical Therapeutic Chemical Classification
The ontology is an OWL representation of the ATC classification provided by WHO used for the classification of drugs. Used by KEGG and PharmGKB.
ATO
phylogenomics'laboratory animal science'Amphibians
ClassifiedAmphibian taxonomy
A taxonomy of Amphibia
ATOL
phenomicsvertebrates'developmental biology'physiology'nutritional science''reproductive health'Animalia
ClassifiedAnimal Trait Ontology for Livestock
ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientific and educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production
AURA
'data management'All life
ClassifiedKB_Bio_101
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
BAO
'compound libraries and screening''computational chemistry''cell biology'phenomics'molecular biology'biochemistryAll life
ClassifiedBioAssay Ontology
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.
BAO-GPCR
biochemistryphysiologypharmacology'drug discovery'moleculesproteinslipidsproteomicsAll life
ClassifiedG Protein-Coupled Receptor BioAssays Ontology
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.
BATHMATE
Unloadablekenzi pump
Bathmate is the world best product for penis health and enlargement, with our new Hydromax you can get outstanding results. here is an a solid best penis pump guide http://bathmatepenispump.com/
BCGO
oncologyanatomyHuman
ClassifiedBreast Cancer Grading Ontology
assigns a grade to a tumor starting from the 3 criteria of the NGS
BCO
ecologyAll life
ClassifiedBiological Collections Ontology
An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.
BCTEO
bioengineeringphysiology'developmental biology''mass spectrometry'medicine'cell biology'biomaterials'musculoskeletal medicine'Human
ClassifiedBone and Cartilage Tissue Engineering Ontology
Ontology that describes the field of Tissue Engineering for what concerns bone and cartilage tissues.
BCTT
ClassifiedBehaviour Change Technique Taxonomy
BCT Taxonomy v0.4
BCTTV1
psychiatryneurobiologyneurologyHuman
UnknownBehaviour change technique taxonomy
BDO
'developmental biology''cell biology''musculoskeletal medicine'phenomicsoncology'quantitative genetics'anatomyHuman
ClassifiedBone Dysplasia Ontology
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.
BFO
'data management'All life
ClassifiedBasic Formal Ontology
The upper level ontology upon which OBO Foundry ontologies are built.
BHN
anatomypathology'population genetics'enzymesimmunologymicrobiologyhaematologyproteomicsviruses'biomedical science''microbial collection'proteinHuman
ClassifiedBiologie Hors Nomenclature
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).
BHO
haematologyphenomicspathologyHuman
ClassifiedBleeding History Phenotype Ontology
An application ontology devoted to the standardized recording of phenotypic data related to hemorrhagic disorders.
BILA
anatomyphysiology'laboratory animal science'Bilateria
ClassifiedBilateria anatomy
BIM
'medical imaging''biological imaging'Human
ClassifiedBiomedical Image Ontology
BIM is an open biomedical image features ontology, it provides semantic vocabularies to represent the biomedical images and their features. BIM specifically addresses the provenance and crowd image annotation issues during biomedical image manipulation.
BIOMO
'sample collections'genetics'functional genomics''function analysis''metabolic pathways'Human
ClassifiedBiological Observation Matrix Ontology
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
BIOMODELS
'molecular modelling''computational biology''computational chemistry'biochemistryAll life
UnloadableBioModels Ontology
OWL Representation of the models in the BioModels repository.
BIRNLEX
anatomypathologyphenomics'cell biology'neurobiologyneurologyphysiologyphylogenetics'medical informatics'Human
ClassifiedBiomedical Informatics Research Network Project Lexicon
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.
BMO
biomarkerspharmacologypathology'drug discovery''pharmacokinetics and pharmacodynamics''translational medicine'All life
ClassifiedBiomarker Ontology
Biomarker ontology is a first attempt to organize the biomarker knowledge domain in collaboration with pharmaceutical companies.
BMT
'biomedical science''ontology and terminology'biologyHuman
ClassifiedBiomedical Topics
An ontology of biological and biomedical topics, created from merging the EDAM Topics sub-ontology with auxiliary topics that are out of scope of EDAM.
BNO
'nutritional science''preclinical and clinical studies'Human
ClassifiedBionutrition Ontology
The Bionutrition Ontology relates concepts and terminologies used for human nutrition in a clinical and biomedical setting.
BOF
biodiversityAll life
UnknownBiodiversity Ontology
An ontology of biodiversity of INPA
BOOTSTREP
'gene regulation'All life
UnloadableGene Regulation Ontology
BP
'protein interactions''molecular interactions, pathways and networks'geneticsmoleculesAll life
ClassifiedBioPAX Ontology of Biological Pathways
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.
BP-METADATA
'ontology and terminology''data identity and mapping''data integration and warehousing''information retrieval'All life
ClassifiedBioPortal Metadata Ontology
This ontology represents the structure that BioPortal uses to represent all of its metadata (ontology details, mappings, notes, reviews, views)
BRCT
'cell biology'anatomyneurobiologyneurologyHuman
ClassifiedBrain Region & Cell Type terminology
The BRCT stands for Brain Region and Cell Type terminology, which was built with the purpose of organizing the knowledge domain of brain anatomy with a top-down granularity, from gross regions to cell types.
BRIDG
'data management'pharmacologyphysiologypsychiatry'preclinical and clinical studies'pharmacovigilenceAll life
ClassifiedBiomedical Research Integrated Domain Group Model
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&
BRO
'statistics and probability'bioinformatics'computational biology''public health and epidemiology'pathology'pharmacokinetics and pharmacodynamics'physiologytoxicology'ontology and terminology''preclinical and clinical studies'paediatricsHuman
ClassifiedBiomedical Resource Ontology
A controlled terminology of resources, which is used to improve the sensitivity and specificity of web searches.
BRO_ACRONYM
ClassifiedBro_Name
Uploading ontology for the first time
BSAO
'marine biology'anatomy'developmental biology'physiologyeukaryotesBotryllus schlosseri
ClassifiedBotryllus schlosseri anatomy and development ontology
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
BSPO
anatomybiophysics'structural biology'All life
ClassifiedBiological Spatial Ontology
An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces
BT
'population genetics'eukaryotesviruses'prokaryotes and archae'Human
ClassifiedBioTop Ontology
A top-domain ontology that provides definitions for the foundational entities of biomedicine as a basic vocabulary to unambiguously describe facts in this domain.
BTO
enzymes'cell biology'physiologyAll life
ClassifiedBRENDA tissue / enzyme source
A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.
CABRO
'trauma medicine'neurologyneurobiology'software engineering''preclinical and clinical studies'Human
ClassifiedComputer Assisted Brain Injury Rehabilitation Ontology
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.
CADSRVS
UnloadableNCI caDSR Value Sets
Value Sets extracted from caDSR Common Data Elements (CDEs)
CANCO
oncology'medicinal chemistry'Human
ClassifiedCancer Chemoprevention Ontology
The Cancer Chemoprevention Ontology constitutes a vocabulary that is able to describe and semantically interconnect the different paradigms of the cancer chemoprevention domain.
CANONT
oncologyHuman
ClassifiedUpper-Level Cancer Ontology
Providing an upper-level ontology for cancer.
CAO
genetics'functional genomics''evolutionary biology''statistics and probability'eukaryotesproteins'prokaryotes and archae'All life
ClassifiedClusters of Orthologous Groups (COG) Analysis Ontology
CAO ontology is designed for supporting the COG enrichment study by using Fisher's exact test
CARELEX
oncology'preclinical and clinical studies''medical informatics''data management''statistics and probability''medical imaging'Human
ClassifiedContent Archive Resource Exchange Lexicon
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
CARO
anatomy'structural biology'All life
ClassifiedCommon Anatomy Reference Ontology
An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species
CARRE
'preclinical and clinical studies''laboratory techniques''laboratory information management'Human
ClassifiedCARRE Risk Factor ontology
Clinical risk factors, evidence and observables
CBO
'molecular modelling''cell biology''molecular biology'All life
ClassifiedCell Behavior Ontology
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.
CCO
'cell biology'eukaryotes'data integration and warehousing'genetics'molecular interactions, pathways and networks'proteinsEukaryota
ClassifiedCell Cycle Ontology
An application ontology integrating knowledge about the eukaryotic cell cycle.
CCON
plantsecology'molecular dynamics'Plants
ClassifiedCerrado concepts and plant community dynamics
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.
CCONT
'cell culture collection''cell biology'All life
ClassifiedCell Culture Ontology
CCONT is an ontology for the formal representation of cell lines and their correspnding culture conditions.
CDAO
'evolutionary biology''comparative genomics'phylogenetics'data architecture, analysis and design'genetics'sequence comparison'All life
ClassifiedComparative Data Analysis Ontology
a formalization of concepts and relations relevant to evolutionary comparative analysis
CEDARPC
UnloadableCEDAR Provisional Classes
CEDAR Provisional Classes
CEDARVS
ClassifiedCEDAR Value Sets
Value Sets used by the CEDAR project
CEPH
anatomy'developmental biology''cell biology''membrane and lipoproteins'eukaryotes'metabolic pathways'metabolomics'marine biology'Cephalopods
ClassifiedCephalopod Ontology
An anatomical and developmental ontology for cephalopods
CHD
cardiologygeneticsHuman
ClassifiedCongenital Heart Defects Ontology
An ontology that describes the Congenital Heart Defects data.
CHEBI
'compound libraries and screening''molecular biology'biochemistrybiophysics'structural biology'All life
ClassifiedChemical Entities of Biological Interest
A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds.
CHEMBIO
genomics'molecular interactions, pathways and networks''synthetic chemistry''chemical biology''structural biology'pathologygeneticspharmacovigilenceAll life
ClassifiedSystems Chemical Biology and Chemogenomics Ontology
Ontology for Systems Chemical Biology and Chemogenomics
CHEMINF
cheminformatics'software engineering'All life
UnloadableChemical Information Ontology
Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.
CHMO
'synthetic chemistry''mass spectrometry''electron microscopy'All life
UnloadableChemical Methods Ontology
CHMO, the chemical methods ontology, describes methods used to
CIINTEADO
'marine biology'anatomy'developmental biology'eukaryotesCiona intestinalis
UnknownCiona intestinalis Anatomy and Development Ontology
CISAVIADO
'marine biology'anatomy'developmental biology'eukaryotesCiona savignyi
Unknown Ciona savignyi Anatomy and Development Ontology
CL
eukaryotes'cell biology'anatomy'molecular biology''chemical biology''molecular interactions, pathways and networks'proteinsAnimalia
ClassifiedCell Ontology
The Cell Ontology is a structured controlled vocabulary for cell types in animals.
CLO
'cell culture collection''cell biology''data integration and warehousing'All life
ClassifiedCell Line Ontology
An ontology to standardize and integrate cell line information and to support computer-assisted reasoning.
CMF
surgerydentistryHuman
UnloadableCranioMaxilloFacial ontology
CMO
physiology'preclinical and clinical studies'Human
ClassifiedClinical measurement ontology
Morphological and physiological measurement records generated from clinical and model organism research and health programs.
CMPO
'cell biology'phenomics'molecular interactions, pathways and networks''molecular biology'All life
ClassifiedCellular microscopy phenotype ontology
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).
CN
'computer science'All life
Classifiedcomputer network
Computer networks ontology
CNO
neurologyneurobiology'computational biology'Human
ClassifiedComputational Neuroscience Ontology
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.
CNO_ACRONYM
ClassifiedCNO_NAME
test
CO
ecology'data identity and mapping'eukaryotesPlants
UnknownCrop Ontology
CO-WHEAT
plantsphysiologyWheat
ClassifiedWheat Trait Ontology
This ontology defines traits of the International Wheat Information System (IWIS) database and wheat descriptor.
COGAT
psychiatryneurologyneurobiologyHuman
ClassifiedCognitive Atlas Ontology
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.
COGPO
psychiatryneurologyneurobiology'laboratory techniques''laboratory information management'Human
ClassifiedCognitive Paradigm Ontology
This ontology is used to describe the experimental conditions within cognitive/behavioral experiments, primarily in humans.
COMODI
ClassifiedCOMODI
An ontology to characterise differences in versions of computational models in biology
COSTART
pharmacovigilencepharmacology'pharmacokinetics and pharmacodynamics'pathologyphysiologyanatomyAll life
ClassifiedCoding Symbols for a Thesaurus of Adverse Reaction Terms
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.
CPMO
UnknownCare Plan Metadata Ontology
CPRO
medicine'computer science'physiologypathology'data management''systems biology'Human
ClassifiedComputer-Based Patient Record Ontology
A uniform core set of data elements (whose formal semantics are captured in OWL) for use in a Computer-Based Patient Record (CPR)
CPT
surgeryanaesthesiologypathology'laboratory techniques''laboratory information management'Human
UnloadableCurrent Procedural Terminology
Current Procedural Terminology
CPTAC
proteomics'preclinical and clinical studies'oncology'laboratory techniques'biomarkers'mass spectrometry''laboratory information management'Human
ClassifiedCPTAC Proteomics Pipeline Infrastructure Ontology
a basic ontology which describes the proteomics pipeline infrastructure for CPTAC project
CRISP
'computer science'anatomychemistryphysicsbiologypathologymedicinemathematics'data management'All life
ClassifiedComputer Retrieval of Information on Scientific Projects Thesaurus
Computer Retrieval of Information on Scientific Projects (CRISP)
CSEO
'medical toxicology'toxicology'respiratory medicine'Human
ClassifiedCigarette Smoke Exposure Ontology
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.
CSO
'preclinical and clinical studies'Human
UnknownClinical Study Ontology
CSSO
'preclinical and clinical studies'neurologyneurobiologyimmunology'musculoskeletal medicine''reproductive health''respiratory medicine'dermatology'urology and nephrology'Human
ClassifiedClinical Signs and Symptoms Ontology
An ontology for describing clinical signs and symptoms.
CTCAE
oncologypharmacologypharmacovigilencetoxicology'pharmacokinetics and pharmacodynamics''medical toxicology'All life
ClassifiedCommon Terminology Criteria for Adverse Events
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).
CTENO
anatomy'developmental biology''marine biology'eukaryotes'cell biology''molecular interactions, pathways and networks'Ctenophores
ClassifiedCtenophore Ontology
An anatomical and developmental ontology for ctenophores (Comb Jellies)
CTO
'preclinical and clinical studies'neurologypathologyneurobiology'laboratory information management''laboratory techniques'Human
ClassifiedClinical Trials Ontology
The CTO-NDD stands for Clinical Trial Ontology-Neurodegenerative Diseases, which was built with the purpose of organizing the knowledge domain of clinical trials in neurodegeneration field.
CTONT
'preclinical and clinical studies''laboratory techniques''laboratory information management'Human
ClassifiedEpoch Clinical Trial Ontology
CTX
'genotype and phenotype''preclinical and clinical studies'neurologyneurobiologyHuman
UnloadableCerebrotendinous Xanthomatosis Ontology
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.
CU-VO
toxicologybiochemistry'medical toxicology'pharmacologyAll life
UnknownVenom Ontology
CVDO
cardiologypathologyhaematologyinsdxmlHuman
UnloadableCardiovascular Disease Ontology
An ontology to describe entities related to cardiovascular diseases
CYTO
proteomicsmolecules'data integration and warehousing'proteinsAll life
ClassifiedCYTOKINE
It is flat ontology showing cytokine synonyms. It has been produced by merging cytokine branches, using SOMA (Synonym Ontology Mapping Approach) method, of 11 Bioportal ontologies.
DCM
'medical imaging''biological imaging''ontology and terminology'Human
UnloadableDICOM Controlled Terminology
DICOM Controlled Terminology (PS3.16 2016b Annex D)
DCO
'rare diseases''data management''molecular interactions, pathways and networks''pharmacokinetics and pharmacodynamics'Human
ClassifiedDispedia Core Ontology
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).
DCO-DEBUGIT
'infectious disease''preclinical and clinical studies'insdxmlHuman
ClassifiedDebugIT Core Ontology
The Debugit Core Ontology (dco) covers the complete conceptual space of the domain of interest in the DebugIT project. It focuses on the management of antibiotics resistance within hospitals and infectious diseases to cover the clinical monitoring use cases. The ontology shall provide a semantic reference as logically defined classes in a formal and computer understandable format. It is supposed to formally represent all basic kinds of entities in the domain of interest, together with their invariant and context-independent properties. The ontology is therefore distinct from the representation of clinical knowledge as targeted by the DebugIT WP 4. Instead, it has a supportive semantic glue Function as it provides standardized and formally described meaning identifiers across the whole project, hence serving the Interoperability platform as well.
DC_CL
'cell biology''immunoproteins, genes and antigens'immunology'laboratory animal science'Mammalia
ClassifiedDendritic cell
DDANAT
'cell biology'anatomyeukaryotes'laboratory animal science'Dictyostelium discoideum
ClassifiedDictyostelium discoideum anatomy
A structured controlled vocabulary of the anatomy of the slime-mould <i>Dictyostelium discoideum</i>.
DDI
'drug discovery'All life
ClassifiedOntology for Drug Discovery Investigations
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).
DDO
ClassifiedDiabetes Mellitus Diagnosis Ontology
An ontology for diagnosis of diabetes containing the diabetes related complications, symptoms, drugs, lab tests, etc.
DDPHENO
phenomics'cell biology''laboratory animal science'Dictyostelium discoideum
ClassifiedDictyostelium discoideum phenotype
A structured controlled vocabulary of phenotypes of the slime-mould <i>Dictyostelium discoideum</i>.
DERMLEX
'laboratory techniques'dermatology'laboratory information management'Human
ClassifiedDermatology Lexicon
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.
DERMO
dermatologypathologyHuman
ClassifiedHuman Dermatological Disease Ontology
Ontology of human dermatologic disease
DIAB
pathology'urology and nephrology''endocrinology and metabolism''public health and epidemiology'Human
ClassifiedWP7 Diabetes Ontology
Diabetes ontology
DIAGONT
surgeryneurology'data architecture, analysis and design''public health and epidemiology'Human
ClassifiedDiagnostic Ontology
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.
DIDEO
pharmacology'pharmacokinetics and pharmacodynamics''molecular interactions, pathways and networks'All life
ClassifiedDrug Interaction and Evidence Ontology
The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology
DIKB
pharmacology'pharmacokinetics and pharmacodynamics''molecular interactions, pathways and networks'enzymesmetabolomics'molecular interactions, pathways and networks''drug development''drug formulation and delivery''preclinical and clinical studies''drug discovery'All life
ClassifiedDrug Interaction Knowledge Base Ontology
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.
DINTO
pharmacology'pharmacokinetics and pharmacodynamics''molecular interactions, pathways and networks'All life
UnloadableThe Drug-drug Interactions Ontology
DLORO
ClassifiedDependency Layered Ontology for Radiation Oncology
Dependency Layered Ontology for Radiation Oncology
DOCCC
'preclinical and clinical studies'physiologypsychiatryHuman
ClassifiedDiagnosis Ontology of Clinical Care Classification
Diagnosis Ontology of Clinical Care Classification (CCC)
DOID
pathologyanatomy'cell biology'geneticspsychiatry'endocrinology and metabolism'Human
ClassifiedHuman Disease Ontology
An ontology for describing the classification of human diseases organized by etiology.
DPO
phenomicsinvertebrates'laboratory animal science'Drosophila
ClassifiedDrosophila Phenotype Ontology
An ontology of commonly encountered and/or high level Drosophila phenotypes.
DRON
pharmacology'pharmacokinetics and pharmacodynamics''molecular interactions, pathways and networks'All life
ClassifiedThe Drug Ontology
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.
ECG
'laboratory techniques'cardiology'laboratory information management'All life
ClassifiedElectrocardiography Ontology
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.
ECO
'laboratory techniques'genomics'literature and reference''data deposition, annotation and curation'All life
ClassifiedEvidence ontology
An ontology for experimental and other evidence statements.
ECP
'laboratory techniques'informatics'preclinical and clinical studies'Human
ClassifiedElectronic Care Plan
ECSO
ecologychemistryAll life
ClassifiedThe Ecosystem Ontology
EDAM
'ontology and terminology'All life
ClassifiedEDAM bioinformatics operations, data types, formats, identifiers and topics
EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries
EDAMTO
'ontology and terminology'All life
ClassifiedEDAM Topics
An ontology of bioinformatics, biological and biomedical topics (EDAM Topics)
EDDA
'literature and reference'All life
ClassifiedEDDA Study Design Terminology
The EDDA Study Designs Taxonomy (v2.0) was developed by the Evidence in Documents, Discovery, and Analytics (EDDA) Group: Tanja Bekhuis (Principal Scientist); Eugene Tseytlin (Systems Developer); Ashleigh Faith (Taxonomist); Faina Linkov (Epidemiologist). The EDDA Group is a division of TCB Research & Indexing LLC. This work was made possible, in part, by the US National Library of Medicine, National Institutes of Health, grant no. R00LM010943. Foundational research is described in Bekhuis T, Demner Fushman D, Crowley RS. Comparative effectiveness research designs: an analysis of terms and coverage in Medical Subject Headings (MeSH) and Emtree. Journal of the Medical Library Association (JMLA). 2013 April;101(2):92-100. PMC3634392. Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries. A PDF of this taxonomy is available in ResearchGate DOI: 10.13140/RG.2.1.3769.2406/1. The EDDA Study Designs Taxonomy by Tanja Bekhuis and Eugene Tseytlin is licensed under a Creative Commons Attribution–NonCommercial–ShareAlike 4.0 International License (CC BY-NC-SA 4.0). For information about this license, see https://creativecommons.org/licenses/by-nc-sa/4.0/.
EDDA_PT
ClassifiedEDDA Publication Types Taxonomy
The EDDA Publication Types Taxonomy (v1.0) was developed by Tanja Bekhuis (Principal Scientist) and Eugene Tseytlin (Systems Developer) of the Evidence in Documents, Discovery, and Analytics (EDDA) Group. The EDDA Group is a division of TCB Research & Indexing LLC. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCIT, Emtree, and dictionaries. The EDDA Publication Types Taxonomy by Tanja Bekhuis and Eugene Tseytlin is licensed under a Creative Commons Attribution–NonCommercial–ShareAlike 4.0 International License (CC BY-NC-SA 4.0). For information about this license, see https://creativecommons.org/licenses/by-nc-sa/4.0/.
EFO
'drugs and target structures'pathologyanatomy'laboratory techniques'phenomics'cell biology''laboratory information management'All life
ClassifiedExperimental Factor Ontology
The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental variables in multiple resources at the EBI and the Centre for Therapeutic Target Validation. The ontology has been developed to increase the richness of the annotations that are currently made in resources and to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology pulls together classes from reference ontologies such as disease, cell line, cell type and anatomy and adds axiomatisation as necessary to connect areas such as disease to phenotype. Contact EFO users list for information: efo-users@lists.sourceforge.net
EGO
ClassifiedEpigenome Ontology
The Epigenome Ontology (EGO) a biomedical ontology for integrative epigenome knowledge representation and data analysis.
EHDA
anatomy'developmental biology'Human
ClassifiedHuman developmental anatomy, timed version
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.
EHDAA
anatomy'developmental biology'Human
ClassifiedHuman developmental anatomy, abstract version
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 <i>heart</i> really means <i>heart (CS 9-20)</i>. Timing details will be added to the abstract version of the ontology in a future release.
EHDAA2
anatomy'developmental biology'Human
ClassifiedHuman developmental anatomy, abstract
A structured controlled vocabulary of stage-specific anatomical structures of the developing human.
ELIG
oncology'preclinical and clinical studies'pathologyHuman
ClassifiedEligibility Feature Hierarchy
We derived a set of 1,437 eligibility features that were organized into a feature hierarchy using 80 breast cancer trials.
EMAP
anatomy'developmental biology''mouse clinic''laboratory animal science'Mouse
ClassifiedMouse gross anatomy and development, timed
A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).
EMAPA
anatomy'developmental biology''mouse clinic''laboratory animal science'Mouse
ClassifiedMouse gross anatomy and development, timed
Abstract (i.e. non-stage specific) stage-specific anatomical structures of the mouse.
EMO
enzymes'molecular interactions, pathways and networks''protein interactions'All life
ClassifiedEnzyme Mechanism Ontology
ENM
'toxins and targets'toxicology'data identity and mapping'All life
ClassifiedeNanoMapper
The eNanoMapper ontology covers the full scope of terminology needed to support research into nanomaterial safety. It builds on multiple pre-existing external ontologies such as the NanoParticle Ontology.
ENTITY
ClassifiedISO-15926-2_2003_entityMembership
Entity Membership
ENTITYCANDIDATES
ClassifiedISO-15926-2_2003_entityMembershipCandidates
ISO entity candidates for oil and gas
ENVO
ecologyAll life
ClassifiedEnvironment Ontology
Ontology of environmental features and habitats
EO
ecologyplants'developmental biology''laboratory techniques'Plants
ClassifiedPlant Environment Ontology
A structured, controlled vocabulary which ≠≠describes the treatments, growing conditions, and/or study types used in various types of plant biology experiments.
EOL
'nutritional science'ecologyeukaryotes'developmental biology'Animalia
ClassifiedEnvironment Ontology for Livestock
L'ontologie EOL décrit les conditions d'environnement des élevages d'animaux domestiques. Elle décrit plus particulièrement les modalités de l'alimentation, de l'environnement, de la structure des élevages et des systèmes d'élevage
EP
cardiologyphysiologyanatomyimagingHuman
ClassifiedCardiac Electrophysiology Ontology
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.
EPILONT
neurologyneurobiologypsychiatryHuman
ClassifiedEpilepsy Ontology
Ontology about the epilepsy domain and epileptic seizures. Based on the diagnosis proposed by the International League Against Epilepsy (ILAE).
EPO
'public health and epidemiology'insdxmlHuman
ClassifiedEpidemiology Ontology
An ontology designed to support the semantic annotation of epidemiology resources
ERO
'laboratory information management'biologymedicineAll life
Classifiedeagle-i resource ontology
An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.
ESSO
Incoherent (structural)Epilepsy Syndrome Seizure Ontology
This ontology contains epilepsy syndromes, seizure types, and data elements associated with them.
EV
pathologyanatomy'developmental biology''cell biology''laboratory techniques''data deposition, annotation and curation'Human
UnloadableeVOC (Expressed Sequence Annotation for Humans)
EXACT
'laboratory techniques'insdxml'laboratory information management'All life
ClassifiedAn ontology for experimental actions
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.
EXO
ecologychemistrybiologyphysicsHuman
ClassifiedExposure ontology
Vocabularies for describing exposure data to inform understanding of environmental health.
FALL
biophysicsmedicineHuman
ClassifiedMyOntoServiceFull_FallDetection
FAO
anatomyfungiFungi
ClassifiedFungal gross anatomy
A structured controlled vocabulary for the anatomy of fungi.
FB-BT
anatomyinvertebratesgenetics'molecular interactions, pathways and networks'Drosophila melanogaste
ClassifiedDrosophila Gross Anatomy Ontology
A structured controlled vocabulary of the anatomy of <i>Drosophila melanogaster</i>.
FB-CV
anatomyinvertebratesphenomics'molecular interactions, pathways and networks'Drosophila
ClassifiedFlyBase Controlled Vocabulary
A structured controlled vocabulary used for various aspects of annotation by FlyBase.<br>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.
FB-DV
anatomyinvertebrates'developmental biology''molecular interactions, pathways and networks'Drosophila melanogaste
ClassifiedDrosophila Development Ontology
A structured controlled vocabulary of the development of <i>Drosophila melanogaster</i>.
FB-SP
invertebratesDrosophila
ClassifiedFly Taxonomy
The taxonomy of the family <i>Drosophilidae</i> (largely after Baechli) and of other taxa referred to in FlyBase.
FBBI
'sample collections'visualisation'biological imaging''medical imaging'Human
ClassifiedBiological imaging methods
A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.
FBBT
anatomyinvertebratesgenetics'molecular interactions, pathways and networks'Drosophila melanogaste
ClassifiedDrosophila gross anatomy
An ontology representing the gross anatomy of Drosophila melanogaster.
FBCV
anatomyinvertebratesphenomics'molecular interactions, pathways and networks'Drosophila
ClassifiedFlyBase Controlled Vocabulary
A structured controlled vocabulary used for various aspects of annotation by FlyBase.
FBDV
anatomyinvertebrates'molecular interactions, pathways and networks''developmental biology'Drosophila melanogaste
ClassifiedDrosophila development
A structured controlled vocabulary of the development of Drosophila melanogaster.
FBSP
ClassifiedFly taxonomy
The taxonomy of the family <i>Drosophilidae</i> (largely after Baechli) and of other taxa referred to in FlyBase.
FBbi
'sample collections'visualisation'biological imaging''medical imaging'Human
ClassifiedBiological Imaging Methods Ontology
A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.
FBbt
anatomyinvertebratesgenetics'molecular interactions, pathways and networks'Drosophila
Classifieddrosophila_anatomy_ontology_full
The complete, and latest, Drosophila anatomy ontology. Loaded via a purl specifying the standard OWL translation. This version is NOT pre-reasoned.
FDSAJFAHSJK
ClassifiedOWL_XML_Tool5
dasf
FHHO
pathologygenetics'public health and epidemiology''population genetics'Human
ClassifiedFamily Health History Ontology
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.
FIRE
ecologyphysiology'molecular dynamics'plantsPlants
ClassifiedFire Ontology
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.
FIX
physiologybiophysicsproteins'data identity and mapping'chemistryAll life
ClassifiedPhysico-chemical methods and properties
An ontology of physico-chemical methods and properties.
FLOPO
phenomics'developmental biology'anatomyPlants
ClassifiedFlora Phenotype Ontology
The Flora Phenotype Ontology is intended to describe the whole range of traits and phenotypes of flowering plants. The original version was developed at the pro-iBiosphere Hackathon in Leiden. 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/
FLU
'infectious disease''respiratory medicine'viruses'public health and epidemiology'phenomics'ear, nose and throat medicine''allergy, clinical immunology and immunotherapeutics.'Human, vertebrata
ClassifiedInfluenza Ontology
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)
FMA
anatomy'cell biology'phenomics'structural biology'All life
ClassifiedFoundational Model of Anatomy (subset)
This is currently a slimmed down version of FMA
FO
anatomy'developmental biology'plantsTracheophyta
ClassifiedFern Ontology
FOD
UnknownFoodofDiabetics
FOODO
'nutritional science''analytical chemistry'All life
ClassifiedFood Ontology
An ontology representation of parts of the FooDB database.
FTC
Classified Functional Therapeutic Chemical Classification System
The Functional Therapeutic Chemical Classification System (FTC) defines over 20'000 mechanisms and modes of action for approuved drugs. The resource abstracts away from the traditional chemical structure-based approach and focuses solely on the mode of action of drugs. The classification sorts therapeutic agents based on their function in the human body.
FYPO
phenomics'molecular interactions, pathways and networks'geneticsfungiSchizosaccharomyces pombe
ClassifiedFission Yeast Phenotype Ontology
FYPO is a formal ontology of phenotypes observed in fission yeast.
GALEN
'data management'medicinebiologyAll life
ClassifiedGalen Ontology
A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.
GAZ
ecologyAll life
ClassifiedGazetteer
Gazetteer
GBM
neurologyneurobiologypathologysurgeryphysiologyoncologybiomarkersHuman
ClassifiedGlioblastoma
GCO
genetics'functional genomics''data integration and warehousing'insdxmlAll life
ClassifiedGenome Component Ontology
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.
GENE-CDS
'preclinical and clinical studies''functional genomics'pharmacogenomicsmap'genetic variation'Human
ClassifiedGenomic Clinical Decision Support Ontology
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)
GEO
ecologyAll life
ClassifiedGeographical Entity Ontology
An ontology of geographical entities
GEOSPECIES
ecology'model organisms'imaging'data integration and warehousing'All life
ClassifiedGeoSpecies Ontology
This ontology was designed to help integrate species concepts with species occurrences, gene sequences, images, references and geographical information. See also Taxonconcept.org
GEXO
'gene expression''data integration and warehousing'All life
ClassifiedGene Expression Ontology
An application ontology for the domain of gene expression. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, and orthology relations using ontological properties from RO and ISO.
GFO
'data integration and warehousing''ontology and terminology'All life
ClassifiedGeneral Formal Ontology
The General Formal Ontology (GFO) is a top-level ontology integrating objects and processes.
GFO-BIO
'data integration and warehousing''ontology and terminology'All life
ClassifiedGeneral Formal Ontology for Biology
GFO-Bio is a biological core ontology built on the General Formal Ontology.
GFVO
'genetic variation'genomicsAll life
ClassifiedGenomic Feature and Variation Ontology
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
GLYCO
'structural biology'carbohydrateslipids'data deposition, annotation and curation'proteins'molecular biology''compound libraries and screening'All life
ClassifiedGlycomics Ontology
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).
GLYCORDF
'structural biology'carbohydrateslipids'data deposition, annotation and curation'proteins'molecular biology''compound libraries and screening'All life
ClassifiedGlycoRDF
GMM
'functional genomics'plants'molecular genetics''data deposition, annotation and curation'nrrdPlants
ClassifiedGoMapMan
GoMapMan is an open web-accessible resource for gene functional annotations in the plant sciences. It was developed to facilitate improvement, consolidation and visualization of gene annotations across several plant species.
GMO
microbiology'developmental biology''microbial collection'All life
ClassifiedGrowth Medium Onotology
A structured controlled vocabulary for describing ingredients that constitute microbial growth media used in biological research centers.
GO
'functional genomics''molecular genetics''data deposition, annotation and curation''molecular interactions, pathways and networks''cell biology''molecular biology'All life
ClassifiedGene Ontology
An ontology for describing the function of genes and gene products
GO-EXT
'functional genomics''molecular genetics''data deposition, annotation and curation''molecular interactions, pathways and networks''cell biology''molecular biology'All life
ClassifiedGene Ontology Extension
Gene Ontology Extension
GO-PLUS
'functional genomics''molecular genetics''data deposition, annotation and curation''molecular interactions, pathways and networks''cell biology''molecular biology'anatomyAll life
Classifiedgo-plus
GPML
visualisation'molecular interactions, pathways and networks''data architecture, analysis and design'All life
ClassifiedGraphical Pathway Markup Language
GPML is the file format used to store pathway content at WikiPathways. GPML is short for Graphical Pathway Markup Language, and it is a custom XML format compatible with pathway visualization and analysis tools such as Cytoscape and PathVisio. Get it as RDFa in HTML: <http://vocabularies.wikipathways.org/gpml> Or get it translated to RDF/XML from either of these URLs: <http://getschema.org/rdfaliteextractor?url=http%3A%2F%2Fvocabularies.wikipathways.org%2Fgpml&out=rdf> or <http://rdf-translator.appspot.com/convert/rdfa/xml/http%3A%2F%2Fvocabularies.wikipathways.org%2Fgpml>.
GRO
anatomy'gene regulation''transcription factors and regulatory sites'plantsPoaceae
ClassifiedCereal Plant Gross Anatomy
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.
GRO-CPD
'developmental biology'plantsPoaceae
ClassifiedCereal Plant Development Ontology
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.
GRO-CPGA
anatomy'structural biology'plantsPoaceae
ClassifiedCereal Plant Gross Anatomy Ontology
A structured controlled vocabulary for the anatomy of Gramineae. Please note that this ontology has now been superseded by the <a http://bioportal.bioontology.org/ontologies/1587> Plant Ontology</a>.
GTO
'laboratory techniques'genetics'laboratory information management''data integration and warehousing'All life
UnknownGenetic Test
GTO_TESTING
'laboratory techniques'genetics'laboratory information management''data integration and warehousing'phenomicsAll life
UnknownGenetic Testing
HAAURAADO
'developmental biology'anatomy'marine biology'eukaryotes'laboratory animal science'Halocynthia aurantium
UnknownHalocynthia aurantium Anatomy and Development Ontology
HABRONATTUS
invertebrates'laboratory animal science'biologyHabronattus
UnloadableHabronattus courtship
HAO
anatomyinvertebratesHymenoptera
ClassifiedHymenoptera Anatomy Ontology
A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)
HAROREADO
'developmental biology''marine biology'anatomyeukaryotesHalocynthia roretzi
UnknownHalocynthia roretzi Anatomy and Development Ontology
HC
invertebrates'laboratory animal science'biologyHabronattus
UnknownHabronattus Courtship Ontology
HCPCS
'public health and epidemiology''laboratory techniques'surgeryanaesthesiologypathology'laboratory information management''data integration and warehousing'Human
ClassifiedHealthcare Common Procedure Coding System
Healthcare Common Procedure Coding System
HEIO
'data integration and warehousing''public health and epidemiology''laboratory techniques''laboratory information management'Human
ClassifiedRegional Healthcare System Interoperability and Information Exchange Measurement Ontology
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.
HFO
ClassifiedHeart Failure Ontology
Heart failure ontology is an attempt to define heart-failure-relevant information including the causes and risk factors, signs and symptoms, diagnostic tests and results, and treatment.
HINO
'molecular interactions, pathways and networks''protein interactions'Human
ClassifiedHuman Interaction Network Ontology
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.
HIV
virusesimmunology'public health and epidemiology''infectious disease''allergy, clinical immunology and immunotherapeutics.''reproductive health'HIV, human
UnloadableHIV ontology
The HIV ontology encompasses all knowledge about HIV
HIVO004
virusesimmunology'public health and epidemiology''infectious disease''allergy, clinical immunology and immunotherapeutics.''reproductive health'HIV, human
ClassifiedHIVOntologymain.owl
This HIV ontology has been started to be imported by other AIDS relating ontologies.
HL7
'medical imaging''public health and epidemiology''preclinical and clinical studies''data management'All life
ClassifiedHealth Level Seven Reference Implementation Model, Version 3
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.
HOM
'functional genomics'biologyAll life
ClassifiedHomology Ontology
This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.
HP
phenomicspathologyanatomybiochemistryHuman
Classifiedhuman phenotype ontology
A structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease.
HPIO
pathologyeukaryotes'molecular interactions, pathways and networks'Animalia
ClassifiedHost Pathogen Interactions Ontology
Ontology for host pathogen interactions in farmed animals
HRDO
'rare diseases''molecular interactions, pathways and networks'geneticsphenomicsAll life
ClassifiedDisease core ontology applied to Rare Diseases
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). </ br> 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.
HSAPDV
'developmental biology'Human
ClassifiedHuman Developmental Stages
Life cycle stages for Human
HUGO
genomicsgeneticsphenomicsrnaHuman
ClassifiedHuman Genome Organization Gene Symbols
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.
HUPSON
physiologyHuman
ClassifiedHuman Physiology Simulation Ontology
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.
IAO
'data management'All life
ClassifiedInformation Artifact Ontology
An ontology of information entities.
ICD10
pathology'statistics and probability'Human
UnloadableInternational Classification of Diseases, Version 10
International Statistical Classification of Diseases and Related Health Problems (ICD-10). 10th rev. Geneva
ICD10CM
pathology'statistics and probability''preclinical and clinical studies''laboratory techniques'Human
ClassifiedInternational Classification of Diseases, Version 10 - Clinical Modification
International Classification of Diseases, 10th Edition, Clinical Modification, 2011_01
ICD10PCS
'laboratory techniques'pathology'statistics and probability''preclinical and clinical studies'surgeryHuman
ClassifiedInternational Classification of Diseases, Version 10 - Procedure Coding System
ICD-10-PCS, 2009
ICD11-BODYSYSTEM
'systems biology''systems medicine'Human
ClassifiedBody System Terms from ICD11
This is a set of body-system terms used in the ICD 11 revision
ICD9CM
'laboratory techniques'pathology'statistics and probability''preclinical and clinical studies'surgeryHuman
ClassifiedInternational Classification of Diseases, Version 9 - Clinical Modification
The ICD is the international standard diagnostic classification for all general epidemiological, many health management purposes and clinical use.
ICECI
'data management'paediatrics'statistics and probability''trauma medicine'Human
ClassifiedInternational Classification of External Causes of Injuries
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.
ICF
ecology'data management''public health and epidemiology'physiologyHuman
ClassifiedInternational Classification of Functioning, Disability and Health
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. <br><br> Source: <a href="http://www.who.int/classifications/icf/en/">http://www.who.int/classifications/icf/en/</a>
ICNP
'laboratory techniques''laboratory information management'Human
UnloadableInternational Classification for Nursing Practice
International Classification for Nursing Practice
ICNP2015
ClassifiedICNP
ICO
'data integration and warehousing'Human
ClassifiedInformed Consent Ontology
An ontology of clinical informed consents
ICPC
'data management'medicinebiologyAll life
ClassifiedInternational Classification of Primary Care
The International Classification of Primary Care (ICPC). Denmark: World Organisation of Family Doctors, 1993.
ICPC2P
'data management'medicinebiologyAll life
UnloadableInternational Classification of Primary Care - 2 PLUS
ICPC-2 PLUS
ICPS
'safety sciences''data management'Human
UnloadableInternational Classification for Patient Safety
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.
IDO
'infectious disease''public health and epidemiology'Human
ClassifiedInfectious disease
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. <br><br> To import,<br> Latest version: <a href="http://purl.obolibrary.org/obo/ido.owl">http://purl.obolibrary.org/obo/ido.owl</a><br> This version (2010-12-02): <a href="http://purl.obolibrary.org/obo/ido/2010-12-02/ido.owl">http://purl.obolibrary.org/obo/ido/2010-12-02/ido.owl</a><br> Previous versions:<br> 2010-05-26 <a href="http://purl.obolibrary.org/obo/ido/2010-05-26/ido.owl">http://purl.obolibrary.org/obo/ido/2010-05-26/ido.owl</a><br> 2009-08-14 <a href="http://purl.obolibrary.org/obo/ido/2009-08-14/ido.owl">http://purl.obolibrary.org/obo/ido/2009-08-14/ido.owl</a><br> <br> <br> Latest release notes at <a href="http://infectiousdiseaseontology.org/page/Download">http://infectiousdiseaseontology.org/page/Download</a><br> Please note: The ontology metrics displayed by BioPortal do not distinguish IDO-developed terms from terms imported from other ontologies.
IDOBRU
'infectious disease''veterinary medicine'vertebrates'prokaryotes and archae'gastroenterologyHuman, vertebrata, brucella
ClassifiedBrucellosis Ontology
Brucellosis Ontology is a biomedical ontology in the domain of zoonotic disease brucellosis that is caused by Brucella, a facultative intracellular baterium.
IDODEN
'infectious disease'virusesinvertebrates'public health and epidemiology'Human, culicidae
ClassifiedDengue Fever Ontology
An ontology for dengue fever.
IDOMAL
'infectious disease'virusesinvertebrates'public health and epidemiology'Human, culicidae
ClassifiedMalaria Ontology
An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.
IDOPlant
ClassifiedInfectious Disease Ontology Plant
The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease.
IDQA
'data management'All life
ClassifiedImage and Data Quality Assessment Ontology
Image and Data Quality Assessment for scientific data management
IEV
'molecular interactions, pathways and networks''protein interactions'All life
ClassifiedEvent (INOH pathway ontology)
IFAR
'musculoskeletal medicine'pathologygeneticsHuman
ClassifiedFanconi Anemia Ontology
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.
IGTO
'laboratory techniques''laboratory information management'genetics'data integration and warehousing'All life
UnknownScientific Evidence Based Genetic Testing Ontology
IMGT-ONTOLOGY
immunology'population genetics''systems biology''immunoproteins, genes and antigens''allergy, clinical immunology and immunotherapeutics.''medical informatics'proteomicsgenomicsAll life
ClassifiedImmunogenetics Ontology
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.
IMMDIS
immunology'allergy, clinical immunology and immunotherapeutics.'pathologyinsdxml'immunoproteins, genes and antigens'Human
UnloadableImmune Disorder Ontology
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. <br><br> <b>Lineage(s)</b> <br><br> 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. <br><br> <b>Annotations</b> <br><br> Specific information may be available about a class, including Preferred_Name, DEFINITION, Synonym, etc. The following provides more detail on annotation information presented:<br> DEFINITION: A human-readable definition is provided for each class in the ontology and the displayed format is Owner|Definition (Source).<br> 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.<br> 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.<br> ICD-9_Code: Code of International Classification of Diseases and Related Health Problems, 9th revision.<br> 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.<br> Preferred_Name: A human-friendly and commonly used name in plain English.<br> 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.<br> 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. <br><br> <b>Relationships (Object Properties)</b> <br><br> 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. <br><br> <b>Datatype Properties</b> <br><br> 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.
IMR
'protein families'proteomics'molecular biology'All life
ClassifiedMolecule role (INOH Protein name/family name ontology)
INM-NPI
ClassifiedINM - NPI ontology
Interventionnelle Non Médicamenteuse, Non-Pharmacological Interventions
INO
'molecular interactions, pathways and networks''protein interactions''molecular biology'All life
ClassifiedInteraction Network Ontology
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.
INSECTH
ClassifiedinsectH
NeuroMorpho.Org insect brain regions ontology is compiled to create data annotation standard for depositing insect data. Currently at v6.2, NeuroMorpho.Org hosts over 17k neuronal reconstructions mostly from the fly. The insect ontology follows the standard nomenclature of the insect brain (Ito et al., 2013) and the virtualfly.org.
INVERSEROLES
ClassifiedISO-15926-2_2003_inverseRoles
ISO inverse roles ontology for oil and gas
IPR
'protein families'proteomics'molecular biology''protein domains and folds'All life
UnloadableProtein Domains
ISO-15926-2_2003
ClassifiedISO-15926-2_2003_oil
This ontology describes gas and oil field process level descriptions
ISO-ANNOTATIONS
ClassifiedISO-15926-2_2003_annotations
Oil and Gas Annotations
IXNO
'molecular interactions, pathways and networks''protein interactions''molecular biology''toxins and targets'toxicology'data deposition, annotation and curation'Human
ClassifiedInteraction Ontology
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.
InterNano
moleculesAll life
ClassifiedInterNano Nanomanufacturing Taxonomy
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
JERM
microbiology'systems biology''data management''microbial collection'All life
ClassifiedSysMO JERM Ontology of Systems Biology for Micro-Organisms
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/
JLVO
ClassifiedJennifer Ontology
JOCHEM
Unknownjoint chemical dictionary
KISAO
biophysics'molecular modelling''systems biology''molecular dynamics'All life
ClassifiedKinetic Simulation Algorithm Ontology
A classification of algorithms available for the simulation of models in biology.
LBO
ClassifiedLivestock Breed Ontology
A vocabulary for buffalo, cattle, chicken, goat, horse, pig, and sheep breeds.
LDA
neurobiologyneurologypsychiatrypaediatrics'text mining'Human
ClassifiedOntology of Language Disorder in Autism
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.
LEGALAPA
psychiatry'data management'Human
Classifiedlegalapa
this is a test with the legal cluster of apa ontology
LEGALAPATEST2
'data management'psychiatryHuman
Classifiedapalegal
Legal cluster for APA ontology
LHN
'marine biology'anatomy'developmental biology'physiologyeukaryotesCaretta caretta
ClassifiedLoggerhead Nesting Ontology
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 (<i>Caretta caretta</i>) nesting behavior, based on the published ethogram of Hailman and Elowson.
LIPRO
lipids'systems biology''functional genomics'All life
ClassifiedLipid Ontology
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.
LOGGERHEAD
'marine biology'anatomy'developmental biology'physiologyeukaryotesCaretta caretta
ClassifiedLoggerhead nesting
LOINC
'laboratory information management''laboratory techniques'All life
ClassifiedLogical Observation Identifier Names and Codes
Logical Observation Identifier Names and Codes (LOINC)
LPT
eukaryotesbiology'data management'Animalia
ClassifiedLivestock Product Trait Ontology
MA
anatomy'laboratory animal science'biologyeukaryotes'mouse clinic'Mouse
ClassifiedMouse adult gross anatomy
A structured controlled vocabulary of the adult anatomy of the mouse (Mus).
MAMO
mathematics'systems biology'biochemistry'computational biology''computational chemistry'All life
ClassifiedMathematical modeling ontology
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.
MAO
UnloadableMultiple alignment
MAT
anatomy'model organisms'biologyAll life
ClassifiedMinimal anatomical terminology
Minimal set of terms for anatomy
MATR
ClassifiedMaterial
List of material Objects from SWEET ontology
MATRCOMPOUND
ClassifiedMaterial Compound
Material Compound details from SWEET ontology
MATRELEMENT
ClassifiedMaterial Element
Material Element part of SWEET ontology
MATRROCK
ClassifiedMaterial Rock
RocK material
MATRROCKIGNEOUS
ClassifiedMaterial Rock Igneouus
matrRockIgneous
MCBCC
pathology'genetic variation'oncology'cell biology''cell culture collection''pharmacokinetics and pharmacodynamics''medicinal chemistry'anatomybiochemistryAll life
ClassifiedBreast Tissue Cell Lines Ontology
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
MCCL
pathology'genetic variation''cell biology''cell culture collection''pharmacokinetics and pharmacodynamics''medicinal chemistry'anatomybiochemistryAll life
ClassifiedCell Line Ontology [by Mahadevan]
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.
MCCV
microbiology'cell culture collection''microbial collection'All life
ClassifiedMicrobial Culture Collection Vocabulary
Structured controlled vocabulary for describing meta information of microbial calture collection maintained in biological research centers
MDDB
'preclinical and clinical studies'pharmacology'pharmacokinetics and pharmacodynamics'All life
UnloadableMaster Drug Data Base Clinical Drugs
Master Drug Data Base, 2009_08_05
MEDDRA
'preclinical and clinical studies'pharmacology'pharmacokinetics and pharmacodynamics'pharmacovigilence'regulatory affairs'All life
UnloadableMedical Dictionary for Regulatory Activities
Medical Dictionary for Regulatory Activities Terminology (MedDRA)
MEDEON
ClassifiedMedical Error Ontology
This is a demo version of the patient safety ontology.
MEDLINEPLUS
'public health and epidemiology'pathologypharmacology'ontology and terminology'Human
ClassifiedMedlinePlus Health Topics
MedlinePlus Health Topics;National Library of Medicine;June 14, 2008;Bethesda, MD
MEDO
'laboratory animal science''laboratory techniques'geneticsphenomics'mouse clinic'Mouse
ClassifiedMouse Experimental Design Ontology
A representation of experimental design for high-throughput mouse analysis pipelines.
MEGO
'protein families'geneticsinsdxmlAll life
ClassifiedMobile Genetic Element Ontology
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.
MEO
ecologymicrobiology'model organisms'metagenomics'microbial collection'All life
ClassifiedMetagenome and Microbes Environmental Ontology
An Ontology for organismal habitats (especially focused on microbes)
MERA
'data integration and warehousing'biologymedicineAll life
ClassifiedMedical Educational Resource Aggregator
MESH
'data management'biologypathologyAll life
ClassifiedMedical Subject Headings
Medical Subject Headings (MeSH);National Library of Medicine; 2011
MF
psychiatrypathologyinsdxmlAll life
ClassifiedMental Functioning Ontology
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.
MFMO
anatomy'musculoskeletal medicine''ear, nose and throat medicine'dentistryMammalia
ClassifiedMammalian Feeding Muscle Ontology
The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors.
MFO
'developmental biology'anatomy'marine biology'eukaryotesOryzias latipes
UnloadableMedaka fish anatomy and development
A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, <i>Oryzias latipes</i>.
MFOEM
psychiatryHuman
ClassifiedEmotion Ontology
An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings.
MFOMD
pathologypsychiatryHuman
ClassifiedMFO Mental Disease Ontology
An ontology to describe and classify mental diseases
MHC
physiologygenetics'immunoproteins, genes and antigens'vertebratesmoleculesGnathostomata
ClassifiedMajor Histocompatibility Complex Ontology
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.
MI
'protein interactions''molecular interactions, pathways and networks''laboratory techniques''data deposition, annotation and curation'All life
ClassifiedMolecular interactions
A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions.
MIAPA
phylogeneticsgeneticsAll life
ClassifiedMIAPA Ontology
An application ontology to formalize annotation of phylogenetic data.
MICRO
Unloadableprokaryotic phenotypic and metabolic characters
An ontology of prokaryotic phenotypic and metabolic characters
MIM
phenomicsmetabolomicsmetabolites'metabolic pathways''prokaryotes and archae'Bacteria, archaea
ClassifiedMolecular Interaction Map
The Molecular Interaction Map (MIM) notation seeks to provide a standardized method to draw diagrams for bioregulatory networks with features similar to technical diagrams in other fields. This vocabulary uses the term hierarchy from the Formal MIM Notation Specification. Where possible, Systems Biology Ontology (SBO) and Biological Pathway Exchange (BioPAX) terms and IRIs are used. If no SBO or BioPAX term is available, a new term and IRI are created. This is currently only a partial implementation. Many elements still need to be added to cover the full the specification.
MINERAL
ClassifiedMaterial Mineral
Material Mineral
MIRNAO
'functional, regulatory and non-coding rna'metabolitesmetabolomicsAll life
UnloadablemicroRNA Ontology
An application ontology for use with miRNA databases.
MIRO
invertebrates'laboratory animal science'pharmacologybiologyCulicidae
ClassifiedMosquito insecticide resistance
Application ontology for entities related to insecticide resistance in mosquitos
MIXS
sequencing'sequence analysis'All life
ClassifiedMinimal Information about any Sequence Ontology
An RDF representation of the MIxS Family of Checklists
MIXSCV
sequencing'sequence analysis'All life
ClassifiedMinimal Information about any Sequence (MIxS) Controlled Vocabularies
Controlled vocabularies for the MIxS family of metadata checklists. See http://gensc.org/gc_wiki/index.php/MIxS for details on the MIxS checklists.
MMO
'laboratory techniques'phenomics'preclinical and clinical studies'All life
ClassifiedMeasurement method ontology
A representation of the variety of methods used to make clinical and phenotype measurements.
MMUSDV
anatomy'developmental biology''mouse clinic''laboratory animal science'Mouse
ClassifiedMouse Developmental Stages
Life cycle stages for Mus Musculus
MNR
ClassifiedMaterial Natural Resource
Natural Resource
MO
'laboratory techniques''gene expression'All life
ClassifiedMicroarray and Gene Expression Data Ontology
Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1.
MOC
ClassifiedMaterial Organic Compound
Organic Compound
MOD
'protein modifications''molecular biology''chemical biology'All life
ClassifiedProtein modification
PSI-MOD is an ontology consisting of terms that describe protein chemical modifications
MOOCCIADO
'marine biology'anatomy'developmental biology'physiologyeukaryotesMolgula occidentalis
UnknownMolgula occidentalis Anatomy and Development Ontology
MOOCCUADO
'marine biology'anatomy'developmental biology'physiologyeukaryotesMolgula occulta
UnknownMolgula occulta Anatomy and Development Ontology
MOOCULADO
'marine biology'anatomy'developmental biology'physiologyeukaryotesMolgula occulta
UnknownMolgula oculata Anatomy and Development Ontology
MOP
'molecular interactions, pathways and networks''molecular biology''chemical biology'All life
ClassifiedMolecular Process Ontology
Processes at the molecular level
MP
eukaryotesphenomicsanatomypathology'chemical biology'Mammalia
ClassifiedMammalian phenotype
Standard terms for annotating mammalian phenotypic data.
MPATH
anatomyphenomics'mouse clinic''laboratory animal science'pathologyMouse
ClassifiedMouse pathology
A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes
MRO
genetics'immunoproteins, genes and antigens'moleculesAll life
ClassifiedMHC Restriction Ontology
An ontology for Major Histocompatibility Complex (MHC) restriction in experiments
MS
proteomics'mass spectrometry''laboratory information management'All life
ClassifiedMass spectrometry ontology
A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.
MSO
pathologyneurobiologypsychiatryneurologyHuman
ClassifiedMultiple sclerosis ontology
Multiple sclerosis ontology integrated with Basic formal ontology.
MSTDE
'laboratory techniques'gastroenterology'systems medicine'pathologyHuman
ClassifiedMinimal Standard Terminology of Digestive Endoscopy
Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy. Bethesda, MD: National Library of Medicine, 2001.
MSTDE-FRE
'laboratory techniques'gastroenterology'systems medicine'pathologyHuman
ClassifiedMinimal Standard Terminology of Digestive Endoscopy, French
Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy, French Translation, 2001
MSV
metagenomics'sample collections'All life
ClassifiedMetagenome Sample Vocabulary
An ontology for metagenome sample metadata. This ontology mainly defines predicates.
MWLA
'data management'Human
ClassifiedMedical Web Lifestyle Aggregator
NATPRO
'chemical biology'biologyAll life
ClassifiedNatural Products Ontology
An ontology for describing biological activities of natural products.
NBO
neurobiologyneurologypsychiatryphenomicsbiochemistry'chemical biology'Human
ClassifiedNeuro Behavior Ontology
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
NCBITAXON
'data management''model organisms'All life
ClassifiedNCBI organismal classification
An ontology representation of the NCBI organismal taxonomy
NCCO
'laboratory information management'medicineHuman
ClassifiedNursing Care Coordination Ontology
Nursing Care Coordination Ontology contains activities that nurses use while coordinating care among patients.
NCIT
oncology'translational medicine''preclinical and clinical studies'bioinformaticspathologyHuman
ClassifiedNational Cancer Institute Thesaurus
A vocabulary for clinical care, translational and basic research, and public information and administrative activities.
NCITHESAURUS
oncologypathologyHuman
UnloadableNCI Thesaurus
an ontology-like vocabulary that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities
NCRO
'functional, regulatory and non-coding rna'All life
ClassifiedNon-coding RNA Ontology
NDDF
'medicine research and development''medicinal chemistry'pharmacologyAll life
UnloadableNational Drug Data File
National Drug Data File Plus Source Vocabulary
NDFRT
'medicine research and development''medicinal chemistry'pharmacologyAll life
UnloadableNational Drug File - Reference Terminology
National Drug File - Reference Terminology Public Inferred Edition, 2008_03_11
NEMO
neurobiologyneurologypsychiatrybiophysicsHuman
ClassifiedNeural ElectroMagnetic Ontology
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/.
NEOMARK3
oncologydentistrypathology'medical informatics'Human
ClassifiedNeomark Oral Cancer Ontology, version 3
Ontology that describes the medical information necessary for early detection of the oral cancer reoccurrence extracted from the NeoMark Project.
NEOMARK4
oncologydentistrypathology'medical informatics'Human
ClassifiedNeomark Oral Cancer Ontology, version 4
Ontology that describes the medical information necessary for early detection of the oral cancer reoccurrence extracted from the NeoMark Project.
NEUMORE
biophysicsneurologyneurobiologyHuman
ClassifiedNeural Motor Recovery Ontology
Neural Functional Motor Recovery Ontology
NGSONTO
'laboratory information management'genomicssequencingdnaAll life
ClassifiedNGS ontology
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.
NHSQI2009
'quality affairs''data management'Human
UnknownNHS Quality Indicators
NIC
'laboratory information management'medicineHuman
UnknownNursing Interventions Classification
NIDM-RESULTS
ClassifiedNIDM-Results
NIDM-Results is a data model that enable sharing neuroimaging results using a common descriptive standard across neuroimaging software. NIDM-Results focuses on mass-univariate studies and is mostly targeted at fMRI but is also suitable for anatomical MRI (with Voxel-Based Morphometry), and Positron Emission Tomography (PET). NIDM-Results packs provide a lightweight solution to share maps generated by neuroimaging studies along with their metadata. Export to NIDM-Results is natively implemented in SPM, NeuroVault and CBRAIN and a Python library is ready for integration in FSL. NeuroVault additionally can import NIDM-Results packs.
NIFCELL
'cell biology'neurologyneurobiology'data integration and warehousing''biomedical science'All life
ClassifiedNeuroscience Information Framework (NIF) Cell Ontology
Cell types from NIFSTD
NIFDYS
pathologyneurologyneurobiology'biomedical science'Human
ClassifiedNeuroscience Information Framework (NIF) Dysfunction Ontlogy
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.
NIFSTD
neurology'cell biology'neurobiology'data integration and warehousing''biomedical science'All life
UnknownNeuroscience Information Framework (NIF) Standard Ontology
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.
NIFSUBCELL
'structural biology''cell biology'neurologyproteins'data integration and warehousing''biomedical science'neurobiologyAll life
ClassifiedNeuroscience Information Framework (NIF) Subcellular Ontology
http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl
NIF_CELL
'cell biology'neurologyneurobiology'data integration and warehousing'All life
ClassifiedNIF Cell
Neuronal cell types
NIF_DYSFUNCTION
pathologyneurologyneurobiology'biomedical science'Human
ClassifiedNIF Dysfunction
NIF_GROSSANATOMY
neurologyneurobiology'data integration and warehousing'anatomyAll life
ClassifiedNIF Gross Anatomy
NIGO
'systems biology''systems medicine'neurologyneurobiology'data integration and warehousing'immunology'immunoproteins, genes and antigens'geneticsHuman, rat, mouse
ClassifiedNeural-Immune Gene Ontology
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.
NIHSS
neurologyneurobiology'data integration and warehousing'Human
ClassifiedNational Institutes of Health Stroke Scale Ontology
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.
NLMVS
'data management'medicineHuman
UnloadableNIH NLM Value Sets
NMOBR
neurologyneurobiology'data integration and warehousing'All life
ClassifiedNeuroMorpho.Org brain region ontologies
NMOSP
neurologyneurobiology'data integration and warehousing'genetics'model organisms'All life
ClassifiedNeuroMorpho.Org species ontology
The species ontology of NeuroMorpho.Org was updated (OntoSearch v1.3) to map the new species and strains added in NeuroMorpho.Org v6.3 release.
NMR
metabolomicsmetabolites'data integration and warehousing'All life
ClassifiedNMR-Instrument Component of Metabolomics Investigations Ontology
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.
NONRCTO
'preclinical and clinical studies'Human
ClassifiedNon-Randomized Controlled Trials Ontology
We built an ontology to help the systematic review and meta-analysis process of non randomized clinical trials.
NORREG
UnloadableNorwegian national quality registries- Variabelbibliotek for medisinske kvalitetsregistre
Norway has 52 national quality registers with over 5000 different variables, which each has their own value set. This is a mapping between similar variables and to other ontologies.
NPHO
plantsphenomicsanatomy'developmental biology'Solanaceae
ClassifiedNightshade Phenotype Ontology
first draft
NPI
ClassifiedNon-Pharmacological Interventions (NPIs)
Terminologies of Non-Pharmacological Interventions
NPO
oncologybiophysicschemistrypathologyAll life
ClassifiedNanoParticle Ontology
An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.
NTDO
'infectious tropical disease''public health and epidemiology'Human
ClassifiedNeglected Tropical Disease Ontology
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.
OAE
pharmacologypharmacovigilenceAll life
ClassifiedOntology of Adverse Events
A biomedical ontology in the domain of adverse events
OBA
anatomy'chemical biology''model organisms'biologyAll life
ClassifiedOntology of Biological Attributes
A collection of biological attributes (traits) covering all kingdoms of life.
OBCS
'preclinical and clinical studies''statistics and probability'biology'chemical biology''biomedical science'All life
ClassifiedOntology of Biological and Clinical Statistics
A biomedical ontology in the domain of biological and clinical statistics.
OBI
'preclinical and clinical studies''functional genomics''biomedical science'biology'data deposition, annotation and curation'Human
ClassifiedOntology for Biomedical Investigations
An integrated ontology for the description of life-science and clinical investigations
OBIB
biobank'laboratory information management''biomedical science''data deposition, annotation and curation'Human
ClassifiedOntology for Biobanking
An ontology built for annotation and modeling of biobank repository and biobanking administration
OBIWS
bioinformatics'biomedical science'biology'data deposition, annotation and curation'All life
ClassifiedBioinformatics Web Service Ontology
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.
OBI_BCGO
'cell biology'genomics'data deposition, annotation and curation'All life
ClassifiedBeta Cell Genomics Ontology
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.
OBOE-SBC
ecologyAll life
ClassifiedSanta Barbara Coastal Observation Ontology
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.
OBOREL
biology'biomedical science''data management'All life
ClassifiedOpen Biological and Biomedical Ontologies Relationship Types
Defines core relations used in all OBO ontologies. Obsolete. Replaced with RO.
OBO_REL
biology'biomedical science''data management'All life
ClassifiedOBO relationship types (legacy)
OCHV
ClassifiedOntology of Consumer Health Vocabulary
A SKOS-encoded implementation of the "Open Access, Collaborative Consumer Health Vocabulary Initiative" by the University of Utah (consumerhealthvocab.org and layhealthinformatics.com)
OCRE
'data management''preclinical and clinical studies''biomedical science'Human
UnloadableOntology of Clinical Research
OCRe is an ontology designed to support systematic description of, and interoperable queries on, human studies and study elements.
OCVDAE
ClassifiedOntology of Cardiovascular Drug Adverse Events
OCVDAE is a biomedical ontology of cardiovascular disease drug-associated adverse events
ODNAE
pharmacovigilencepharmacologyneurobiologyneurologyAll life
ClassifiedOntology of Drug Neuropathy Adverse Events
OF
ClassifiedOntoFood
This is an ontology with SWRL rules of nutrition for diabetic patient. We can import the value of Blood Sugar and Weight by .xls and use that like instance for generate the rules with rule engine Jess.
OFSMR
ClassifiedOpen Food Safety Model Repository
ontology
OGDI
'population genetics'pathologygenomics'genetic variation''endocrinology and metabolism'Human
UnknownOntology for Genetic Disease Investigations
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) .
OGG
geneticsgenomics'model organisms'All life
UnloadableThe Ontology of Genes and Genomes
A formal ontology of genes and genomes of biological organisms.
OGG-MM
geneticsgenomics'laboratory animal science''mouse clinic'Mouse
ClassifiedOntology of Genes and Genomes - Mouse
OGG-Mm is the OGG Mus musculus (mouse) subset. The OGG (Ontology of Genes and Genomes) is a formal ontology of genes and genomes of biological organisms. OGG is developed by following OBO Foundry principles and aligning with the BFO top ontology.
OGI
geneticsgenomicsbiomarkersrnadnainsdxmlAll life
UnloadableOntology for genetic interval
An ontology that formalizes the genomic element by defining an upper class genetic interval
OGMD
pathologyphenomics'endocrinology and metabolism'metabolomicsmetabolitesHuman
ClassifiedOntology of Glucose Metabolism Disorder
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.
OGMS
oncologypathologyHuman
ClassifiedOntology for General Medical Science
An ontology for representing treatment of disease and diagnosis and on carcinomas and other pathological entities
OGR
ecologyAll life
ClassifiedOntology of Geographical Region
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.
OGSF
pharmacologypharmacovigilencepathologygeneticsHuman
UnloadableOntology of Genetic Susceptibility Factor
An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.
OLATDV
'marine biology'anatomy'developmental biology'physiologyeukaryotesOryzias latipes
ClassifiedMedaka Developmental Stages
Life cycle stages for Medaka
OMIM
'population genetics''biomedical science'Human
ClassifiedOnline Mendelian Inheritance in Man
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
OMIT
'cell biology'pathologyrnabioinformaticsgeneticsHuman
ClassifiedOntology for MIRNA Target
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.
OMP
microbiologyphenomics'microbial collection'All life
ClassifiedOntology of Microbial Phenotypes
An ontology of phenotypes covering microbes
OMRSE
'public health and epidemiology''data management'Human
ClassifiedOntology of Medically Related Social Entities
This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations.
ONL-DP
imagingneurologyneurobiology'data integration and warehousing'Human
ClassifiedDataset processing
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.
ONL-MR-DA
imagingneurologyneurobiology'data integration and warehousing'Human
ClassifiedMagnetic Resonance Dataset Acquisition Ontology
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.
ONL-MSA
psychiatryimagingneurologyneurobiology'data integration and warehousing'Human
ClassifiedMental State Assessment
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).
ONLIRA
'hepatic and biliary medicine''medical imaging'Human
ClassifiedOntology of Liver for Radiology
ONLIRA (Ontology of the Liver for Radiology) focuses on a semantic specification of imaging observations of CT scans for the liver. ONLIRA extends RadLex with semantic relationships that describe and relate the concepts. Thus, automated processing tasks, such as identifying similar patients, are supported.
ONSTR
'translational medicine'paediatrics'data integration and warehousing'Human
ClassifiedOntology for Newborn Screening Follow-up and Translational Research
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).
ONTOAD
neurobiologyneurologypathologypsychiatry'geriatric medicine'pathologyHuman
ClassifiedBilingual Ontology of Alzheimer's Disease and Related Diseases
OntoAD is a bilingual (English-French) domain ontology for modeling knowledge about Alzheimer's Disease and Related Syndromes.
ONTODM-CORE
'data deposition, annotation and curation''computer science''data architecture, analysis and design'All life
ClassifiedOntology of Core Data Mining Entities
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.
ONTODM-KDD
'data deposition, annotation and curation''data architecture, analysis and design''computer science'All life
ClassifiedOntology of Data Mining Investigations
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.
ONTODT
'data deposition, annotation and curation''computer science''data architecture, analysis and design'All life
ClassifiedOntology of General Purpose Datatypes
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.
ONTOKBCF
'molecular modelling''molecular genetics''respiratory medicine''hepatic and biliary medicine''urology and nephrology'gastroenterologypathology'public health and epidemiology'Human
ClassifiedOntological Knowledge Base Model for Cystic Fibrosis
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.
ONTOLURGENCES
'public health and epidemiology''data management'Human
ClassifiedEmergency care ontology
Emergency care ontology build during LERUDI project. http://www.ncbi.nlm.nih.gov/pubmed/25160343 (v4.0)
ONTOMA
'complementary medicine'Human
ClassifiedOntology of Alternative Medicine, French
Common concepts for communication between traditional medicine and western medicine. (In French)
ONTONEO
ClassifiedOntology of the Obstetric and Neonatal Domain
The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby.
ONTOPNEUMO
'respiratory medicine'Human
ClassifiedOntology of Pneumology
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/.
ONTOTOXNUC
toxicology'toxins and targets''medical toxicology'Human
ClassifiedOntology of Nuclear Toxicity
Ontology of nuclear toxicity developed during ToxNuc project <>.
OOEVV
'laboratory techniques''laboratory information management'All life
ClassifiedOntology of Experimental Variables and Values
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.
OPB
biophysics'molecular dynamics''systems biology'All life
ClassifiedOntology of Physics for Biology
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.
OPE
'musculoskeletal medicine'biologyAll life
ClassifiedOntology of Physical Exercises
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.
OPL
'developmental biology'parasitology'model organisms'All life
ClassifiedOntology for Parasite LifeCycle
A reference ontology for parasite life cycle stages.
ORDO
'rare diseases''computational biology''medical informatics'geneticsphenomics'literature and reference''public health and epidemiology'Human
ClassifiedOrphanet Rare Disease Ontology
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 <http://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).
ORTH
ClassifiedOrthology Ontology
Orthology Ontology
ORTHO
'population genetics'bioinformaticsAll life
ClassifiedOrtholog Ontology
Ortholog Ontology (OrthO)
OVAE
pharmacologypharmacovigilence'immunoproteins, genes and antigens'immunologypathologyHuman
ClassifiedOntology of Vaccine Adverse Events
A biomedical ontology in the domain of vaccine adverse events.
OntoVIP
'medical imaging''public health and epidemiology''data management'anatomypathologyHuman
ClassifiedMedical image simulation
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.
OpenToxAlgorithm
ClassifiedOpenTox Algorithm Ontology
Algorithm Ontology, as specified by the OpenTox project, and described in http://www.opentox.org/dev/apis/api-1.2/Ontology and http://www.opentox.org/dev/apis/api-1.2/Algorithms
OpenTox_Resource
ClassifiedOpenTox Resource Ontology
Ontology for resources of the OpenTox project, as described in http://www.opentox.org/dev/apis/api-1.2/Ontology
PAE
plantsanatomy'developmental biology''cell biology'Plants
ClassifiedPlant Anatomy
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/
PAO
plantsanatomy'developmental biology''cell biology'Plants
ClassifiedPlant Anatomy Ontology
PATHLEX
anatomypathologyHuman
ClassifiedAnatomic Pathology Lexicon
PathLex, a comprehensive lexicon—a unified language of anatomic pathology terms—for standardized indexing and retrieval of anatomic pathology information resources.
PATO
phenomicsAll life
ClassifiedPhenotypic quality
An ontology of phenotypic qualities (properties, attributes or characteristics)
PAV
'data deposition, annotation and curation'All life
ClassifiedPAV Provenance, Authoring and Versioning
PAV is a lightweight ontology for tracking Provenance, Authoring and Versioning. PAV specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources. This ontology describes the defined PAV properties and their usage. Note that PAV does not define any explicit classes or domain/ranges, as every property is meant to be used directly on the described online resource.
PCO
'data management''model organisms'All life
ClassifiedPopulation and Community Ontology
A taxon-neutral ontology of material entities, qualities, and processes related to collections of interacting organisms such as populations and communities.
PDO
microbiology'infectious disease''microbial collection'Human
ClassifiedPathogenic Disease Ontology
An ontology for describing both human infectious diseases caused by microbes and the diseases that is related to microbial infection.
PDON
neurobiologyneurologypathologypsychiatry'geriatric medicine''biomedical science''molecular medicine''molecular biology'Human
ClassifiedParkinson's Disease Ontology
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.
PDO_CAS
plantsbiodiversityPlants
ClassifiedPlant Diversity Ontology
PDQ
oncology'preclinical and clinical studies'geneticspharmacology'information retrieval'Human
ClassifiedPhysician Data Query
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.
PDUMDV
'marine biology'anatomy'developmental biology'anatomyinvertebratesPlatynereis
ClassifiedPlatynereis Developmental Stages
Life cycle stages for Platynereis dumerilii
PD_ST
'marine biology'anatomy'developmental biology'anatomyinvertebratesPlatynereis
ClassifiedPlatynereis stage ontology
PE
ClassifiedPulmonary Embolism Ontology
A controlled vocabulary of PE-relevant information. Currently, only treatment information is available.
PEAO
'laboratory techniques'plants'developmental biology'anatomyPlants
ClassifiedPlant Experimental Assay Ontology
The Plant domain has been the subject of several attempts to structure and formally define terms and corresponding relations, such as their anatomical features, developmental stages, and the application of particular experimental procedures to a biological problem. However, a focus on experimental assays in order to describe the whole experimental procedure, to the best of our knowledge, has only been attempted in the context of a very general description based on classical views of the scientific method. In this study, we focus on the development and proposal of an ontology dedicated to the description of these experimental procedures, regardless of the scientific questions that prompted the assays. This ontology includes entities from three distinct realms (biological, physical and data), which include both experimental products, their relations and the protocols describing their manipulation. The final outcome is a useful and comprehensive ontology in the plant domain, to be used as a log book by experimentalists, providing a formal relation between entities.
PECO
ecologyplants'developmental biology'Plants
ClassifiedPlant Environmental Conditions
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.
PEDTERM
paediatrics'gynaecology and obstetrics''developmental biology'anatomyHuman
ClassifiedPediatric Terminology
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.
PEO
'developmental biology'parasitology'model organisms''laboratory animal science''gene expression'All life
ClassifiedParasite Experiment Ontology
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.
PGDSO
ecologyplants'developmental biology'Plants
ClassifiedPlant Growth and Development Stage
PHAGE
ClassifiedPhylogenetics Ontology
This ontology represent the seven steps of phylogenetic analyses. Each root concept step is composed from a set of resource annotations (to represent the data-flow) and programs (to represent the control flow). Object properties serve to represent relations to annotate data (e.g. has_RetrievedInDatabase, has_ModeledBy, etc.) and reorder the sequence of programs (e.g. has_InputOutput).This ontology has been collected in a semi-automated way from well-known databases such as NCBI, GeneOntology, UniProtKB and Felsenstein’s Web site through Web crawling and mapping techniques.
PHARE
pharmacogenomicsphenomicsAll life
ClassifiedPharmacogenomic Relationships Ontology
The PHArmacogenomic RElationships Ontology (or PHARE) proposes concepts and roles to represent relationships of pharmacogenomics interest.
PHARMGKB
'chemical biology'phenomicsbiologypharmacologyAll life
UnknownPharmGKB Ontology
PHENOMEBLAST
pathologyphenomicsanatomyAll life
UnloadablePhenomeBLAST Ontology
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.
PHENX
ecologyphenomicspathologyHuman
ClassifiedPhenX Phenotypic Terms
Standard measures related to complex diseases, phenotypic traits and environmental exposures
PHFUMIADO
'marine biology'eukaryotes'developmental biology'anatomyPhallusia fumigata
UnknownPhallusia fumigata Anatomy and Development Ontology
PHMAMMADO
'marine biology'eukaryotes'developmental biology'anatomyPhallusia fumigata
UnknownPhallusia mammillata Anatomy and Development Ontology
PHYLONT
phylogenetics'computational biology'bioinformaticsAll life
ClassifiedPhylogenetic Ontology
Ontology for Phylogenetic Analysis
PIERO
'data deposition, annotation and curation'enzymes'molecular interactions, pathways and networks'metabolomicsmetabolitesAll life
ClassifiedEnzyme Reaction Ontology for annotating Partial Information of chemical transformation
Enzyme Reaction Ontology for annotating Partial Information of chemical transformation
PLIO
'protein interactions''data deposition, annotation and curation''molecular interactions, pathways and networks'proteomicsAll life
ClassifiedProtein-ligand interaction ontology
The protein--ligand interaction ontology (PLIO) was developed around three main concepts, namely target, ligand and interaction, and was enriched by adding synonyms, useful annotations and references.
PLO
microbiology'developmental biology'parasitologyPlasmodium
UnloadablePlasmodium life cycle
PLOSTHES
'ontology and terminology'All life
ClassifiedPLOS Thesaurus
The PLOS Thesaurus includes over 10,000 Subject Area terms covering the wide range of research topics included the PLOS journals. It was initially built for us over the course of 2012 by Access Innovations (http://www.accessinn.com/). The entire corpus of PLOS articles was analysed to ensure that the thesaurus covers the research domain comprehensively. We release updates several times a year.
PMA
'data management'All life
ClassifiedPortfolio Management Application
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
PMR
'medical informatics''preclinical and clinical studies''data integration and warehousing'All life
ClassifiedPhysical Medicine and Rehabilitation
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.
PO
anatomygenomicsplants'developmental biology'Plants
ClassifiedPlant Ontology
The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.
PORO
'marine biology'eukaryotes'developmental biology'anatomyPorifera
ClassifiedPorifera Ontology
An ontology covering the anatomy of the taxon Porifera (sponges)
PP
'data management'All life
ClassifiedPipeline Patterns Ontology
To answer the need for a workflow representing a sequence of data transformations, a high-level process ontology was defined, denoted Pipeline Patterns (PP) ontology. Every concept is generically a Data (class from EDAM), which can be further specified as an Entry (P:00002) or an Exit (P:00009). All Entries can be subjected to an Operation (class from EDAM) producing an Intermediate (P:00010). An Intermediate has a TemporalEntity associated to represent its time of creation. Some Entries are specifically of the type Exit, meaning that they will represent concepts that exit the current category and be passed to the next one on the workflow. Additionally, in order to permit the treatment of a set of objects as a single entity, this high-level ontology considers the concept of List (P:00004) and more specifically an Aggregate (P:00005), containing a set of Data or Entry, respectively. The concept Intermediate is an Entry, allowing for the successive application of an operation to an Element. This is particularly useful in the case of the application of sequential set of operations.
PPIO
'protein interactions''data deposition, annotation and curation''molecular interactions, pathways and networks'proteomicsAll life
UnloadableProtein-Protein Interaction Ontology
A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Developed by the HUPO Proteomics Standards Initiative.
PR
proteomics'evolutionary biology'proteinsAll life
ClassifiedProtein Ontology
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).
PROCCHEMICAL
ClassifiedChemical Process
Chemical process
PROPREO
proteomicsproteinsAll life
ClassifiedProteomics data and process provenance
A comprehensive proteomics data and process provenance ontology.
PROVO
'data deposition, annotation and curation'All life
ClassifiedProvenance Ontology
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.
PSDS
plants'developmental biology'Plants
ClassifiedPlant Structure Development Stage
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/
PSIMOD
'molecular biology''protein modifications''chemical biology''peptides and amino acids'All life
ClassifiedProtein Modification Ontology
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.
PTO
plantsphenomics'developmental biology'Plants
ClassifiedPlant Trait Ontology
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.
PTRANS
pathologypathogens'public health and epidemiology'Human
ClassifiedPathogen Transmission Ontology
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.
PTS
'chemical biology''molecular interactions, pathways and networks'All life
Incoherent (structural)Pathway Terminology System
PVONTO
pharmacovigilencepathology'molecular biology'pharmacologyAll life
ClassifiedPharmacovigilance Ontology
A pharmacovigilance ontology to connect known facts on drugs, disease, ADEs, and their molecular mechanisms.
PW
'molecular interactions, pathways and networks''chemical biology'genetics'data deposition, annotation and curation'All life
ClassifiedPathway ontology
A controlled vocabulary for annotating gene products to pathways.
PXO
ClassifiedProteasix Ontology
The Proteasix Ontology (PxO) is a new application ontology that supports the Proteasix tool (http://www.proteasix.org/). Proteasix is an open-source peptide-centric tool that can be used to predict automatically and in a large-scale fashion in silico the proteases involved in the generation of proteolytic cleavage fragments (peptides).
PhenomeNET
ClassifiedPhenomeNET Ontology
The ontology used in PhenomeNET: an integrated, cross-species phenotype ontology.
QIBO
biomarkerspharmacology'medical imaging''biological imaging'Human
ClassifiedQuantitative Imaging Biomarker Ontology
An ontology that describes various concepts in quantitative imaging biomarkers.
QUDT
'data management'All life
ClassifiedQuantities, Units, Dimensions, and Types Ontology
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.
RADLEX
'laboratory techniques'Human
ClassifiedRadiology Lexicon
RadLex is a controlled terminology for radiology-a single unified source of radiology terms for radiology practice, education, and research. For license information see : <a href="http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/RadLex_License_Agreement_and_Terms_of_Use_V2_Final.pdf">http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/RadLex_License_Agreement_and_Terms_of_Use_V2_Final.pdf</a> Converted to use OWL format submissions
RAO
ClassifiedRheumatoid Arthritis ontology
A controlled vocabulary of RA-relevant information. Currently, only treatment information is available.
RB
'trauma medicine'neurologyneurobiologyHuman
ClassifiedRegenBase ontology
The RegenBase ontology describes biological entities and processes studied in spinal cord injury (SCI) research.
RCD
'public health and epidemiology''data management''preclinical and clinical studies'Human
UnloadableRead Codes, Clinical Terms Version 3 (CTV3)
Clinical Terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre
RCTONT
'preclinical and clinical studies''laboratory techniques'Human
ClassifiedRandomized Controlled Trials Ontology
We developed and evaluated an ontology specifically for Randomized Controlled Trials in order to facilitate the production of systematic reviews and metaanalysis.
RCTV2
ClassifiedRead Clinical Terminology Version 2
NHS UK Read Codes Version 2
RDL
UnloadableRDL
RDL
REPO
'reproductive health'phenomicsAnimalia
ClassifiedReproductive Trait and Phenotype Ontology
Ontology for livestock reproductive traits and phenotypes
RESID
'protein structure analysis''structural biology'proteinsAll life
UnloadableProtein covalent bond
For the description of covalent bonds in proteins.
RETO
'transcription factors and regulatory sites''data integration and warehousing'All life
ClassifiedRegulation of Transcription Ontology
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 and orthological properties from RO and SIO.
REX
physicschemistryAll life
ClassifiedPhysico-chemical process
An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time.
REXO
'gene regulation''data integration and warehousing'All life
ClassifiedRegulation of Gene Expression Ontolology
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, and orthology relations using ontological properties from RO and ISO.
RH-MESH
pharmacology'data integration and warehousing'pathologyphysiology'systems medicine'psychiatryAll life
ClassifiedRobert Hoehndorf Version of MeSH
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. <p><p> -------------------------- <p> 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.
RNAO
'structural biology''sequence sites, features and motifs'rnaAll life
ClassifiedRNA ontology
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.
RNPRIO
'data management''public health and epidemiology''preclinical and clinical studies'Human
ClassifiedResearch Network and Patient Registry Inventory Ontology
Ontology for Inventories of Clinical Data Research Networks, Patient-Powered Research Networks, and Patient Registries
RNRMU
ClassifiedRNRMU
The terms of RNRMU
RO
'data management'All life
ClassifiedRelations Ontology
Relationship types shared across multiple ontologies
ROLEO
'data management'All life
ClassifiedRole Ontology
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.
ROO
oncologypathologyHuman
ClassifiedRadiation Oncology Ontology
The Radiation Oncology Ontology aims to cover the radiation oncology domain with a strong focus on re-using existing ontologies.
RP
UnloadableResep Project
RPO
'public health and epidemiology'phenomicsimmunology'allergy, clinical immunology and immunotherapeutics.'Human
ClassifiedResource of Asian Primary Immunodeficiency Diseases (RAPID) Phenotype Ontology
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
RS
'laboratory animal science'eukaryotesRat
ClassifiedRat Strain Ontology
Ontology of rat strains
RSA
'data deposition, annotation and curation''sequence analysis'insdxmlAll life
ClassifiedReference Sequence Annotation
An ontology for sequence annotations and how to preserve them with reference sequences.
RXNO
'synthetic chemistry'biochemistry'molecular interactions, pathways and networks'All life
UnloadableName Reaction Ontology
Connects organic name reactions to their roles in an organic synthesis and to processes in MOP
RXNORM
'preclinical and clinical studies''medicinal chemistry'pharmacology'medicine research and development'All life
ClassifiedRxNORM
RxNorm Vocabulary
SAO
'cell biology'anatomymolecules'structural biology'All life
ClassifiedSubcellular Anatomy Ontology
SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules.
SBO
'systems biology''computational biology'bioinformaticsAll life
ClassifiedSystems Biology
Terms commonly used in Systems Biology, and in particular in computational modeling.
SBOL
'synthetic chemistry''data deposition, annotation and curation'visualisation'nucleic acid sequence analysis'dnaAll life
ClassifiedSynthetic Biology Open Language Visual Ontology
Synthetic Biology Open Language Visual (SBOLv) is an ontology to represent standardized graphical notation for synthetic biology.
SCHEMA
'data management'All life
Classifiedschema.org
A collection of schemas that webmasters can use to markup HTML pages in ways recognized by major search providers, and that can also be used for structured data interoperability (e.g. in JSON).
SD3
'documentation and help''data management'All life
ClassifiedSimulation Delivery and Documentation Deviations
SDO
neurologyneurobiologypsychiatryinsdxmlHuman
ClassifiedSleep Domain Ontology
An application ontology for the domain of Sleep Medicine.
SEDI
'biological imaging''medical imaging'Human
ClassifiedSemantic DICOM Ontology
An ontology for DICOM as used in the SeDI project.
SEP
'sample collections''laboratory techniques''data deposition, annotation and curation'All life
ClassifiedSample processing and separation techniques
A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments.
SHR
'public health and epidemiology'pathology'laboratory techniques'Human
ClassifiedStudent Health Record Ontology
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 ... .
SIBO
'developmental biology'invertebratesanatomyInsecta
ClassifiedSocial Insect Behavior Ontology
Social Behavior in insects
SIO
'data integration and warehousing'All life
ClassifiedSemanticscience Integrated Ontology
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.
SITBAC
'public health and epidemiology''data management'Human
ClassifiedSituation-Based Access Control Ontology
Context-based healthcare access-control policies
SMASH
'text mining''public health and epidemiology'biologyHuman
ClassifiedSemantic Mining of Activity, Social, and Health data Project
SNMI
'veterinary medicine''data management''model organisms'All life
ClassifiedSystematized Nomenclature of Medicine, International Version
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.
SNOMEDCT
'data management''preclinical and clinical studies'Human
UnloadableSystematized Nomenclature of Medicine - Clinical Terms
SNOMED Clinical Terms
SNPO
mapgenomics'data integration and warehousing'All life
ClassifiedSingle-Nucleotide Polymorphism (SNP) Ontology
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.
SO
'data deposition, annotation and curation''sequence analysis'insdxmlAll life
ClassifiedSequence types and features
A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases.
SOPHARM
pharmacogenomicsphenomics'preclinical and clinical studies'genomicsAll life
ClassifiedSuggested Ontology for Pharmacogenomics
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.
SOY
plants'developmental biology'Glycine max
ClassifiedSoy Ontology
Growth, trait and development ontology for soybean
SOnt
ClassifiedStroke
represent the Stroke domain
SP
ClassifiedSMART Protocols
The SeMAntic RepresenTation for Protocols, SMART Protocols, provides a structured OWL vocabulary of experimental protocols. SMART Protocols ontology includes two modules, SP-document and SP-workflow. SP-document, aims to provide a structured vocabulary of concepts to represent information necessary and sufficient for reporting an experimental protocol. SP-workflow, represents basic instructions carried out in experimental protocols.
SPD
invertebratesanatomybiologyAraneae
ClassifiedSpider Ontology
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).
SPO
dermatologyphysiologyHuman
ClassifiedSkin Physiology Ontology
SPTO
plantsphenomicsSolanaceae
ClassifiedSolanaceae Phenotype Ontology
Solanaceae crop phenotypes and traits, developed in collaboration with the research community, especially for breeder traits of agronomic importance.
SSE
surgerypharmacovigilenceHuman
ClassifiedSurgical Secondary Events
Memorial Sloan-Kettering Cancer Center Surgical Secondary Events Ontology (Adverse Events)
SSO
'public health and epidemiology''data management'Human
ClassifiedSyndromic Surveillance Ontology
The SSO encodes agreement among experts about how Emergency Department (ED) chief complaints are grouped into syndromes of public health importance (consensus definitions).
STATO
'statistics and probability'visualisation'laboratory techniques'All life
ClassifiedThe Statistical Methods Ontology
STATO is a general-purpose STATistics Ontology. Its aim is to provide coverage for processes such as statistical tests, their conditions of application, and information needed or resulting from statistical methods, such as probability distributions, variables, 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.
STUFF
'data management'All life
ClassifiedStuff Ontology
a core ontology of types of macroscopic stuff (types of masses/matter)
STY
'data management'All life
ClassifiedSemantic Types Ontology
Fixed hierarchy.
SURGICAL
surgeryHuman
UnknownNurse Surgical
SWEET
'data management'ecologyAll life
ClassifiedSemantic Web for Earth and Environment Technology Ontology
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.
SWO
'software engineering'bioinformatics'data management'All life
ClassifiedSoftware ontology
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
SYMP
'public health and epidemiology'pathologyHuman
ClassifiedSymptom Ontology
An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease.
SYN
neurologyneurobiologyoncologypathologyanatomyHuman
ClassifiedSage Bionetworks Synapse Ontology
The controlled vocabulary used for various entity properties in the Synapse platform.
TADS
parasitologyanatomyinvertebratesIxodida
ClassifiedTick gross anatomy
The anatomy of the Tick, <i>Families: Ixodidae, Argassidae</i>
TAHE
embryologyanatomyHuman
UnloadableTerminology of Anatomy of Human Embryology
TAHH
'cell biology'anatomyHuman
UnloadableTerminology of Anatomy of Human Histology
TAO
'marine biology'eukaryotesanatomyTeleostei
ClassifiedTeleost Anatomy Ontology
Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa
TAXRANK
'model organisms''data management'All life
ClassifiedTaxonomic rank vocabulary
A vocabulary of taxonomic ranks (species, family, phylum, etc)
TEDDY
'systems biology''synthetic chemistry''molecular dynamics'All life
ClassifiedTerminology for the Description of Dynamics
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.
TEO
'data management'All life
ClassifiedTime Event Ontology
The Time Event Ontology (TEO) is an ontology for representing events, time, and their relationships.
TGMA
anatomyinvertebratesCulicidae
ClassifiedMosquito gross anatomy
A structured controlled vocabulary of the anatomy of mosquitoes.
TM-CONST
'complementary medicine''data management'Human
ClassifiedTraditional Medicine Constitution Value Set
The value set for the Constitution property of the International Classification of Traditional Medicine (ICTM).
TM-MER
'complementary medicine''data management'Human
ClassifiedTraditional Medicine Meridian Value Sets
The meridian value set used in the International Classification of Traditional Medicine.
TM-OTHER-FACTORS
'complementary medicine''data management'Human
ClassifiedTraditional Medicine Other Factors Value Set
The value set for the Other Factors property of the International Classification of Traditional Medicine (ICTM).
TM-SIGNS-AND-SYMPTS
'complementary medicine''data management'Human
ClassifiedTraditional Medicine Signs and Symptoms Value Set
The value set for the Signs and Symptoms property of the International Classification of Traditional Medicine (ICTM).
TMA
'translational medicine''data integration and warehousing''gene expression'All life
ClassifiedTissue Microarray Ontology
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.
TMO
pharmacology'translational medicine''data integration and warehousing''drug development''drug discovery'Human
ClassifiedTranslational Medicine Ontology
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.
TO
plantsphenomicsPlants
ClassifiedPlant Trait Ontology
A controlled vocabulary of describe phenotypic traits in plants.
TOK
'data deposition, annotation and curation'All life
ClassifiedTerminological and Ontological Knowledge Resources Ontology
An Ontology describing Resources having different formats. This Ontology can be used to annotate and describe Terminological, Ontological Knowledge resources.
TOP-MENELAS
'medical informatics''preclinical and clinical studies''data management'pathologyHuman
ClassifiedMenelas Project Top-Level Ontology
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.
TRAK
'preclinical and clinical studies''musculoskeletal medicine''public health and epidemiology'Human
ClassifiedTaxonomy for Rehabilitation of Knee Conditions
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.
TRANS
pathology'public health and epidemiology'pathogensHuman
ClassifiedPathogen Transmission Ontology
An ontology representing the disease transmission process during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host.
TRIAGE
'data management''public health and epidemiology'Human
UnknownNurse triage
TRON
anatomyinvertebrates'developmental biology'Tribolium castaneum
ClassifiedTribolium Ontology
TrOn is an ontology about the anatomical structures of the red flour beetle Tribolium castaneum in the developmental stages larva, pupa and adult.
TTO
'marine biology'eukaryotesTeleostei
ClassifiedTeleost taxonomy
An ontology covering the taxonomy of teleosts (bony fish)
TYPON
microbiology'microbial collection''data integration and warehousing'All life
ClassifiedMicrobial Typing Ontology
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.
UBERON
anatomyeukaryotesAnimalia
ClassifiedUberon multi-species anatomy ontology
An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies
UNITSONT
'laboratory techniques''data management'All life
ClassifiedUnits Ontology
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.
UO
'laboratory techniques''data management'All life
ClassifiedUnits of measurement
Metrical units for use in conjunction with PATO
UPHENO
'data management'phenomicsAll life
ClassifiedCombined phenotype ontology
VANDF
'veterinary medicine''medicine research and development'pharmacologyAll life
ClassifiedVeterans Health Administration National Drug File
NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes.
VARIO
proteins'nucleic acids''genetic variation'All life
ClassifiedVariation Ontology
Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations.
VFB
ClassifiedVirtual Fly Brain Knowledge Base
A Knowledge Base of Drosophila brain anatomy images: including 3D images of neurons, clones, expression patterns.
VFB_Ind
ClassifiedVFB
VirtualFlyBrain.org individuals
VFB_test
UnloadableVFB_test
A small, test version of the VFB Knowledge Base
VHOG
vertebrates'data identity and mapping'anatomyVertebrata
ClassifiedVertebrate Homologous Ontology Group Ontology
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.
VICO
'allergy, clinical immunology and immunotherapeutics.''public health and epidemiology'Human
ClassifiedVaccination Informed Consent Ontology
VIVO
'data management'Human
ClassifiedVIVO Ontology for Researcher Discovery
The VIVO ontology represents researchers in the context of their experience, outputs, interests, accomplishments, and associated institutions.
VIVO-ISF
'data integration and warehousing'All life
ClassifiedVIVO-Integrated Semantic Framework
VO
'allergy, clinical immunology and immunotherapeutics.''public health and epidemiology''data integration and warehousing'Human
ClassifiedVaccine Ontology
a biomedical ontology in the domain of vaccine and vaccination
VSAO
vertebratesanatomy'musculoskeletal medicine'Vertebrata
ClassifiedVertebrate Skeletal Anatomy Ontology-
Vertebrate skeletal anatomy ontology.
VSO
anatomymedicineHuman
ClassifiedVital Sign Ontology
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.
VT
vertebratesVertebrata
ClassifiedVertebrate trait
An ontology of traits covering vertebrates
VTO
'data integration and warehousing'vertebratesgeneticsVertebrata
ClassifiedVertebrate Taxonomy Ontology
Comprehensive hierarchy of extinct and extant vertebrate taxa.
WB-BT
anatomyinvertebratesC. Elegans
ClassifiedC. elegans Gross Anatomy Vocabulary
A structured controlled vocabulary of the anatomy of <i>Caenorhabditis elegans</i>.
WB-LS
invertebrates'developmental biology'C. Elegans
ClassifiedC. elegans Development Vocabulary
A structured controlled vocabulary of the development of <i>Caenorhabditis elegans</i>.
WB-PHENOTYPE
invertebratesphenomicsC. Elegans
ClassifiedC. elegans Phenotype Vocabulary
A structured controlled vocabulary of <i>Caenorhabditis elegans</i> phenotypes
WBBT
anatomyinvertebratesC. Elegans
ClassifiedC. elegans gross anatomy
A structured controlled vocabulary of the anatomy of <i>Caenorhabditis elegans</i>.
WBLS
invertebrates'developmental biology'C. Elegans
ClassifiedC. elegans development
A structured controlled vocabulary of the development of <i>Caenorhabditis elegans</i>.
WBPHENOTYPE
invertebratesphenomicsC. Elegans
ClassifiedC. elegans phenotype
A structured controlled vocabulary of <i>Caenorhabditis elegans</i> phenotypes
WHO-ART
pharmacovigilencepharmacologyHuman
UnloadableWorld Health Organization (WHO) Adverse Reaction Terminology
WHO Adverse Reaction Terminology, 1997
WIKIPATHWAYS
'molecular interactions, pathways and networks'All life
UnloadableWikiPathways
WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways.
WSIO
'software engineering''data management'All life
ClassifiedWeb-Service Interaction Ontology
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.
XAO
anatomy'developmental biology'vertebratesXenopus
ClassifiedXenopus anatomy and development
Anatomy and development of the African clawed frog (<i>Xenopus laevis</i>).
XCO
'laboratory techniques'physiology'preclinical and clinical studies''model organisms'All life
ClassifiedExperimental condition ontology
Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.
XEO
ecologyplantsPlants
ClassifiedXEML Environment Ontology
XeO has been created to help plant scientists in documenting and sharing metadata describing the abiotic environment.
YPO
fungiphenomicsSaccharomyces cerevisiae
ClassifiedYeast phenotypes
ZEA
anatomyplantsZea mays
ClassifiedMaize Gross Anatomy Ontology
ZFA
'marine biology'eukaryotesanatomy'developmental biology''laboratory animal science'Zebrafish
ClassifiedZebrafish anatomy and development
A structured controlled vocabulary of the anatomy and development of the Zebrafish
ZFS
'marine biology'eukaryotes'developmental biology''laboratory animal science'Zebrafish
ClassifiedZebrafish developmental stages
Developmental stages of the Zebrafish
aids
Unloadabledevelopment of an hiv/aids ontology
information on hiv and aids
chear
UnloadableChildren's Health Exposure Analysis Resource Ontology
Children's health and wellbeing are influenced by interactions between environmental and genetic factors. NIEHS is establishing an infrastructure, the Children's Health Exposure Analysis Resource (CHEAR), to provide the extramural research community access to laboratory and data analyses that add or expand the inclusion of environmental exposures in children’s health research. The goal of CHEAR is to provide tools so researchers can assess the full range of environmental exposures which may affect children's health. We anticipate that CHEAR will be used by children's health researchers conducting epidemiological or clinical studies that currently have limited consideration of environmental exposures, or those who have collected exposure data but seek more extensive analyses. Read more at: https://www.niehs.nih.gov/research/supported/exposure/chear/
go-plus
'functional genomics''molecular genetics''data deposition, annotation and curation''molecular interactions, pathways and networks''cell biology''molecular biology'All life
Classifiedgo-plus.owl
The official, fully axiomatised, OWL version of the gene ontology
pseudo
geneticsdnaAll life
ClassifiedPseudogene
suicideo
psychiatry'data management'Human
Classifiedsuicideonto
ontology for suicidology
test
Classifiedtest
test