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| An ontology of behavioral phenotypes of animals.
| An ontology of behavioral phenotypes of animals.
| [https://github.com/obo-behavior/behavior-ontology/]
| [https://github.com/obo-behavior/behavior-ontology/]
|-
| Neuroscience Information Framework Cell Ontology
| Ontology to describe cell types in animals in general.
| [http://bioportal.bioontology.org/ontologies/NIFCELL?p=classes&amp;conceptid=root]<br>[https://github.com/obophenotype/cell-ontology]
|-
|-
| NOMEN - A nomenclatural ontology for biological names
| NOMEN - A nomenclatural ontology for biological names
| An ontology of the rules of nomenclature for biological names.
| An ontology of the rules of [[Taxonomy (biology)|nomenclature]] for biological names.
| [https://github.com/SpeciesFileGroup/nomen]
| [https://github.com/SpeciesFileGroup/nomen]
|-
|-
| Non-Coding RNA Ontology <ref>{{Cite journal|last=Huang|first=Jingshan|last2=Eilbeck|first2=Karen|last3=Smith|first3=Barry|last4=Blake|first4=Judith A.|last5=Dou|first5=Dejing|last6=Huang|first6=Weili|last7=Natale|first7=Darren A.|last8=Ruttenberg|first8=Alan|last9=Huan|first9=Jun|last10=Zimmermann|first10=Michael T.|last11=Jiang|first11=Guoqian|date=2016-05-04|title=The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology|url=https://doi.org/10.1186/s13326-016-0066-0|journal=Journal of Biomedical Semantics|volume=7|issue=1|pages=24|doi=10.1186/s13326-016-0066-0|issn=2041-1480|pmc=PMC4857245|pmid=27152146}}</ref>
| Non-Coding RNA Ontology
| An ontology for RNA function
| An ontology for [[non-coding RNA]] function
|[https://github.com/bgsu-rna/rnao]
|[https://github.com/OmniSearch/ncro]
|-
|-
| Ontologized MIABIS
| Ontologized MIABIS
Line 379: Line 375:
| [https://github.com/OMIABIS/omiabis-dev]
| [https://github.com/OMIABIS/omiabis-dev]
|-
|-
| Ontology for Biobanking <ref>{{Cite journal|last=Brochhausen|first=Mathias|last2=Zheng|first2=Jie|last3=Birtwell|first3=David|last4=Williams|first4=Heather|last5=Masci|first5=Anna Maria|last6=Ellis|first6=Helena Judge|last7=Stoeckert|first7=Christian J.|date=2016-05-02|title=OBIB-a novel ontology for biobanking|url=http://dx.doi.org/10.1186/s13326-016-0068-y|journal=Journal of Biomedical Semantics|volume=7|issue=1|doi=10.1186/s13326-016-0068-y|issn=2041-1480}}</ref>
| Ontology for Biobanking
| An ontology for concepts related to biobanks
| An ontology for concepts related to [[Biobank|biobanks]]
| [https://github.com/biobanking/biobanking/wiki]<br>[https://github.com/biobanking/biobanking]
| [https://github.com/biobanking/biobanking/wiki]<br>
|-
|-
| Ontology for Biomedical Investigations
| Ontology for Biomedical Investigations

Revision as of 17:26, 18 February 2020

This is a list of ontologies that are part of the OBO Foundry as of January 2020.

OBO Foundry ontologies

title description official page
Agronomy Ontology Ontology of concepts relevant to agronomy experiments [1]
An ontology of core ecological entities An ontology for ecological entities. [2]
Anatomical Entity Ontology Ontology of anatomical structures that expand CARO, the Common Anatomy Reference Ontology. [3]
Antibiotic Resistance Ontology Ontology for antibiotic resistance genes and mutations [4]
Apollo Structured Vocabulary [1] Ontology for enabling interoperability of epidemic models and public health application software.
[5]
Ascomycete phenotype ontology A structured controlled vocabulary for the phenotypes of Ascomycete fungi. [6]
Basic Formal Ontology [2] The upper-level ontology upon which OBO Foundry ontologies are built.
[7]
Beta Cell Genomics Ontology An application ontology built for beta cell genomics studies. [8]
Biological Collections Ontology [3] An ontology for biodiversity data [9]
[10]
Biological Imaging Methods Ontology Ontology for methods involved in biomedical imaging, including preparation and acquisition. [11]
Biological Spatial Ontology An ontology for respresenting spatial concepts used in biology [12]
BRENDA tissue / enzyme source An ontology for the source of enzymes. [13]
C. elegans development ontology An ontology for the development of Caenorhabditis elegans [14]
C. elegans Gross Anatomy Ontology An ontology for the anatomy of Caenorhabditis elegans. [15]
C. elegans phenotype An ontology for the phenotypes of Caenorhabditis elegans [16]
Cardiovascular Disease Ontology ontology [17]
[18]
Cell Line Ontology [4] Ontology fo describe cell lines [19]
[20]
Cell Ontology [5] Ontology for metazoan cell types [21]
[22]
Chemical Entities of Biological Interest Ontology of small molecular entities of biological interest [23]
Chemical Information Ontology Ontology for descriptors used in chemoinformatics database [24]
[25]
Chemical Methods Ontology ontology [26]
Exposure Ontology [6] Ontology to describe exposure to environmental factors (such as cigarette smoke) that might influence clinical outcomes.
[27]
clinical LABoratory Ontology An ontology of prescriptions and reports in clinical laboratories. [28]
Clinical measurement ontology Ontology to calssify clinical measurements of experimental animals [29]
Common Anatomy Reference Ontology [7] ontology
[30]
Comparative Data Analysis Ontology [8] Ontology of concepts and relations relevant to evolutionary comparative analysis [31]
[32]
Confidence Information Ontology [9] An ontology to describe confidence information in sequence annotations. [33]
Contributor Role Ontology An ontology for the diverse roles behind a scientific research article. [34]
[35]
Ctenophore Ontology An anatomical and developmental ontology for ctenophores (Comb Jellies) [36]
Dictyostelium discoideum anatomy [10] A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum [37]
Dictyostelium discoideum phenotype ontology An ontology for phenotypes of the slime-mould Dictyostelium discoideum. [38]
Drosophila development An ontology of the development of Drosophila melanogaster. [39]
Drosophila gross anatomy [11] An ontology for the anatomy of Drosophila melanogaster. [40]
Drosophila Phenotype Ontology An ontology of common Drosophila phenotypes. [41]
Drug-drug Interaction and Drug-drug Interaction Evidence Ontology [12] Ontology for drug-drug interaction evidence. [42]
Evidence & Conclusion Ontology [13] An ontology for types evidence used to support scientific claims.
[43]
eagle-i resource ontology An ontology of research equipment, protocols and consumables. . [44]

[45]

Emotion Ontology [14] An ontology of emotions, moods, and other kinds of feelings. [46]
Environment Ontology [15] Ontology of environmental features and habitats
[47]
Experimental condition ontology [16] An ontology for the different conditions in which experimental measurements are taken. [48]
Fission Yeast Phenotype Ontology [17] An ontology of phenotypes of fission yeast. [49]
[50]
Flora Phenotype Ontology [18] An ontology for traits and phenotypes of flowering plants [51]
FlyBase Controlled Vocabulary An ontology to support the FlyBase project. [52]
Food Ontology [19] An ontology to represent entities that play a food role or related to foods. [53]
Foundational Model of Anatomy Ontology (subset) Subset of the Foundational Model of Anatomy Ontology. [54]
Fungal gross anatomy An ontology for the anatomy of fungi. [55]
Gazetteer An ontology that acts as a gazetteer (geographical dictionary) [56]
Gene Ontology An ontology for describing the function of genes and gene products. [57]
[58]
Genomic Epidemiology Ontology An ontology for foodborne pathogens and associated outbreaks. [59]
Genotype Ontology An ontology for genotypes and their related phenotypes and diseases. [60]
Geographical Entity Ontology An ontology of geographical entities [61]
Glycan Naming Ontology [20] An ontology for glycans based on GlyTouCan [62]
Homology Ontology An ontology for concepts related to homology [63]
Human Ancestry Ontology [21] An ontology of ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies. [64]
Human Developmental Stages An ontology of stages of the human life. [65]
Human Disease Ontology An ontology for describing human diseases [66]
Human Phenotype Ontology An ontology for human phenotypes in hereditary and non-hereditary diseases. [67]
[68]
HUPO-PSI cross-linking and derivatization reagents controlled vocabulary An ontology for reagents used to cross-link molecules in mass spectrometry experiments. [69]
Hymenoptera Anatomy Ontology [22] An ontology of the anatomy of the Hymenoptera (bees, wasps, and ants) [70]
Hypertension Ontology An ontology for clinical data about hypertension [71]
Infectious Disease Ontology [23] A set of ontologies related to infectious diseases. [72]
Information Artifact Ontology [24] An ontology of information entities.
[73]
Informed Consent Ontology An ontology for concepts related to informed consent, such as forms and policies.
[74]
Integrative and Conjugative Element Ontology An ontology of bacterial integrative and conjugative elements (ICEs). [75]
Interaction Network Ontology [25] An ontology for gene-gene interactions
[76]
Malaria Ontology [26] An ontology for concepts related to malaria
[77]
Mammalian Feeding Muscle Ontology An ontology for the mammalian muscles that play a role in feeding behavior. [78]
Mammalian Phenotype Ontology Standard terms for annotating mammalian phenotypic data. [79]
Mass spectrometry ontology An ontology for concepts to describe mass spectrometry in the context of proteomics. [80]
Measurement method ontology An ontology for methods of clinical and laboratory measurements. [81]
Medaka Developmental Stages An ontology of life stages for the medaka fish. [82]
Mental Disease Ontology [27] An ontology for mental diseases
[83]
Mental Functioning Ontology An ontology for concepts related to mental functioning [84]
[85]
MHC Restriction Ontology [28] An ontology for Major Histocompatibility Complex (MHC) restriction in experiments [86]
MIAPA Ontology[29] An ontology for phylogenetic data [87]
Microbial Conditions Ontology[30] An ontology for microbial growth conditions [88]
microRNA Ontology An application ontology for use with miRNA databases. [89]
Minimum PDDI Information Ontology An ontology of the minimum information to describe drug-drug interactions [90]
Molecular Interactions Controlled Vocabulary An ontology for concepts related to the study of protein-protein interactions. [91]
Mondo Disease Ontology An ontology for the integration of information on disease [92]
Mosquito gross anatomy ontology An ontology for the anatomy of mosquitoes. [93]
Mouse adult gross anatomy An ontology for the adult anatomy of the mouse (Mus). [94]
Mouse Developmental Stages An ontology of stages of the mouse (Mus) life. [95]
Mouse gross anatomy and development, timed Ontology of anatomical structures of the mouse (Mus musculus). [96]
Mouse Pathology Ontology [31] An ontology of mouse pathology phenotypes. [97]
[98]
Name Reaction Ontology An ontology for organic reactions in organic synthesis. [99]
NCBI organismal classification [32] An ontology representation of the NCBI organismal taxonomy. [100]
Neuro Behavior Ontology An ontology of behavioral phenotypes of animals. [101]
NOMEN - A nomenclatural ontology for biological names An ontology of the rules of nomenclature for biological names. [102]
Non-Coding RNA Ontology [33] An ontology for non-coding RNA function [103]
Ontologized MIABIS An ontological version of MIABIS (Minimum Information About BIobank data Sharing) [104]
Ontology for Biobanking [34] An ontology for concepts related to biobanks [105]
Ontology for Biomedical Investigations An ontology which describes biological processes, cellular components and molecular functions in living organisms [106]
[107]
Ontology for General Medical Science An ontology for general aspects of medicine, with a focus on cancer. [108]
[109]
Ontology for MIRNA Target An ontology for data elements related to microRNA (miR) [110]
Ontology for Parasite LifeCycle A reference ontology for parasite life cycle stages. [111]
Ontology of Adverse Events An ontology for adverse events of drug regimens [112]
Ontology of Arthropod Circulatory Systems An ontology for the circulatory systems of arthropods. [113]
Ontology of Biological and Clinical Statistics An ontology to describe biomedical statistics [114]
Ontology of Biological Attributes An ontology for biological traits [115]
Ontology of Medically Related Social Entities ontology [116]
[117]
Ontology of Microbial Phenotypes An ontology of phenotypes of microbes [118]
Ontology of Organizational Structures of Trauma centers and Trauma systems An ontology for the organizational structures of trauma centers and trauma systems. [119]
Ontology of Precision Medicine and Investigation An ontology for concepts related to precision medicine [120]
Ontology of Prokaryotic Phenotypic and Metabolic Characters An ontology of prokaryotic phenotypic and metabolic characters [121]
Ontology of RNA Sequencing An ontology built for annotation of RNA Sequencing experiments. [122]
Ontology of Vaccine Adverse Events An ontology for adverse events of vaccines. [123]
[124]
Pathogen Host Interaction Phenotype Ontology An ontology of phenotypes that occur in pathogen-host interactions [125]
Pathogen Transmission Ontology An ontology for disease transmission processes [126]
Pathway ontology An ontology for annotating gene products to pathways. [127]
Performance Summary Display Ontology An ontology for concepts related to clinical performance [128]
Phenotype And Trait Ontology FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data. [129]
planaria-ontology An ontology for the anatomy and developmental stages of the planaria (Schmidtea mediterranea.) [130]
Planarian Phenotype Ontology An ontology for phenotypes of the planaria (Schmidtea mediterranea.) [131]
Plant Experimental Conditions Ontology An ontology for concepts related to plant biology experiments. [132]
Plant ontology database resource that links plant traits to genomics data. [133]
Plant Phenology Ontology An ontology for describing the cyclic phenomena of plants. [134]
Plant Trait Ontology An ontology for phenotypic traits in plants. [135]
Platynereis Developmental Stages An ontology for life stages of Platynereis dumerilii [136]
Population and Community Ontology An ontology for describing groups of interacting organisms. [137]
[138]
Porifera Ontology An ontology for the anatomy of sponges (Porifera) [139]
Protein modification An ontology for protein chemical modifications [140]
PRotein Ontology (PRO) An ontological representation of protein-related entities [141]
Rat Strain Ontology An ontology for laboratorial rat strains. [142]
Relation Ontology An ontology for relations between ontologies. [143]
Scientific Evidence and Provenance Information Ontology An ontology for the provenance of scientific claims and supporting evidence. [144]
Sequence types and features ontology An ontology for annotation of sequences [145]
Software Ontology An ontology to describe software applications with a focus on bioinformatics tools. [146]
[147]
Spider Ontology An ontology for anatomy and behavior of spiders as well as spider-derived products. [148]
Symptom Ontology An ontology of disease symptoms [149]
Taxonomic rank vocabulary An ontology of taxonomic ranks in systematics [150]
Teleost taxonomy ontology An ontology for the taxonomy of teleost fish. [151]
The Data Use Ontology Ontology for conditions of data use. [152]
The Drug Ontology An ontology for drug products. [153]
The Drug-Drug Interactions Ontology Ontology for drug-drug interactions. [154]
The Ontology of Genes and Genomes An ontology of genes and genomes of biological organisms. [155]
The Oral Health and Disease Ontology An ontology for the content of teeth-related health records. [156]
The Prescription of Drugs Ontology An ontology for concepts related to prescription of drugs [157]
The Statistical Methods Ontology An ontology for statistical methods, such as tests and experimental desigens [158]
Tick Anatomy Ontology An ontology for the anatomy of the tick families Ixodidae and Argassidae. [159]
Uberon multi-species anatomy ontology An integrative, cross species ontology for anatomical terms [160]
Unified phenotype ontology (uPheno) An ontology for unified phenotypical descriptictions [161]
Units of measurement ontology An ontology of metrical units, couplet to the PATO ontology. [162]
Vaccination Informed Consent Ontology An ontology of clinical informed consents [163]
[164]
Vaccine Ontology An ontology for concepts related to vaccines and vaccination [165]
Vertebrate Taxonomy Ontology An ontology for the taxonomy of vertebrates. [166]
Vertebrate trait ontology An ontology for traits covering vertebrates [167]
VEuPathDB ontology An ontology for the support of the Eukaryotic Pathogen, Host & Vector Genomics Resource. [168]
Xenopus Anatomy Ontology[35] Ontology of the anatomy of the African clawed frog (Xenopus laevis).
[169]
Xenopus Phenotype Ontology An ontology for anatomical, cellular, and gene function phenotypes in Xenopus, the African clawed frogs. [170]
Zebrafish anatomy and development ontology Ontology for the anatomy and development of the Zebrafish. [171]
Zebrafish developmental stages ontology An ontology for developmental stages of zebrafish [172]
Zebrafish Experimental Conditions Ontology An ontology for experimental conditions used in zebrafish research and described in ZFIN. [173]
Zebrafish Phenotype Ontology An ontology for the phenotypes of the Zebrafish. [174]

References

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