Table 2.
List of ontologies, CVs and thesaurus of interest for AgBioData member databases
| Name | Domain | ID space | URL |
|---|---|---|---|
| Amphibian Gross Anatomy Ontology | Amphibian anatomy | AAO | http://purl.bioontology.org/ontology/AAO |
| Agronomy Ontology | agronomy trials | AGRO | http://obofoundry.org/ontology/agro.html |
| AGROVOC | a controlled vocabulary covering all areas of interest of the Food and Agriculture Organization | AGROVOC | http://aims.fao.org/vest-registry/vocabularies/agrovoc-multilingual-agricultural-thesaurus |
| Animal Trait Ontology for Livestock | phenotypic traits of farm animals | ATOL | http://purl.bioontology.org/ontology/ATOL |
| CAB Thesaurus | bibliographic databases of CABI (Centre for Agriculture and Biosciences International) | CABT | http://www.cabi.org/cabthesaurus/ |
| Cephalopod Ontology | cephalopod anatomy and development | CEPH | http://obofoundry.org/ontology/ceph.html |
| Chemical Entities of Biological Interest | molecular entities | CHEBI | http://obofoundry.org/ontology/chebi.html |
| Cell Ontology | Metazoan (not plant) cell types | CL | http://obofoundry.org/ontology/cl.html |
| Clinical Measurement Ontology | morphological and physiological measurement records generated from clinical and model organism research and health programs | CMO | http://obofoundry.org/ontology/cmo.html |
| Crop Ontology | a collection of vocabularies that describe breeders’ traits for agriculturally important plants: banana, barley, beets, Brachiaria, brassica, cassava, castor bean, chickpea, common bean, cowpea, grapes, groundnut, lentil, maize, mung bean, pearl millet, pigeon pea, potato, rice, sorghum, soybean, sugar kelp, sweet potato, wheat, woody plant and yam | CO | http://www.cropontology.org/ |
| Drosophila Phenotype Ontology | Drosophila phenotypes | DPO | http://obofoundry.org/ontology/dpo.html |
| Evidence and Conclusion Ontology | types of scientific evidence | ECO |
http://www.evidenceontology.org/Welcome.html
http://obofoundry.org/ontology/eco.html |
| Experimental Factor Ontology | anatomy, disease and chemical compounds | EFO | http://www.ebi.ac.uk/efo/ |
| Environment Ontology | biomes, environmental features and environmental materials | ENVO | http://obofoundry.org/ontology/envo.html |
| Feature Annotation Location Description Ontology | FALDO is the Feature Annotation Location Description Ontology. It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt and many other bioinformatics resources. | FALDO | https://github.com/JervenBolleman/FALDO |
| Drosophila Gross Anatomy Ontology | Drosophila melanogaster anatomy | FB-BT | http://obofoundry.org/ontology/fbbt.html |
| Flora Phenotype Ontology | traits and phenotypes of flowering plants occurring in digitized floras | FLOPO | http://obofoundry.org/ontology/flopo.html |
| Gene Ontology | gene function, biological processes and cellular components | GO | http://obofoundry.org/ontology/go.html |
| Hymenoptera Anatomy Ontology | anatomy of Hymenoptera | HAO |
http://hymao.org
http://obofoundry.org/ontology/hao.html |
| Infectious Disease Ontology | infectious diseases | IDO | http://infectiousdiseaseontology.org/page/Download |
| Dengue fever | disease ontology for Dengue fever | IDODEN | VectorBase Ontologies |
| Malaria | disease ontology for malaria | IDOMAL | VectorBase Ontologies |
| Livestock Breed Ontology | buffalo, cattle, chicken, goat, horse, pig and sheep breeds | LBO | http://purl.bioontology.org/ontology/LBO |
| Livestock Product trait Ontology | traits of products from agricultural animals or birds | LPT | http://purl.bioontology.org/ontology/LPT |
| Mammalian Feeding Muscle Ontology | an anatomy ontology for the muscles of the head and neck that participate in feeding, swallowing and other oral-pharyngeal behaviors | MFMO | http://obofoundry.org/ontology/mfmo.html |
| Molecular interactions | protein–protein interactions | MI | http://www.obofoundry.org/ontology/mi.html |
| Mosquito Insecticide Resistance | mosquito insecticide resistance | MIRO | VectorBase Ontologies |
| MONDO Disease Ontology | diseases (currently mostly human but also animal diseases) | MONDO | http://obofoundry.org/ontology/mondo.html |
| Mammalian phenotype | mammalian phenotypes | MP | http://obofoundry.org/ontology/mp.html |
| Mouse Pathology Ontology | mutant and transgenic mouse pathological lesions and processes | MPATH | http://obofoundry.org/ontology/mpath.html |
| National Agricultural Library Thesaurus | vocabulary tools of agricultural terms | NALT | https://agclass.nal.usda.gov/ |
| Neuro Behavior Ontology | behavior terms | NBO | http://www.obofoundry.org/ontology/nbo.html |
| Ontology of Arthropod Circulatory Systems | arthropod circulatory system | OARCS | http://obofoundry.org/ontology/oarcs.html |
| Ontology of Biological Attributes | traits (all species) | OBA | http://obofoundry.org/ontology/oba.html |
| Ontology of Host-Microbe interactions | host–microbe interactions | OHMI | http://www.obofoundry.org/ontology/ohmi.html |
| Ontology of Microbial Phenotypes | microbial phenotypes | OMP | http://obofoundry.org/ontology/omp.html |
| Ontology for Parasite Lifecycle | parasite life cycle stages | OPL | http://www.obofoundry.org/ontology/opl.html |
| Phenotype and Trait Ontology | phenotypic qualities | PATO | http://obofoundry.org/ontology/pato.html |
| Population and Community Ontology | populations and communities | PCO | http://obofoundry.org/ontology/pco.html |
| Plant Experimental Conditions Ontology | plant treatments, growing conditions and/or study types | PECO |
http://browser.planteome.org/amigo
http://obofoundry.org/ontology/peco.html |
| Plant Ontology | plant anatomy and growth stages | PO |
http://browser.planteome.org/amigo
http://obofoundry.org/ontology/po.html |
| Protein Ontology | protein-related entities | PR | http://obofoundry.org/ontology/pr.html |
| Social Insect Behavior Ontology | chemical, anatomy and behavior of social insects | SIBO | http://www.obofoundry.org/ontology/sibo.html |
| Sequence Ontology | sequence types and features | SO | http://obofoundry.org/ontology/so.html |
| SOY Ontology | soybean traits, growth and development | SOY | https://www.soybase.org/ontology.php |
| Spider anatomy and behavior ontology | spider anatomy, behavior and products | SPD | http://obofoundry.org/ontology/spd.html |
| Tick anatomy | Tick gross anatomy | TADS | VectorBase Ontologies |
| Mosquito anatomy | Mosquito gross anatomy | TGMA | VectorBase Ontologies |
| Plant Trait Ontology | plant traits | TO |
http://browser.planteome.org/amigo
http://obofoundry.org/ontology/to.html |
| Tribolium Ontology | anatomy of the red flour beetle Tribolium castaneum | TRON | http://ibeetle-base.uni-goettingen.de/ontology/overview.jsf |
| Teleost Taxonomy Ontology | Teleost phenotypes specifically for zebrafish | TTO | http://obofoundry.org/ontology/tto.html |
| Uberon multispecies anatomy ontology | animal anatomical structures | Uberon | http://obofoundry.org/ontology/uberon.html |
| Variation Ontology | variations in DNA, RNA and/or protein | VARIO | http://purl.obolibrary.org/obo/vario.owl |
| VectorBase controlled vocabulary | controlled vocabulary for vector biology | VBCV | VectorBase Ontologies |
| Vertebrate Trait Ontology | morphology, physiology or development of vertebrates | VT | http://obofoundry.org/ontology/vt.html |
| Xenopus anatomy and development ontology | anatomy and development of Xenopus sp. | XAO |
http://www.xenbase.org/anatomy/xao.do?method=display
http://obofoundry.org/ontology/xao.html |
| Zebrafish Anatomy and Development Ontology | Zebrafish anatomy and development | ZFA |
http://zfin.org/zf_info/anatomy/dict/sum.html
http://obofoundry.org/ontology/zfa.html |
| Zebrafish Developmental Stages | Zebrafish (Danio rerio) developmental stages | ZFS | http://obofoundry.org/ontology/zfs.html |