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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SEGS Resource Report Resource Website 1+ mentions |
SEGS (RRID:SCR_003554) | SEGS | data analysis service, production service resource, service resource, analysis service resource | A web tool for descriptive analysis of microarray data. The analysis is performed by looking for descriptions of gene sets that are statistically significantly over- or under-expressed between different scenarios within the context of a genome-scale experiments (DNA microarray). Descriptions are defined by using the terms from the Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and gene-gene interactions found in the ENTREZ database. Gene annotations by GO and KEGG terms can also be found in the ENTREZ database. The tool provides three procedures for testing the enrichment of the gene sets (over- or under-expressed): Fisher's exact test, GSEA and PAGE, and option for combining the results of the tests. Because of the multiple-hypothesis testing nature of the problem, all the p-values are computed using the permutation testing method. | microarray, pathway, gene-gene interaction, gene, interaction, annotation, gene expression, ortholog, molecular function, biological process, cellular component, enriched gene set, gene set |
is related to: Gene Ontology is related to: Entrez Gene is related to: KEGG is related to: GoMapMan has parent organization: Jozef Stefan Institute; Ljubljana; Slovenia |
PMID:18234563 | nlx_157688 | SCR_003554 | Search for Enriched Gene Sets | 2026-02-14 02:05:50 | 3 | |||||||
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Rat Gene Symbol Tracker Resource Report Resource Website 10+ mentions |
Rat Gene Symbol Tracker (RRID:SCR_003261) | RGST | data or information resource, database | 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 2, 2016. Database for defining official rat gene symbols. It includes rat gene symbols from three major sources: the Rat Genome Database (RGD), Ensembl, and NCBI-Gene. All rat symbols are compared with official symbols from orthologous human genes as specified by the Human Gene Nomenclature Committee (HGNC). Based on the outcome of the comparisons, a rat gene symbol may be selected. Rat symbols that do not match a human ortholog undergo a strict procedure of comparisons between the different rat gene sources as well as with the Mouse Genome Database (MGD). For each rat gene this procedure results in an unambiguous gene designation. The designation is presented as a status level that accompanies every rat gene symbol suggested in the database. The status level describes both how a rat symbol was selected, and its validity. Rat Gene Symbol Tracker approves rat gene symbols by an automatic procedure. The rat genes are presented with links to RGD, Ensembl, NCBI Gene, MGI and HGNC. RGST ensures that each acclaimed rat gene symbol is unique and follows the guidelines given by the RGNC. To each symbol a status level associated, describing the gene naming process. | gene, orthology, naming, gene symbol, nomenclature, human, mouse |
is related to: Rat Genome Database (RGD) is related to: Entrez Gene is related to: Ensembl is related to: Mouse Genome Informatics (MGI) is related to: HGNC has parent organization: RatMap |
Swedish MRC ; Nilsson-Ehle Foundation ; Sven and Lilly Lawski Foundation ; Erik Philip-Sorensen Foundation ; Wilhelm and Martina Lundgren Research Foundation ; SWEGENE Foundation |
PMID:18215257 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31426 | SCR_003261 | RGST (Rat Gene Symbol Tracker), RGST - Rat Gene Symbol Tracker | 2026-02-14 02:06:11 | 14 | |||||
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ASAP: the Alternative Splicing Annotation Project Resource Report Resource Website 10+ mentions |
ASAP: the Alternative Splicing Annotation Project (RRID:SCR_003415) | ASAP | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. Database to access and mine alternative splicing information coming from genomics and proteomics based on genome-wide analyses of alternative splicing in human (30 793 alternative splice relationships found) from detailed alignment of expressed sequences onto the genomic sequence. ASAP provides precise gene exon-intron structure, alternative splicing, tissue specificity of alternative splice forms, and protein isoform sequences resulting from alternative splicing. They developed an automated method for discovering human tissue-specific regulation of alternative splicing through a genome-wide analysis of expressed sequence tags (ESTs), which involves classifying human EST libraries according to tissue categories and Bayesian statistical analysis. They use the UniGene clusters of human Expressed Sequence Tags (ESTs) to identify splices. The UniGene EST's are clustered so that a single cluster roughly corresponds to a gene (or at least a part of a gene). A single EST represents a portion of a processed (already spliced) mRNA. A given cluster contains many ESTs, each representing an outcome of a series of splicing events. The ESTs in UniGene contain the different mRNA isoforms transcribed from an alternatively spliced gene. They are not predicting alternative splicing, but locating it based on EST analysis. The discovered splices are further analyzed to determine alternative splicing events. They have identified 6201 alternative splice relationships in human genes, through a genome-wide analysis of expressed sequence tags (ESTs). Starting with 2.1 million human mRNA and EST sequences, they mapped expressed sequences onto the draft human genome sequence and only accepted splices that obeyed the standard splice site consensus. After constructing a tissue list of 46 human tissues with 2 million human ESTs, they generated a database of novel human alternative splices that is four times larger than our previous report, and used Bayesian statistics to compare the relative abundance of every pair of alternative splices in these tissues. Using several statistical criteria for tissue specificity, they have identified 667 tissue-specific alternative splicing relationships and analyzed their distribution in human tissues. They have validated our results by comparison with independent studies. This genome-wide analysis of tissue specificity of alternative splicing will provide a useful resource to study the tissue-specific functions of transcripts and the association of tissue-specific variants with human diseases. | gene, genome, human, isoform, mechanism, metazoa, molecular, mrna, nucleus, process, protein, sequence, splice, tissue specificity, transcription, transcript, alternate splicing, microarray, alternative splicing, biological process, alternatively spliced isoform, contig, cancer, image |
is listed by: Biositemaps is related to: Alternative Splicing Annotation Project II Database has parent organization: University of California at Los Angeles; California; USA |
NSF 0082964; NSF DGE-9987641; DOE DEFG0387ER60615 |
PMID:12519958 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33105 | SCR_003415 | Alternative Splicing, Alternative Splicing Annotation Project, Alternative Splicing Annotation Project database | 2026-02-14 02:05:49 | 33 | |||||
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PHI-base Resource Report Resource Website 100+ mentions |
PHI-base (RRID:SCR_003331) | PHI-base | data or information resource, database | Database that catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. It is an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, it also includes antifungal compounds and their target genes. Each entry is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes have been annotated using controlled vocabularies and links to external sources (Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC). | gene expression, pathogenic bacteria, virulence, infection, target site, gene, pathogen-host interaction, interaction, phenotype, pathogen, disease, host, anti-infective, nucleotide sequence, amino acid sequence, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian |
BBSRC BB/1000488/1 | PMID:17942425 PMID:17153929 PMID:16381911 |
Free, Freely available | nif-0000-03276, r3d100011301, biotools:phi-base | https://bio.tools/phi-base https://doi.org/10.17616/R35D1V |
http://www4.rothamsted.bbsrc.ac.uk/phibase/ | SCR_003331 | Pathogen Host Interaction base, Pathogen Host Interaction, Pathogen Host Interaction-Base | 2026-02-14 02:05:43 | 198 | |||
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T-profiler Resource Report Resource Website 10+ mentions |
T-profiler (RRID:SCR_003452) | T-profiler | data analysis service, production service resource, service resource, analysis service resource | One of the key challenges in the analysis of gene expression data is how to relate the expression level of individual genes to the underlying transcriptional programs and cellular state. The T-profiler tool hosted on this website uses the t-test to score changes in the average activity of pre-defined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif, and location on the same chromosome, respectively. If desired, an iterative procedure can be used to select a single, optimal representative from sets of overlapping gene groups. A jack-knife procedure is used to make calculations more robust against outliers. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters. Currently, gene expression data from Saccharomyces cerevisiae and Candida albicans are supported. Users can submit their microarray data for analysis by clicking on one of the two organism-specific tabs above. Platform: Online tool | expression, gene, binding, cellular, transcriptional, gene expression, microarray, gene ontology, transcription factor, binding motif, chip-chip, chip, motif, t-test, statistical analysis, transcriptome, bio.tools |
is listed by: Biositemaps is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Columbia University; New York; USA has parent organization: University of Amsterdam; Amsterdam; Netherlands |
Netherlands Foundation for Technical Research APB.5504; NHGRI R01HG003008 |
PMID:15980543 | Free for academic use | nif-0000-33354, biotools:t-profiler | https://bio.tools/t-profiler | SCR_003452 | T-profiler: Scoring the Activity of Pre-defined Groups of Genes Using Gene Expression Data | 2026-02-14 02:06:14 | 11 | ||||
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Distant Regulatory Elements Resource Report Resource Website 10+ mentions |
Distant Regulatory Elements (RRID:SCR_003058) | DiRE | data analysis service, production service resource, service resource, analysis service resource | Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data. | regulatory element, enhancer identification, genome, prediction, transcription factor binding site, gene, co-expression, co-function, function, transcription factor, comparative genomics, regulatory function, gene locus, chromosome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
NLM ; Intramural Research Program |
PMID:18487623 | Free, Freely available | nif-0000-30448, biotools:dire | https://bio.tools/dire | SCR_003058 | Distant Regulatory Elements of co-regulated genes | 2026-02-14 02:06:10 | 25 | ||||
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MITOMAP - A human mitochondrial genome database Resource Report Resource Website 100+ mentions |
MITOMAP - A human mitochondrial genome database (RRID:SCR_002996) | MITOMAP | data or information resource, database | Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf. | gene, genome, diabetes, disease, disease-association, high resolution screening, human, inversion, metabolism, mitochondrial dna, mutation, phenotype, polymorphism, polypeptide assignment, pseudogene, restriction site, rna, sequence, trna, unpublished, variation, mitochondria, dna, insertion, deletion, FASEB list |
is used by: HmtVar is listed by: OMICtools is related to: Hereditary Hearing Loss Homepage has parent organization: Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA has parent organization: Emory University School of Medicine; Atlanta; Georgia; USA |
NIH ; Muscular Dystrophy Foundation ; Ellison Foundation ; Diputacion General de Aragon Grupos consolidados B33 ; NIGMS GM46915; NINDS NS21328; NHLBI HL30164; NIA AG10130; NIA AG13154; NINDS NS213L8; NHLBI HL64017; NIH Biomedical Informatics Training Grant T15 LM007443; NSF EIA-0321390; Spanish Fondo de Investigacion Sanitaria PI050647; Ciber Enfermedades raras CB06/07/0043 |
PMID:17178747 PMID:15608272 PMID:9399813 PMID:9016535 PMID:8594574 |
Except where otherwise noted, Creative Commons Attribution License, The community can contribute to this resource | nif-0000-00511, OMICS_01641 | SCR_002996 | 2026-02-14 02:05:42 | 368 | ||||||
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NetPath Resource Report Resource Website 50+ mentions |
NetPath (RRID:SCR_003567) | NetPath | data or information resource, database | A manually curated resource of signal transduction pathways in humans. All pathways are freely available for download in BioPAX level 3.0, PSI-MI version 2.5 and SBML version 2.1 formats. The slim pathway models representing only core reactions in each pathway are available at NetSlim. All the NetPath pathway models are also submitted to WikiPathways., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathway, signal transduction, molecule, physical interaction, gene, transcriptional regulation, transport, enzyme catalysis, immune, signaling pathway, FASEB list |
is related to: WikiPathways is related to: ConsensusPathDB has parent organization: Johns Hopkins University; Maryland; USA has parent organization: Institute of Bioinformatics; Bangalore; India |
Cancer | PMID:20067622 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157701, r3d100011009 | https://doi.org/10.17616/R34G98 | SCR_003567 | 2026-02-14 02:05:44 | 90 | |||||
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ExAc Resource Report Resource Website 1000+ mentions |
ExAc (RRID:SCR_004068) | ExAC | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. An aggregated data platform for genome sequencing data created by a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data set provided on this website spans 61,486 unrelated individuals sequenced as part of various disease-specific and population genetic studies. They have removed individuals affected by severe pediatric disease, so this data set should serve as a useful reference set of allele frequencies for severe disease studies. All of the raw data from these projects have been reprocessed through the same pipeline, and jointly variant-called to increase consistency across projects. They ask that you not publish global (genome-wide) analyses of these data until after the ExAC flagship paper has been published, estimated to be in early 2015. If you''re uncertain which category your analyses fall into, please email them. The aggregation and release of summary data from the exomes collected by the Exome Aggregation Consortium has been approved by the Partners IRB (protocol 2013P001477, Genomic approaches to gene discovery in rare neuromuscular diseases). | exome sequencing, exome, sequencing, variant, grch37/hg19, gene, region, transcript, multi-allelic variant, FASEB list |
uses: dbSNP has parent organization: Broad Institute |
PMID:27899611 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158505, r3d100010468 | https://doi.org/10.17616/R3QP53 | SCR_004068 | Exome Aggregation Consortium, ExAC Browser | 2026-02-14 02:06:16 | 4800 | |||||
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ChannelPedia Resource Report Resource Website 1+ mentions |
ChannelPedia (RRID:SCR_003807) | Channelpedia | data or information resource, database | An information management framework for comprehensive ion channel information. It is a knowledge base system centered on genetically expressed ion channel models and it encourages researchers of the field to contribute, build and refine the information through an interactive wiki-like interface. It is web-based, freely accessible and currently contains 187 annotated ion channels with 50 Hodgkin-Huxley models (September 2014). Channelepdia provides an ideal platform to collectively build ion channel knowledge base by accommodating both structured and unstructured data. The current version of Channelpedia contains the following sections : Introduction, Genes, Ontologies, Interactions, Structure, Expression, Distribution, Function, Kinetics and Models. Newly published literature related to ion channels is automatically queried every week from PubMed and added to respective categories. Currently, Channelpedia contains ~180,000 abstracts related to ion channels from Pubmed. | ion channel, model, cell, gene, transcript, ontology, interaction, hodgkinhuxley model, kinetics |
uses: PubMed uses: Gene Ontology uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: UniProt uses: Ensembl uses: IntAct uses: Rat Genome Database (RGD) has parent organization: Blue Brain Project |
PMID:22232598 | The community can contribute to this resource, Free, Public | nlx_158108 | SCR_003807 | Channel pedia | 2026-02-14 02:05:45 | 9 | ||||||
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INMEX Resource Report Resource Website 10+ mentions |
INMEX (RRID:SCR_004173) | INMEX | data analysis service, production service resource, service resource, analysis service resource | A web-based tool to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments. INMEX contains three functional modules. The data preparation module supports flexible data processing, annotation and visualization of individual data sets. The statistical analysis module allows researchers to combine multiple data sets based on P-values, effect sizes, rank orders and other features. The significant genes can be examined in functional analysis module for enriched Gene Ontology terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, or expression profile visualization. INMEX has built-in support for common gene/metabolite identifiers (IDs), as well as 45 popular microarray platforms for human, mouse and rat. Complex operations are performed through a user-friendly web interface in a step-by-step manner. | gene expression, meta-analysis, metabolomics, pathway, gene, metabolite, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: KEGG is related to: Human Metabolome Database has parent organization: University of British Columbia; British Columbia; Canada |
Killam Trust ; Canadian Institutes of Health Research |
PMID:23766290 | Acknowledgement requested | biotools:inmex, OMICS_01546 | https://bio.tools/inmex | SCR_004173 | INtegrative Meta-analysis of EXpression data, INMEX - INtegrative Meta-analysis of EXpression data | 2026-02-14 02:06:16 | 19 | ||||
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FlyTF.org Resource Report Resource Website 10+ mentions |
FlyTF.org (RRID:SCR_004123) | FlyTF | data or information resource, database | A database of genomic and protein data for Drosophila site-specific transcription factors. | transcription factor, gene, annotation, genome, protein |
is listed by: OMICtools has parent organization: MRC Laboratory of Molecular Biology |
PMID:16613907 | The community can contribute to this resource, Acknowledgement requested | OMICS_00534 | SCR_004123 | FlyTF.org - The Drosophila Transcription Factor Database | 2026-02-14 02:05:50 | 12 | ||||||
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Integrated Brain Gene Expression Resource Report Resource Website |
Integrated Brain Gene Expression (RRID:SCR_004197) | data or information resource, database | Virtual database indexing brain region gene expression data from mice from: Gene Expression Nervous System Atlas (GENSAT), Allen Mouse Brain Atlas, and Mouse Genome Institute (MGI). | database, brain gene expression, molecular neuroanatomy resource, brain, gene expression, mouse, gene |
is used by: NIF Data Federation is related to: Gene Expression Nervous System Atlas is related to: Allen Mouse Brain Reference Atlas is related to: Mouse Genome Informatics (MGI) is related to: Allen Institute for Brain Science has parent organization: Integrated |
Restricted | nlx_22354 | https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-4 http://neuinfo.org/nif/nifgwt.html?query=nlx_22354, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_22354-1, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-4 | SCR_004197 | NIF Integrated Brain Gene Expression View, NIF Integrated Brain Gene Expression, Integrated BGE, Integrated Brain Gene Expression View, NIF Brain Gene Expression, Brain Gene Expression | 2026-02-14 02:05:51 | 0 | |||||||
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Nephromine Resource Report Resource Website 10+ mentions |
Nephromine (RRID:SCR_003813) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE; REPLACED BY NEPHROSEQ; A growing database of publicly available renal gene expression profiles, a sophisticated analysis engine, and a powerful web application designed for data mining and visualization of gene expression. It provides unique access to datasets from the Personalized Molecular Nephrology Research Laboratory incorporating clinical data which is often difficult to collect from public sources and mouse data. | kidney, gene expression, visualization, clinical, expression profile, gene, mouse model, microarray |
is listed by: NIDDK Information Network (dkNET) is related to: Nephroseq has parent organization: University of Michigan; Ann Arbor; USA has parent organization: Life Technologies |
Kidney disease, Healthy, Lupus nephritis, Chronic kidney disease, Diabetic nephropathy | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158114 | SCR_003813 | 2026-02-14 02:06:13 | 20 | ||||||||
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LINCS Information Framework Resource Report Resource Website 1+ mentions |
LINCS Information Framework (RRID:SCR_003937) | data or information resource, database | LIFE search engine contains data generated from LINCS Pilot Phase, to integrate LINCS content leveraging semantic knowledge model and common LINCS metadata standards. LIFE makes LINCS content discoverable and includes aggregate results linked to Harvard Medical School and Broad Institute and other LINCS centers, who provide more information including experimental conditions and raw data. Please visit LINCS Data Portal. | bioassay, cell, small molecule, kinase protein, compound, cell, gene, metadata standard, cell line, primary cell, rnai reagent, rnai, reagent, protein reagent, protein, antibody reagent, antibody, perturbagen, growth factor, ligand, linked data, organ, disease, data set |
uses: HMS LINCS Database uses: Bioassay Ontology uses: Molecular Libraries Program is related to: Broad Institute is related to: Harvard Medical School; Massachusetts; USA is related to: Columbia University; New York; USA is related to: Yale University; Connecticut; USA is related to: Arizona State University; Arizona; USA has parent organization: University of Miami; Florida; USA |
NHLBI U01 HL111561; NHGRI |
PMID:29140462 | Free, Freely available | nlx_158348 | http://dev3.ccs.miami.edu:8080/datasets-beta/ | http://lifekb.org/ | SCR_003937 | lifekb, LIFE LINCS Information Framework | 2026-02-14 02:06:16 | 1 | ||||
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Multiple Myeloma Genomics Portal Resource Report Resource Website 1+ mentions |
Multiple Myeloma Genomics Portal (RRID:SCR_003722) | MMGP | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Database providing access and limited analysis to the MMGP portal data sets. These include the MMRC funded reference array comparative genomic hybridization (aCGH) and gene expression data and additional public multiple myeloma datasets. The MMGP will be updated with new features such as additional data and analysis tools as they become available. | gene, genomics, mutation, single-nucleotide polymorphism, array comparative genomic hybridization, gene expression, resequencing, rnai, sample annotation, differential expression |
is used by: MMRF CoMMpass Study has parent organization: Broad Institute |
Multiple myeloma | Multiple Myeloma Research Foundation | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157900 | SCR_003722 | MMRC Multiple Myeloma Genomics Portal | 2026-02-14 02:05:45 | 3 | |||||
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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 | 2026-02-14 02:05:48 | 3 | |||||||
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IntegromeDB Resource Report Resource Website 1+ mentions |
IntegromeDB (RRID:SCR_004620) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016. Search engine that integrates over 100 curated and publicly contributed data sources and provides integrated views on the genomic, proteomic, transcriptomic, genetic and functional information currently available. Information featured in the database includes gene function, orthologies, gene expression, pathways and protein-protein interactions, mutations and SNPs, disease relationships, related drugs and compounds. | catalog, search engine, gene, protein, gene regulation, gene expression, protein-protein interaction, pathway, metagenomics, mutation, disease, transcriptional regulation, genomics, transcriptomics, genetics, function, interaction, ortholog |
is related to: ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters has parent organization: University of California at San Diego; California; USA |
NIH ; NIGMS R01 GM084881 |
PMID:22260095 PMID:20427517 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_63198 | SCR_004620 | Integrome DB | 2026-02-14 02:05:49 | 3 | ||||||
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SGD Resource Report Resource Website 1000+ mentions |
SGD (RRID:SCR_004694) | SGD, SGD LOCUS, SGD REF | data or information resource, database | A curated database that provides comprehensive integrated biological information for Saccharomyces cerevisiae along with search and analysis tools to explore these data. SGD allows researchers to discover functional relationships between sequence and gene products in fungi and higher organisms. The SGD also maintains the S. cerevisiae Gene Name Registry, a complete list of all gene names used in S. cerevisiae which includes a set of general guidelines to gene naming. Protein Page provides basic protein information calculated from the predicted sequence and contains links to a variety of secondary structure and tertiary structure resources. Yeast Biochemical Pathways allows users to view and search for biochemical reactions and pathways that occur in S. cerevisiae as well as map expression data onto the biochemical pathways. Literature citations are provided where available. | database, yeast, pathway, analysis, gene, nomenclature, predicted sequence, fungi, functional relationship, protein structure, bio.tools, FASEB list |
uses: InterMOD is used by: NIF Data Federation is used by: PhenoGO is listed by: re3data.org is listed by: OMICtools is listed by: InterMOD is listed by: bio.tools is listed by: Debian is affiliated with: InterMOD is related to: AmiGO is related to: Yeast Search for Transcriptional Regulators And Consensus Tracking is related to: HomoloGene is related to: TXTGate is related to: PhenoGO has parent organization: Stanford University School of Medicine; California; USA has parent organization: Stanford University; Stanford; California is parent organization of: Ascomycete Phenotype Ontology is parent organization of: SGD Gene Ontology Slim Mapper |
NHGRI 5P41HG001315-11; NHGRI 5P41HG002273-05; NHGRI 5U41HG001315-18; NHGRI 2U41HG002273-13; NHGRI 5R01HG004834-04 |
PMID:24265222 PMID:12519985 PMID:9399804 |
Free for academic use, The community can contribute to this resource, Non-commercial | nif-0000-03456, biotools:sgd, r3d100010419, OMICS_01661 | https://bio.tools/sgd https://doi.org/10.17616/R3N313 |
http://genome-www.stanford.edu/Saccharomyces/ | SCR_004694 | SGD LOCUS, Saccharomyces Genome Database, SGD REF | 2026-02-14 02:06:21 | 1920 | |||
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Ancestrymap Resource Report Resource Website 10+ mentions |
Ancestrymap (RRID:SCR_004353) | ANCESTRYMAP | software resource, source code, software application | Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux. | disease gene, ancestry, gene, genomic, unix, linux, admixture mapping, admixture, genome, linkage disequilibrium, population |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools has parent organization: Harvard Medical School; Massachusetts; USA |
Burroughs Wellcome Fund ; NHGRI K-01 HG002758-01 |
PMID:15088269 | Restricted | nlx_39116, biotools:ancestrymap, OMICS_02083 | https://reich.hms.harvard.edu/software https://bio.tools/ancestrymap |
http://genepath.med.harvard.edu/~reich/Software.htm, http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html | SCR_004353 | 2026-02-14 02:05:47 | 12 |
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