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http://archive.gramene.org/plant_ontology/ontology_browse.html#to

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.

Proper citation: Plant Trait Ontology (RRID:SCR_003461) Copy   

•   Source: SciCrunch Registry

http://www.loria.fr/~coulet/sopharm2.0_description.php

A domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. It articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables the representation of pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables the representation of a patient and more largely a panel included in trials, and populations. SO-Pharm enables the representation of measured items on 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.

Proper citation: Suggested Ontology for Pharmacogenomics (RRID:SCR_003497) Copy   

•   Source: SciCrunch Registry

https://bioportal.bioontology.org/ontologies/REX?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FREX_0000000

An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. It includes both microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes. Some biochemical processes from Gene Ontology (GO Biological process) can be described as instances of REX.

Proper citation: Physico-Chemical Process (RRID:SCR_003530) Copy   

•   Source: SciCrunch Registry

http://theswo.sourceforge.net

An ontology for describing software tools, their types, tasks, versions, provenance and data associated (the input and output data types and the uses the software can be put to).

Proper citation: Software Ontology (RRID:SCR_003493) Copy   

•   Source: SciCrunch Registry

http://ccdb.ucsd.edu/SAO

An ontology that describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules. It is built according to ontology development best practices (re-use of existing ontologies; formal definitions of terms; use of foundational ontologies). It describes the parts of neurons and glia and how these parts come together to define supracellular structures such as synapses and neuropil. Molecular specializations of each compartment and cell type are identified. The SAO was designed with the goal of providing a means to annotate cellular and subcellular data obtained from light and electron microscopy, including assigning macromolecules to their appropriate subcellular domains. The SAO thus provides a bridge between ontologies that describe molecular species and those concerned with more gross anatomical scales. Because it is intended to integrate into ontological efforts at these other scales, particular care was taken to construct the ontology in a way that supports such integration.

Proper citation: Subcellular Anatomy Ontology (RRID:SCR_003486) Copy   

•   Source: SciCrunch Registry

http://biomodels.net/kisao/

An ontology that classifies algorithms available for the simulation of models in biology, their characteristics and the parameters required for their use.

Proper citation: Kinetic Simulation Algorithm Ontology (RRID:SCR_003361) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/VTO

An ontology that includes both extinct and extant vertebrates, aiming to provide one comprehensive hierarchy. The hierarchy backbone for extant taxa is based on the NCBI taxonomy. Since the NCBI taxonomy only includes species associated with archived genetic data, to complement this, they also incorporate taxonomic information across the vertebrates from the Paleobiology Database (PaleoDB). The Teleost Taxonomy Ontology (TTO) and AmphibiaWeb (AWeb) are incorporated to provide a more authoritative hierarchy and a richer set of names for specific taxonomic groups.

Proper citation: Vertebrate Taxonomy Ontology (RRID:SCR_003518) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ICPS

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.

Proper citation: International Classification for Patient Safety (RRID:SCR_003553) Copy   

•   Source: SciCrunch Registry

https://bioportal.bioontology.org/ontologies/NEMO/?p=summary

Ontology that 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). Its aim is to support data sharing, logic-based queries and mapping/integration of patterns across data from different labs, experiment paradigms, and modalities (EEG/MEG).

Proper citation: NEMO Ontology (RRID:SCR_003386) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/SBOL

Ontology to represent standardized graphical notation for synthetic biology.

Proper citation: Synthetic Biology Open Language Visual Ontology (RRID:SCR_001261) Copy   

•   Source: SciCrunch Registry

http://phenoscape.org/wiki/Teleost_Taxonomy_Ontology

An ontology of taxonomic terms (names of taxonomic groups) used in the systematics of fish, including non-teleost groups such as Chondrichthys (sharks and rays), Sarcopterygii (lungfish and coelacanths), lampreys, and hagfish. It contains (as of August 2010) over 38,500 names, and over 44,000 taxonomic synonyms. A majority of the taxonomic names and synonyms were made available from the Catalog of Fishes. In July 2010 they added nearly 15,000 common names provided by Fishbase. Additional names and synonyms are added as a result of their curation activities. The ontology is being used to facilitate annotation of phenotypes, particularly for taxa that are not covered by NCBI because no submissions of molecular data have been made. Taxonomy ontologies can also be valuable in annotating legacy data, where authors make phenotype or ecological assertions (e.g., host-parasite associations) that refer to groups that are reorganized or no longer recognized. The taxonomy ontology serves as the source of taxa for their project's use for identifying evolutionary changes that match the phenotype of a zebrafish mutant.

Proper citation: Teleost Taxonomy Ontology (RRID:SCR_001611) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/SDO

An application ontology for the domain of Sleep Medicine.

Proper citation: Sleep Domain Ontology (RRID:SCR_006808) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CBO

Ontology that 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.

Proper citation: Cell Behavior Ontology (RRID:SCR_007055) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CTX

Ontology that represents CTX phenotypes, genetic variants, and bidirectional relationships between them though a patient model. The CTX ontology was built 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.

Proper citation: Cerebrotendinous Xanthomatosis Ontology (RRID:SCR_007067) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CANCO

A vocabulary that is able to describe and semantically interconnect the different paradigms of the cancer chemoprevention domain.

Proper citation: Cancer Chemoprevention Ontology (RRID:SCR_006966) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CAO

Ontology designed for supporting the COG enrichment study by using Fisher''s exact test

Proper citation: Clusters of Orthologous Groups Analysis Ontology (RRID:SCR_007232) Copy   

•   Source: SciCrunch Registry

http://www.ifomis.org/bfo

A small, upper level ontology that is designed for use in supporting information retrieval, analysis and integration in scientific and other domains. BFO is a genuine upper integration in scientific and other domains. Thus it does not contain physical, chemical, biological or other terms which would properly fall within the coverage domains of the special sciences.

Proper citation: BFO (RRID:SCR_004818) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/OBIWS

Ontology that extends the Ontology for Biomedical Investigations (OBI) to support consistent annotation of Bioinformatics Web services.

Proper citation: Bioinformatics Web Service Ontology (RRID:SCR_004529) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/PHENOMEBLAST

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.

Proper citation: PhenomeBLAST Ontology (RRID:SCR_005139) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/searches/MP_form.shtml

Community ontology to provide standard terms for annotating mammalian phenotypic data. It has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria. Your input is welcome.

Proper citation: MPO (RRID:SCR_004855) Copy   

•   Source: SciCrunch Registry