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

A web ontology for the semantic representation of the computer assisted brain trauma rehabilitation domain. This is a novel and emerging domain, since it employs the use of robotic devices, adaptation software and machine learning to facilitate interactive, adaptive and personalized rehabilitation care, patient monitoring and assisted living.

Proper citation: Computer Assisted Brain Injury Rehabilitation Ontology (RRID:SCR_005288) Copy   

•   Source: SciCrunch Registry

http://bmir.stanford.edu/

Mark Musen''s laboratory studies components for building knowledge-based systems, controlled terminologies and ontologies, and technology for the Semantic Web. For more than two decades, Musen''s group has worked to elucidate reusable building blocks of intelligent systems, and to develop scalable computational architectures for systems with significant applications in biomedicine. Informatics is the study of information: its structure, its communication, and its use. As society becomes increasingly information intensive, the need to understand, create, and apply new methods for modeling, managing, and acquiring information has never been greater especially in biomedicine. BMIR is home to world class scientists and trainees developing cutting-edge ways to acquire, represent, process, and manage knowledge and data related to health, health care, and the biomedical sciences. Our faculty, students, and staff are committed to ensuring the biomedical community is properly equipped for the information age, and believe our efforts will provide the structure for the burgeoning revolution of health care and the biomedical sciences.

Proper citation: Stanford Center for Biomedical Informatics Research (RRID:SCR_005698) Copy   

•   Source: SciCrunch Registry

http://www.clo-ontology.org/

A community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. Its focus is on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications. The CLO development has become a community effort with international collaborations. The development consortium includes experts from all over the world: the USA, Europe, and Japan.

Proper citation: Cell Line Ontology (RRID:SCR_005840) Copy   

•   Source: SciCrunch Registry

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

Ontology of clinical terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre

Proper citation: Read Codes Clinical Terms Version 3 (RRID:SCR_006055) Copy   

•   Source: SciCrunch Registry

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

Ontology specifically for Randomized Controlled Trials in order to facilitate the production of systematic reviews and metaanalysis.

Proper citation: Randomized Controlled Trials Ontology (RRID:SCR_005992) Copy   

•   Source: SciCrunch Registry

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

An application ontology for the domain of gene transcription regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations.

Proper citation: Regulation of Transcription Ontology (RRID:SCR_006238) Copy   

•   Source: SciCrunch Registry

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://www.stanford.edu/

Private, non profit university in Stanford, California, USA for research and undergraduate and graduate studies. Known for its academic strength, wealth, proximity to Silicon Valley, and ranking as one of the world's top universities. Particularly noted for its entrepreneurship and is one of the most successful universities in attracting funding for start-ups.

Proper citation: Stanford University; Stanford; California (RRID:SCR_011538) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/chebi/beta/

Collection of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

Proper citation: CHEBI (RRID:SCR_002088) 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://purl.bioontology.org/ontology/ICNP

Ontology of the international classification for nursing practice.

Proper citation: International Classification for Nursing Practice (RRID:SCR_003099) Copy   

•   Source: SciCrunch Registry

https://genenames.org

Only worldwide authority that provides standardized nomenclature, i.e. gene names and symbols (short form abbreviations), for all known human genes, and stores all approved symbols in the HGNC database. Approved human gene nomenclature. Database of gene symbols and names. Manually curated genes into groups based on shared characteristics such as homology, function or phenotype. Data for protein-coding genes, pseudogenes and non-coding RNAs.

Proper citation: HGNC (RRID:SCR_002827) Copy   

•   Source: SciCrunch Registry

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

Ontology to enable curation of chemical-gene and chemical-protein interactions for the Comparative Toxicogenomics Database (CTD), a freely available resource that aims to promote understanding and novel hypothesis development about the effects of the environment on human health.

Proper citation: Interaction Ontology (RRID:SCR_003055) 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://purl.bioontology.org/ontology/SPD

An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).

Proper citation: Spider Ontology (RRID:SCR_003117) 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