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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

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://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

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

Ontology of master drug data base, 2009_08_05

Proper citation: Master Drug Data Base Clinical Drugs (RRID:SCR_003668) 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

https://www.ebi.ac.uk/chebi/beta/

Collection of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

Proper citation: CHEBI (RRID:SCR_002088) Copy   

•   Source: SciCrunch Registry

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

Ontology of suicidology.

Proper citation: suicideonto (RRID:SCR_010452) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/EHDAA2

A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just ''heart'' really means ''heart (CS 9-20)''. Timing details will be added to the abstract version of the ontology in a future release.

Proper citation: Human Developmental Anatomy Ontology abstract version 2 (RRID:SCR_010337) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ONTODM-KDD

Ontology for representing data mining investigations. Its goal is to allow the representation of knowledge discovery processes and be general enough to represent the data mining investigations. The ontology is based on the CRISP-DM process methodology.

Proper citation: Ontology of Data Mining Investigations (RRID:SCR_010394) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/TM-MER

Ontology of the meridian value set used in the International Classification of Traditional Medicine.

Proper citation: Traditional Medicine Meridian Value Sets (RRID:SCR_010436) Copy   

•   Source: SciCrunch Registry

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

A comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format.

Proper citation: Cell Line Ontology by Mahadevan (RRID:SCR_010281) Copy   

•   Source: SciCrunch Registry

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

Ontology of National Drug File - Reference Terminology Public Inferred Edition, 2008_03_11

Proper citation: National Drug File - Reference Terminology (RRID:SCR_010372) Copy   

•   Source: SciCrunch Registry

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

Ontology that provides an up-to-date knowledge base of experimentally verified glycan structures. Glycan (oligosaccharide or polysaccharide) structures are represented as trees of monosaccharide residues. Linkage to proteins and lipids is supported as well. Insertion of a new glycan is controlled by curation process that includes matching the new glycan against a canonical glyco-tree (a highly branched representation for a family of glycans).

Proper citation: Glycomics Ontology (RRID:SCR_010333) Copy   

•   Source: SciCrunch Registry

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

A domain ontology that provides a formal representation (OWL-DL) of genomic variations. Despite its name it is not limited to the representation of SNPs but it encompasses genomic variations in a broader meaning. SNP-Ontology is general enough to enable the representation of variations observed in genome of various species. Latest versions of SNP-Ontology include the representation of haplotype and of CNV. The unambiguous representation of genomic variations provided by SNP-Ontology enables to integrate heterogeneous data related to genomic variations. To achieve this goal SNP-Ontology enables (1) to represent one variation in accordance with various ways that exist for describing it, (2) to represent the equivalence between two distinct descriptions of one variation, and (3) to represent correspondence between a genomic variation and its outcome at the transcriptome and proteome levels.

Proper citation: Single-Nucleotide Polymorphism Ontology (RRID:SCR_010428) Copy   

•   Source: SciCrunch Registry

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

An Ontology describing Resources having different formats. This Ontology can be used to annotate and describe Terminological, Ontological Knowledge resources.

Proper citation: Terminological and Ontological Knowledge Resources Ontology (RRID:SCR_010432) Copy   

•   Source: SciCrunch Registry

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

Ontology terms useful for machine learning experiments. The terminology appearing in JMLA has been enriched with terms from MeSH and Emtree, the controlled vocabularies for MEDLINE and Embase, respectively. Synonyms include American and British variants and some inverted terms.

Proper citation: EDDA Study Design Terminology (RRID:SCR_010312) Copy   

•   Source: SciCrunch Registry