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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PubMed Resource Report Resource Website 10000+ mentions |
PubMed (RRID:SCR_004846) | bibliography, database, data or information resource | Public bibliographic database that provides access to citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. PubMed citations and abstracts include fields of biomedicine and health, covering portions of life sciences, behavioral sciences, chemical sciences, and bioengineering. Provides access to additional relevant web sites and links to other NCBI molecular biology resources. Publishers of journals can submit their citations to NCBI and then provide access to full-text of articles at journal web sites using LinkOut. | biomedical, literature, publication, open, access, bibliography, gold standard |
is used by: Knowledgebase for Addiction Related Genes is used by: Drug Related Gene Database is used by: ChannelPedia is used by: Molecular Imaging and Contrast Agent Database is used by: Colwiz is used by: Nowomics is used by: PINT is listed by: OMICtools is listed by: FORCE11 is listed by: LabWorm is related to: Chilibot: Gene and Protein relationships from MEDLINE is related to: ImpactStory is related to: Automated recognition of brain region mentions in neuroscience literature. is related to: Information Hyperlinked Over Proteins is related to: PubMed Central is related to: PIE the search is related to: Anne O'Tate is related to: PubBrain is related to: Europe PubMed Central is related to: ResearchGate is related to: CBioC is related to: CiteAb is related to: LitInspector is related to: RefMED is related to: Pubmed Commons is related to: iBIOFind is related to: Ensembl Variation is related to: MEDLINE is related to: XplorMed is related to: Linked Neuron Data is related to: NCBI Structure is related to: MeSH is related to: MEDLINE is related to: EBIMed is related to: Coremine Medical is related to: NIF Literature is related to: GoPubMed is related to: Integrated Auto-Extracted Annotation is related to: Polbase is related to: Integrated Manually Extracted Annotation is related to: DaTo is related to: NIF Registry Automated Crawl Data has parent organization: NCBI works with: Open Regulatory Annotation Database works with: rentrez |
NLM | Free, Freely available | nlx_82958, OMICS_01195 | http://www.force11.org/node/4652, http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed | SCR_004846 | Pub Med | 2026-08-12 10:49:03 | 106635 | ||||||
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QUEST Resource Report Resource Website 500+ mentions |
QUEST (RRID:SCR_005210) | QUEST | video resource, portal, data or information resource, podcast, narrative resource, outreach program, training resource, training material, community building portal | An award-winning multimedia science and environment series created by KQED, San Francisco, the public media station serving Northern California. Launched in February 2007, by the end of its fourth season (in September 2010), QUEST had reached approximately 36 million viewers and listeners through its traditional TV and radio broadcasts and its growing Web audience. QUEST''s ultimate aim is to raise science literacy in the San Francisco Bay Area and beyond, inspiring audiences to discover and explore science and environment issues for themselves. Every season, KQED''s QUEST produces: * half-hour television episodes episodes that air weekly, exploring the cutting-edge work of Northern California scientists and researchers (QUEST airs Wednesdays 7:30pm on KQED Public Television 9); * weekly radio reports covering urban environmental issues which often include multimedia slide shows, and interactive online maps (QUEST airs Mondays 6:30am and 8:30am on KQED Public Radio 88.5 FM); * Educational resources, for use by formal and informal educators; QUEST also provides professional development for science educators to support multimedia and technology integration in science classrooms and programs; * 20 six-minute stories for its new web only series, Science on the SPOT, which takes a fresh, fast and curious look at science with stories about albino redwoods, the science of fog and banana slugs, to name a few. (launched in 2010); * A daily science blog written by Northern California scientists, QUEST producers and science enthusiasts; * Exclusive web extras, featuring extended interviews with scientists; Flickr photos, and science hikes. Formal and informal Educators who would like to become involved withthe educational outreach program should contact: ScienceEd (at) kqed.org. | science, environment, astronomy, biology, chemistry, climate, engineering, environment, geology, health, physics, news, television, radio, digital media |
is used by: NIF Data Federation is used by: Integrated Blogs is parent organization of: QUEST Community Science Blog |
NSF ; Corporation for Public Broadcasting ; Richard and Rhoda Goldman Fund ; S. D. Bechtel Jr. Foundation ; Dirk and Charlene Kabcenell Foundation ; Vadasz Family Foundation ; Wyncote Foundation ; George and Jeanette Stuart Charitable Trust |
nlx_144230 | SCR_005210 | QUEST Northern California, KQED QUEST | 2026-08-12 10:49:08 | 806 | |||||||
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Lawson Brain Tumour Tissue Bank Resource Report Resource Website |
Lawson Brain Tumour Tissue Bank (RRID:SCR_004881) | Lawson Brain Tumour Bank | biomaterial supply resource, tissue bank, brain bank, material resource | To aid researchers, the Brain Tumour Tissue Bank, located located in London Health Sciences Centre in London, Ontario, Canada has been collecting human brain tumor specimens and matching clinical data for neuro-oncology research in Canada and internationally since its establishment in 1991. A wide variety of primary and secondary brain tumors, spinal tumors, peritumors and normal brain tissues are available for molecular, protein, enzyme and immunohistochemical studies. Interested researchers can review the information provided at the website and can contact the tissue bank for information about what is currently available. In order to complete a request, an application must be completed. |
is listed by: One Mind Biospecimen Bank Listing is related to: Brain Tumour Foundation of Canada |
Brain tumor | Brain Tumour Foundation of Canada | nlx_85555 | http://www.lawsonresearch.com/v1.0/website/clinical_research/brain_tumour_bank.htm | SCR_004881 | Lawson Health Research Institute Brain Tumour Tissue Bank, Lawson Health Research Institute Brain Tumour Bank, Lawson Brain Tumor Tissue Bank | 2026-08-12 10:49:03 | 0 | ||||||
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Organ Procurement and Transplantation Network Resource Report Resource Website 50+ mentions |
Organ Procurement and Transplantation Network (RRID:SCR_004883) | OPTN | data or information resource, people resource, database, patient registry | The only national patient waiting list and an online database system, called UNet, that links all of the professionals involved in the donation and transplantation system for the collection, storage, analysis, and publication of all OPTN data pertaining to the patient waiting list, organ matching, and transplants. The system contains data regarding every organ donation and transplant event occurring in the U.S. since October 1, 1987. UNet is a fail-safe, 24/7, secure Internet-based transplant information database created to enable the nation''''s organ transplant institutions to: * register patients for transplants * match donated organs to waiting patients * manage the time-sensitive, life-critical data of all patients, before and after their transplants Data reports are available by type: National Data, Regional Data, State Data, Center Data, Build Advanced Report, and Annual Report Data. UNet is being used right now by all of the nation''''s organ transplant programs, organ procurement organizations, and histocompatibility (tissue typing) laboratories working cooperatively to efficiently share a limited number of donated organs among thousands of patients. | transplant, organ, kidney, pancreas, liver, heart, lung, intestine, adult, pediatric, adult human, young human, child, thoracic, waiting list, donation, transplantation, data set, medical data, FASEB list |
is listed by: NIDDK Research Resources is listed by: NIDDK Information Network (dkNET) has parent organization: UNOS - United Network for Organ Sharing is parent organization of: LifeBanc |
Health Resources and Services Administration | nlx_143932 | http://www.optn.org/ | SCR_004883 | Organ Procurement Transplantation Network | 2026-08-12 10:49:04 | 50 | ||||||
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Open PHACTS Resource Report Resource Website 10+ mentions |
Open PHACTS (RRID:SCR_005050) | OPS | organization portal, portal, data or information resource, database, software resource, consortium | Project that developed an open access discovery platform, called Open Pharmacological Space (OPS), via a semantic web approach, integrating pharmacological data from a variety of information resources and tools and services to question this integrated data to support pharmacological research. The project is based upon the assimilation of data already stored as triples, in the form subject-predicate-object. The software and data are available for download and local installation, under an open source and open access model. Tools and services are provided to query and visualize this data, and a sustainability plan will be in place, continuing the operation of the Open PHACTS Discovery Platform after the project funding ends. Throughout the project, a series of recommendations will be developed in conjunction with the community, building on open standards, to ensure wide applicability of the approaches used for integration of data. | drug, enzyme family, structure, receptor, target, ki, pathway, pharmacology, enzyme, small molecule, data mining, annotation, drug discovery, drug development, pharmacological profile, pharmacokinetic, admet data, biological target, chemical, linked data, rdf, nanopublication, platform, semantic technology, text mining, bioinformatics, cheminformatics, interoperability, chemistry, data provenance, compound, small molecule, semantic integration, drug discovery |
uses: CHEBI uses: ChemSpider uses: ConceptWiki uses: DrugBank uses: ENZYME uses: UniProt uses: Gene Ontology uses: WikiPathways is listed by: Consortia-pedia is listed by: FORCE11 is related to: Nanopub.org is related to: eTRIKS is related to: Janssen Research and Development is related to: Almirall is related to: ESTEVE is related to: Merck is related to: Pfizer Animal Genetics is related to: VU University; Amsterdam; Netherlands is related to: European Bioinformatics Institute is related to: Maastricht University; Maastricht; Netherlands is related to: University of Bonn; Bonn; Germany is related to: Royal Society of Chemistry is related to: Spanish National Cancer Research Center is related to: Netherlands Bioinformatics Centre is related to: SIB Swiss Institute of Bioinformatics is related to: Technical University of Denmark; Lyngby; Denmark is related to: University of Santiago de Compostela; Santiago de Compostela; Spain is related to: University of Vienna; Vienna; Austria is related to: University of Hamburg; Hamburg; Germany is related to: University of Manchester; Manchester; United Kingdom is related to: BioSolveIT is related to: ConnectedDiscovery is related to: OpenLink Software is related to: SciBite is related to: Open PHACTS Foundation has parent organization: University of Vienna; Vienna; Austria |
Innovative Medicines Initiative grant 115191; EFPIA ; Open PHACTS Foundation |
PMID:22683805 | Open unspecified license, Registration required, Non-commercial | r3d100011550, nlx_144033 | https://www.force11.org/node/4684, http://www.imi.europa.eu/content/open-phacts, https://doi.org/10.17616/R3T63F | SCR_005050 | Open PHACTS - Open Pharmacological Space, OpenPhacts.org, Open Pharmacological Space, Open Pharmacological Concepts Triple Store, OpenPHACTS, Open PHACTS: Open Pharmacological Space | 2026-08-12 10:49:06 | 11 | ||||
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HMP Data Analysis and Coordination Center Resource Report Resource Website 100+ mentions |
HMP Data Analysis and Coordination Center (RRID:SCR_004919) | HMP DACC | service resource, data or information resource, database, data repository, storage service resource | Common repository for diverse human microbiome datsets and minimum reporting standards for Common Fund Human Microbiome Project. | Repository, diverse, human, microbiome, minimum, reporting, standard, common, fund, microbiome, project, dataset, FASEB list |
is recommended by: National Library of Medicine has parent organization: University of Maryland School of Medicine; Maryland; USA has parent organization: Human Microbiome Project |
NIH | nlx_88368 | SCR_004919 | Data Analysis and Coordination Center for the Human Microbiome Project, HMPDACC, Human Microbiome Project Data Analysis and Coordination Center | 2026-08-12 10:49:04 | 239 | |||||||
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UCSF Laboratory for Visual Neuroscience Resource Report Resource Website |
UCSF Laboratory for Visual Neuroscience (RRID:SCR_004913) | Laboratory for Visual Neuroscience | video resource, portal, image, data or information resource, organization portal, laboratory portal | Devise better ways to prevent and treat vision loss due to amblyopia and strabismus, and to advance medical science by understanding the human visual system. Various Images, Videos and Talks related to the research are available. In the Laboratory for Visual Neuroscience at the University of California, San Francisco, we are seeking to discover how visual perception occurs in the human brain. The function of the visual system is to guide our behavior by providing an efficient means for the rapid assimilation of information from the environment. As we navigate through our surroundings, a continuous stream of light images impinges on our eyes. In the back of each eye a light-sensitive tissue, the retina, converts patterns of light energy into electrical discharges known as action potentials. These signals are conveyed along the axons of retinal ganglion cells to the lateral geniculate body, a relay nucleus in the thalamus. Most of the output of the lateral geniculate body is relayed directly to the primary visual cortex (striate cortex, V1), and then to surrounding visual association areas. To understand the function of the visual pathways, our research is focused on 5 major themes: * Organization of Primary Visual Cortex * Mapping of Extrastriate Visual Cortex * Amblyopia and Visual Development * Strabismus and Visual Suppression * The Human Visual Cortex | amblyopia, strabismus, human, visual system, ophthalmology, monkey, eye, vision loss, patient, research, education, pediatric ophthalmology, neuro-ophthalmology, pediatric, primary visual cortex, vision |
is used by: NIF Data Federation is used by: Integrated Videos has parent organization: University of California at San Francisco; California; USA |
PMID:17898211 | nlx_143941 | SCR_004913 | University of California San Francisco Laboratory for Visual Neuroscience | 2026-08-12 10:49:04 | 0 | |||||||
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BBMRI Wiki Resource Report Resource Website |
BBMRI Wiki (RRID:SCR_004994) | BBMRI Wiki | ontology, data or information resource, narrative resource, controlled vocabulary, standard specification, wiki, international standard specification | The BBMRI Wiki is intended to help establish a standard vocabulary within the European BBMRI (Biobanking and Biomolecular Resources Research Infrastructure) project. This Wiki also facilitates the definition and updating of new terms as well as the Minimum Information About BIobank data Sharing: MIABIS. MIABIS represents the minimum information required to enable the exchange of biological samples and data between biobanks. | biobank, biomedical, lexicon, miabis, sample, study | has parent organization: Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) | nlx_143999 | SCR_004994 | BBMRI Wiki: For a global biomedical research, Biobanking Biomolecular Resources Research Infrastructure Wiki, Biobanking and Biomolecular Resources Research Infrastructure Wiki | 2026-08-12 10:49:05 | 0 | ||||||||
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NCBI Popset Resource Report Resource Website 1+ mentions |
NCBI Popset (RRID:SCR_005049) | PopSet | service resource, data or information resource, database, data repository, storage service resource | Database containing a set of DNA sequences that have been collected to analyse the evolutionary relatedness of a population. The population could originate from different members of the same species, or from organisms from different species. Users may submit a Popset using Sequin. | nucleotide sequence, nucleotide, sequence, dna sequence, dna, evolution, population, genomics, eukaryotic cell, mutation, phylogenetic, ecosystem, gold standard |
is listed by: re3data.org has parent organization: NCBI |
nlx_99613, r3d100010777 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=popset, https://doi.org/10.17616/R3S901 | SCR_005049 | Entrez PopSet | 2026-08-12 10:49:05 | 9 | |||||||
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Tropical Botanic Garden and Research Institute Resource Report Resource Website |
Tropical Botanic Garden and Research Institute (RRID:SCR_005162) | TBGRI | data or information resource, topical portal, database, portal | Tropical Botanic Garden & Research Institute (TBGRI) is an autonomous Institute established by the Government of Kerala on 17th November 1979 and registered on 23rd November 1979 under the Travancore-Cochin Literary, Scientific and Charitable Societies Registration Act, 1955. It functions under the umbrella of the Science, Technology and Environment Department, Government of Kerala. Prof. A. Abraham, a visionary and a great Botanist, conceived the idea of establishing a Botanic Garden and Research Institute to study and conserve the rare and vanishing wild plant genetic resources of the country. Kinded by the spirit of his concept, the Government of Kerala took a far sighted decision resulting in the establishment of Tropical Botanic Garden & Research Institute (TBGRI) as an autonomous organization at Thiruvananthapuram, the capital City of Kerala. In the beginning, the Institute functioned at Thiruvananthapuram city on a rented duplex building. Thanks to the Forests & Wildlife Department, the land for establishment of the garden was allotted in 1983 and the foundation stone was laid on 27th May 1983 by the then Chief Minister, Shri K. Karunakaran. The then Education Minister, the late C. H. Mohammed Koya laid the foundation stone for the construction of the Visiting Scientists'' Guest House. The meeting was presided over by the Minister for Forests, Shri K. P. Noorudeen. With the recruitment of a skeletal scientific and technical staff, the Institute made a modest beginning. Biotechnology and Taxonomy were the two subjects considered to have immediate relevance to the development of the garden. While taxonomists prepared a flora of the garden documenting the native plant wealth before mass introduction and face lift which subsequently followed, the bio-technologists mass multiplied plants of commercial importance, especially orchids for cultivation and distribution to the public. The Royal Botanic Gardens (RBG), Kew played an exemplary and significant role in shaping and design of garden lay out of TBGRI in its formative stages. RBG, Kew not only lent its best men to train our technical staff in gardening and landscaping but also generously supplied books and living plants as gifts to enrich the respective collections. Undoubtedly, the continuing support of RBG, Kew is of special mention in the development of the Garden. | botany, biotechnology, taxonomy | is parent organization of: TheScienceJobs.com | nlx_144192 | SCR_005162 | Tropical Botanic Garden and Research Institute, Tropical Botanic Garden Research Institute, Tropical Botanic Garden & Research Institute (TBGRI), Tropical Botanic Garden & Research Institute, Jawaharlal Nehru Tropical Botanic Garden and Research Institute | 2026-08-12 10:49:06 | 0 | ||||||||
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Ivy Glioblastoma Atlas Project Resource Report Resource Website 100+ mentions |
Ivy Glioblastoma Atlas Project (RRID:SCR_005044) | Ivy GAP | data or information resource, atlas, database, image collection | Platform for exploring the anatomic and genetic basis of glioblastoma at the cellular and molecular levels that includes two interactive databases linked together by de-identified tumor specimen numbers to facilitate comparisons across data modalities: * The open public image database, here, providing in situ hybridization data mapping gene expression across the anatomic structures inherent in glioblastoma, as well as associated histological data suitable for neuropathological examination * A companion database (Ivy GAP Clinical and Genomic Database) offering detailed clinical, genomic, and expression array data sets that are designed to elucidate the pathways involved in glioblastoma development and progression. This database requires registration for access. The hope is that researchers all over the world will mine these data and identify trends, correlations, and interesting leads for further studies with significant translational and clinical outcomes. The Ivy Glioblastoma Atlas Project is a collaborative partnership between the Ben and Catherine Ivy Foundation, the Allen Institute for Brain Science and the Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment. | glioblastoma, in situ hybridization, hematoxylin and eosin stain, brain, tumor, gene expression, anatomic structure, histology, clinical, genomic, expression array, gene, FASEB list | has parent organization: Allen Institute for Brain Science | Brain cancer, Cancer | Ben and Catherine Ivy Foundation | nlx_99161 | SCR_005044 | 2026-08-12 10:49:05 | 158 | |||||||
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UCSD Experimental Neuropath Laboratory Resource Report Resource Website |
UCSD Experimental Neuropath Laboratory (RRID:SCR_004906) | biomaterial supply resource, tissue bank, brain bank, material resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. The Laboratory of Experimental Neuropathology is engaged in the study of neurodegenerative disease, including Alzheimer's, Parkinson's, and the dementia of HIV encephalitis. It contains a large bank of materials available to fellow investigators including images, publications, and lab safety. Fellow Investigators and Collaborators may request materials from the brain bank. Technologies employed by the laboratory include immunocytochemistry, neurochemistry, molecular genetics, transgenic models of disease, and imaging by scanning laser confocal microscopy. | brain, tissue, neurodegenerative disease, alzheimer'disease, parkinson's disease, huntington's disease, hiv dementia, dementia, human immunodeficiency virus, encephalitis, neuronal degeneration, postmortem, brain bank |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of California at San Diego; California; USA |
Neurodegenerative disease, Alzheimer's disease, Parkinson's disease, Huntington's disease, HIV dementia | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143937 | http://neurosci.ucsd.edu/materials-request-form.aspx http://neurosci.ucsd.edu/faculty/eliezer_masliah.aspx | SCR_004906 | UCSD Experimental Neuropathology Laboratory, Laboratory of Experimental Neuropathology | 2026-08-12 10:49:04 | 0 | ||||||
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Brain Research Institute Resource Report Resource Website |
Brain Research Institute (RRID:SCR_004988) | BRI | portal, postdoctoral program resource, data or information resource, training resource, topical portal, graduate program resource | Portal touching on all aspects of neuroscience from molecules to the mind, from the laboratory bench to the patient's bedside. Members study the normal structure and workings of the nervous system, its development, its cognitive functions, its derangement by disease and injury, and the means of its repair and protection. Projects span traditional disciplinary boundaries, as do graduate and postdoctoral training programs. Its major achievement has been to foster and improve multidisciplinary collaborations which has increasingly permitted the identification of pathogenic mechanisms and the formulation of new therapeutic approaches. | one mind tbi, one mind ptsd, neuroscience, nervous system, genomics, proteomics, magnetic resonance imaging assay, positron emission tomography, biosensor, microelectromechanical system, brain, spinal cord |
has parent organization: University of California at Los Angeles; California; USA is parent organization of: Numerical Fibre Generator is parent organization of: cortex is parent organization of: SOCK is parent organization of: Brain Research Institute Biobank Resources |
Brain disorder, Parkinson's disease, Huntington's disease, Alzheimer's disease, Neurofibromatosis, Stroke, Spinal cord injury, Traumatic brain injury, Post-Traumatic Stress Disorder | nlx_143995 | http://www.bri.ucla.edu/index_02.asp | SCR_004988 | Brain Research Institute UCLA | 2026-08-12 10:49:05 | 0 | ||||||
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UnoSeq Resource Report Resource Website 1+ mentions |
UnoSeq (RRID:SCR_005116) | UnoSeq | software library, software toolkit, software resource | A Java library to analyze next generation sequencing data and especially perform expression profiling in organisms where no well-annotated reference genome exists. | java, expression profile, next generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20194116 | OMICS_01296 | SCR_005116 | UnoSeq - Expression profiling with next generation sequencing without a reference genome | 2026-08-12 10:49:06 | 1 | |||||||
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Genomic Datasharing Resource Report Resource Website 1+ mentions |
Genomic Datasharing (RRID:SCR_005233) | GDS | data or information resource, listserv, feed, narrative resource, standard specification | NIH established expectations for sharing data obtained through NIH-funded genome-wide association studies (GWAS) with the implementation of the GWAS Policy. Information and resources related to the GWAS Policy can be found on this website. | genome-wide association study, genome, data sharing |
is listed by: OMICtools has parent organization: National Institutes of Health |
NIH | OMICS_00272 | SCR_005233 | GWAS, Genome-Wide Association Studies | 2026-08-12 10:49:07 | 5 | |||||||
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BioPortfolio Resource Report Resource Website 1+ mentions |
BioPortfolio (RRID:SCR_005230) | BioPortfolio | portal, data or information resource, database, narrative resource, job resource, blog | BioPortfolio is a leading news, information and knowledge resource covering the global life science industries impacted on by biotechnology. The site aims to provide the lay person, the researcher and the management executive with a single location to source core information on specific bio-related topics, to collate relevant data associated with each topic and to point the user to relevant knowledge resources. We publish up to the minute news (see biotechnology news categories) and regularly update content across our information databases. BioPortfolio promotes and sells market research and management reports from 30+ publishers. In addition our unique corporate database lists 40,000+ companies and organizations. BioPortfolio aims to bring together high quality information about marketed drugs - medication and relevant clinical trials, research papers and recent news from PubMed, ClinicalTrials.gov, and DailyMed. Additionally, resources include biotech, pharma and medical job listings. When the BioPortfolio site was launched in February 1997 the company aimed to provide a global free-to-use resource with defined aims and mission statement: to meet the increasing demand of consumers, scientists, investors, commerce and government for timely, accurate and commercially useful information and intelligence on biotechnology companies, technologies and products world-wide. Driven by the success of the site we have made major investments and improvements to enhance our content and to apply the latest web technologies to improve functionality and site utility. We believe this unique depth and breadth of content is supporting individuals, organizations and policy-makers to become more aware of the role of biotechnology on the global economy. With 97,000 users visiting the site more than once per month we are confident that we are providing information our users need. We hope you the users find the site of value for both personal and professional reasons. Please enjoy this free resource and email your comments! | news, information, knowledge, life science, biotechnology, pubmed, corporate, clinical trial, drug, career, pharmaceutical, healthcare, medicine, clinical, industry |
is used by: NIF Data Federation is used by: Integrated Blogs |
For personal non-commercial use only | nlx_144235 | SCR_005230 | 2026-08-12 10:49:07 | 1 | ||||||||
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VARIANT Resource Report Resource Website 1000+ mentions |
VARIANT (RRID:SCR_005194) | VARIANT | service resource, production service resource, software application, data processing software, analysis service resource, software resource, data analysis service, data analysis software | Analysis tool that can report the functional properties of any variant in all the human, mouse or rat genes (and soon new model organisms will be added) and the corresponding neighborhoods. Also other non-coding extra-genic regions, such as miRNAs are included in the analysis. It not only reports the obvious functional effects in the coding regions but also analyzes noncoding SNVs situated both within the gene and in the neighborhood that could affect different regulatory motifs, splicing signals, and other structural elements. These include: Jaspar regulatory motifs, miRNA targets, splice sites, exonic splicing silencers, calculations of selective pressures on the particular polymorphic positions, etc. Software analysis pipelines used in the analysis of NGS data are highly modular, heterogeneous, and rapidly evolving. VARIANT can easily be incorporated into a NGS resequencing pipeline either as a CLI or invoked a webservice. It inputs data directly from the most widely used programs for SNV detection., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional property, variant, gene, non-coding region, mirna, function, single nucleotide variant, next generation sequencing, command line |
is listed by: OMICtools has parent organization: Principe Felipe Research Centre; Valencia; Spain |
Spanish Ministry of Science and Innovation BIO2011-27069 | PMID:22693211 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00193 | SCR_005194 | Variant effect, VARIant ANalysis Tool | 2026-08-12 10:49:07 | 1366 | |||||
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SNPdbe Resource Report Resource Website 1+ mentions |
SNPdbe (RRID:SCR_005190) | SNPdbe | service resource, data or information resource, database, data repository, storage service resource | A database to fill the annotation gap left by the high cost of experimental testing for functional significance of protein variants. It joins related bits of knowledge, currently distributed throughout various databases, into a consistent, easily accessible, and updatable resource. It currently covers over 155,000 protein sequences which come from more than 2,600 organisms. Overall more than one million single amino acid substitutions (SAASs) are referenced consisting of natural variants, SAASs from mutagenesis experiments and sequencing conflicts. SNPdbe offers the following pieces of information (if available) on each SAAS: * Experimentally derived functional and structural impact * Predicted functional effect * Associated disease * Average heterozygosity * Experimental evidence of the nsSNP * Evolutionary conservation of wildtype and mutant amino acid * Link-outs to external databases A convenient webinterface to query SAASs on the following levels is offered: * Protein and gene identifiers and keywords * Disease keywords * Protein sequence on different sequence identity thresholds * Variant identifier (dbSNP rs, SwissVar, PMD) or specific mutant like XposY and specified sequence They offer the possibility to submit protein sequences along with experimentally substantiated mutations in order to predict their functional effect and inclusion into our database. | single amino acid substitution, protein variant, protein, variant, protein sequence, natural variant, mutagenesis, sequencing, mutation |
is listed by: OMICtools has parent organization: ROSTLAB |
PMID:22210871 | Free for academic use, Non-commercial, Commercial use with permission, The community can contribute to this resource | OMICS_00185 | SCR_005190 | SNPdbe - nsSNP database of functional effects, nsSNP database of functional effects | 2026-08-12 10:49:07 | 4 | ||||||
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Protocol Online - Your labs reference book Resource Report Resource Website 10+ mentions |
Protocol Online - Your labs reference book (RRID:SCR_004937) | Protocol Online | data or information resource, narrative resource, experimental protocol | Database of research protocols in a variety of life science fields, it contains protocols contributed by worldwide researchers as well as links to web protocols hosted by worldwide research labs, biotech companies, personal web sites. The data is stored in a MySql relational database. Protocol Online also hosts discipline specific discussion forums (BioForum), and provides a free PubMed search and alerting service (PubAlert). | bioinformatics, molecular biology, immunology, microbiology, proteomics, cell biology, database |
is used by: NIF Data Federation is used by: Integrated Blogs |
Eppendorf ; Invitrogen ; Chang Bioscience ; Mirus ; KPL ; Oligomaster ; Abcam ; Nature Publishing Group |
nlx_90492 | SCR_004937 | Protocol Online Your lab''s reference book, Protocol-Online | 2026-08-12 10:49:04 | 11 | |||||||
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CTSAconnect Resource Report Resource Website |
CTSAconnect (RRID:SCR_005225) | CTSAconnect | ontology, service resource, data or information resource, narrative resource, controlled vocabulary, source code, knowledge environment, standard specification, software resource | THIS RESOURCE IS NO LONGER IS SERVICE. Documented on December 5th, 2022. Semantic framework to integrate information about research activities, clinical activities, and scientific resources to facilitate the production and consumption of Linked Open Data about investigators, physicians, biomedical research resources, services, and clinical activities. The goal is to enable software to consume data from multiple sources and allow the broadest possible representation of researchers'''' and clinicians'''' activities and research products. Current research tracking and networking systems rely largely on publications, but clinical encounters, reagents, techniques, specimens, model organisms, etc., are equally valuable for representing expertise. CTSAConnect will provide linkage between semantic representations of a wide range of clinical and research data using controlled vocabularies mapped to the Unified Medical Language System (UMLS) as a bridge between the two subject areas. The data sources include data from Medicaid, hospital billing systems, CTSAShareCenter, and other CTSA resource data, eagle-i and VIVO. It allows institutions to leverage existing tools and data sources by making the information they contain more discoverable and easier to integrate. For instance, with the ISF, researchers can be characterized by organizational affiliations, grant and project participation, research resources that they have generated, and publications that they have (co)-authored. Clinicians can be characterized by training and credentials, by clinical research topic, and by the kinds of procedures and specialization that can be inferred from encounter data. LOD refers to data that has been given a specific Uniform Resource Identifier (URI), for the purpose of sharing and linking data and information on the Semantic Web. While a large amount of data is published as LOD, there remains a significant gap in the representation of research resources and clinical expertise. Researchers can be characterized by the organization to which they belong, the grants and research in which they have participated, the research topics and research resources (reagents, biospecimens, animal models) they have generated, as well as the publications they have (co)-authored. Clinician profiles on the other hand, can be defined by their credentials, clinical research topics, and the kinds of procedures and specialization that can be inferred from clinical encounter data. They believe that integrating and relating this diversity of information sources and platforms requires addressing the overlap between research resources and the attributes and activities of researchers and clinicians. CTSAconnect aims to promote integration and discovery of research activities, resources, and clinical expertise. To this end, they will publish their ontologies and LOD via their website, which will also illustrate repeatable methods and examples of how to extract, consume, and utilize this valuable new LOD using freely available tools like VIVO, eagle-i, and Google APIs. CTSAconnect is a collaboration between Oregon Health & Science University, Stony Brook University, Cornell University, Harvard University, University at Buffalo, and the University of Florida, and leverages the work of eagle-i (eagle-i.net), VIVO (vivoweb.org), and ShareCenter (ctsasharecenter.org). | data sharing, clinical, research, semantic framework, linked open data, collaborate |
is related to: Eagle I is related to: VIVO is related to: CTSA ShareCenter is related to: Clinical and Translational Science Awards Consortium is related to: CTSA ShareCenter has parent organization: Oregon Health and Science University; Oregon; USA has parent organization: Harvard University; Cambridge; United States |
Booz Allen Hamilton ; National Center for Advancing Translational Sciences |
THIS RESOURCE IS NO LONGER IS SERVICE | nlx_144228 | SCR_005225 | CTSAconnect: A Linked Open Data approach to represent clinical and research expertise activities and resources, CTSA Connect, Clinical and Translational Science Awards Connect | 2026-08-12 10:49:08 | 0 |
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