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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Burroughs Wellcome Fund Resource Report Resource Website 50+ mentions |
Burroughs Wellcome Fund (RRID:SCR_005772) | BWF | institution | The Burroughs Wellcome Fund is an independent private foundation dedicated to advancing the biomedical sciences by supporting research and other scientific and educational activities. Within this broad mission, BWF has two primary goals: * To help scientists early in their careers develop as independent investigators * To advance fields in the basic biomedical sciences that are undervalued or in need of particular encouragement BWF''s financial support is channeled primarily through competitive peer-reviewed award programs. * BWF''s endowment: $586.8 million at the end of FY 2009 * BWF approved $26.4 million in grants during FY 2009 BWF makes grants primarily to degree-granting institutions on behalf of individual researchers, who must be nominated by their institutions. To complement these competitive award programs, BWF also makes grants to nonprofit organizations conducting activities intended to improve the general environment for science. A Board of Directors comprising distinguished scientists and business leaders governs BWF. BWF was founded in 1955 as the corporate foundation of the pharmaceutical firm Burroughs Wellcome Co. In 1993, a generous gift from the Wellcome Trust in the United Kingdom, enabled BWF to become fully independent from the company, which was acquired by Glaxo in 1995. BWF has no affiliation with any corporation. | biomedical sciences, research, science, education | Wellcome Trust | nlx_149371, grid.427464.7, Wikidata: Q5000488, ISNI: 0000 0000 8727 8697, Crossref funder ID: 100000861 | https://ror.org/01d35cw23 | SCR_005772 | 2026-02-07 02:06:51 | 99 | ||||||||
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NeuronVisio Resource Report Resource Website 1+ mentions |
NeuronVisio (RRID:SCR_006839) | Neuronvisio | d visualization software | A Graphical User Interface for NEURON simulator environment with 3D capabilities. Neuronvisio makes easy to select and investigate sections'''' properties and it offers easy integration with matplotlib for plotting the results. The geometry can be saved using NeuroML and the computational results in a customized and extensible HDF5 format; the results can then be reload in the software and analyzed in a later stage, without re-running the simulation. Featuring 3D visualization of the model with the possibility to change it runtime; creation of vectors to record any variables present in the section; pylab integration to plot directly the result of the simulation; exploration of the timecourse of any variable among time using a color coded scale; saving the results simulation for later analysis; automatic download and running of models in ModelDB. | 3d visualization, electrophysiological model, hdf storage, matplotlib integration, neuron model, visualization, neuron, visualization, electrophysiology |
is related to: INCF Software Center is related to: NEURON is related to: ModelDB has parent organization: European Bioinformatics Institute |
Wellcome Trust | PMID:22685429 | GNU General Public License, Acknowledgement requested | nlx_156723 | SCR_006839 | Neuron visio | 2026-02-07 02:07:34 | 3 | |||||
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POAS4SPM Resource Report Resource Website 1+ mentions |
POAS4SPM (RRID:SCR_010469) | POAS4SPM | software resource | Software toolbox for SPM to denoise diffusion MRI data. Used for diffusion weighted magnetic resonance imaging data enhancement based on structural adaptive smoothing in both voxel space and diffusion-gradient space.Part of the ACID-toolbox. | denoise diffusion MRI data, diffusion weighted, magnetic resonance imaging data, MRI data, |
is related to: ACID works with: SPM |
Wellcome Trust ; Deutsche Forschungsgemeinschaft |
PMID:24993814 | nlx_157718 | http://www.diffusiontools.com/ | SCR_010469 | Position Orientation Adaptive Smoothing for SPM | 2026-02-07 02:08:01 | 4 | |||||
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ACT: Artemis Comparison Tool Resource Report Resource Website 10+ mentions |
ACT: Artemis Comparison Tool (RRID:SCR_004507) | ACT | software resource | A free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyze regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It is based on the software for Artemis, the genome viewer and annotation tool. ACT runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequences in FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format. | dna sequence, genome, synteny, pairwise comparison |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust | PMID:15976072 | GNU General Public License | OMICS_00928, nlx_48986 | SCR_004507 | Artemis Comparison Tool | 2026-02-07 02:06:48 | 46 | |||||
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European Bioinformatics Institute Resource Report Resource Website 1000+ mentions |
European Bioinformatics Institute (RRID:SCR_004727) | EMBL-EBI | institution | Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL. | organization, academic, bioinformatics, research, service, data, computational, biology, training, database, DNA, protein |
is used by: Blueprint Epigenome is listed by: re3data.org is related to: AgedBrainSYSBIO is related to: ProteomeXchange is related to: Open PHACTS is related to: RHEA is related to: TraCeR is related to: 3D-Beacons is related to: RNAcentral has parent organization: European Molecular Biology Laboratory is parent organization of: CoGenT++ is parent organization of: ENA Sequence Version Archive is parent organization of: Reaper - Demultiplexing trimming and filtering sequencing data is parent organization of: PeakAnalyzer is parent organization of: Tally is parent organization of: Clustal Omega is parent organization of: Biocatalogue - The Life Science Web Services Registry is parent organization of: Experimental Network for Functional Integration: A European Network of Excellence for Data Integration and Systems Biology is parent organization of: The Alternatve Splicing Database is parent organization of: BioModels is parent organization of: CHEBI is parent organization of: MAGE is parent organization of: Ensembl is parent organization of: MIAME is parent organization of: UniProt is parent organization of: Ligand-Gated Ion Channel Database is parent organization of: EBI Genomes is parent organization of: IMEx - The International Molecular Exchange Consortium is parent organization of: Toolbox at the European Bioinformatics Institute is parent organization of: Clustal W2 is parent organization of: ArrayExpress is parent organization of: IMGT/HLA is parent organization of: IntEnz- Integrated relational Enzyme database is parent organization of: IPD - Immuno Polymorphism Database is parent organization of: IPI is parent organization of: MicroArray and Gene Expression Markup Language is parent organization of: DaliLite Pairwise comparison of protein structures is parent organization of: Chemical Information Ontology is parent organization of: PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees is parent organization of: Proteomics Identifications (PRIDE) is parent organization of: Software Ontology is parent organization of: FSSP - Families of Structurally Similar Proteins is parent organization of: Experimental Factor Ontology is parent organization of: Identifiers.org is parent organization of: HipSci is parent organization of: ProteomeXchange is parent organization of: Taxonomy is parent organization of: PDBe - Protein Data Bank in Europe is parent organization of: EBI Dbfetch is parent organization of: ProFunc is parent organization of: WSDbfetch (SOAP) is parent organization of: QuickGO is parent organization of: SAS - Sequence Annotated by Structure is parent organization of: UniProt DAS is parent organization of: UniParc at the EBI is parent organization of: Patent Abstracts is parent organization of: BioSample Database at EBI is parent organization of: Database of Genomic Variants Archive (DGVa) is parent organization of: European Genome phenome Archive is parent organization of: UniSave is parent organization of: ArchSchema is parent organization of: UniRef at the EBI is parent organization of: EBIMed is parent organization of: Kraken is parent organization of: SIMBioMS is parent organization of: Expression Profiler is parent organization of: Whatizit is parent organization of: InterProScan is parent organization of: VectorBase is parent organization of: DRCAT Resource Catalogue is parent organization of: FunTree is parent organization of: CREATE is parent organization of: BioMedBridges is parent organization of: PSICQUIC Registry is parent organization of: PDBsum is parent organization of: European Nucleotide Archive (ENA) is parent organization of: DrugPort is parent organization of: Ontology Lookup Service is parent organization of: EDAM Ontology is parent organization of: InterPro is parent organization of: MIRIAM Resources is parent organization of: EB-eye Search is parent organization of: SBO is parent organization of: Ensembl Genomes is parent organization of: NeuronVisio is parent organization of: IntAct is parent organization of: WSsas - Web Service for the SAS tool is parent organization of: Enzyme Structures Database is parent organization of: EMBOSS CpGPlot/CpGReport/Isochore is parent organization of: PaperMaker is parent organization of: CluSTr is parent organization of: Genome Reviews is parent organization of: GOA is parent organization of: Integr8 : Access to complete genomes and proteomes is parent organization of: IPD-ESTDAB- The European Searchable Tumour Line Database is parent organization of: IPD-HPA - Human Platelet Antigens is parent organization of: IPD-KIR - Killer-cell Immunoglobulin-like Receptors is parent organization of: IPD-MHC- Major Histocompatibility Complex is parent organization of: HilbertVis is parent organization of: Gene Expression Atlas is parent organization of: Parasite genome databases and genome research resources is parent organization of: Alternative Exon Database is parent organization of: AltExtron Database is parent organization of: Patent Data Resources is parent organization of: Pompep is parent organization of: Mouse finder is parent organization of: Gene Regulation Ontology is parent organization of: CiteXplore literature searching is parent organization of: MaxSprout is parent organization of: SRS is parent organization of: MicroCosm Targets is parent organization of: Kalign is parent organization of: MUSCLE is parent organization of: FASTA is parent organization of: WU-BLAST is parent organization of: Oases is parent organization of: HTS Mappers is parent organization of: CRAM is parent organization of: CSA - Catalytic Site Atlas is parent organization of: ArrayExpress (R) is parent organization of: WiggleTools is parent organization of: vsn is parent organization of: rlsim is parent organization of: ISA Infrastructure for Managing Experimental Metadata is parent organization of: BioMart Project is parent organization of: BioPerl is parent organization of: BioJS is parent organization of: EMDataResource.org is parent organization of: HTqPCR is parent organization of: Reactome is parent organization of: Europe PubMed Central is parent organization of: h5vc is parent organization of: LexGrid is parent organization of: Consensus CDS is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: OrChem is parent organization of: Orphanet Rare Disease Ontology is parent organization of: Reflect is parent organization of: BioLayout Express 3D is parent organization of: Virtual Fly Brain is parent organization of: GeneWise is parent organization of: PhenoMeNal is parent organization of: Ensembl Metazoa is parent organization of: Velvet |
EMBL member states ; European Union ; NIH ; Wellcome Trust ; UK Research Councils ; Industry Programme partners ; BBSRC |
grid.225360.0, Wikidata: Q1341845, ISNI: 0000 0000 9709 7726, nlx_72386 | https://ror.org/02catss52 | SCR_004727 | EBI, European Molecular Biology Laboratory - European Bioinformatics Institute | 2026-02-07 02:06:30 | 3689 | ||||||
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InterMine Resource Report Resource Website 10+ mentions |
InterMine (RRID:SCR_001772) | software resource | An 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, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Cambridge; Cambridge; United Kingdom |
Wellcome Trust | PMID:24753429 | Free, Freely available | OMICS_03840, biotools:intermine | https://github.com/intermine/intermine https://bio.tools/intermine |
http://intermine.github.io/intermine.org/ | SCR_001772 | 2026-02-07 02:05:43 | 21 | |||||
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Wellcome Trust Case Control Consortium Resource Report Resource Website 100+ mentions |
Wellcome Trust Case Control Consortium (RRID:SCR_001973) | WTCCC | data or information resource | Consortium 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, disease |
is related to: Psychiatric Genomics Consortium has parent organization: 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 dysfunction, Diabetes | Wellcome Trust ; Bill and Melinda Gates Foundation ; Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:17554300 | Access to summary data and individual-level genotype data is available by application to the Wellcome Trust Case Control Consortium Data Access Committee. Access to data will be granted to qualified investigators for appropriate use. | nif-0000-10551 | SCR_001973 | Wellcome Trust Case-Control Consortium (WTCCC) | 2026-02-07 02:05:38 | 212 | ||||
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ChEMBL Resource Report Resource Website 1000+ mentions |
ChEMBL (RRID:SCR_014042) | data or information resource, database | Collection of bioactive drug-like small molecules that contains 2D structures, calculated properties and abstracted bioactivities. Used for drug discovery and chemical biology research. Clinical progress of new compounds is continuously integrated into the database. | database, compound, data, bioassay, bioactive, molecule, drug, discovery |
is used by: GEROprotectors is used by: PubChem is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Wellcome Trust ; EMBL Member States ; Medicines for Malaria Ventures ; EU Innovative Medicines Initiative ; GSK ; Syngenta ; Pfizer |
PMID:21948594 | Public, Free, Freely available, Acknowledgement requested | r3d100010539 | https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 https://doi.org/10.17616/R3C320 |
SCR_014042 | ChEMBLdb, Chembl, ChEMBL Database | 2026-02-11 10:58:51 | 2433 | |||||
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FlyMine Resource Report Resource Website 100+ mentions |
FlyMine (RRID:SCR_002694) | FlyMine | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java API | anopheles, genome, c. elegans, drosophila, gene, chromosomal location, genomics, proteomics, gene expression, interaction, homology, function, regulation, protein, phenotype, pathway, disease, publication, FASEB list |
is related to: FlyBase is related to: UniProt is related to: Ensembl is related to: InterPro is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Tree families database is related to: IntAct is related to: Gene Ontology is related to: GOA is related to: ArrayExpress is related to: REDfly Regulatory Element Database for Drosophilia is related to: KEGG is related to: Reactome has parent organization: University of Cambridge; Cambridge; United Kingdom |
Wellcome Trust 067205; NHGRI |
PMID:17615057 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02845 | SCR_002694 | 2026-02-11 10:56:31 | 104 | ||||||
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Potassium Channel Database Resource Report Resource Website 1+ mentions |
Potassium Channel Database (RRID:SCR_011960) | KDB | data or information resource, data set | A Database of Potassium Ion Channel Homology Models & Molecular Dynamics Simulations. | potassium ion channel, homology model, crystal structure, molecular dynamics, simulation, structure, image |
is listed by: OMICtools has parent organization: University of Oxford; Oxford; United Kingdom |
BBSRC ; Wellcome Trust |
OMICS_01609 | SCR_011960 | Potassium Channel Database - Structures and Simulations | 2026-02-11 10:58:28 | 2 | |||||||
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GeneDB Spombe Resource Report Resource Website |
GeneDB Spombe (RRID:SCR_010639) | GeneDB_Spombe, GeneDB Spombe, GeneDB S. pombe | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE documented June 6, 2013 Database of all S. pombe (fission yeast) known and predicted protein coding genes, pseudogenes, transposons, tRNAs, rRNAs, snRNAs, snoRNAs and other known and predicted non-coding RNAs. Curation of new and existing literature is ongoing and changes are incorporated weekly. User feedback is welcome. The genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824, has been sequenced and annotated. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved 1.8-kb element. Regions upstream of genes are longer than in budding yeast (Saccharomyces cerevisiae), possibly reflecting more-extended control regions. Some 43% of the genes contain introns, of which there are 4,730. Fifty genes have significant similarity with human disease genes; half of these are cancer related. We identify highly conserved genes important for eukaryotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing. These genes may have originated with the appearance of eukaryotic life. Few similarly conserved genes that are important for multicellular organization were identified, suggesting that the transition from prokaryotes to eukaryotes required more new genes than did the transition from unicellular to multicellular organization. | fission yeast |
is related to: PomBase has parent organization: GeneDB |
Wellcome Trust | PMID:11859360 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_62442 | SCR_010639 | Schizosaccharomyces pombe GeneDB, GDB S. pombe | 2026-02-11 10:58:16 | 0 | |||||
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Genomics of Drug Sensitivity in Cancer Resource Report Resource Website 1000+ mentions |
Genomics of Drug Sensitivity in Cancer (RRID:SCR_011956) | Genomics of Drug Sensitivity in Cancer | data or information resource, database | A genomics database project is an academic research program to identify molecular features of cancers that predict response to anti-cancer drugs. | compound, gene, molecule, drug, FASEB list |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Cancer | Wellcome Trust | OMICS_01581 | SCR_011956 | 2026-02-11 10:58:26 | 1418 | |||||||
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SHERPA RoMEO Resource Report Resource Website |
SHERPA RoMEO (RRID:SCR_013815) | data or information resource, database | A database which houses publisher policies regarding the self- archiving of journal articles on the web and in Open Access repositories. RoMEO contains publishers' general policies on self-archiving of journal articles and certain conference series. Each entry provides a summary of the publisher's policy, including what version of an article can be deposited, where it can be deposited, and any conditions that are attached to that deposit. | database, publisher policy, open access |
is listed by: Connected Researchers is related to: Connected Researchers has parent organization: University of Nottingham; Nottingham; United Kingdom |
JISC ; Wellcome Trust |
Free, Public | SCR_013815 | RoMEO | 2026-02-11 10:58:57 | 0 | ||||||||
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3DSwap Resource Report Resource Website 1+ mentions |
3DSwap (RRID:SCR_004133) | data or information resource, database | Curated knowledegbase of protein structures that are reported to be involved in 3-dimensional domain swapping. 3DSwap provides literature curated information and structure related information about 3D domain swapping in proteins. Information about swapping, hinge region, swapped region, extent of swapping, etc. are extracted from original research publications after extensive literature curation. | protein structure, protein, structure, 3d domain swapping, function, sequence, domain swap, 3d spatial image | has parent organization: Tata Institute of Fundamental Research; Mumbai; India | Tata Institute of Fundamental Research; Mumbai; India ; National Centre for Biological Sciences ; Wellcome Trust |
PMID:21959866 PMID:21592079 |
nlx_143564 | SCR_004133 | 3DSwap: Knowledgebase of 3D Domain Swapping in Proteins, 3DSwap - Knowledgebase of proteins involved in 3D domain swapping, 3D Swap, 3DSwap Database | 2026-02-11 10:56:49 | 5 | |||||||
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HapMap 3 and ENCODE 3 Resource Report Resource Website 1+ mentions |
HapMap 3 and ENCODE 3 (RRID:SCR_004563) | HapMap 3 and ENCORE 3 | data or information resource, database | Draft 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, software |
is listed by: 3DVC is related to: NHGRI Sample Repository for Human Genetic Research has parent organization: Baylor University; Texas; USA |
Wellcome Trust ; NHGRI ; NIDCD |
nlx_143820 | http://www.hgsc.bcm.tmc.edu/project-medseq-hm-hapmap3encode3.hgsc?pageLocation=hapmap3encode3 | SCR_004563 | 2026-02-11 10:56:55 | 3 | |||||||
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Pfam Resource Report Resource Website 10000+ mentions |
Pfam (RRID:SCR_004726) | data or information resource, database | A 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, domain, bio.tools, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is used by: MobiDB is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Conserved Domain Database is related to: SUPFAM is related to: DBD: Transcription factor prediction database is related to: DOMINE: Database of Protein Interactions is related to: GeneSpeed- A Database of Unigene Domain Organization is related to: Eukaryotic Linear Motif is related to: TopoSNP is related to: GOTaxExplorer is related to: TrED is related to: ProOpDB is related to: Algal Functional Annotation Tool has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
EMBL core funds ; Howard Hughes Medical Institute ; BBSRC BB/L024136/1; Wellcome Trust 108433/Z/15/Z |
PMID:24288371 PMID:19920124 |
Acknowledgement requested, Available via FTP | biotools:pfam, OMICS_01696, r3d100012850, nlx_72111 | https://bio.tools/pfam https://doi.org/10.17616/R3QV4F |
http://pfam.sanger.ac.uk/ | SCR_004726 | Pfam Database, Protein Families Database, PFAM, Pfam protein families database | 2026-02-11 10:57:02 | 15523 | ||||
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FunTree Resource Report Resource Website 1+ mentions |
FunTree (RRID:SCR_006014) | FunTree | data or information resource, database | FunTree provides a range of data resources to detect the evolution of enzyme function within distant structurally related clusters within domain super families as determined by CATH. To access the resource enter a specific CATH superfamily code or search for a structure / sequence / function (either via a EC code or KEGG ligand / reaction ID, PDB ID or UniProtKB ID). Or browse the resource via superfamily / function / structure / metabolites & reactions via the menu on the left panel. FunTree is a new resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies. Gathering together this range of data into a single resource allows the investigation of how novel enzyme functions have evolved within a structurally defined superfamily as well as providing a means to analyse trends across many superfamilies. This is done not only within the context of an enzyme''''s sequence and structure but also the relationships of their reactions. Developed in tandem with the CATH database, it currently comprises 276 superfamilies covering 1800 (70%) of sequence assigned enzyme reactions. Central to the resource are phylogenetic trees generated from structurally informed multiple sequence alignments using both domain structural alignments supplemented with domain sequences and whole sequence alignments based on commonality of multi-domain architectures. These trees are decorated with functional annotations such as metabolite similarity as well as annotations from manually curated resources such the catalytic site atlas and MACiE for enzyme mechanisms. | enzyme function, enzyme superfamily, enzyme, sequence, structure, phylogenetic, chemical, mechanistic, functional annotation, superfamily, gold standard, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CATH: Protein Structure Classification is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: KEGG is related to: UniProtKB has parent organization: European Bioinformatics Institute |
European Molecular Biology Laboratory; Heidelberg; Germany ; BBSRC ; Wellcome Trust 081989/Z/07/A; DOE contract DE-AC02-06CH11357 |
PMID:22006843 | Free | biotools:funtree, nlx_151402 | https://bio.tools/funtree | SCR_006014 | 2026-02-11 10:57:13 | 4 | |||||
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GeneDB Pfalciparum Resource Report Resource Website 1+ mentions |
GeneDB Pfalciparum (RRID:SCR_006567) | GeneDB_Pfalciparum, GeneDB Pfalciparum, GeneDB P. falciparum | data or information resource, database | Database of the most recent sequence updates and annotations for the P. falciparum genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Plasmodium research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. The P. falciparum 3D7 nuclear genome is 23.3 Mb in size, with a karyotype of 14 chromosomes. The G+C content is approximately 19%. The P. falciparum genome is undergoing re-annotation. This process started in October 2007 with a weeklong workshop co-organized by staff from the Wellcome Trust Sanger Intistute and the EuPathDB team. Ongoing curation and sequence checking is being carried out by the Pathogen Genomics group. Plasmodium falciparum is the most deadly of the five Plasmodium species that cause human malaria. Malaria has a massive impact on human health; it is the worlds second biggest killer after tuberculosis. Around 300 million clinical cases occur each year resulting in between 1.5 - 2.7 million deaths annually, the majority in sub-saharan Africa. It is estimated that 3,000 children under the age of five years fall victim to malaria each day. Around 40% of the worlds population are at risk. In collaboration with EuPathDB, genomic sequence data and annotations are regularly deposited on PlasmoDB where they can be integrated with other datasets and queried using customized queries. |
is used by: NIF Data Federation is related to: AmiGO is related to: PlasmoDB has parent organization: GeneDB |
Wellcome Trust | PMID:12368864 | nlx_13809 | SCR_006567 | Plasmodium falciparum homepage on GeneDB, Plasmodium falciparum 3D7 on GeneDB | 2026-02-11 10:57:21 | 6 | |||||||
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Worldwide Protein Data Bank (wwPDB) Resource Report Resource Website 1000+ mentions |
Worldwide Protein Data Bank (wwPDB) (RRID:SCR_006555) | wwPDB | data or information resource, database | Public global Protein Data Bank archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by individual member organizations and about projects undertaken by wwPDB. Data available via websites of its member organizations. | 3-dimentional, bioinformatics, protein, research, structure, macromolecule, structural data, 3d spatial image, gold standard |
is used by: Ligand Expo is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Proteopedia - Life in 3D is related to: NRG-CING is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DNA DataBank of Japan (DDBJ) is related to: PDBe - Protein Data Bank in Europe is related to: PDBe - Protein Data Bank in Europe is related to: PDBj - Protein Data Bank Japan is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: PDB Validation Server is related to: Structural Antibody Database is parent organization of: PDB-Dev works with: PDB-REDO |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NINDS ; NIDDK ; European Molecular Biology Laboratory ; Heidelberg; Germany ; Wellcome Trust ; BBSRC ; NIH ; European Union ; NBDC - National Bioscience Database Center ; Japan Science and Technology Agency |
PMID:14634627 | Free, Freely available | nif-0000-23903, r3d100011104 | https://doi.org/10.17616/R3462V | SCR_006555 | World Wide Protein DataBank, wwPDB, Worldwide Protein Data Bank (wwPDB), World Wide Protein Data Bank, Worldwide Protein DataBank | 2026-02-11 10:57:20 | 1215 | ||||
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CoCoMac Resource Report Resource Website 50+ mentions |
CoCoMac (RRID:SCR_007277) | CoCoMac | data or information resource, database | Online access (html or xml) to structural connectivity ("wiring") data on the Macaque brain. The database has become by far the largest of its kind, with data extracted from more than four hundred published tracing studies. The main database, contains data from tracing studies on anatomical connectivity in the macaque cerebral cortex. Also available are a variety of tools including a graphical simulation workbench, map displays and the CoCoMac-Paxinos-3D viewer. Submissions are welcome. To overcome the problem of divergent brain maps ORT (Objective Relational Transformation) was developed, an algorithmic method to convert data in a coordinate- independent way based on logical relations between areas in different brain maps. CoCoMac data is used to analyze the organization of the cerebral cortex, and to establish its structure- function relationships. This includes multi-variate statistics and computer simulation of models that take into account the real anatomy of the primate cerebral cortex. This site * Provides full, scriptable open access to the data in CoCoMac (you must adhere to the citation policy) * Powers the graphical interface to CoCoMac provided by the Scalable Brain Atlas * Sports an extensive search/browse wizard, which automatically constructs complex search queries and lets you further explore the database from the results page. * Allows you to get your hands dirty, by using the custom SQL query service. * Displays connectivity data in tabular form, through the axonal projections service. CoCoMac 2 was initiated at the Donders Institute for Brain, Cognition and Behaviour, and is currently supported by the German neuroinformatics node and the Computational and Systems Neuroscience group at the Juelich research institute. | brain, macaque, non-human primate, connectivity, microcircuitry, prefrontal cortex, neural network, structure, function, neuroanatomy, brain circuitry, axonal projection, data repository, visualization, atlas application, computational neuroscience, magnetic resonance, ontology, php, tractography, web environment, software, FASEB list |
is used by: NIF Data Federation is used by: Integrated Nervous System Connectivity is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Scalable Brain Atlas has parent organization: German Neuroinformatics Node (G-Node) is parent organization of: CoCoMac-Paxinos3D viewer |
DFG ; Heinrich-Heine University of Dusseldorf; Dusseldorf; Germany ; Wellcome Trust |
PMID:23293600 PMID:11545697 PMID:15319511 PMID:15971361 PMID:10703043 |
Open Access | nif-0000-00022 | http://www.nitrc.org/projects/cocomac http://134.95.56.239/home.asp |
http://cocomac.org/, http://cocomac.g-node.org/drupal/ | SCR_007277 | CoCoMac Brain Connectivity Database, Collations of Connectivity Data on the Macaque Brain, CoCoMac (Collations of Connectivity Data on the Macaque Brain) | 2026-02-11 10:57:35 | 57 |
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