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| Beta Cell Genomics Ontology
| Beta Cell Genomics Ontology
| An application ontology built for beta cell genomics studies.
| An application ontology built for [[beta cell]] genomic studies.
| [https://github.com/obi-bcgo/bcgo]
| [https://github.com/obi-bcgo/bcgo]
|-
|-
Line 54: Line 54:
| [https://github.com/obophenotype/biological-spatial-ontology]
| [https://github.com/obophenotype/biological-spatial-ontology]
|-
|-
|[[BRENDA|BRENDA tissue / enzyme source]]
|[[BRENDA tissue ontology|BRENDA tissue / enzyme source]]
| An ontology for the source of enzymes.
| An ontology for the source of enzymes.
| [http://www.brenda-enzymes.org]
| [http://www.brenda-enzymes.org]
Line 220: Line 220:
|-
|-
| Homology Ontology
| Homology Ontology
| An ontology for concepts related to homology
| An ontology for concepts related to [[Homology (biology)|homology]]
| [https://github.com/BgeeDB/homology-ontology]
| [https://github.com/BgeeDB/homology-ontology]
|-
|-
Line 379: Line 379:
| [https://github.com/biobanking/biobanking/wiki]<br>
| [https://github.com/biobanking/biobanking/wiki]<br>
|-
|-
| Ontology for Biomedical Investigations
|[[Ontology for Biomedical Investigations]]
| An ontology which describes biological processes, cellular components and molecular functions in living organisms
| An ontology which describes biological processes, cellular components and molecular functions in living organisms
| [http://obi.sf.net]<br>[http://obi-ontology.org]
|[http://obi-ontology.org]
|-
|-
| Ontology for General Medical Science
| Ontology for General Medical Science
| An ontology for general aspects of medicine, with a focus on cancer.
| An ontology for general aspects of medicine, with a focus on cancer.
| [http://code.google.com/p/ogms]<br>[https://github.com/OGMS/ogms]
|[https://github.com/OGMS/ogms]
|-
|-
| Ontology for MIRNA Target
| Ontology for MIRNA Target
| An ontology for data elements related to microRNA (miR)
| An ontology for data elements related to [[microRNA]] (miR)
| [http://omit.cis.usouthal.edu/]
| [http://omit.cis.usouthal.edu/]
|-
|-
| Ontology for Parasite LifeCycle <ref>{{Cite journal|last=Parikh|first=Priti P|last2=Zheng|first2=Jie|last3=Logan-Klumpler|first3=Flora|last4=Stoeckert|first4=Christian J|last5=Louis|first5=Christos|last6=Topalis|first6=Pantelis|last7=Protasio|first7=Anna V|last8=Sheth|first8=Amit P|last9=Carrington|first9=Mark|last10=Berriman|first10=Matthew|last11=Sahoo|first11=Satya S|date=2012-05-23|title=The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms|url=http://dx.doi.org/10.1186/2041-1480-3-5|journal=Journal of Biomedical Semantics|volume=3|issue=1|doi=10.1186/2041-1480-3-5|issn=2041-1480}}</ref>
| Ontology for Parasite LifeCycle
| A reference ontology for parasite life cycle stages.
| A reference ontology for parasite life cycle stages.
| [https://github.com/OPL-ontology/OPL]
| [https://github.com/OPL-ontology/OPL]
|-
|-
| Ontology of Adverse Events <ref>{{Cite journal|last=He|first=Yongqun|last2=Sarntivijai|first2=Sirarat|last3=Lin|first3=Yu|last4=Xiang|first4=Zuoshuang|last5=Guo|first5=Abra|last6=Zhang|first6=Shelley|last7=Jagannathan|first7=Desikan|last8=Toldo|first8=Luca|last9=Tao|first9=Cui|last10=Smith|first10=Barry|date=2014|title=OAE: The Ontology of Adverse Events|url=http://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-5-29|journal=Journal of Biomedical Semantics|language=en|volume=5|issue=1|pages=29|doi=10.1186/2041-1480-5-29|issn=2041-1480|pmc=PMC4120740|pmid=25093068}}</ref>
| Ontology of Adverse Events
| An ontology for adverse events of drug regimens
| An ontology for adverse events of drug regimens
| [https://github.com/OAE-ontology/OAE/]
| [https://github.com/OAE-ontology/OAE/]

Revision as of 19:55, 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 genomic 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]
Ontology for General Medical Science An ontology for general aspects of medicine, with a focus on cancer. [107]
Ontology for MIRNA Target An ontology for data elements related to microRNA (miR) [108]
Ontology for Parasite LifeCycle [35] A reference ontology for parasite life cycle stages. [109]
Ontology of Adverse Events [36] An ontology for adverse events of drug regimens [110]
Ontology of Arthropod Circulatory Systems An ontology for the circulatory systems of arthropods. [111]
Ontology of Biological and Clinical Statistics An ontology to describe biomedical statistics [112]
Ontology of Biological Attributes An ontology for biological traits [113]
Ontology of Medically Related Social Entities ontology [114]
[115]
Ontology of Microbial Phenotypes An ontology of phenotypes of microbes [116]
Ontology of Organizational Structures of Trauma centers and Trauma systems An ontology for the organizational structures of trauma centers and trauma systems. [117]
Ontology of Precision Medicine and Investigation An ontology for concepts related to precision medicine [118]
Ontology of Prokaryotic Phenotypic and Metabolic Characters An ontology of prokaryotic phenotypic and metabolic characters [119]
Ontology of RNA Sequencing An ontology built for annotation of RNA Sequencing experiments. [120]
Ontology of Vaccine Adverse Events An ontology for adverse events of vaccines. [121]
[122]
Pathogen Host Interaction Phenotype Ontology An ontology of phenotypes that occur in pathogen-host interactions [123]
Pathogen Transmission Ontology An ontology for disease transmission processes [124]
Pathway ontology An ontology for annotating gene products to pathways. [125]
Performance Summary Display Ontology An ontology for concepts related to clinical performance [126]
Phenotype And Trait Ontology FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data. [127]
planaria-ontology An ontology for the anatomy and developmental stages of the planaria (Schmidtea mediterranea.) [128]
Planarian Phenotype Ontology An ontology for phenotypes of the planaria (Schmidtea mediterranea.) [129]
Plant Experimental Conditions Ontology An ontology for concepts related to plant biology experiments. [130]
Plant ontology database resource that links plant traits to genomics data. [131]
Plant Phenology Ontology An ontology for describing the cyclic phenomena of plants. [132]
Plant Trait Ontology An ontology for phenotypic traits in plants. [133]
Platynereis Developmental Stages An ontology for life stages of Platynereis dumerilii [134]
Population and Community Ontology An ontology for describing groups of interacting organisms. [135]
[136]
Porifera Ontology An ontology for the anatomy of sponges (Porifera) [137]
Protein modification An ontology for protein chemical modifications [138]
PRotein Ontology (PRO) An ontological representation of protein-related entities [139]
Rat Strain Ontology An ontology for laboratorial rat strains. [140]
Relation Ontology An ontology for relations between ontologies. [141]
Scientific Evidence and Provenance Information Ontology An ontology for the provenance of scientific claims and supporting evidence. [142]
Sequence types and features ontology An ontology for annotation of sequences [143]
Software Ontology An ontology to describe software applications with a focus on bioinformatics tools. [144]
[145]
Spider Ontology An ontology for anatomy and behavior of spiders as well as spider-derived products. [146]
Symptom Ontology An ontology of disease symptoms [147]
Taxonomic rank vocabulary An ontology of taxonomic ranks in systematics [148]
Teleost taxonomy ontology An ontology for the taxonomy of teleost fish. [149]
The Data Use Ontology Ontology for conditions of data use. [150]
The Drug Ontology An ontology for drug products. [151]
The Drug-Drug Interactions Ontology Ontology for drug-drug interactions. [152]
The Ontology of Genes and Genomes An ontology of genes and genomes of biological organisms. [153]
The Oral Health and Disease Ontology An ontology for the content of teeth-related health records. [154]
The Prescription of Drugs Ontology An ontology for concepts related to prescription of drugs [155]
The Statistical Methods Ontology An ontology for statistical methods, such as tests and experimental desigens [156]
Tick Anatomy Ontology An ontology for the anatomy of the tick families Ixodidae and Argassidae. [157]
Uberon multi-species anatomy ontology An integrative, cross species ontology for anatomical terms [158]
Unified phenotype ontology (uPheno) An ontology for unified phenotypical descriptictions [159]
Units of measurement ontology An ontology of metrical units, couplet to the PATO ontology. [160]
Vaccination Informed Consent Ontology An ontology of clinical informed consents [161]
[162]
Vaccine Ontology An ontology for concepts related to vaccines and vaccination [163]
Vertebrate Taxonomy Ontology An ontology for the taxonomy of vertebrates. [164]
Vertebrate trait ontology An ontology for traits covering vertebrates [165]
VEuPathDB ontology An ontology for the support of the Eukaryotic Pathogen, Host & Vector Genomics Resource. [166]
Xenopus Anatomy Ontology[37] Ontology of the anatomy of the African clawed frog (Xenopus laevis).
[167]
Xenopus Phenotype Ontology An ontology for anatomical, cellular, and gene function phenotypes in Xenopus, the African clawed frogs. [168]
Zebrafish anatomy and development ontology Ontology for the anatomy and development of the Zebrafish. [169]
Zebrafish developmental stages ontology An ontology for developmental stages of zebrafish [170]
Zebrafish Experimental Conditions Ontology An ontology for experimental conditions used in zebrafish research and described in ZFIN. [171]
Zebrafish Phenotype Ontology An ontology for the phenotypes of the Zebrafish. [172]

References

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  26. ^ Topalis, Pantelis; Mitraka, Elvira; Bujila, Ioana; Deligianni, Elena; Dialynas, Emmanuel; Siden-Kiamos, Inga; Troye-Blomberg, Marita; Louis, Christos (2010-08-10). "IDOMAL: an ontology for malaria". Malaria Journal. 9: 230. doi:10.1186/1475-2875-9-230. ISSN 1475-2875. PMC 2925367. PMID 20698959.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  27. ^ Ceusters, Werner Smith, Barry (2010-12-09). Foundations for a realist ontology of mental disease. BioMed Central Ltd. OCLC 754495600.{{cite book}}: CS1 maint: multiple names: authors list (link)
  28. ^ Vita, Randi; Overton, James A.; Seymour, Emily; Sidney, John; Kaufman, Jim; Tallmadge, Rebecca L.; Ellis, Shirley; Hammond, John; Butcher, Geoff W.; Sette, Alessandro; Peters, Bjoern (2016). "An ontology for major histocompatibility restriction". Journal of Biomedical Semantics. 7: 1. doi:10.1186/s13326-016-0045-5. ISSN 2041-1480. PMC 4709943. PMID 26759709.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  29. ^ Leebens-Mack, Jim; Vision, Todd; Brenner, Eric; Bowers, John E.; Cannon, Steven; Clement, Mark J.; Cunningham, Clifford W.; DePamphilis, Claude; DeSalle, Rob; Doyle, Jeff J.; Eisen, Jonathan A. (June 2006). "Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)". OMICS: A Journal of Integrative Biology. 10 (2): 231–237. doi:10.1089/omi.2006.10.231. ISSN 1536-2310.
  30. ^ Tierrafría, V H; Mejía-Almonte, C; Camacho-Zaragoza, J M; Salgado, H; Alquicira, K; Ishida, C; Gama-Castro, S; Collado-Vides, J (2019-03-01). Wren, Jonathan (ed.). "MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions". Bioinformatics. 35 (5): 856–864. doi:10.1093/bioinformatics/bty689. ISSN 1367-4803.
  31. ^ Schofield, Paul N; Sundberg, John P; Sundberg, Beth A; McKerlie, Colin; Gkoutos, Georgios V (2013). "The mouse pathology ontology, MPATH; structure and applications". Journal of Biomedical Semantics. 4 (1): 18. doi:10.1186/2041-1480-4-18. ISSN 2041-1480. PMC 3851164. PMID 24033988.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  32. ^ Federhen, S. (2012-01-01). "The NCBI Taxonomy database". Nucleic Acids Research. 40 (D1): D136–D143. doi:10.1093/nar/gkr1178. ISSN 0305-1048. PMC 3245000. PMID 22139910.{{cite journal}}: CS1 maint: PMC format (link)
  33. ^ Huang, Jingshan; Eilbeck, Karen; Smith, Barry; Blake, Judith A.; Dou, Dejing; Huang, Weili; Natale, Darren A.; Ruttenberg, Alan; Huan, Jun; Zimmermann, Michael T.; Jiang, Guoqian (2016-05-04). "The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology". Journal of Biomedical Semantics. 7 (1): 24. doi:10.1186/s13326-016-0066-0. ISSN 2041-1480. PMC 4857245. PMID 27152146.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  34. ^ Brochhausen, Mathias; Zheng, Jie; Birtwell, David; Williams, Heather; Masci, Anna Maria; Ellis, Helena Judge; Stoeckert, Christian J. (2016-05-02). "OBIB-a novel ontology for biobanking". Journal of Biomedical Semantics. 7 (1). doi:10.1186/s13326-016-0068-y. ISSN 2041-1480.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  35. ^ Parikh, Priti P; Zheng, Jie; Logan-Klumpler, Flora; Stoeckert, Christian J; Louis, Christos; Topalis, Pantelis; Protasio, Anna V; Sheth, Amit P; Carrington, Mark; Berriman, Matthew; Sahoo, Satya S (2012-05-23). "The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms". Journal of Biomedical Semantics. 3 (1). doi:10.1186/2041-1480-3-5. ISSN 2041-1480.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  36. ^ He, Yongqun; Sarntivijai, Sirarat; Lin, Yu; Xiang, Zuoshuang; Guo, Abra; Zhang, Shelley; Jagannathan, Desikan; Toldo, Luca; Tao, Cui; Smith, Barry (2014). "OAE: The Ontology of Adverse Events". Journal of Biomedical Semantics. 5 (1): 29. doi:10.1186/2041-1480-5-29. ISSN 2041-1480. PMC 4120740. PMID 25093068.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  37. ^ Segerdell E, Ponferrada VG, James-Zorn C, Burns KA, Fortriede JD, Dahdul WM, et al. (October 2013). "Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase". Journal of Biomedical Semantics. 4 (1): 31. doi:10.1186/2041-1480-4-31. PMC 3816597. PMID 24139024.{{cite journal}}: CS1 maint: unflagged free DOI (link)
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