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

Ontology that encodes agreement among experts about how Emergency Department (ED) chief complaints are grouped into syndromes of public health importance (consensus definitions).

Proper citation: Syndromic Surveillance Ontology (RRID:SCR_010409) Copy   

•   Source: SciCrunch Registry

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

Ontology to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It derived from the Orphanet database (http://www.orpha.net) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, SNOMED CT, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10). The ontology will be maintained by Orphanet and further populated with new data. Orphanet classifications can be browsed in the OLS view. The Orphanet Rare Disease Ontology is updated monthly and follows the OBO guidelines on deprecation of terms. It constitutes the official ontology of rare diseases produced and maintained by Orphanet (INSERM, US14).

Proper citation: Orphanet Rare Disease Ontology (RRID:SCR_010402) Copy   

•   Source: SciCrunch Registry

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

Ontology that models provenance metadata associated with experiment protocols used in parasite research. The PEO extends the upper-level Provenir ontology (http://knoesis.wright.edu/provenir/provenir.owl) to represent parasite domain-specific provenance terms. The PEO (v 1.0) includes Proteome, Microarray, Gene Knockout, and Strain Creation experiment terms along with other terms that are used in pathway.

Proper citation: Parasite Experiment Ontology (RRID:SCR_010403) Copy   

•   Source: SciCrunch Registry

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

Ontology that proposes concepts and roles to represent relationships of pharmacogenomics interest.

Proper citation: Pharmacogenomic Relationships Ontology (RRID:SCR_010406) Copy   

•   Source: SciCrunch Registry

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

Ontology for the description of drug discovery investigations. DDI aims to follow to the OBO (Open Biomedical Ontologies) Foundry principles, uses relations laid down in the OBO Relation Ontology, and be compliant with Ontology for biomedical investigations (OBI).

Proper citation: Ontology for Drug Discovery Investigations (RRID:SCR_010383) Copy   

•   Source: SciCrunch Registry

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

Application ontology to model / represent the notion of genetic susceptibility to a specific disease or an adverse event or a pathological biological process. It is developed using BFO2.0''s framwork. The ontology is under the domain of genetic epidemiology.

Proper citation: Ontology for Genetic Susceptibility Factor (RRID:SCR_010386) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ACGT-MO

Ontology to represent the domain of cancer research and management in a computationally tractable manner.

Proper citation: Cancer Research and Management ACGT Master Ontology (RRID:SCR_006953) Copy   

•   Source: SciCrunch Registry

http://www.evidenceontology.org

A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2

Proper citation: ECO (RRID:SCR_002477) Copy   

•   Source: SciCrunch Registry

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

Ontology that describes the content of the models used in medical image simulation developed in the context of the Virtual Imaging Platform project (VIP), a french project aiming at sharing medical image simulation resources. This ontology can be used to annotate such models in order to highlight the different entities that are present in the 3D scene to be imaged, i.e. anatomical structures, pathological structures, foreign bodies, contrast agents etc. The model allows also to associate to these entities information about their physical qualities, which are used in the medical image simulation process (to mimick physical phenomena involved in CT, MR, US and PET imaging). This ontology partly relies on the OntoNeuroLOG ontology (ONL-DP ONL-MR-DA), as well as PATO, RadLex, FMA and ChEBI.

Proper citation: Medical image simulation (RRID:SCR_010355) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ONL-MSA

Ontology that is a module of the OntoNeuroLOG ontology that covers the field of mental state assessments, i.e. instruments, instrument variables, assessments, and resulting scores, developed in the context of the NeuroLOG project, a french project aiming at integrating distributed heterogeous resources in neuroimaging. It includes a generic domain core ontology, that provides a general model of such entities and a general taxonomy of behavioural, neurosychological and neuroclinical instruments, that can be easily extended to model any particular kind of instrument. It also includes such extensions for 8 relatively standard instruments, namely: (1) the Beck-depression-inventory-(BDI-II), (2) the Expanded-Disability-Status-Scale, (3) the Controlled-oral-word-association-test, (4) the Free-and-Cued-Selective-Reminding-Test-with-Immediate-Recall-16-item-version-(The-Grober-and-Buschke-test), (5) the Mini-Mental-State, (6) the Stroop-color-and-word-test, (7) the Trail-making-test-(TMT), (8) the Wechsler-Adult-Intelligence-Scale-third-edition, (9) the Clinical-Dementia-Rating-scale, (10) the Category-verbal-fluency, (11) the Rey-Osterrieth-Complex-Figure-Test-(CFT).

Proper citation: Mental State Assessment (RRID:SCR_010357) Copy   

•   Source: SciCrunch Registry

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

An ontology for metagenome sample metadata that mainly defines predicates.

Proper citation: Metagenome Sample Vocabulary (RRID:SCR_010358) Copy   

•   Source: SciCrunch Registry

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

A structured controlled vocabulary of the anatomy of mosquitoes.

Proper citation: Mosquito Gross Anatomy Ontology (RRID:SCR_003839) Copy   

•   Source: SciCrunch Registry

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

A basic ontology which describes the proteomics pipeline infrastructure for CPTAC project

Proper citation: CPTAC Proteomics Pipeline Infrastructure Ontology (RRID:SCR_006945) Copy   

•   Source: SciCrunch Registry

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

A structured controlled vocabulary for the phenotypes of Ascomycete fungi.

Proper citation: Ascomycete Phenotype Ontology (RRID:SCR_003254) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/bcgo-ontology/

An application ontology built for the Beta Cell Genomics database aiming to support database annotation, complicated semantic queries, and automated cell type classification. The ontology is developed using Basic Formal Ontology (BFO) as upper ontology, Ontology for Biomedical Investigations (OBI) as ontology framework and integrated subsets of multiple OBO Foundry (candidate) ontologies. Current the BCGO contains 2383 classes including terms referencing to 24 various OBO Foundry ontologies including CL, CLO, UBERON, GO, PRO, UO, etc.

Proper citation: Beta Cell Genomics Ontology (RRID:SCR_003259) Copy   

•   Source: SciCrunch Registry

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

A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum.

Proper citation: Dictyostelium Discoideum Anatomy Ontology (RRID:SCR_003309) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/bco/

Ontology developed as an application ontology as part of the Biocode Commons project whose goal is to support the interoperability of biodiversity data, including data on museum collections, environmental and metagenomic samples, and ecological surveys. It includes consideration of the distinctions between individuals, organisms, voucher specimens, lots, and samples the relations between these entities, and processes governing the creation and use of samples. Within scope as well are properties including collector, location, time, storage environment, containers, institution, and collection identifiers.

Proper citation: Biological Collections Ontology (RRID:SCR_003262) Copy   

•   Source: SciCrunch Registry

http://www.bioontology.org/wiki/index.php/CARO:Main_Page

An ontology developed to facilitate interoperability between existing anatomy ontologies for different species, and to provide a template for building new anatomy ontologies.

Proper citation: Common Anatomy Reference Ontology (RRID:SCR_003296) Copy   

•   Source: SciCrunch Registry

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

An ontology designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs.

Proper citation: Clinical Measurement Ontology (RRID:SCR_003291) Copy   

•   Source: SciCrunch Registry

https://github.com/rsc-ontologies/rsc-cmo

An ontology that describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy; preparing and separating material for further analysis, such as sample ionization, chromatography, and electrophoresis; and synthesizing materials, such as epitaxy and continuous vapor deposition. It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI).

Proper citation: Chemical Methods Ontology (RRID:SCR_003286) Copy   

•   Source: SciCrunch Registry