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http://obi-ontology.org/

An ontology for the description of biological and clinical investigations built with international, collaborative effort. The ontology represents the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. This includes a set of universal terms that are applicable across various biological and technological domains, and domain-specific terms relevant only to a given domain. Currently OBI is being built under the Basic Formal Ontology (BFO). This project was formerly titled the Functional Genomics Investigation Ontology (FuGO) project.

Proper citation: Ontology for Biomedical Investigations (RRID:SCR_006266) Copy   

•   Source: SciCrunch Registry

http://omim.org

Online catalog of human genes and genetic disorders, for clinical features, phenotypes and genes. Collection of human genes and genetic phenotypes, focusing on relationship between phenotype and genotype. Referenced overviews in OMIM contain information on all known mendelian disorders and variety of related genes. It is updated daily, and entries contain copious links to other genetics resources.

Proper citation: OMIM (RRID:SCR_006437) Copy   

•   Source: SciCrunch Registry

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

Ontology of SNOMED (Systematized Nomenclature of Medicine) clinical terms.

Proper citation: Systematized Nomenclature of Medicine - Clinical Terms (RRID:SCR_003915) Copy   

•   Source: SciCrunch Registry

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

A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes

Proper citation: Mouse Pathology Ontology (RRID:SCR_003950) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/NHSQI2009

Ontology to organise a 2009 set of over 200 NHS quality indicators from different sources. Relationships between indicators, a basic set of inclusion / exclusion criteria, clinical pathway, clinical code and purpose (per 1992 Institute of Medicine, originally intended to categorise clinical guidelines) are identifies and made searchable.

Proper citation: NHS Quality Indicators (RRID:SCR_004005) Copy   

•   Source: SciCrunch Registry

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

A reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.

Proper citation: Ontology of Physics for Biology (RRID:SCR_004144) Copy   

•   Source: SciCrunch Registry

http://www.xenbase.org/anatomy/xao.do?method=display

A structured, controlled vocabulary of the anatomy and development of the African clawed frogs (Xenopus laevis and tropicalis), organized in a graphical structure. Tissues are shown as being part of other tissues and the timing of their development is indicated by start and end stages. The lineage of tissues is represented by develops from relationships between different tissues at different developmental stages. Many items have been classified according to the Common Anatomy Reference Ontology. The Xenopus Anatomical Ontology will be used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes. Its robust developmental map will enable powerful database searches and data analyses. They encourage community recommendations for updates and improvements to the ontology.

Proper citation: Xenopus Anatomy Ontology (RRID:SCR_004337) Copy   

•   Source: SciCrunch Registry

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

An ontology to describe the entities and relationships in the SEEK database, a Systems Biology environment for the sharing and exchange of data and models. The SysMO-SEEK database contains the work of the SysMO consortium (Systems Biology of Micro-Organisms) https://seek.sysmo-db.org/

Proper citation: SysMO JERM Ontology of Systems Biology for Micro-Organisms (RRID:SCR_004569) 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://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://purl.bioontology.org/ontology/LIPRO

An ontology that describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define membership requirements for sub classes of lipid according to appropriate functional groups. Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied.

Proper citation: Lipid Ontology (RRID:SCR_003349) Copy   

•   Source: SciCrunch Registry

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

An ontology designed to represent the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms.

Proper citation: Measurement Method Ontology (RRID:SCR_003373) Copy   

•   Source: SciCrunch Registry

http://sig.biostr.washington.edu/projects/fm/

A domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Its ontological framework can be applied and extended to all other species. The description of how the OWL version was generated is in Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy by N. F. Noy, J. L. Mejino, C. Rosse, M. A. Musen: http://bmir.stanford.edu/publications/view.php/pushing_the_envelope_challenges_in_a_frame_based_representation_of_human_anatomy The Foundational Model of Anatomy ontology has four interrelated components: # Anatomy taxonomy (At), # Anatomical Structural Abstraction (ASA), # Anatomical Transformation Abstraction (ATA), # Metaknowledge (Mk), The ontology contains approximately 75,000 classes and over 120,000 terms; over 2.1 million relationship instances from over 168 relationship types link the FMA's classes into a coherent symbolic model.

Proper citation: FMA (RRID:SCR_003379) Copy   

•   Source: SciCrunch Registry

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

An application ontology to cover all aspects of malaria (clinical, epidemiological, biological, etc) as well as the intervention attempts to control it, extending the infectious disease ontology (IDO).

Proper citation: Malaria Ontology (RRID:SCR_003369) 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://purl.bioontology.org/ontology/MAT

An ontology of minimal set of terms for anatomy.

Proper citation: Minimal Anatomical Terminology (RRID:SCR_003385) 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