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

Ontology for standard measures related to complex diseases, phenotypic traits and environmental exposures

Proper citation: PhenX Phenotypic Terms (RRID:SCR_004518) 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://www.obofoundry.org/ontology/pato.html

Ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. The new PATO differs from the old in that the system of attributes and values has been abandoned in favor of a single hierarchy of qualities. PATO is designed to be used in conjunction with ontologies of quality-bearing entities. An example of such an entity is an insect eye (taken from the fly_anatomy ontology), which could be the bearer of the quality ''red'' (PATO:0000322). This combination is the red eye phenotype. We say that the phenotype term is ''post-coordinated'', as it is formed by coordinating two terms together. This is in contrast to ontologies of pre-coordinated phenotypes, such as the Mammalian Phenotype (MP) ontology. PATO is independent of any exchange format or database schema. One way of expressing phenotype annotation using PATO is pheno-syntax, or pheno-xml. They will also post recommendations for representing phenotypes using OWL. All representations share the same basic formal underpinnings, a combination of quality-bearing entity and a quality (the EQ model).

Proper citation: PATO (RRID:SCR_004782) 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/PVONTO

A pharmacovigilance ontology to connect known facts on drugs, disease, ADEs, and their molecular mechanisms.

Proper citation: Pharmacovigilance Ontology (RRID:SCR_004499) 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

https://github.com/SciCrunch/NIF-Ontology

The NIF Standard Ontology (NIFSTD) is a collection of modular ontologies that provides an extensive set of terms and concepts important for the domains of neuroscience and biology, as well as the data and resources relevant for the life sciences. It is a core component of the Neuroscience Information Framework (NIF) project, a semantically enhanced portal for accessing and integrating neuroscience data, tools and information.

Proper citation: NIFSTD (RRID:SCR_005414) Copy   

•   Source: SciCrunch Registry

http://vivoweb.org/

Open source semantic web application that enables the discovery of research and scholarship across disciplines at a particular institution and across institutions by creating a semantic cloud of information that can be searched and browsed. Participants include institutions with local installations of VIVO or those with research discovery and profiling applications that can provide semantic web-compliant data. The information accessible through the national network''''s search and browse capability will therefore reside and be controlled locally within institutional VIVOs or other semantic web applications. The VIVO ontology provides a set of types (classes) and relationships (properties) to represent researchers and the full context of their experience, outputs, interests, accomplishments, and associated institutions. https://wiki.duraspace.org/display/VIVO/VIVO-ISF+Ontology VIVO is populated with detailed profiles of faculty and researchers including information such as publications, teaching, service, and professional affiliations. It also supports browsing and a search function which returns faceted results for rapid retrieval of desired information. The rich semantically structured data in VIVO support and facilitate research discovery. Examples of applications that consume these rich data include: visualizations, enhanced multi-site search through VIVO Search, and applications such as VIVO Searchlight, a browser bookmarklet which uses text content of any webpage to search for relevant VIVO profiles, and the Inter-Institutional Collaboration Explorer, an application which allows visualization of collaborative institutional partners, among others. Institutions are free to participate in the national network by installing and using the application. The application provides linked data via RDF data making users a part of the semantic web! or any other application that provides linked data can be used. Users can also get involved with developing applications that provide enhanced search, new collaboration capabilities, grouping, finding and mapping scientists and their work.

Proper citation: VIVO (RRID:SCR_005246) Copy   

•   Source: SciCrunch Registry

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

Ontology of Computer retrieval of Information on Scientific Projects (CRISP).

Proper citation: Computer Retrieval of Information on Scientific Projects Thesaurus (RRID:SCR_005301) Copy   

•   Source: SciCrunch Registry

http://force11.org/

A collaboration which works to transform scholarly communications through advanced use of computers and the Web. FORCE11 advocates the digital publishing of papers in order to enable more effective scholarly communication. The virtual community also advocates the publication of software tools and research communication by means of social media channels. As such, FORCE11 provides access to information and tools for the wider scientific community.

Proper citation: FORCE11 (RRID:SCR_005334) Copy   

•   Source: SciCrunch Registry

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

Ontology of clinical trial terminology.

Proper citation: Epoch Clinical Trial Ontology (RRID:SCR_000366) Copy   

•   Source: SciCrunch Registry

http://aclame.ulb.ac.be/Classification/mego.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Gene Ontology dedicated to the functions of mobile genetic elements. The terms defined are used to annotate phage and plasmid protein families in ACLAME. Note: The phage ontology PhiGO has now been incorporated in MeGO and can thus be accessed in MeGO version 1.0 and up.

Proper citation: MeGO (RRID:SCR_000110) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An anatomy ontology covering the vertebrate skeletal system that integrates terms for skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system.

Proper citation: Vertebrate Skeletal Anatomy Ontology (RRID:SCR_000313) Copy   

•   Source: SciCrunch Registry

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

Ontology for Inventories of Clinical Data Research Networks, Patient-Powered Research Networks, and Patient Registries

Proper citation: Research Network and Patient Registry Inventory Ontology (RRID:SCR_000308) Copy   

•   Source: SciCrunch Registry

http://environmentontology.org/

Community ontology for the concise, controlled description of environmental features and habitats. It provides a structured vocabulary that is designed to support the annotation of any organism or biological sample with environment descriptors. EnvO contains terms for biomes, environmental features, and environmental material.

Proper citation: EnvO (RRID:SCR_000182) Copy   

•   Source: SciCrunch Registry

https://github.com/information-artifact-ontology/IAO

An ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. Please note: The ontology metrics displayed by BioPortal do not distinguish IAO-developed terms from terms imported from other ontologies.

Proper citation: Information Artifact Ontology (RRID:SCR_000477) Copy   

•   Source: SciCrunch Registry

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

Ontology of nursing interventions classification.

Proper citation: Nursing Interventions Classification (RRID:SCR_000911) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ICPC2P

Ontology of the international classification of primary care -2 PLUS

Proper citation: International Classification of Primary Care - 2 PLUS (RRID:SCR_000909) 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