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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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bulkAnalyseR Resource Report Resource Website |
bulkAnalyseR (RRID:SCR_027647) | software toolkit, software resource | Software R package for most bulk sequencing datasets. Creates shiny app for interactive data analysis and visualisation. Used for analysing and sharing bulk sequencing results. | bulk sequencing results, analysing and sharing results, sequencing data, | uses: Shiny | Wellcome Trust | PMID:36583521 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/bulkAnalyseR/ | SCR_027647 | 2026-02-15 09:24:19 | 0 | |||||||
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Ensembl Resource Report Resource Website 10000+ mentions |
Ensembl (RRID:SCR_002344) | data or information resource, database | Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species. | collection, genome, dataset, database, vertebrate, eukaryotic, DNA, protein, sequence, search, automaticly, annotate, data, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: Animal QTLdb is used by: ChannelPedia is used by: Blueprint Epigenome is used by: HmtPhenome lists: Ensembl Covid-19 is listed by: OMICtools is listed by: Biositemaps is listed by: re3data.org is listed by: LabWorm is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Ensembl Genomes is related to: GermOnline is related to: CandiSNPer is related to: Human Splicing Finder is related to: NGS-SNP is related to: Sanger Mouse Resources Portal is related to: DECIPHER is related to: Ensembl Genomes is related to: PeptideAtlas is related to: AnimalTFDB is related to: Bgee: dataBase for Gene Expression Evolution is related to: FlyMine is related to: Rat Gene Symbol Tracker is related to: UniParc at the EBI is related to: go-db-perl is related to: UniParc is related to: g:Profiler is related to: RIKEN integrated database of mammals is related to: VBASE2 is related to: p300db is related to: ShinyGO has parent organization: European Bioinformatics Institute has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: Ensembl Metazoa is parent organization of: Ensembl Variation is parent organization of: Pre Ensembl is parent organization of: Variant Effect Predictor is parent organization of: Ensembl Bacteria is parent organization of: Ensembl Plants is parent organization of: Ensembl Fungi is parent organization of: Ensembl Protists is parent organization of: Ensembl Genome Browser works with: Genotate works with: CellPhoneDB works with: Open Regulatory Annotation Database works with: Database of genes related to Repeat Expansion Diseases works with: TarBase |
Wellcome Trust ; EMBL ; European Union ; FP7 ; FP6 ; MRC ; NHGRI ; BBSRC |
PMID:24316576 PMID:23203987 |
nif-0000-21145, OMICS_01647, biotools:ensembl, r3d100010228 | https://bio.tools/ensembl https://sources.debian.org/src/ensembl/ https://doi.org/10.17616/R39K5B |
SCR_002344 | ENSEMBL | 2026-02-14 02:00:23 | 11652 | ||||||
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OME-TIFF Format Resource Report Resource Website |
OME-TIFF Format (RRID:SCR_002636) | OME-TIFF | data or information resource, narrative resource, standard specification | A standardized file format for multidimensional microscopy image data. OME-TIFF maximizes the respective strengths of OME-XML and TIFF. It takes advantage of the rich metadata defined in OME-XML while retaining the pixel structure in multi-page TIF format for compatibility with many image-processing applications. An OME-TIFF dataset has the following characteristics: * Image planes are stored within one multi-page TIFF file, or across multiple TIFF files. Any image organization is feasible. * A complete OME-XML metadata block describing the dataset is embedded in each TIFF file's header. Thus, even if some of the TIFF files in a dataset are misplaced, the metadata remains intact. * The OME-XML metadata block may contain anything allowed in a standard OME-XML file. * OME-TIFF uses the standard TIFF mechanism for storing one or more image planes in each of the constituent files, instead of encoding pixels as base64 chunks within the XML. Since TIFF is an image format, it makes sense to only use OME-TIFF as opposed to OME-XML, when there is at least one image plane. | microscopy, format, archiving, data management, annotation, mark up, metadata standard, standard, tiff, ome-xml |
is listed by: FORCE11 is related to: JCB DataViewer is related to: Cell Image Library (CIL) is related to: HMS LINCS Database is related to: Stowers Original Data Repository is related to: Bio-Formats has parent organization: OME - Open Microscopy Environment |
Wellcome Trust 68046 | PMID:15892875 | Free, Available for download, Freely available | nlx_156061 | SCR_002636 | OME-TIFF: Open Microscopy Environment Tagged Image File Format, Open Microscopy Environment Tagged Image File Format | 2026-02-14 02:00:28 | 0 | |||||
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Artemis: Genome Browser and Annotation Tool Resource Report Resource Website 100+ mentions |
Artemis: Genome Browser and Annotation Tool (RRID:SCR_004267) | Artemis | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is free software and is distributed under the terms of the GNU General Public License. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format. | training tool, genome browser, gene annotation, java, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: DNAPlotter has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom works with: Alien-hunter |
Wellcome Trust | PMID:11120685 DOI:10.1093/bioinformatics/btr703 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_28554, OMICS_00903, biotools:artemis | https://bio.tools/artemis https://sources.debian.org/src/art-nextgen-simulation-tools/ |
SCR_004267 | 2026-02-14 02:00:56 | 421 | |||||
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IBMA toolbox Resource Report Resource Website |
IBMA toolbox (RRID:SCR_003772) | software resource | Image-Based Meta-Analysis toolbox for SPM. Implementation of z-based statistics: Fisher's, Stouffer's. |
is listed by: GitHub is related to: SPM has parent organization: University of Warwick; Coventry; United Kingdom |
Wellcome Trust | nlx_158042 | SCR_003772 | 2026-02-14 02:00:51 | 0 | ||||||||||
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Wellcome Trust Sanger Institute; Hinxton; United Kingdom Resource Report Resource Website 500+ mentions |
Wellcome Trust Sanger Institute; Hinxton; United Kingdom (RRID:SCR_011784) | WTSI, Sanger | institution | Non profit research organization for genome sequences to advance understanding of biology of humans and pathogens in order to improve human health globally. Provides data which can be translated for diagnostics, treatments or therapies including over 100 finished genomes, which can be downloaded. Data are publicly available on limited basis, and provided more extensively upon request. | research, genome, sequence, human, health, project, global, data, treatment, therapy |
is listed by: re3data.org is affiliated with: Open Targets is related to: Clonalframe is related to: ClonalOrigin is related to: TraCeR is parent organization of: ILLUMINUS is parent organization of: ARNIE is parent organization of: Sequence Search and Alignment by Hashing Algorithm is parent organization of: Sequencing of Idd regions in the NOD mouse genome is parent organization of: CAROL is parent organization of: DINDEL is parent organization of: Wellcome Trust Case Control Consortium is parent organization of: OLORIN is parent organization of: Exomiser is parent organization of: COSMIC - Catalogue Of Somatic Mutations In Cancer is parent organization of: GeneDB is parent organization of: Breast Cancer Somatic Genetics Study is parent organization of: Artemis: Genome Browser and Annotation Tool is parent organization of: ACT: Artemis Comparison Tool is parent organization of: Alien hunter is parent organization of: Pfam is parent organization of: DNAPlotter is parent organization of: VAGrENT is parent organization of: SMALT is parent organization of: LookSeq is parent organization of: ZMP is parent organization of: Deciphering Developmental Disorders is parent organization of: Sanger Mouse Resources Portal is parent organization of: SpliceDB is parent organization of: DECIPHER is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: Genes to Cognition: Neuroscience Research Programme is parent organization of: MEROPS is parent organization of: Rfam is parent organization of: VEGA is parent organization of: Bacterial Genomes is parent organization of: Caenorhabditis Genome Sequencing Projects is parent organization of: D. rerio Blast Server is parent organization of: Fungi Sequencing Projects is parent organization of: PEER is parent organization of: Alfresco - FRont-End for Sequence COmparison is parent organization of: AutoCSA (Automatic Comparative Sequence Analysis) is parent organization of: AceDB is parent organization of: CnD is parent organization of: Genomics of Drug Sensitivity in Cancer is parent organization of: Zebrafish Genome Project is parent organization of: Tree families database is parent organization of: Ensembl is parent organization of: BamView is parent organization of: SVMerge is parent organization of: RetroSeq is parent organization of: Consensus CDS is parent organization of: WormBase is parent organization of: Belvu is parent organization of: Bio-tradis is parent organization of: Blixem is parent organization of: Dotter is parent organization of: Exonerate is parent organization of: Fastaq is parent organization of: Gubbins is parent organization of: CellPhoneDB is parent organization of: Ensembl Metazoa is parent organization of: Scmap is parent organization of: Scfind is parent organization of: Recognition of Errors in Assemblies using Paired Reads is parent organization of: SAMTOOLS is parent organization of: Cell Model Passports |
Wellcome Trust | ISNI: 0000 0004 0606 5382, nlx_91258, grid.10306.34, Wikidata: Q1142544 | https://ror.org/05cy4wa09 | SCR_011784 | Wellcome Trust Sanger Institute, Genome Research Limited, The Wellcome Sanger Institute, Sanger Institute, Wellcome Trust Sanger Institute Genome Research Limited | 2026-02-14 02:02:04 | 527 | ||||||
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Dietary Restriction Gene Database Resource Report Resource Website 1+ mentions |
Dietary Restriction Gene Database (RRID:SCR_013720) | GenDR | Database of genes associated with dietary restriction. It includes genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of dietary restriction and genes robustly altered due to dietary restriction, derived from a meta-analysis of microarray studies in mammals. | gene, dietary restriction, microarray | has parent organization: University of Liverpool; Liverpool; United Kingdom | Wellcome Trust MEB050495MES; Biotechnology and Biological Sciences Research Council H0084971 |
Free, Public | SCR_013720 | The GenDR Database of Dietary Restriction-Related Genes | 2026-02-14 02:02:54 | 3 | ||||||||
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SUPFAM Resource Report Resource Website 10+ mentions |
SUPFAM (RRID:SCR_005304) | SUPFAM | data or information resource, database | SUPFAM is a database that consists of clusters of potentially related homologous protein domain families, with and without three-dimensional structural information, forming superfamilies. The present release (Release 3.0) of SUPFAM uses homologous families in Pfam (Version 23.0) and SCOP (Release 1.69) which are examples of sequence -alignment and structure classification databases respectively. The two steps involved in setting up of SUPFAM database are * Relating Pfam and SCOP families using a new profile-profile alignment algorithm AlignHUSH. This results in identifying many Pfam families which could be related to a family or superfamily of known structural information. * An all-against-all match among Pfam families with yet unknown structure resulting in identification of related Pfam families forming new potential superfamilies. The SUPFAM database can be used in either the Browse mode or Search mode. In Browse mode you can browse through the Superfamilies, Pfam families or SCOP families. In each of these modes you will be presented with a full list which can be easily browsed. In Search mode, you can search for Pfam families, SCOP families or Superfamilies based on keywords or SCOP/Pfam identifiers of families and superfamilies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | duf/upf connections, 3-d structure, alignment, amino acid sequence, bioinformatics, clustering, homologous protein family, multiple sequence alignment, nmr, pali, pfam, phylogeny, protein classification, protein domain database, protein families, protein sequence database, rps_blast, scop, structural genomics, structure determination, superfamily, three-dimensional, x-ray crystalography |
is related to: Pfam is related to: SCOP: Structural Classification of Proteins has parent organization: Indian Institute of Science; Bangalore; India |
Council of Scientific and Industrial Research New Delhi ; Wellcome Trust |
PMID:15113407 PMID:11752317 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03517 | http://pauling.mbu.iisc.ernet.in/~supfam | SCR_005304 | 2026-02-14 02:06:23 | 13 | |||||
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Major depressive disorder neuroimaging database Resource Report Resource Website 1+ mentions |
Major depressive disorder neuroimaging database (RRID:SCR_005835) | MaND | data or information resource, database | The Major Depressive Disorder Neuroimaging Database (MaND) contains information of 225 studies which have investigated brain structure (using MRI and CT scans) in patients with major depressive disorder compared to a control group. 143 studies and 63 brain structures are included in the meta-analysis. The database and meta-analysis are contained in an Excel spreadsheet file which may be freely downloaded from this website. | mri, brain, ct, neuroimaging, image, normal control | has parent organization: King's College London; London; United Kingdom | Major depressive disorder | Wellcome Trust ; National Institute for Health Research ; EPSRC |
PMID:21727252 | nlx_149353 | SCR_005835 | Major Depressive Disorder Neuroimaging Database (MaND) | 2026-02-14 02:06:25 | 2 | |||||
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DECIPHER Resource Report Resource Website 1000+ mentions |
DECIPHER (RRID:SCR_006552) | DECIPHER | data or information resource, database | Interactive database which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance. Used to enhance clinical diagnosis by retrieving information from bioinformatics resources relevant to the imbalance found in the patient. Contributing to the DECIPHER database is a Consortium, comprising an international community of academic departments of clinical genetics. Each center maintains control of its own patient data (which are password protected within the center''''s own DECIPHER project) until patient consent is given to allow anonymous genomic and phenotypic data to become freely viewable within Ensembl and other genome browsers. Once data are shared, consortium members are able to gain access to the patient report and contact each other to discuss patients of mutual interest, thus facilitating the delineation of new microdeletion and microduplication syndromes. | chromosomal imbalance, phenotype, chromosome, gene, genome, deletion, duplication, copy number, genotype, polymorphism, FASEB list |
is used by: MARRVEL is listed by: OMICtools is related to: Deciphering Developmental Disorders is related to: Ensembl has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Developmental disorder, Microdeletion Syndrome, Overgrowth syndrome, Microduplication syndrome, Deletion syndrome, Duplication syndrome, Wolf-Hirschhorn Syndrome, Williams-Beuren Syndrome, Smith-Magenis Syndrome, Etc | Wellcome Trust WT077008 | PMID:19344873 | Acknowledgement required | nlx_151653, OMICS_00265 | SCR_006552 | Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources, DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources, Database of Chromosomal Imbalance Phenotype in Humans using Ensembl Resources, Decipher | 2026-02-14 02:05:56 | 1797 | ||||
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MEROPS Resource Report Resource Website 500+ mentions |
MEROPS (RRID:SCR_007777) | MEROPS, MEROPS fam | data or information resource, database | An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. The MEROPS database uses an hierarchical, structure-based classification of the peptidases. In this, each peptidase is assigned to a Family on the basis of statistically significant similarities in amino acid sequence, and families that are thought to be homologous are grouped together in a Clan. There is a Summary page for each family and clan, and these have indexes. Each of the Summary pages offers links to supplementary pages. About 3000 individual peptidases and inhibitors are included in the database, and there is a Summary page describing each one. You can navigate to this by any of several routes. There are indexes of Name, MEROPS Identifier and source Organism on the menu bar. Each Summary page describes the classification and nomenclature of the peptidase or inhibitor, and provides links to supplementary pages showing sequence identifiers, the structure if known, literature references and more. | peptidase, protease, proteinase, proteolytic enzyme, protein, inhibitor, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: TopFIND has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust WT077044/Z/05/Z | PMID:19892822 | biotools:merops, r3d100012783, nif-0000-03112 | https://bio.tools/merops https://doi.org/10.17616/R33225 https://doi.org/10.17616/R33225 |
SCR_007777 | MEROPS- the Peptidase Database, MEROPS - the Peptidase Database, MEROPS database, MEROPS fam | 2026-02-14 02:06:03 | 736 | |||||
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MLST Resource Report Resource Website 1000+ mentions |
MLST (RRID:SCR_010245) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms via the internet. The aim of MLST is to provide a portable, accurate, and highly discriminating typing system that can be used for most bacteria and some other organisms. It is envisaged that this approach will be particularly helpful for the typing of bacterial pathogens. To achieve this aim we have taken the proven concepts of multilocus enzyme electrophoresis (MLEE) and have adapted them so that alleles at each locus are defined directly, by nucleotide sequencing, rather than indirectly from the electrophoretic moblity of their gene products. MLST was developed in the laboratories of Martin Maiden, Dominique Caugant, Ian Feavers, Mark Achtman and Brian Spratt. This site is hosted at Imperial College with funding from the Wellcome Trust. The location of the subsites for the individual species are shown on their respective front pages. | has parent organization: Imperial College London; London; United Kingdom | Wellcome Trust | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_156883 | SCR_010245 | 2026-02-14 02:06:11 | 1230 | |||||||||
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TREES toolbox Resource Report Resource Website 10+ mentions |
TREES toolbox (RRID:SCR_010457) | TREES toolbox | software resource | Software package, written in Matlab (Mathworks, Natick, MA), providing tools to automatically reconstruct neuronal branching from microscopy image stacks and to generate synthetic axonal and dendritic trees. It provides the basic tools to edit, visualize and analyze dendritic and axonal trees, methods for quantitatively comparing branching structures between neurons, and tools for exploring how dendritic and axonal branching depends on local optimization of total wiring and conduction distance. | neuronal branching, microscopy, neuron, matlab, visualization, rendering, reconstruction, analysis, modeling, morphology, dendrite, axon, computational neuroanatomy, tree |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University College London; London; United Kingdom |
Max Planck Society ; Wellcome Trust ; Gatsby Charitable Foundation ; Alexander von Humboldt-Stiftung ; European Research Council |
PMID:20700495 | GNU General Public License v3, Creative Commons Attribution-NonCommercial-ShareAlike License v3, The community can contribute to this resource | nlx_157723 | http://www.nitrc.org/projects/treestoolbox | SCR_010457 | treestoolbox - A Matlab toolbox to generate edit visualize and analyze neuronal structure | 2026-02-14 02:01:59 | 28 | ||||
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eVOC Resource Report Resource Website 1+ mentions |
eVOC (RRID:SCR_010704) | eVOC | data or information resource, ontology, controlled vocabulary | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., 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, anatomy |
is related to: OBO is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: University of the Western Cape; Bellville; South Africa |
South African National Research Foundation ; European Union ; Wellcome Trust ; South African Department of Arts Culture Science and Technology 32146 |
PMID:12799354 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_84448 | SCR_010704 | Expressed Sequence Annotation for Humans, eVOC (Expressed Sequence Annotation for Humans), eVOC Ontologies, eVOContology.org | 2026-02-14 02:01:48 | 4 | |||||
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Genes to Cognition Database Resource Report Resource Website |
Genes to Cognition Database (RRID:SCR_002735) | G2Cdb | data or information resource, database | Database 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, synapse | Wellcome Trust ; MRC ; BBSRC ; Gatsby Charitable Foundation ; Human Frontiers Science Programme ; European Union ; Framework Programme ; EPSRC ; NSF |
PMID:18984621 | Free, Freely available | nif-0000-02864 | http://www.genes2cognition.org/cgi-bin/SearchView | SCR_002735 | Genes-to-Cognition Database | 2026-02-14 02:06:11 | 0 | |||||
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PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees Resource Report Resource Website 1+ mentions |
PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees (RRID:SCR_003321) | PANDIT | data or information resource, database | PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains: * the seed protein sequence alignments from the Pfam-A (curated families) database (version 17.0) * nucleotide sequence alignments derived from sequences available for the above and using the protein alignments as "templates"; * protein sequence alignments restricted to the family members for which nucleotide sequences are available * inferred phylogenetic trees for each alignment The data in PANDIT and the dataset's development have been frozen owing to a lack of funding support. The existing data, version 17.0 corresponding to Pfam 17.0, remain stable and, we hope, useful. The entire database is also available for download as a flatfile from this website. | gold standard, database, protein, associated nucleotide domain | has parent organization: European Bioinformatics Institute | Wellcome Trust | PMID:16381879 PMID:12912837 |
Free, Available for download, Freely available | r3d100010570, nif-0000-03241 | https://doi.org/10.17616/R3GP69 | SCR_003321 | Protein and Associated Nucleotide Domains with Inferred Trees | 2026-02-14 02:06:11 | 4 | ||||
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GeneDB Gmorsitans Resource Report Resource Website 1+ mentions |
GeneDB Gmorsitans (RRID:SCR_004310) | GeneDB Gmorsitans, GeneDB G. morsitans | data or information resource, database | As of 12th March 2009, GeneDB provides access to the transcriptome of the Tsetse fly Glossina morsitans morsitans, the biological vector of African trypanosomiases. The current data set includes: >>7,015 contigs comprised of ESTs from Trypanosoma brucei infected midgut tissue (Lehane et al, Genome Biol. 2003;4(10):R63) >>7,493 contigs comprised of ESTs from salivary gland tissue >>18,404 contigs comprised of EST pooled from a range of different tissue- and developmental stage-specific libraries: head (2,700 ESTs), midgut (21,662 ESTs), reproductive organs (3, 438 ESTs), salivary gland (27,426 ESTs), larvae (2,304 ESTs), pupae (2,304 ESTs), fatbody (20,257 ESTs) (Attardo et al, Insect Molecular Biology 2006, 15(4):411-424), male and female whole bodies (19,968 ESTs). These data include the midgut and salivary gland ESTs used in the library specific clustering for the contig sets listed above. Initial automated annotations of product descriptions were manually revised by participants in two community annotation jamborees held under the auspice of the International Glossina Genome Initiative (IGGI) with funding by TDR. A Glossina morsitans morsitans genome project is currently also underway. To date, 2.4M capillary shotgun reads have been produced and the initial assembly is available to download via the ftp server and for blast analysis. | has parent organization: GeneDB | Wellcome Trust ; TDR |
nlx_32209 | SCR_004310 | Glossina morsitans GeneDB | 2026-02-14 02:05:51 | 2 | ||||||||
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Retinal wave repository Resource Report Resource Website |
Retinal wave repository (RRID:SCR_010462) | Retinal wave repository | data or information resource, data set | A subset of the CARMEN repository, a curated set of data and code of multielectrode array recordings of spontaneous activity in developing mouse and ferret retina. The data have been annotated with minimal metadata and converted into HDF5 (Hierarchical data format, version 5) including the essential features of the recordings, such as developmental age, and genotype. All code and tools used in the analyses are also fully available for reuse, giving the ability to regenerate each figure and table and know exactly how the results were calculated, adding confidence in the research output and allowing others to easily build upon previous work. The addition of published data to the repository is encouraged. | hdf5, development, neural circuit, retina, eye, multielectrode, array recording, spontaneous activity, reproducible research, retinal wave, electrophysiology, multielectrode array, developmental age, genotype |
has parent organization: GigaScience has parent organization: Code Analysis Repository and Modelling for e-Neuroscience has parent organization: University of Cambridge; Cambridge; United Kingdom |
Developing retina, Aging | EPSRC EP/E002331/1; BBSRC BB/H023577/1; BBSRC BB/I000984/1; Wellcome Trust 083205/B/07/Z |
PMID:24666584 | Registration required, (CARMEN), Acknowledgement required, The community can contribute to this resource | nlx_157664 | http://www.damtp.cam.ac.uk/user/eglen/waverepo/ | SCR_010462 | A data repository and analysis framework for spontaneous neural activity recordings in developing retina | 2026-02-14 02:08:15 | 0 | |||
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BIGSdb Resource Report Resource Website 1+ mentions |
BIGSdb (RRID:SCR_023551) | data or information resource, database | Platform for gene-by-gene bacterial population annotation and analysis. Designed to store and analyse sequence data for bacterial isolates. Used for scalable analysis of bacterial genome variation at population level. | sequence data, bacterial isolates, gene-by-gene bacterial population, annotation and analysis, bacterial genome variation, | Wellcome Trust | PMID:21143983 | Free, Freely available | https://bigsdb.readthedocs.io/en/latest/ | SCR_023551 | Bacterial Isolate Genome Sequence Database | 2026-02-14 02:06:35 | 1 | |||||||
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Wellcome-CTC Mouse Strain SNP Genotype Set Resource Report Resource Website 1+ mentions |
Wellcome-CTC Mouse Strain SNP Genotype Set (RRID:SCR_003216) | Wellcome-CTC Mouse Strain SNP Genotype Set | data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Data set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34. | genome, genotype, snp, chromosome, haplotype, haplotype structure, recombinant inbred mouse strain | has parent organization: Wellcome Trust Centre for Human Genetics | Wellcome Trust ; NCRR R24RR015116; NIGMS R01GM072863; NIAAA U01AA014425; NINDS R01NS049445; NIMH P20-MH 62009; NIAAA U24AA13513 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156947 | SCR_003216 | 2026-02-14 02:07:20 | 3 |
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We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
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If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
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