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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Congenital Heart Defects Ontology Resource Report Resource Website 50+ mentions |
Congenital Heart Defects Ontology (RRID:SCR_007584) | CHD | data or information resource, controlled vocabulary, ontology | An ontology that describes the Congenital Heart Defects data. | owl | is listed by: BioPortal | Congenital Heart Defect | nlx_157376 | SCR_007584 | 2026-08-09 09:04:46 | 61 | ||||||||
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Surgical Secondary Events Resource Report Resource Website |
Surgical Secondary Events (RRID:SCR_007894) | SSE | data or information resource, controlled vocabulary, ontology | Memorial Sloan-Kettering Cancer Center''s ontology of surgical secondary events (adverse events). | owl | is listed by: BioPortal | SCR_007894 | 2026-08-09 09:04:48 | 0 | ||||||||||
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University of Washington Integrated Brain Project Resource Report Resource Website 1+ mentions |
University of Washington Integrated Brain Project (RRID:SCR_008075) | data or information resource, software resource, controlled vocabulary, ontology | 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. | functional mri, anatomy, brain, imaging, neuroanatomy, neuroscience, open source license, pet, technology | Aging | nif-0000-10536 | SCR_008075 | UW Brain Project | 2026-08-09 09:04:57 | 1 | |||||||||
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Prodigal Resource Report Resource Website 1000+ mentions |
Prodigal (RRID:SCR_011936) | Prodigal | simulation software, software application, software resource | Software tool for protein coding gene prediction for prokaryotic genomes. |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: Oak Ridge National Laboratory |
PMID:20211023 | Free, Available for download, Freely available | SCR_021246, OMICS_01493 | https://sources.debian.org/src/prodigal/ | http://prodigal.ornl.gov/ | SCR_011936 | , PROkaryotic DYnamic programming Gene-finding ALgorithm, Prokaryotic Dynamic Programming Genefinding Algorithm | 2026-08-09 09:05:48 | 3398 | |||||
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ZFIN Antibody Wiki Resource Report Resource Website |
ZFIN Antibody Wiki (RRID:SCR_013326) | data or information resource, wiki, narrative resource | 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. | has parent organization: Zebrafish Information Network (ZFIN) | nlx_38706 | SCR_013326 | ZFIN Community Antibody Wiki | 2026-08-09 09:06:16 | 0 | ||||||||||
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InnoCentive Resource Report Resource Website 1+ mentions |
InnoCentive (RRID:SCR_013851) | people resource, software resource | 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. | group, crowdsourcing, Challenge Drive Innovation, software, tools, idea management |
is used by: Scientific American is listed by: Connected Researchers is related to: Connected Researchers |
Must pay for resource | SCR_013851 | 2026-08-09 09:06:20 | 9 | ||||||||||
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Vienna Drosophila Resource Center Resource Report Resource Website 100+ mentions |
Vienna Drosophila Resource Center (RRID:SCR_013805) | VDRC | material resource, biomaterial supply resource | 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. | RIN, Resource Information Network, biomaterial supply resource, drosophila, fly lines, RRID Community Authority | is listed by: Resource Information Network | Free, Public, Must create an account, Acknowledgment required | https://drive.google.com/file/d/1VvsxJMXBDPlO5M_HWGOkeYXbg7zk_68E/view?usp=drivesdk | http://www.csf.ac.at/facilities/vienna-drosophila-resource-center/, http://stockcenter.vdrc.at/control/main | SCR_013805 | 2026-08-09 09:06:13 | 396 | |||||||
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Brodmann's Interactive Atlas Resource Report Resource Website 1+ mentions |
Brodmann's Interactive Atlas (RRID:SCR_006368) | data or information resource, mri d image, atlas | 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. | neuroanatomy, fmri, interactive, mri, pet, brain, brodmann's areas, brodmann partition scheme region, cerebral cortex, function, brain activation, atlas | fMRI consulting | nlx_152117 | SCR_006368 | Broadmann's Interactive Atlas | 2026-08-09 09:04:21 | 3 | |||||||||
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cTAKES Resource Report Resource Website 10+ mentions |
cTAKES (RRID:SCR_006379) | cTAKES | text-mining software, software application, source code, software resource | 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. | natural language processing, information extraction, electronic medical record, medical record, clinical, free-text, annotation, unstructured information management architecture, uima |
is related to: Clinical and Translational Science Awards Consortium has parent organization: Mayo Clinic Minnesota; Minnesota; USA has parent organization: National Cancer Institute |
IBM UIMA ; SHARPn Strategic Health IT Advanced Research Projects Area 4: Secondary Use of EHR Data Cooperative Agreement from the HHS Office of the National Coordinator Washington DC DHHS 90TR000201 |
PMID:23286462 PMID:20819853 |
Open-source | nlx_152159 | https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5 | SCR_006379 | cTAKES - clinical Text Analytics and Knowledge Extraction System, Clinical Text Analysis and Knowledge Extraction System | 2026-08-09 09:04:21 | 45 | ||||
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EDAM Ontology Resource Report Resource Website 1+ mentions |
EDAM Ontology (RRID:SCR_006620) | EDAM | data or information resource, controlled vocabulary, ontology | 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. | bioinformatics, operation, data, topic, type, identifier, format, semantic annotation, obo format, owl |
is listed by: BioPortal is related to: DRCAT Resource Catalogue is related to: bioDBcore has parent organization: European Bioinformatics Institute |
Acknowledgement required, Permission required | nlx_151281 | http://purl.bioontology.org/ontology/EDAM | SCR_006620 | EMBRACE Data and Methods Ontology, EDAM Ontology - Bioinformatics operations types of data topics and data formats, EMBRACE Data And Methods | 2026-08-09 09:04:30 | 9 | ||||||
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Bone Dysplasia Ontology Resource Report Resource Website |
Bone Dysplasia Ontology (RRID:SCR_006588) | BDO | data or information resource, controlled vocabulary, ontology | 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. | owl | is listed by: BioPortal | Bone Dysplasia | nlx_157340 | SCR_006588 | 2026-08-09 09:04:32 | 0 | ||||||||
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RxNorm Resource Report Resource Website 500+ mentions |
RxNorm (RRID:SCR_006645) | RxNorm | data or information resource, controlled vocabulary, ontology | 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 | umls, drug, pharmacy, clinical, drug pack, medicine, unique identifier, prescribable drug, web service, metathesaurus, generic drug, branded drug, data set, web service, database |
is listed by: BioPortal has parent organization: National Library of Medicine |
PMID:22426081 | Account required, (UMLS Terminology Services (UTS)) | nif-0000-02575 | SCR_006645 | Rx Norm | 2026-08-09 09:04:26 | 760 | ||||||
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Diabetes in America Resource Report Resource Website |
Diabetes in America (RRID:SCR_006754) | Diabetes in America | data or information resource, book, resource, narrative resource | 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. | epidemiology, prevalence, incidence, sociodemographic, metabolic, risk factor, mortality, complication, therapy, medical care, economic, health insurance, health care cost, african american, hispanic, asian, pacific islander, native american, pregnant, clinical, pdf, medical care |
is related to: NIDDK Information Network (dkNET) has parent organization: National Diabetes Information Clearinghouse |
Diabetes | NIDDK | Public, Not copyrighted. The Clearinghouse encourages users of this publication to duplicate and distribute as many copies as desired. | nlx_152695 | SCR_006754 | Diabetes in America 2nd Edition | 2026-08-09 09:04:35 | 0 | |||||
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Botryllus schlosseri anatomy and development ontology Resource Report Resource Website |
Botryllus schlosseri anatomy and development ontology (RRID:SCR_006602) | BSAO | data or information resource, controlled vocabulary, ontology | Ontology describing the anatomy and the development of Botryllus schlosseri. | obo | is listed by: BioPortal | nlx_157342 | SCR_006602 | 2026-08-09 09:04:30 | 0 | |||||||||
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Breast Tissue Cell Lines Ontology Resource Report Resource Website |
Breast Tissue Cell Lines Ontology (RRID:SCR_006686) | MCBCC | data or information resource, controlled vocabulary, ontology | 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 | owl | is listed by: BioPortal | nlx_157344 | SCR_006686 | 2026-08-09 09:04:27 | 0 | |||||||||
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Resource of Asian Primary Immunodeficiency Diseases Phenotype Ontology Resource Report Resource Website |
Resource of Asian Primary Immunodeficiency Diseases Phenotype Ontology (RRID:SCR_006776) | RPO | data or information resource, controlled vocabulary, ontology | 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 | owl | is listed by: BioPortal | Primary Immunodeficiency Disease | nlx_157576 | SCR_006776 | Resource of Asian Primary Immunodeficiency Diseases (RAPID) Phenotype Ontology, RAPID phenotype ontology | 2026-08-09 09:04:35 | 0 | |||||||
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C. elegans Development Vocabulary Resource Report Resource Website |
C. elegans Development Vocabulary (RRID:SCR_006811) | WB-LS | data or information resource, controlled vocabulary, ontology | A structured controlled vocabulary of the development of Caenorhabditis elegans. | obo |
is listed by: BioPortal has parent organization: WormBase |
nlx_157346 | SCR_006811 | 2026-08-09 09:04:29 | 0 | |||||||||
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Adverse Event Ontology Resource Report Resource Website |
Adverse Event Ontology (RRID:SCR_006807) | AEO | data or information resource, controlled vocabulary, ontology | 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 | has parent organization: SourceForge | nlx_44108 | SCR_006807 | 2026-08-09 09:04:29 | 0 | ||||||||||
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C. elegans Phenotype Vocabulary Resource Report Resource Website |
C. elegans Phenotype Vocabulary (RRID:SCR_006924) | WB-PHENOTYPE | data or information resource, controlled vocabulary, ontology | A structured controlled vocabulary of Caenorhabditis elegans phenotypes. | obo |
is listed by: BioPortal has parent organization: WormBase |
nlx_157348 | SCR_006924 | 2026-08-09 09:04:31 | 0 | |||||||||
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C. elegans Gross Anatomy Vocabulary Resource Report Resource Website |
C. elegans Gross Anatomy Vocabulary (RRID:SCR_006835) | WB-BT | data or information resource, controlled vocabulary, ontology | A structured controlled vocabulary of the anatomy of Caenorhabditis elegans. | obo |
is listed by: BioPortal has parent organization: WormBase |
nlx_157347 | SCR_006835 | 2026-08-09 09:04:33 | 0 |
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