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

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 timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once.

Proper citation: Human Developmental Anatomy Ontology timed version (RRID:SCR_010338) Copy   

•   Source: SciCrunch Registry

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

Ontology as a basis for shared semantics and interoperability of simulations, of models, of algorithms and of other resources in this domain. The ontology is based on the Basic Formal Ontology, and adheres to the MIREOT principles.

Proper citation: Human Physiology Simulation Ontology (RRID:SCR_010340) Copy   

•   Source: SciCrunch Registry

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

Ontology of logical observation identifier names and codes (LOINC); Version 2.26; January 2, 2009

Proper citation: Logical Observation Identifier Names and Codes (RRID:SCR_010341) Copy   

•   Source: SciCrunch Registry

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

DICOM Controlled Terminology (PS3.16 2013 Annex D)

Proper citation: DICOM Controlled Terminology (RRID:SCR_010302) Copy   

•   Source: SciCrunch Registry

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

A computational diagnostic ontology containing 91 elements, including classes and sub-classes, which are required to conduct SR-MA (Systematic Review - Meta Analysis) for diagnostic studies, that will assist in standardized reporting of diagnostic articles. They also report high percentage of agreement among five observers as a result of the inter-observer agreement that they conducted among them to tag 13 articles using the diagnostic ontology. Moreover, they extend their existing repository CERR-N (Center of Excellence in Research Reporting in Neurosurgery) to include diagnostic studies.

Proper citation: Diagnostic Ontology (RRID:SCR_010307) Copy   

•   Source: SciCrunch Registry

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

A high level patient-centric ontology for the pharmaceutical industry. The ontology should enable silos in discovery research, hypothesis management, experimental studies, compounds, formulation, drug development, market size, competitive data, population data, etc. to be brought together. This would enable scientists to answer new questions, and to answer existing scientific questions more quickly. This will help pharmaceutical companies to model patient-centric information, which is essential for the tailoring of drugs, and for early detection of compounds that may have sub-optimal safety profiles. The ontology should link to existing publicly available domain ontologies.

Proper citation: Translational Medicine Ontology (RRID:SCR_010439) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/BP-METADATA

Ontology that represents the structure that BioPortal uses to represent all of its metadata (ontology details, mappings, notes, reviews, views)

Proper citation: BioPortal Metadata Ontology (RRID:SCR_010167) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/sbo/

A set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. The ontology consists of seven orthogonal vocabularies defining: the roles of reaction participants (eg. substrate), quantitative parameters (eg. Michaelis constant), a precise classification of mathematical expressions that describe the system (eg. mass action rate law), the modeling framework used (eg. logical framework), and a branch each to describe entity (eg. macromolecule) and interaction (eg. process) types, and a branch to define the different types of metadata that may be present within a model. SBO terms can be used to introduce a layer of semantic information into the standard description of a model, or to annotate the results of biochemical experiments in order to facilitate their efficient reuse. SBO is an Open Biomedical Ontologies (OBO) candidate ontology, and is free for use. A programmatic access to the content of the Systems Biology Ontology is provided by Web Services.

Proper citation: SBO (RRID:SCR_006753) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/WHO-ART

Ontology of the WHO adverse reaction terminology, 1997.

Proper citation: WHO Adverse Reaction Terminology (RRID:SCR_010447) Copy   

•   Source: SciCrunch Registry

http://www.nlm.nih.gov/mesh

A controlled vocabulary thesaurus that consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. MeSH, in machine-readable form, is provided at no charge via electronic means. MeSH descriptors are arranged in both an alphabetic and a hierarchical structure. At the most general level of the hierarchical structure are very broad headings such as Anatomy or Mental Disorders. More specific headings are found at more narrow levels of the twelve-level hierarchy, such as Ankle and Conduct Disorder. There are 27,149 descriptors in 2014 MeSH. There are also over 218,000 entry terms that assist in finding the most appropriate MeSH Heading, for example, Vitamin C is an entry term to Ascorbic Acid. In addition to these headings, there are more than 219,000 headings called Supplementary Concept Records (formerly Supplementary Chemical Records) within a separate thesaurus. The MeSH thesaurus is used by NLM for indexing articles from 5,400 of the world''''s leading biomedical journals for the MEDLINE/PubMED database. It is also used for the NLM-produced database that includes cataloging of books, documents, and audiovisuals acquired by the Library. Each bibliographic reference is associated with a set of MeSH terms that describe the content of the item. Similarly, search queries use MeSH vocabulary to find items on a desired topic.

Proper citation: MeSH (RRID:SCR_004750) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/FB-SP

The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.

Proper citation: Fly Taxonomy (RRID:SCR_003317) Copy   

•   Source: SciCrunch Registry

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

Ontology of human dermatologic disease

Proper citation: Human Dermatological Disease Ontology (RRID:SCR_007648) Copy   

•   Source: SciCrunch Registry

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

Ontology for host pathogen interactions in farmed animals

Proper citation: Host Pathogen Interactions Ontology (RRID:SCR_007647) Copy   

•   Source: SciCrunch Registry

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

A small ontology for anatomical spatial references, such as dorsal, ventral, axis, and so forth.

Proper citation: Spatial Ontology (RRID:SCR_007860) Copy   

•   Source: SciCrunch Registry

http://cogpo.org

Ontology used to describe the experimental conditions within cognitive and behavioral experiments, primarily in humans for application and use in the functional neuroimaging community. CogPO has been developed through the integration of the Functional Imaging Biomedical Informatics Research Network (FBIRN) Human Imaging Database (HID) and the BrainMap Database. The design of CogPO concentrates on what can be observed directly: categorization of each paradigm in terms of (1) the stimulus presented to the subjects, (2) the requested instructions, and (3) the returned response.

Proper citation: Cognitive Paradigm Ontology (RRID:SCR_002235) Copy   

•   Source: SciCrunch Registry

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

An ontology to capture all aspects of RNA - from primary sequence to alignments, secondary and tertiary structure from base pairing and base stacking to sophisticated motifs.

Proper citation: RNA Ontology (RRID:SCR_003470) Copy   

•   Source: SciCrunch Registry

http://purl.obolibrary.org/obo/flu/

An application ontology established by a collaborative group of influenza researchers that includes consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS)

Proper citation: Influenza Ontology (RRID:SCR_003346) Copy   

•   Source: SciCrunch Registry

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

Ontology of experimental design for high-throughput mouse analysis pipelines.

Proper citation: Mouse Experimental Design Ontology (RRID:SCR_003879) Copy   

•   Source: SciCrunch Registry

http://cellontology.org

Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases.

Proper citation: Cell Type Ontology (RRID:SCR_004251) Copy   

•   Source: SciCrunch Registry

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

An ontology for describing clinical signs and symptoms.

Proper citation: Clinical Signs and Symptoms Ontology (RRID:SCR_007226) Copy   

•   Source: SciCrunch Registry