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|-
|[[FlyBase|FlyBase Controlled Vocabulary]]
|[[FlyBase|FlyBase Controlled Vocabulary]]
|FBCV
⚫
|FOODON
| An ontology to support the [[FlyBase]] project.
| An ontology to support the [[FlyBase]] project.
| [http://purl.obolibrary.org/obo/fbcv]
| [http://purl.obolibrary.org/obo/fbcv]
|-
|-
| Food Ontology <ref>{{cite journal | vauthors = Dooley DM, Griffiths EJ, Gosal GS, Buttigieg PL, Hoehndorf R, Lange MC, Schriml LM, Brinkman FS, Hsiao WW | display-authors = 6 | title = FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration | journal = NPJ Science of Food | volume = 2 | issue = 1 | pages = 23 | date = December 2018 | pmid = 31304272 | pmc = 6550238 | doi = 10.1038/s41538-018-0032-6 }}</ref>
| Food Ontology <ref>{{cite journal | vauthors = Dooley DM, Griffiths EJ, Gosal GS, Buttigieg PL, Hoehndorf R, Lange MC, Schriml LM, Brinkman FS, Hsiao WW | display-authors = 6 | title = FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration | journal = NPJ Science of Food | volume = 2 | issue = 1 | pages = 23 | date = December 2018 | pmid = 31304272 | pmc = 6550238 | doi = 10.1038/s41538-018-0032-6 }}</ref>
⚫
|FOODON
|
| An ontology to represent entities that play a [[food]] role or related to foods.
| An ontology to represent entities that play a [[food]] role or related to foods.
|[https://foodon.org/]
|[https://foodon.org/]
|-
|-
|[[Foundational Model of Anatomy|Foundational Model of Anatomy Ontology]] (subset)
|[[Foundational Model of Anatomy|Foundational Model of Anatomy Ontology]] (subset)
|FMAO
|
| Subset of the Foundational Model of Anatomy Ontology.
| Subset of the Foundational Model of Anatomy Ontology.
| [http://si.washington.edu/projects/fma]
| [http://si.washington.edu/projects/fma]
|-
|-
| Fungal gross anatomy
| Fungal Anatomy Ontology
|
|FAO
| An ontology for the anatomy of [[fungi]].
| An ontology for the anatomy of [[fungi]].
| [https://github.com/obophenotype/fungal-anatomy-ontology/]
| [https://github.com/obophenotype/fungal-anatomy-ontology/]
|-
|-
| Gazetteer
| Gazetteer
|
|GAZ
| An ontology that acts as a gazetteer (geographical dictionary)
| An ontology that acts as a gazetteer (geographical dictionary).
| [http://environmentontology.github.io/gaz/]
| [http://environmentontology.github.io/gaz/]
|-
|-
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| [http://geneontology.org]<br>[http://geneontology.org/]
| [http://geneontology.org]<br>[http://geneontology.org/]
|-
|-
| Genomic Epidemiology Ontology <ref>{{Cite journal|last=Griffiths|first=Emma|last2=Dooley|first2=Damion|last3=Graham|first3=Morag|last4=Van Domselaar|first4=Gary|last5=Brinkman|first5=Fiona S. L.|last6=Hsiao|first6=William W. L.|date=2017-06-26|title=Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance|url=http://dx.doi.org/10.3389/fmicb.2017.01068|journal=Frontiers in Microbiology|volume=8|doi=10.3389/fmicb.2017.01068|issn=1664-302X}}</ref>
| Genomic Epidemiology Ontology
|GENEPIO
|
| An ontology for foodborne pathogens and associated outbreaks.
| An ontology for foodborne pathogens and associated outbreaks.
| [http://genepio.github.io/genepio]<br>
| [http://genepio.github.io/genepio]<br>

Revision as of 18:33, 7 March 2020

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

OBO Foundry ontologies

title code description official page
Agronomy Ontology AGRO Ontology of concepts relevant to agronomy experiments [1]
An ontology of core ecological entities ECOCORE An ontology for ecological entities. [2]
Anatomical Entity Ontology AEO Ontology of anatomical structures that expand CARO, the Common Anatomy Reference Ontology. [3]
Antibiotic Resistance Ontology ARO Ontology for antibiotic resistance genes and mutations [4]
Apollo Structured Vocabulary [1] APOLLO-SV Ontology for enabling interoperability of epidemic models and public health application software.
[5]
Ascomycete phenotype ontology APO A structured controlled vocabulary for the phenotypes of Ascomycete fungi. [6]
Basic Formal Ontology [2] BFO The upper-level ontology upon which OBO Foundry ontologies are built.
[7]
Beta Cell Genomics Ontology BCGO An application ontology built for beta cell genomic studies. [8]
Biological Collections Ontology [3] BCO An ontology for biodiversity data
[9]
Biological Imaging Methods Ontology FBBI Ontology for methods involved in biomedical imaging, including preparation and acquisition. [10]
Biological Spatial Ontology BSPO An ontology for respresenting spatial concepts used in biology. [11]
BRENDA tissue / enzyme source BTO An ontology for the source of enzymes. [12]
C. elegans development ontology WBLS An ontology for the development of Caenorhabditis elegans. [13]
C. elegans Gross Anatomy Ontology WBBT An ontology for the anatomy of Caenorhabditis elegans. [14]
C. elegans phenotype WBPHENOTYPE An ontology for the phenotypes of Caenorhabditis elegans. [15]
Cardiovascular Disease Ontology CVDO An ontology for concepts related to cardiovascular diseases. [16]
[17]
Cell Line Ontology [4] CLO Ontology to describe cell lines. [18]
[19]
Cell Ontology [5] CL Ontology for metazoan cell types. [20]
[21]
Chemical Entities of Biological Interest CHEBI Ontology of small molecular entities of biological interest. [22]
Chemical Information Ontology [6] CHEMINF Ontology for descriptors used in chemoinformatics databases. [23]
[24]
Chemical Methods Ontology CHMO An ontology for the methods used in chemical experiments. [25]
Clinical LABoratory Ontology LABO An ontology of prescriptions and reports in clinical laboratories. [26]
Clinical measurement ontology [7] CMO Ontology to classify clinical measurements of experimental animals. [27]
Common Anatomy Reference Ontology [8] CARO An ontology to improve interoperability between anatomy ontologies for different organisms.
[28]
Comparative Data Analysis Ontology [9] CDAO Ontology of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees. [29]
[30]
Confidence Information Ontology [10] CIO An ontology to describe confidence information in sequence annotations. [31]
Contributor Role Ontology CRO An ontology for the diverse roles behind a scientific research article. [32]
[33]
Ctenophore Ontology CTENO An anatomical and developmental ontology for ctenophores (Comb Jellies) [34]
Dictyostelium discoideum anatomy [11] DDANAT A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum [35]
Dictyostelium discoideum phenotype ontology DDPHENO An ontology for phenotypes of the slime-mould Dictyostelium discoideum. [36]
Drosophila development FBDV An ontology of the development of Drosophila melanogaster. [37]
Drosophila gross anatomy [12] FBBT An ontology for the anatomy of Drosophila melanogaster. [38]
Drosophila Phenotype Ontology FBCV An ontology of common Drosophila phenotypes. [39]
Drug-drug Interaction and Drug-drug Interaction Evidence Ontology [13] DIDEO Ontology for drug–drug interaction evidence. [40]
Evidence & Conclusion Ontology [14] ECO An ontology for types evidence used to support scientific claims.
[41]
eagle-i resource ontology ERO An ontology of research equipment, protocols and consumables. [42]

[43]

Emotion Ontology [15] MFOEM An ontology of emotions, moods, and other kinds of feelings. [44]
Environment Ontology [16] ENVO Ontology of environmental features and habitats.
[45]
Experimental condition ontology [17] XCO An ontology for the different conditions in which experimental measurements are taken. [46]
Exposure Ontology [18] EXO Ontology to describe exposure to environmental factors (such as cigarette smoke) that might influence clinical outcomes.
[47]
Fission Yeast Phenotype Ontology[19] FYPO An ontology of phenotypes of fission yeast. [48]
[49]
Flora Phenotype Ontology [20] FLOPO An ontology for traits and phenotypes of flowering plants. [50]
FlyBase Controlled Vocabulary FBCV An ontology to support the FlyBase project. [51]
Food Ontology [21] FOODON An ontology to represent entities that play a food role or related to foods. [52]
Foundational Model of Anatomy Ontology (subset) FMAO Subset of the Foundational Model of Anatomy Ontology. [53]
Fungal Anatomy Ontology FAO An ontology for the anatomy of fungi. [54]
Gazetteer GAZ An ontology that acts as a gazetteer (geographical dictionary). [55]
Gene Ontology GO An ontology for describing the function of genes and gene products. [56]
[57]
Genomic Epidemiology Ontology [22] GENEPIO An ontology for foodborne pathogens and associated outbreaks. [58]
Genotype Ontology An ontology for genotypes and their related phenotypes and diseases. [59]
Geographical Entity Ontology An ontology of geographical entities [60]
Glycan Naming Ontology [23] An ontology for glycans based on GlyTouCan [61]
Homology Ontology An ontology for concepts related to homology [62]
Human Ancestry Ontology [24] An ontology of ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies. [63]
Human Developmental Stages An ontology of stages of the human life. [64]
Human Disease Ontology An ontology for describing human diseases [65]
Human Phenotype Ontology An ontology for human phenotypes in hereditary and non-hereditary diseases. [66]
[67]
HUPO-PSI cross-linking and derivatization reagents controlled vocabulary An ontology for reagents used to cross-link molecules in mass spectrometry experiments. [68]
Hymenoptera Anatomy Ontology [25] An ontology of the anatomy of the Hymenoptera (bees, wasps, and ants) [69]
Hypertension Ontology An ontology for clinical data about hypertension [70]
Infectious Disease Ontology [26] A set of ontologies related to infectious diseases. [71]
Information Artifact Ontology [27] An ontology of information entities.
[72]
Informed Consent Ontology An ontology for concepts related to informed consent, such as forms and policies.
[73]
Integrative and Conjugative Element Ontology An ontology of bacterial integrative and conjugative elements (ICEs). [74]
Interaction Network Ontology [28] An ontology for gene-gene interactions
[75]
Malaria Ontology [29] An ontology for concepts related to malaria
[76]
Mammalian Feeding Muscle Ontology An ontology for the mammalian muscles that play a role in feeding behavior. [77]
Mammalian Phenotype Ontology Standard terms for annotating mammalian phenotypic data. [78]
Mass spectrometry ontology An ontology for concepts to describe mass spectrometry in the context of proteomics. [79]
Measurement method ontology An ontology for methods of clinical and laboratory measurements. [80]
Medaka Developmental Stages An ontology of life stages for the medaka fish. [81]
Mental Disease Ontology [30] An ontology for mental diseases
[82]
Mental Functioning Ontology An ontology for concepts related to mental functioning [83]
[84]
MHC Restriction Ontology [31] An ontology for Major Histocompatibility Complex (MHC) restriction in experiments [85]
MIAPA Ontology[32] An ontology for phylogenetic data [86]
Microbial Conditions Ontology[33] An ontology for microbial growth conditions [87]
microRNA Ontology An application ontology for use with miRNA databases. [88]
Minimum PDDI Information Ontology An ontology of the minimum information to describe drug–drug interactions [89]
Molecular Interactions Controlled Vocabulary An ontology for concepts related to the study of protein-protein interactions. [90]
Mondo Disease Ontology An ontology for the integration of information on disease [91]
Mosquito gross anatomy ontology An ontology for the anatomy of mosquitoes. [92]
Mouse adult gross anatomy An ontology for the adult anatomy of the mouse (Mus). [93]
Mouse Developmental Stages An ontology of stages of the mouse (Mus) life. [94]
Mouse gross anatomy and development, timed Ontology of anatomical structures of the mouse (Mus musculus). [95]
Mouse Pathology Ontology [34] An ontology of mouse pathology phenotypes. [96]
[97]
Name Reaction Ontology An ontology for organic reactions in organic synthesis. [98]
NCBI organismal classification [35] An ontology representation of the NCBI organismal taxonomy. [99]
Neuro Behavior Ontology An ontology of behavioral phenotypes of animals. [100]
NOMEN - A nomenclatural ontology for biological names An ontology of the rules of nomenclature for biological names. [101]
Non-Coding RNA Ontology [36] An ontology for non-coding RNA function [102]
Ontologized MIABIS An ontological version of MIABIS (Minimum Information About BIobank data Sharing) [103]
Ontology for Biobanking [37] An ontology for concepts related to biobanks [104]
Ontology for Biomedical Investigations An ontology which describes biological processes, cellular components and molecular functions in living organisms [105]
Ontology for General Medical Science An ontology for general aspects of medicine, with a focus on cancer. [106]
Ontology for MIRNA Target An ontology for data elements related to microRNA (miR) [107]
Ontology for Parasite LifeCycle [38] A reference ontology for parasite life cycle stages. [108]
Ontology of Adverse Events [39] An ontology for adverse events of drug regimens [109]
Ontology of Arthropod Circulatory Systems [40] An ontology for the circulatory systems of arthropods. [110]
Ontology of Biological and Clinical Statistics [41] OBCS An ontology to describe statistical tools and methods used in biomedical investigation. [111]
Ontology of Biological Attributes An ontology for biological traits [112]
Ontology of Medically Related Social Entities [42] An ontology for entities (roles and organizations) related to healthcare. [113]
[114]
Ontology of Microbial Phenotypes [43] An ontology of phenotypes of microorganisms [115]
Ontology of Organizational Structures of Trauma centers and Trauma systems An ontology for the organizational structures of trauma centers and trauma systems. [116]
Ontology of Precision Medicine and Investigation An ontology for concepts related to precision medicine [117]
Ontology of Prokaryotic Phenotypic and Metabolic Characters [44] An ontology of prokaryotic phenotypic and metabolic characters [118]
Ontology of RNA Sequencing An ontology to annotate RNA Sequencing experiments. [119]
Ontology of Vaccine Adverse Events [45] An ontology for adverse events of vaccines. [120]
[121]
Pathogen Host Interaction Phenotype Ontology An ontology of phenotypes that occur in pathogen-host interactions [122]
Pathogen Transmission Ontology An ontology for disease transmission processes [123]
Pathway ontology An ontology for annotating gene products to pathways. [124]
Performance Summary Display Ontology An ontology for concepts related to performance information for teams and organizations. [125]
Phenotype And Trait Ontology FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data. [126]
Planaria Ontology An ontology for the anatomy and developmental stages of the planaria (Schmidtea mediterranea.) [127]
Planarian Phenotype Ontology An ontology for phenotypes of the planaria (Schmidtea mediterranea.) [128]
Plant Experimental Conditions Ontology An ontology for concepts related to plant biology experiments. [129]
Plant ontology An ontology and database resource that links plant traits to genomics data. [130]
Plant Phenology Ontology An ontology for describing the cyclic phenomena of plants. [131]
Plant Trait Ontology An ontology for phenotypic traits in plants. [132]
Platynereis Developmental Stages An ontology for life stages of Platynereis dumerilii. [133]
Population and Community Ontology An ontology for describing groups of interacting organisms.
[134]
Porifera Ontology [46] PORO An ontology for the anatomy of sponges (Porifera) [135]
Protein modification An ontology for protein chemical modifications [136]
Protein Ontology[47] PRO An ontological representation of protein-related entities [137]
Rat Strain Ontology An ontology for laboratorial rat strains. [138]
Relation Ontology[48] RO An ontology for relations between terms in the ontologies. [139]
Scientific Evidence and Provenance Information Ontology SEPIO An ontology for the provenance of scientific claims and supporting evidence. [140]
Sequence types and features ontology SO An ontology for annotation of sequences [141]
Software Ontology[49] SWO An ontology to describe software applications with a focus on bioinformatics tools. [142]
Spider Ontology[50] SPD An ontology for anatomy and behavior of spiders as well as spider-derived products. [143]
Symptom Ontology SYMPTOM An ontology of disease symptoms [144]
Taxonomic rank vocabulary TAXRANK An ontology of taxonomic ranks in systematics [145]
Teleost taxonomy ontology [51] TTO An ontology for the taxonomy of teleost fish. [146]
The Data Use Ontology [52] DUO Ontology for conditions of data use. [147]
The Drug Ontology [53] DRON An ontology for drug products. [148]
The Ontology of Genes and Genomes OGG An ontology of genes and genomes of biological organisms. [149]
The Oral Health and Disease Ontology [54] OHD An ontology for the content of teeth-related health records. [150]
The Prescription of Drugs Ontology [55] PDRO An ontology for concepts related to prescription of drugs. [151]
The Statistical Methods Ontology STATO An ontology for statistical methods, such as tests and experimental designs. [152]
Tick Anatomy Ontology [56] TADS An ontology for the anatomy of the tick families Ixodidae and Argasidae. [153]
Uberon multi-species anatomy ontology UBERON An integrative, cross species ontology for anatomical terms [154]
Unified phenotype ontology (uPheno) UPHENO An ontology for unified phenotypical descriptictions [155]
Units of measurement ontology UO An ontology of metrical units, couplet to the PATO ontology. [156]
Vaccination Informed Consent Ontology [57] VICO An ontology of clinical informed consents focused on vaccination procedures. [157]
Vaccine Ontology [58] VO An ontology for concepts related to vaccines and vaccination. [158]
Vertebrate Taxonomy Ontology VTO An ontology for the taxonomy of vertebrates. [159]
Vertebrate Trait Ontology VT An ontology for traits covering vertebrates [160]
VEuPathDB ontology EUPATH An ontology for the support of the Eukaryotic Pathogen, Host & Vector Genomics Resource. [161]
Xenopus Anatomy Ontology[59] XAO Ontology of the anatomy of the African clawed frog (Xenopus laevis).
[162]
Xenopus Phenotype Ontology XPO An ontology for anatomical, cellular, and gene function phenotypes in African clawed frogs (Xenopus laevis). [163]
Zebrafish anatomy and development ontology ZFA Ontology for the anatomy and development of the zebrafish (Danio rerio). [164]
Zebrafish developmental stages ontology ZFS An ontology for developmental stages of the zebrafish (Danio rerio). [165]
Zebrafish Experimental Conditions Ontology ZECO An ontology for experimental conditions used in zebrafish research and described in ZFIN. [166]
Zebrafish Phenotype Ontology ZP An ontology for the phenotypes of the zebrafish (Danio rerio). [167]

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  44. ^ Blank CE, Cui H, Moore LR, Walls RL (December 2016). "MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions". Journal of Biomedical Semantics. 7 (1): 18. doi:10.1186/s13326-016-0060-6. PMC 4830071. PMID 27076900.{{cite journal}}: CS1 maint: unflagged free DOI (link)
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  50. ^ Ramírez, Martín J.; Michalik, Peter (2019-10-22). "The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data". Diversity. 11 (10): 202. doi:10.3390/d11100202. ISSN 1424-2818. {{cite journal}}: Unknown parameter |name-list-format= ignored (|name-list-style= suggested) (help)CS1 maint: unflagged free DOI (link)
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