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

An ontology that describes the Congenital Heart Defects data.

Proper citation: Congenital Heart Defects Ontology (RRID:SCR_007584) Copy   

•   Source: SciCrunch Registry

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

Memorial Sloan-Kettering Cancer Center''s ontology of surgical secondary events (adverse events).

Proper citation: Surgical Secondary Events (RRID:SCR_007894) Copy   

•   Source: SciCrunch Registry

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

The UW Integrated Brain Project is one project within the national Human Brain Project, a national multi-agency effort to develop informatics tools for managing the exploding amount of information that is accumulating about the human brain. The objective of the UW Integrated Brain Project effort is to organize and integrate distributed functional information about the brain around the structural information framework that is the long term goal of our work. This application therefore extends the utility of the Digital Anatomist Project by using it to organize non-structural information. The initial driving neuroscience problem that is being addressed is the management, visualization and analysis of cortical language mapping data. In recent years, advances in imaging technology such as PET and functional MRI have allowed researchers to observe areas of the cortex that are activated when the subject performs language tasks. These advances have greatly accelerated the amount of data available about human language, but have also emphasized the need to organize and integrate the sometimes contradictory sources of data, in order to develop theories about language organization. The hypothesis is that neuroanatomy is the common substrate on which the diverse kinds of data can be integrated. A result of the work done by this project is a set of software tools for generating a 3-D reconstruction of the patient''s own brain from MRI, for mapping functional data to this reconstruction, for normalizing individual anatomy by warping to a canonical brain atlas and by annotating data with terms from an anatomy ontology, for managing individual lab data in local laboratory information systems, for integrating and querying data across separate data management systems, and for visualizing the integrated results. Sponsors: This Human Brain Project research is funded jointly by the National Institute on Deafness and Other Communication Disorders, the National Institute of Mental Health, and the National Institute on Aging.

Proper citation: University of Washington Integrated Brain Project (RRID:SCR_008075) Copy   

•   Source: SciCrunch Registry

https://github.com/hyattpd/Prodigal

Software tool for protein coding gene prediction for prokaryotic genomes.

Proper citation: Prodigal (RRID:SCR_011936) Copy   

•   Source: SciCrunch Registry

https://wiki.zfin.org/display/AB/ZFIN+Antibody+Wiki

A catalog of antibodies important for zebrafish research, maintained by ZFIN. ZFIN Antibody Wiki is where zebrafish researchers can help each other by sharing antibody information - new antibodies, protocols, tips - anything that might be helpful.

Proper citation: ZFIN Antibody Wiki (RRID:SCR_013326) Copy   

•   Source: SciCrunch Registry

https://www.innocentive.com

A global network group resource which provides crowdsourcing services for “innovation solutions.” InnoCentive utilizes an innovation framework, called Challenge Drive Innovation, which is based on leveraging open innovation and crowdsourcing. Software tools are available for idea management, innovation management, and external crowdsourcing programs and competitions.

Proper citation: InnoCentive (RRID:SCR_013851) Copy   

•   Source: SciCrunch Registry

http://stockcenter.vdrc.at/control/main

Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID.

Proper citation: Vienna Drosophila Resource Center (RRID:SCR_013805) Copy   

•   Source: SciCrunch Registry

http://www.fmriconsulting.com/brodmann/

An atlas that facilitates fMRI analysis understanding by providing access to all of the functions that have been associated with each of the 52 Brodmann's areas or corresponding gyri. Links to main publications supporting the findings are provided in PubMed ID format. Brodmann's areas with similar functions and locations have been collapsed into a single page. The word left or right has been added indicating a lateralized function. All the abstracts published on PubMed on fMRI and brain PET studies in which the Brodmann's area or its anatomical correlate were mentioned have been reviewed up to August 2008. Abstracts with poorly described experimental methods or findings clearly conflicting with established knowledge provided by the clinical model were excluded. Studies on patients were also excluded.

Proper citation: Brodmann's Interactive Atlas (RRID:SCR_006368) Copy   

•   Source: SciCrunch Registry

http://ctakes.apache.org

An open-source natural language processing system for information extraction from electronic medical record clinical free-text. This is a system through which one creates one or more pipelines to process clinical notes and to identify clinical named entities. It processes clinical notes, identifying types of clinical named entities, drugs, diseases/disorders, signs/symptoms, anatomical sites and procedures. Each named entity that is found is given attributes for the text span, the ontology mapping code, the context (family history of, current, unrelated to patient), and negated/not negated. cTAKES is built on the UIMA framework. cTAKES 2.5 does not provide a GUI of its own for installation or processing. The cTAKES documentation shows how to use the GUIs provided by the UIMA framework, and how to run cTAKES from a command line. Before using cTAKES you need to know that cTAKES does not provide any mechanisms of its own to handle patient data securely. It is assumed that cTAKES is installed on a system that can process patient data, or that any data being processed by cTAKES has already been through a deidentification step in order to comply with any applicable laws. The tool has been developed and deployed at Mayo Clinic since early 2000.

Proper citation: cTAKES (RRID:SCR_006379) Copy   

•   Source: SciCrunch Registry

http://edamontology.org/

An ontology of bioinformatics operations (tool, application, or workflow functions), types of data including identifiers, topics (application domains), and data formats. The applications of EDAM are within organizing tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web.

Proper citation: EDAM Ontology (RRID:SCR_006620) Copy   

•   Source: SciCrunch Registry

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

Ontology that provides a comprehensive and formal representation of the different domain concepts involved in documenting the full complexity of the skeletal dysplasia domain. It captures and combines the genetic features that discriminate the bone dysplasias with the multitude of phenotypic characteristics manifested by patients and required to be taken into account in order to support the diagnosis process.

Proper citation: Bone Dysplasia Ontology (RRID:SCR_006588) Copy   

•   Source: SciCrunch Registry

http://www.nlm.nih.gov/research/umls/rxnorm/

Ontology that provides a normalized naming system for generic and branded drugs and a tool for supporting semantic interoperation between drug terminologies and pharmacy knowledge base systems. It contains the names of prescription and many over-the-counter drugs available in the United States and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software. It can mediate messages between systems not using the same software and vocabulary. * RxNorm Download Files - contain data consistent with the 2013AB UMLS Metathesaurus Release Files. * RxNorm API - web service for accessing the current RxNorm data set. * RxNorm Browser (RxNav) - a browser for several drug information sources, including RxNorm, RxTerms and National Drug File - Reference Terminology (NDF-RT) . * Current Prescribable Content - subset of currently prescribable drugs found in RxNorm. * RxTerms Drug Interface Terminology - a drug interface terminology derived from RxNorm for prescription writing or medication history recording

Proper citation: RxNorm (RRID:SCR_006645) Copy   

•   Source: SciCrunch Registry

http://diabetes.niddk.nih.gov/dm/pubs/america/

A compilation and assessment of epidemiologic, public health, and clinical data on diabetes and its complications in the United States. Published by the National Diabetes Data Group of the National Institute of Diabetes and Digestive and Kidney Diseases, the book contains 36 chapters organized in five areas: * the descriptive epidemiology of diabetes in the United States based on national surveys and community-based studies, including prevalence, incidence, sociodemographic and metabolic characteristics, risk factors for developing diabetes, and mortality * the myriad complications that affect patients with diabetes * characteristics of therapy and medical care for diabetes * economic aspects, including health insurance and health care costs * diabetes in special populations, including African Americans, Hispanics, Asian and Pacific Islanders, Native Americans, and pregnant women. Diabetes in America, 2nd Edition, has been designed to serve as a reliable scientific resource for assessing the scope and impact of diabetes and its complications, determining health policy and priorities in diabetes, and identifying areas of need in research. The intended audience includes health policy makers at the local and Federal levels who need a sound quantitative base of knowledge to use in decision making; clinicians who need to know the probability that their patients will develop diabetes and the prognosis of the disease for complications and premature mortality; persons with diabetes and their families who need sound information on which to make decisions about their life with diabetes; and the research community which needs to identify areas where important scientific knowledge is lacking.

Proper citation: Diabetes in America (RRID:SCR_006754) Copy   

•   Source: SciCrunch Registry

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

Ontology describing the anatomy and the development of Botryllus schlosseri.

Proper citation: Botryllus schlosseri anatomy and development ontology (RRID:SCR_006602) Copy   

•   Source: SciCrunch Registry

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

Ontology covering a comprehensive list of cell lines derived from breast tissue, both normal and pathological. The ontology in built in OWL with cross relation to classes- genetic variation, pathological condition, genes, chemicals and drugs. The relations built enable semantic query across different classes

Proper citation: Breast Tissue Cell Lines Ontology (RRID:SCR_006686) Copy   

•   Source: SciCrunch Registry

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

A controlled vocabulary of ontology class structures and entities of observed phenotypic terms for primary immunodeficiency diseases (PIDs) that facilitate global sharing and free exchange of PID data with users'' communities

Proper citation: Resource of Asian Primary Immunodeficiency Diseases Phenotype Ontology (RRID:SCR_006776) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/WB-LS

A structured controlled vocabulary of the development of Caenorhabditis elegans.

Proper citation: C. elegans Development Vocabulary (RRID:SCR_006811) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/aeo/

AEO represents the Adverse Event Ontology, a community-driven ontology developed to standardize and integrate data on biomedical adverse events (e.g., vaccine adverse events) and support computer-assisted reasoning. The AEO also can be found in BioPortal, http://bioportal.bioontology.org/ontologies/45534?p=terms

Proper citation: Adverse Event Ontology (RRID:SCR_006807) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/WB-PHENOTYPE

A structured controlled vocabulary of Caenorhabditis elegans phenotypes.

Proper citation: C. elegans Phenotype Vocabulary (RRID:SCR_006924) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/WB-BT

A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.

Proper citation: C. elegans Gross Anatomy Vocabulary (RRID:SCR_006835) Copy   

•   Source: SciCrunch Registry