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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Oct 12, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
eVOCResource, ontology, data or information resource, controlled vocabularyTHIS RESOURCE IS NO LONGER SUPPORTED, documented September 6, 2016. Set of orthogonal controlled vocabularies that unifies gene expression data by facilitating a link between the genome sequence and expression phenotype information. The system associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. The four core eVOC ontologies provide an appropriate set of detailed human terms that describe the sample source of human experimental material such as cDNA and SAGE libraries. These expression terms are linked to libraries and transcripts allowing the assessment of tissue expression profiles, differential gene expression levels and the physical distribution of expression across the genome. Analysis is currently possible using EST and SAGE data, with microarray data being incorporated. The eVOC data is increasingly being accepted as a standard for describing gene expression and eVOC ontologies are integrated with the Ensembl EnsMart database, the Alternate Transcript Diversity Project and the UniProt Knowledgebase. Several groups are currently working to provide shared development of this resource such that it is of maximum use in unifying transcript expression information.mouse, mapping, cdna, development, microarray, expression, expressed sequence, anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation, treatment, gene expression, genome sequence, expression phenotype, genome, sequence, phenotype, anatomical system, cell type, pathology, anatomySCR_010704(eVOC, RRID:SCR_010704)University of the Western Cape; Bellville; South Africa European Union, South African Department of Arts Culture Science and Technology, South African National Research Foundation, Wellcome Trustrelated to: OBO, Bgee: a dataBase for Gene Expression EvolutionPMID:12799354Last checked downnlx_84448
BioMart MartViewResource, data set, web service, software resource, data access protocol, data or information resourceA web server interface of BioMart software and provides a unified view over disparate data sources that enable bioscientists to retrieve data from one or multiple sources in a simple and efficient way. This MartView web server features seamless data federation making cross querying of data sources in a user friendly and unified way. Data sources include major biomolecular sequence, pathway and annotation databases such as Ensembl, Uniprot, Reactome, HGNC, Wormbase, etc. The web server not only provides access through a web interface, it also supports programmatic access through a Perl API as well as RESTful and SOAP oriented web standardSCR_010714(BioMart MartView, RRID:SCR_010714)EMBL, European Union FP6, Ontario Institute for Cancer Research, Wellcome TrustReferences (2)Last checked downnlx_89178
EvidenceFinderResource, software resource, web applicationA web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched.web application, software resource, literature searchSCR_013764(EvidenceFinder, RRID:SCR_013764)Europe PubMed Central Wellcome Trustrelated to: Connected Researchers, Europe PubMed Central, used by: Europe PubMed Central, listed by: Connected ResearchersDOI:10.1093/nar/gku1061Last checked down
GENCODEResource, project portal, dataset, portal, data or information resourceHuman and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation.human, mouse, genome, annotation, sequence, gene featuresSCR_014966(GENCODE, RRID:SCR_014966)NHGRI, Wellcome Trustaffiliated with: ENCODEPMID:22955987Last checked down
Open TrialsResource, data or information resource, databaseDatabase that contains data such as registry entries, portions of regulatory documents describing individual trials, structured data on methods and results, and researchers and papers from and/or related to clinical trials. The initiative aims to locate, match, and share all publicly accessible data and documents, on all trials conducted, on all medicines and other treatments, globally.clinical trial, clinical trial database, clinical trial data, open databaseSCR_015570(Open Trials, RRID:SCR_015570)University of Oxford; Oxford; United Kingdom Laura and John Arnold Foundation, Wellcome Trust, West of England Academic Health Science Network, World Health OrganisationLast checked down
FLIMfitResource, software resource, software application, software toolkitSoftware package for quantitative analysis of large Fluorescence Lifetime Imaging Microscopy (FLIM) data, including global analysis. It is able to routinely analyse multi-well plate FLIM datasets on conventional PC workstations in a reasonable time.fluorescence, lifetime, imaging, microscopy, dataset, global, analysis, multiwell, plate, routineSCR_016298(FLIMfit, RRID:SCR_016298)United Kingdom Biotechnology and Biological Sciences Research Council, United Kingdom Technology Strategy Board, Wellcome TrustDOI:10.1371/journal.pone.0070687, PMID:23940626Last checked down
Genes to Cognition - Biological ResourcesResource, biomaterial supply resource, material resource, organism supplierBiological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline as part of the Genes to Cognition research program are freely-available to interested researchers. Available Transgenic Mouse Lines: *Hras1 (H-ras) knockout,C57BL/6J *Dlg4 (PSD-95) knockout,129S5 *Dlg4 (PSD-95) knockout,C57BL/6J *Dlg3 (SAP102) knockout with hprt mutation,129S5 *Dlg3 (SAP102) knockout (wild-type for hprt,C57BL/6J *Syngap1 (SynGAP) knockout (from 8.24 clone), C57BL/6J *Dlg4 (PSD-95) guanylate kinase domain deletion, C57BL/6J *Ptk2 (FAK) knockout,C57BL/6Jtransgenic, mutant mouse strain, c57bl/6j, 129s5, transgenic mouse line, vector, es cell line, transgenic mouseSCR_001675(Genes to Cognition - Biological Resources, RRID:SCR_001675)University of Edinburgh; Scotland; United Kingdom BBSRC, EPSRC, European Union, Framework Programme, Gatsby Charitable Foundation, Human Frontiers Science Programme, MRC, NSF, Wellcome Trustlisted by: One Mind Biospecimen Bank ListingLast checked downnif-0000-10163
BEAST2Resource, data analysis software, data processing software, software application, sequence analysis software, software resource, software toolkitSoftware package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager.Bayesian, evolutionary, sampling, tree, phylogenic, analysis, Markov, chain, monte carlo, phylogenetic, population, genetic, phylodynamic, sequenceSCR_017307(BEAST2, RRID:SCR_017307)University of Auckland; Auckland; New Zealand EMBL, European Research Council, Max Planck Society, NIGMS, Royal Society of New Zealand Marsden award, Swiss National Science foundationrelated to: BASTA, BEASTPMID:30958812Last checked down
InterMineResource, software resourceAn open source data warehouse system built for the integration and analysis of complex biological data that enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding data. InterMine includes a user-friendly web interface that works "out of the box" and can be easily customized for specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to data.mac os x, unix/linux, windows, javaSCR_001772(InterMine, RRID:SCR_001772)University of Cambridge; Cambridge; United Kingdom Wellcome Trustlisted by: OMICtoolsPMID:24753429Last checked downOMICS_03840
Flybrain at StanfordResource, image analysis software, data processing software, software application, image collection, software resource, data or information resourceProject content including raw image data, neuronal tracings, image registration tools and analysis scripts covering three manuscripts: Comprehensive Maps of DrosophilaHigher Olfactory Centres : Spatially Segregated Fruit and Pheromone Representation which uses single cell labeling and image registration to describe the organization of the higher olfactory centers of Drosophila; Diversity and wiring variability of olfactory local interneurons in the Drosophila antennal lobe which uses single cell labeling to describe the organization of the antennal lobe local interneurons; and Sexual Dimorphism in the Fly Brain which uses clonal analysis and image registration to identify a large number of sex differences in the brain and VNC of Drosophila. Data * Raw Data of Reference Brain (pic, amira) (both seed and average) * Label field of LH and MB calyx and surfaces for these structures * Label field of neuropil of Reference Brain * Traces (before and after registration). Neurolucida, SWC and AmiraMesh lineset. * MB and LH Density Data for different classes of neuron. In R format and as separate amira files. * Registration files for all brains used in the study * MBLH confocal images for all brains actually used in the study (Biorad pic format) * Sample confocal images for antennal lobe of every PN class * Confocal stacks of GABA stained ventral PNs Programs * ImageJ plugins (Biorad reader /writer/Amira reader/writer/IGS raw Reader) * Binary of registration, warp and gregxform (macosx only, others on request) * Simple GUI for registration tools (macosx only at present) * R analysis/visualization functions * Amira Script to show examples of neuronal classes The website is a collaboration between the labs of Greg Jefferis and Liqun Luo and has been built by Chris Potter and Greg Jefferis. The core Image Registration tools were created by Torsten Rohlfing and Calvin Maurer.brain, cell, neuron, neuropil, olfactory, pheromone, confocal image, antennal lobe, axon trace, forum, neuronal tracing, image registration tool, analysis script, single-cell labeling, image registration, mushroom body, lateral horn, olfactory receptor neuronSCR_001877(Flybrain at Stanford, RRID:SCR_001877)Stanford University; Stanford; California Damon Runyon Cancer Research Foundation, NIAAA, NIDCD, Wellcome TrustPMID:17382886Last checked downnif-0000-10437
Wellcome Trust Case Control ConsortiumResource, data or information resourceConsortium of 50 research groups across the UK to harness the power of newly-available genotyping technologies to improve our understanding of the aetiological basis of several major causes of global disease. The consortium has gathered genotype data for up to 500,000 sites of genome sequence variation (single nucleotide polymorphisms or SNPs) in samples ascertained for the disease phenotypes. Analysis of the genome-wide association data generated has lead to the identification of many SNPs and genes showing evidence of association with disease susceptibility, some of which will be followed up in future studies. In addition, the Consortium has gained important insights into the technical, analytical, methodological and biological aspects of genome-wide association analysis. The core of the study comprised an analysis of 2,000 samples from each of seven diseases (type 1 diabetes, type 2 diabetes, coronary heart disease, hypertension, bipolar disorder, rheumatoid arthritis and Crohn's disease). For each disease, the case samples have been ascertained from sites widely distributed across Great Britain, allowing us to obtain considerable efficiencies by comparing each of these case populations to a common set of 3,000 nationally-ascertained controls also from England, Scotland and Wales. These controls come from two sources: 1,500 are representative samples from the 1958 British Birth Cohort and 1,500 are blood donors recruited by the three national UK Blood Services. One of the questions that the WTCCC study has addressed relates to the relative merits of these alternative strategies for the generation of representative population cohorts. Genotyping for this main Case Control study was conducted by Affymetrix using the (commercial) Affymetrix 500K chip. As part of this study a total of 17,000 samples were typed for 500,000 SNPs. There are two additional components to the study. First, the WTCCC award is part-funding a study of host resistance to infectious diseases in African populations. The same approach has been used to type 2,000 cases of tuberculosis (TB) and 2,000 cases of malaria, as well as 2,000 shared controls. As well as addressing diseases of major global significance, and extending WTCCC coverage into the area of infectious disease, the inclusion of samples of African origin has obvious benefits with respect to methodological aspects of genome-wide association analysis. Second, the WTCCC has, for four additional diseases (autoimmune thyroid disease, breast cancer, ankylosing spondylitis, multiple sclerosis), completed an analysis of 15,000 SNPs designed to represent a large proportion of the known non-synonymous coding SNPs across the genome. This analysis has been performed at the WTSI using a custom Infinium chip (Illumina). Data release The genotypic data of the control samples (1958 British Birth Cohort and UK Blood Service) and from seven diseases analyzed in the main study are now available to qualified researchers. Summary genotype statistics for these collections are available directly from the website. Access to the individual-level genotype data and summary genotype statistics is by application to the Consortium Data Access Committee (CDAC) and approval subject to a Data Access Agreement. WTCCC2: A further round of GWA studies were funded in April 2008. These include 15 WTCCC-collaborative studies and 12 independent studies be supported totaling approximately 120,000 samples. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC2 will perform genome-wide association studies in 13 disease conditions: Ankylosing spondylitis, Barrett's oesophagus and oesophageal adenocarcinoma, glaucoma, ischaemic stroke, multiple sclerosis, pre-eclampsia, Parkinson's disease, psychosis endophenotypes, psoriasis, schizophrenia, ulcerative colitis and visceral leishmaniasis. WTCCC2 will also investigate the genetics of reading and mathematics abilities in children and the pharmacogenomics of statin response. Over 60,000 samples will be analyzed using either the Affymetrix v6.0 chip or the Illumina 660K chip. The WTCCC2 will also genotype 3,000 controls each from the 1958 British Birth cohort and the UK Blood Service control group, and the 6,000 controls will be genotyped on both the Affymetrix v6.0 and Illumina 1.2M chips. WTCCC3: The Wellcome Trust has provided support for a further round of GWA studies in January 2009. These include 5 WTCCC-collaborative studies to be carried out in WTCCC3 and 5 independent studies, across a range of diseases. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC3 will perform genome-wide association studies in the following 4 disease conditions: primary biliary cirrhosis, anorexia nervosa, pre-eclampsia in UK subjects, and the interactions between donor and recipient DNA related to early and late renal transplant dysfunction. The WTCCC3 will also carry out a pilot in a study of the genetics of host control of HIV-1 infection. Over 40,000 samples will be analyzed using the Illumina 660K chip. The WTCCC3 will utilize the 6,000 control genotypes generated by the WTCCC2.gene, genomic, genetics, microarray, genome-wide association study, snp, genome-wide association, blood, dna, genotype, variation, genome, sequence variant, copy number variation, genetic variation, phenotype, diseaseSCR_001973(Wellcome Trust Case Control Consortium, RRID:SCR_001973)Wellcome Trust Sanger Institute; Hinxton; United Kingdom Bipolar Disorder, Coronary artery disease, Crohn's disease, Rheumatoid arthritis, Type 1 diabetes, Type 2 diabetes, Hypertension, Control, Multiple sclerosis, Breast cancer, Ankylosing spondylitis, Autoimmune thyroid disease, Malaria, Tuberculosis, Inflammatory bowel disease, Barrett's esophagus, Esophageal adenocarcinoma, Glaucoma, Ischemic stroke, Pre-eclampsia, Parkinson's disease, Psychosis endophenotypes, Psoriasis, Schizophrenia, Ulcerative colitis, Visceral leishmaniasis, Primary biliary cirrhosis, Anorexia nervosa, Human immunodeficiency virus, Renal transplant dysfunctionBill and Melinda Gates Foundation, Wellcome Trust, Wellcome Trust Sanger Institute; Hinxton; United Kingdomrelated to: Psychiatric Genomics ConsortiumPMID:17554300Last checked downnif-0000-10551
Genes to Cognition DatabaseResource, data or information resource, databaseDatabase of protein complexes, protocols, mouse lines, and other research products generated from the Genes to Cognition project, a project focused on understanding molecular complexes involved in synaptic transmission in the brain.allele, gene list, mouse line, human disease, phenotyping, plasticity, behavior, proteonomics, brain, cognition, cognition disorder, learning, memory, neuroscience, experimental protocol, synapse proteomics, synapseSCR_002735(Genes to Cognition Database, RRID:SCR_002735)BBSRC, EPSRC, European Union, Framework Programme, Gatsby Charitable Foundation, Human Frontiers Science Programme, MRC, NSF, Wellcome TrustLast checked downnif-0000-02864
International HapMap ProjectResource, narrative resource, data or information resource, experimental protocol, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project.genetic variant, disease, genetic sequence, genetic variation, single nucleotide polymorphism, genetic diversity, dna, sequence, catalog, genome, chromosomeSCR_002846(International HapMap Project, RRID:SCR_002846)NCBI Chinese Academy of Sciences, Chinese Ministry of Science and Technology, Delores Dore Eccles Foundation, Genome Canada, Genome Quebec, Hong Kong Innovation and Technology Commission, Japanese Ministry of Education Culture Sports Science and Technology MEXT, National Natural Science Foundation of China, NIH, SNP Consortium, University Grants Committee of Hong Kong, Wellcome Trust, W. M. Keck Foundationrelated to: SNAP - SNP Annotation and Proxy Search, Haploview, NHGRI Sample Repository for Human Genetic Research, DistiLD - Diseases and Traits in LD, SNP at Ethnos, GBrowse, used by: BioSample Database at EBI, listed by: OMICtoolsLast checked downnif-0000-02940, OMICS_00273
ShARMResource, organism supplier, database, biomaterial supply resource, biospecimen repository, tissue bank, service resource, portal, storage service resource, data or information resource, material resource, community building portal, material storage repositoryA not for profit organization to accelerate research into aging by sharing resources: providing access to cost and time effective, aged murine tissue through a biorepository and database of live ageing colonies, as well as promoting the networking of researchers and dissemination of knowledge through its online collaborative environment; MiCEPACE. ShARM will provide valuable resources for the scientific community while helping to reduce the number of animals used in vital research into aging. The biobank of tissue and networking facility will enable scientists to access shared research material and data. By making use of collective resources, the number of individual animals required in research experiments can be minimized. The project also has the added value of helping to reduce the costs of research by connecting scientists, pooling resource and combining knowledge. ShARM works in partnership with MRC Harwell and the Centre for Intergrated Research into Musculoskeletal Ageing (CIMA).data sharing, female, male, gut, heart, kidney, livers, lung, mammary fat, muscle, pancreas, bat, bladder, bone, brain, femur, skin, spleen, thymus, tibia, wat, aged tissue, aged mouse, murine modelSCR_003120(ShARM, RRID:SCR_003120)Aging, Control, Young controlWellcome Trustlisted by: One Mind Biospecimen Bank ListingPMID:24085518Last checked downnlx_156767
Wellcome ImagesResource, database, image collection, service resource, storage service resource, image repository, data repository, data or information resourceDigital collection of images, with themes ranging from medical and social history to contemporary healthcare and biomedical science. The collection contains historical images from the Wellcome Library collections, Tibetan Buddhist paintings, ancient Sanskrit manuscripts written on palm leaves, beautifully illuminated Persian books and much more. The Biomedical Collection holds over 40 000 high-quality images from the clinical and biomedical sciences. Selected from the UK''s leading teaching hospitals and research institutions, it covers disease, surgery, general healthcare, sciences from genetics to neuroscience including the full range of imaging techniques. They are always looking for new high quality biomedical images from scientific researchers, clinical photographers and artists in any field of science or medicine. As a contributor you retain your original material and copyright, and receive commission and full credit each time your images are used. The annual Wellcome Images awards (previously known as Biomedical Images Awards) reward contributors for their outstanding work and winners are chosen by a panel of experts. The resulting public exhibitions are always extremely popular and receive widespread acclaim. All images on the Wellcome Images site are available free for use in: * private study and non-commercial research * examination papers * criticism and review, this applies only where there are no multiple copies made * theses submitted by a student at a higher or further education institution for the purposes of securing a degree * personal use by private individualsbiomedical, clinical, disease, surgery, healthcare, genetics, neuroscience, imaging, science, medicine, history, painting, manuscriptSCR_004181(Wellcome Images, RRID:SCR_004181)Wellcome TrustLast checked downnlx_143611
Roslin Wellcome Trust Tick Cell BiobankResource, production service resource, biomaterial supply resource, biospecimen repository, material resource, material service resource, service resource, storage service resource, cell repository, training service resource, biomaterial manufacture, material storage repositoryThe world''s largest collection of tick cell lines, enabling scientists to carry out advanced research. This biobank is establishing a collection of all the continuous cell lines derived from ixodid and argasid ticks of medical and veterinary importance available worldwide now and in future. Ticks are blood feeding arthropods which transmit many human and animal diseases. Research into prevention and cure of these diseases, which are caused by viruses, bacteria and protozoa, is greatly assisted by the use of cell culture systems which enable study of both how tick cells function, and how and why ticks transmit these disease-causing pathogens. Cell lines will always be shipped to recipient laboratories as growing cultures, since we cannot guarantee successful resuscitation of frozen stabilates. Tick cells in culture can tolerate the range of temperatures experienced during transit by air for up to a week. Training: We will provide training in tick cell line care and maintenance. This is an essential component of successful transfer of tick cells to, and their establishment in, laboratories with little or no previous experience of tick cell culture. Recipient scientists (preferably the person who will actually look after the cells) can visit the biobank for between 2 days and 2 weeks, depending on their level of previous experience, to be trained in the specific approach and methods for tick cell cultivation. Establishment of new cell lines: In response to requests and on receipt of suitable starting material (engorged female or moulting nymphal ticks), we will attempt to establish new cell lines from tick species or strains which are not already represented in the collection. Deposition of new tick cell lines: We invite researchers anywhere in the world who have established new tick cell lines to deposit samples for safekeeping free of charge and, if requested, for distribution alongside the existing biobank portfolio.SCR_004228(Roslin Wellcome Trust Tick Cell Biobank, RRID:SCR_004228)University of Edinburgh; Scotland; United Kingdom Wellcome Trustlisted by: One Mind Biospecimen Bank ListingLast checked downnlx_24657
HapMap 3 and ENCODE 3Resource, data or information resource, databaseDraft release 3 for genome-wide SNP genotyping and targeted sequencing in DNA samples from a variety of human populations (sometimes referred to as the HapMap 3 samples). This release contains the following data: * SNP genotype data generated from 1184 samples, collected using two platforms: the Illumina Human1M (by the Wellcome Trust Sanger Institute) and the Affymetrix SNP 6.0 (by the Broad Institute). Data from the two platforms have been merged for this release. * PCR-based resequencing data (by Baylor College of Medicine Human Genome Sequencing Center) across ten 100-kb regions (collectively referred to as ENCODE 3) in 712 samples. Since this is a draft release, please check this site regularly for updates and new releases. The HapMap 3 sample collection comprises 1,301 samples (including the original 270 samples used in Phase I and II of the International HapMap Project) from 11 populations, listed below alphabetically by their 3-letter labels. Five of the ten ENCODE 3 regions overlap with the HapMap-ENCODE regions; the other five are regions selected at random from the ENCODE target regions (excluding the 10 HapMap-ENCODE regions). All ENCODE 3 regions are 100-kb in size, and are centered within each respective ENCODE region. The HapMap 3 and ENCORE 3 data are downloadable from the ftp site.human, gene, genotype, sequence, single nucleotide polymorphism, dna, softwareSCR_004563(HapMap 3 and ENCODE 3, RRID:SCR_004563)Baylor University; Texas; USA NHGRI, NIDCD, Wellcome Trustrelated to: NHGRI Sample Repository for Human Genetic Research, listed by: 3DVCLast checked downnlx_143820
PfamResource, data or information resource, databaseA database of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Users can analyze protein sequences for Pfam matches, view Pfam family annotation and alignments, see groups of related families, look at the domain organization of a protein sequence, find the domains on a PDB structure, and query Pfam by keywords. There are two components to Pfam: Pfam-A and Pfam-B. Pfam-A entries are high quality, manually curated families that may automatically generate a supplement using the ADDA database. These automatically generated entries are called Pfam-B. Although of lower quality, Pfam-B families can be useful for identifying functionally conserved regions when no Pfam-A entries are found. Pfam also generates higher-level groupings of related families, known as clans (collections of Pfam-A entries which are related by similarity of sequence, structure or profile-HMM).database, clan, structure, sequence, protein family, domainSCR_004726(Pfam, RRID:SCR_004726)Wellcome Trust Sanger Institute; Hinxton; United Kingdom BBSRC, EMBL core funds, Howard Hughes Medical Institute, Wellcome Trustrelated to: Conserved Domain Database, Monarch Initiative, SUPFAM, DBD: Transcription factor prediction database, DOMINE: Database of Protein Interactions, GeneSpeed- A Database of Unigene Domain Organization , Eukaryotic Linear Motif, TopoSNP, GOTaxExplorer, TrED, ProOpDB, Algal Functional Annotation Tool, used by: Mutation Annotation and Genomic Interpretation, MobiDB, listed by: OMICtoolsReferences (2)Last checked downnlx_72111, OMICS_01696
GOtchaResource, analysis service resource, data analysis service, service resource, production service resourceGOtcha provides a prediction of a set of GO terms that can be associated with a given query sequence. Each term is scored independently and the scores calibrated against reference searches to give an accurate percentage likelihood of correctness. These results can be displayed graphically. Why is GOtcha different to what is already out there and why should you be using it? * GOtcha uses a method where it combines information from many search hits, up to and including E-values that are normally discarded. This gives much better sensitivity than other methods. * GOtcha provides a score for each individual term, not just the leaf term or branch. This allows the discrimination between confident assignments that one would find at a more general level and the more specific terms that one would have lower confidence in. * The scores GOtcha provides are calibrated to give a real estimate of correctness. This is expressed as a percentage, giving a result that non-experts are comfortable in interpreting. * GOtcha provides graphical output that gives an overview of the confidence in, or potential alternatives for, particular GO term assignments. The tool is currently web-based; contact David Martin for details of the standalone version. Platform: Online toolfunction, protein, prediction, genome, annotation, gene, statistical analysisSCR_005790(GOtcha, RRID:SCR_005790)University of Dundee; Scotland; United Kingdom European Union fifth framework, Wellcome Trustrelated to: Gene Ontology, listed by: Gene Ontology ToolsPMID:15550167Last checked downnlx_149269
Expression ProfilerResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice.other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, geneSCR_005821(Expression Profiler, RRID:SCR_005821)European Bioinformatics Institute Estonian Science Foundation, European Union, Wellcome Trustrelated to: Gene Ontology, listed by: Gene Ontology ToolsPMID:15215431Last checked downnlx_149323
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