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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://sequenceontology.org/

A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl.

Proper citation: SO (RRID:SCR_004374) 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/OBOREL

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Ontology that defines core relations used in all OBO ontologies. Obsolete. Replaced with RO.

Proper citation: Open Biological and Biomedical Ontologies Relationship Types (RRID:SCR_004409) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/searches/MP_form.shtml

Community ontology to provide standard terms for annotating mammalian phenotypic data. It has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria. Your input is welcome.

Proper citation: MPO (RRID:SCR_004855) 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/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://zfin.org/zf_info/anatomy/dict/sum.html

A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio). It includes a list of structures, organized hierarchically into an ontology, with descriptions of each structure. The current version is being written by a consortium of researchers, each serving as an expert for a particular set of anatomical structures. Additional anatomical information derived from the current literature is provided by the ZFIN curation group. Development of a complete and uniform anatomical ontology for the zebrafish is vital to the success of zebrafish science. The anatomical ontology is necessary for: * Effective data dissemination and informatics. * A reference framework. * Interoperability.

Proper citation: Zebrafish Anatomical Ontology (RRID:SCR_005887) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/mental-functioning-ontology/

An ontology for mental functioning, including mental processes such as cognition and traits such as intelligence, and related diseases and disorders. It is developed in the context of the Ontology for General Medical Science and the Basic Formal Ontology. The project is being developed in collaboration between the University of Geneva, Switzerland, and the University at Buffalo, USA. The project is being developed with full involvement of all relevant communities, following best practices laid out by the OBO Foundry. Efforts are currently underway to align with related projects including the Behaviour Ontology, the Cognitive Atlas, the Cognitive Paradigm Ontology and the Neural Electro Magnetic Ontologies.

Proper citation: Mental Functioning Ontology (RRID:SCR_003245) Copy   

•   Source: SciCrunch Registry

http://biomodels.net/kisao/

An ontology that classifies algorithms available for the simulation of models in biology, their characteristics and the parameters required for their use.

Proper citation: Kinetic Simulation Algorithm Ontology (RRID:SCR_003361) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/emotion-ontology/

An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings, designed to support interdisciplinary research by providing unified annotations. The ontology is a domain specialization of the broader Mental Functioning Ontology.

Proper citation: Emotion Ontology (RRID:SCR_003272) Copy   

•   Source: SciCrunch Registry

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

An ontology designed to represent the conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.

Proper citation: Experimental Conditions Ontology (RRID:SCR_003306) Copy   

•   Source: SciCrunch Registry

http://www.bioontology.org

Organization that provides biomedical researchers with online tools and a web portal enabling them to access, review, and integrate disparate ontological resources in all aspects of biomedical investigation and clinical practice. A major focus of the work involves the use of biomedical ontologies to aid in the management and analysis of data derived from complex experiments.

Proper citation: National Center for Biomedical Ontology (RRID:SCR_003304) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/vtontology/

A controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.

Proper citation: Vertebrate Trait Ontology (RRID:SCR_003214) Copy   

•   Source: SciCrunch Registry

https://github.com/egonw/semanticchemistry

An ontology that aims to establish a standard in representing chemical information including chemical structure and the ability to richly describe chemical properties, whether intrinsic or computed. It includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.

Proper citation: Chemical Information Ontology (RRID:SCR_003290) Copy   

•   Source: SciCrunch Registry