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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Human Adenovirus Type Classification Resource Report Resource Website 100+ mentions |
Human Adenovirus Type Classification (RRID:SCR_005753) | HAdV Type Classification | analysis service resource, production service resource, knowledge environment, service resource | The Human Adenovirus Type Classification coordinates the naming of candidate new types, prior to manuscript submission for peer review. This resource contains a method of submitting candidate HAdV, criteria for a new HAdV type, and a Serotyping tool, which displays all potential types corresponding to the query serotype entered by a user. The criteria are based on discussions at the International Adenovirus Meeting (Dobog��k, Hungary; 26-30 April, 2009) and the NIH Human Adenovirus Working Group Workshop (Bethesda, MD. USA; 3 February 2011), which are summarized in a Letter to the Editor. | hadv, human adenovirus, adenovirus, classification, serotyping, genotyping, genome, nucleotide sequence, human adenovirus working group, serotype | has parent organization: George Mason University; Virginia; USA | Adenovirus | nlx_149215 | SCR_005753 | 2026-02-17 10:00:38 | 121 | ||||||||
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CLIPZ Resource Report Resource Website 10+ mentions |
CLIPZ (RRID:SCR_005755) | CLIPZ | data or information resource, production service resource, analysis service resource, database, service resource, data analysis service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets. | rna-binding protein, binding site, protein, functional annotation, cross-linking and immunoprecipitation, short read, mrna-seq, digital gene expression, small rna cloning, visualization, mining, analysis, post-transcriptional regulatory element, genome, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: University of Basel; Basel; Switzerland |
PMID:21087992 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_02256, biotools:clipz | https://bio.tools/clipz | SCR_005755 | 2026-02-17 10:00:59 | 20 | ||||||
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959 Nematode Genomes Resource Report Resource Website 1+ mentions |
959 Nematode Genomes (RRID:SCR_006068) | NematodeGenomes | data or information resource, narrative resource, wiki | A collaborative wiki that collates information on completed, ongoing and planned genome and transcriptome sequencing projects on species from phylum Nematoda. The intention is to encourage genome sequencing across the diversity of the phylum Nematoda. Wiki includes: * Published complete nematode genomes: A dynamically generated table of all species for which the genome is published. * Nematode species with genomes in progress: A dynamically generated table of all species for which a genome project is underway. Users may add species to the list * Proposed nematode genome projects: To propose a species for genome sequencing, edit its species page, and set the genome project status to proposed. * BLAST server: Search a number of the nematode-genomes-in-progress with genes of your choice. Currently there are 12 draft genomes available... * Genomes with Data available: Genomes with data available for download. Users may add more data URLs to strain pages or update the URLs. | nematode, genome, genome sequencing, transcriptome sequencing, blast, genomics, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: nematodes.org has parent organization: University of Edinburgh; Scotland; United Kingdom |
NERC | PMID:22058131 | nlx_151473, biotools:959_nematode_genomes | https://bio.tools/959_nematode_genomes | SCR_006068 | NematodeGenomes | 2026-02-17 10:00:44 | 2 | |||||
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CMHD - Centre for Modeling Human Disease Resource Report Resource Website 10+ mentions |
CMHD - Centre for Modeling Human Disease (RRID:SCR_006101) | CMHD | data or information resource, material service resource, production service resource, analysis service resource, database, service resource, biomaterial manufacture | Multidisciplinary collaboration undertaking genome-wide mutagenesis to functionally annotate the mouse genome and develop new mouse models relevant to human disease. To achieve these goals two major research platforms are carried out: Gene trapping and ENU Mutagenesis. A new challenge is faced in the post-genomic era - the assignment of biological function to the human genome sequence and projecting that assignment into understanding of human health and disease. The Centre for Modeling Human Disease (CMHD) was established to take part in the worldwide initiative to address these challenges. At the CMHD, two fundamentally different, yet complimentary methods are employed to generate mutant mouse models of human disease: chemical mutagenesis by ethylnitrosourea (ENU), and gene trap insertional mutagenesis. The Centre contributes its resources to similar international efforts and is the first of its kind in Canada. The Center is also actively developing other mutagenic strategies including pharmacologic and genetic modifier screens to dissect disease pathways, and novel mutagenic techniques using embryonic stem cells. ENU Database * Statistics for Mouse Physiological Parameters * Search Mutants by Phenotype * Search Mutants by Heritability Gene Trap Database * Search by in vitro Expression Pattern * Search by Gene Trap Sequences CMHD Members Only (must register and login) * Search Mouse Line * Histopathology * Sperm, Tissue, Slide Archiving * CMHD Database Download CMHD Services * Phenotyping * Genetic Mapping * Pathology * Pathology Service Charges | mutant, mouse model, chemical mutagenesis, ethylnitrosourea, gene trap insertion, mutagenesis, genome-wide mutagenesis, mouse genome, genome, phenotype, heritability, expression pattern, sequence, image, neurobiology, behavior, embryonic stem cell, gene trapping, enu mutagenesis, human disease |
has parent organization: Toronto Centre for Phenogenomics is parent organization of: Centre for Modeling Human Disease Gene Trap Resource |
Human disease | CIHR ; Genome Canada |
Non-CMHD users are required to register and log in only if you wish to view images on our mouse models. | nlx_151636 | SCR_006101 | Centre for Modeling Human Disease | 2026-02-17 10:00:52 | 12 | |||||
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GWAS Central Resource Report Resource Website 100+ mentions |
GWAS Central (RRID:SCR_006170) | storage service resource, data or information resource, database, service resource, data repository | Publicly available database of summary level findings from genetic association studies in humans, including genome wide association studies (GWAS). Previously named HGBASE, HGVbase and HGVbaseG2P. | Human Genome Variation database of Genotype-to-Phenotype information, genetic association study, genotype, phenotype, gene, genome region, disease, frequency data, region, genome, marker, single nucleotide polymorphism, genetic variant, allele, genome wide association study, human genome, chromosome, genetics |
is listed by: re3data.org is related to: dbSNP has parent organization: University of Leicester; Leicester; United Kingdom |
European Union GEN2PHEN project ; University of Leicester; Leicester; United Kingdom ; GlaxoSmithKline |
PMID:18948288 | nlx_151672, nif-0000-02958, SCR_007709, r3d100010565 | http://www.hgvbaseg2p.org https://doi.org/10.17616/R34G8W |
SCR_006170 | Genome Wide Association Studies Central, Human Genome Variation database of Genotype to Phenotype information, HGVbaseG2P | 2026-02-17 10:01:01 | 105 | ||||||
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WashU Epigenome Browser Resource Report Resource Website 100+ mentions |
WashU Epigenome Browser (RRID:SCR_006208) | Human Epigenome Browser | software application, data or information resource, data processing software, data analysis software, source code, software resource, data set | Software tool for visualizing and interacting with whole-genome datasets. Browser hosts Human Epigenome Atlas data produced by Roadmap Epigenomics project, but its use of advanced, multi-resolution data formats and its user-friendly interface make it possible for investigators to upload and visualize their own data as custom tracks. Developed and maintained by Epigenome Informatics Group at Washington University in St. Louis. | epigenomics, genome browser, visualization, clustering, genome, sequencing, next-generation sequencing, virus |
is listed by: OMICtools is related to: VizHub is related to: UCSC Genome Browser is related to: Human Epigenome Atlas has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA has parent organization: Roadmap Epigenomics Project |
PMID:22127213 | Free, Freely available | OMICS_00629, nlx_151754 | http://epigenomegateway.wustl.edu/browser/ | SCR_006208 | WashU Epigenome Browser, WashU Genome Browser, Human Epigenome Browser at Washington University | 2026-02-17 10:00:47 | 145 | |||||
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OligoGenome Resource Report Resource Website 1+ mentions |
OligoGenome (RRID:SCR_006025) | OligoGenome | data or information resource, resource, database | The Stanford Human OligoGenome Project hosts a database of capture oligonucleotides for conducting high-throughput targeted resequencing of the human genome. This set of capture oligonucleotides covers over 92% of the human genome for build 37 / hg19 and over 99% of the coding regions defined by the Consensus Coding Sequence (CCDS). The capture reaction uses a highly multiplexed approach for selectively circularizing and capturing multiple genomic regions using the in-solution method developed in Natsoulis et al, PLoS One 2011. Combined pools of capture oligonucleotides selectively circularize the genomic DNA target, followed by specific PCR amplification of regions of interest using a universal primer pair common to all of the capture oligonucleotides. Unlike multiplexed PCR methods, selective genomic circularization is capable of efficiently amplifying hundreds of genomic regions simultaneously in multiplex without requiring extensive PCR optimization or producing unwanted side reaction products. Benefits of the selective genomic circularization method are the relative robustness of the technique and low costs of synthesizing standard capture oligonucleotide for selecting genomic targets. | oligonucleotide, genome, probe, coding region, oligonucleotide sequence, chromosome | has parent organization: Stanford University; Stanford; California | NHGRI RC2 HG005570-01; NCI R21CA12848; NCI 5K08CA96879?6; NIDDK DK56339; NHGRI 2P01HG000205; NLM T15-LM007033; Doris Duke Clinical Foundation ; Reddere Foundation ; Liu Bie Ju Cha and Family Fellowship in Cancer ; Wang Family Foundation ; Howard Hughes Medical Foundation |
PMID:22102592 | nlx_151422 | SCR_006025 | Stanford Human Oligo Genome Project, Human OligoGenome Resource, Stanford Human Oligo Genome, Human Oligo Genome, Human OligoGenome | 2026-02-17 10:00:59 | 2 | ||||||
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ICEberg Resource Report Resource Website 50+ mentions |
ICEberg (RRID:SCR_006026) | ICEberg | data or information resource, production service resource, analysis service resource, database, service resource, data analysis service | ICEberg is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. ICEberg will facilitate efficient, multidisciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community. | dna, protein, sequence, chromosome, element, gene, similarity search, sequence alignment, genome, phylogenetic, functional analysis, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Shanghai Jiao Tong University; Shanghai; China |
National Natural Science Foundation of China 973 program 2009CB118901; National Natural Science Foundation of China 973 program 2012CB721002; National Natural Science Foundation of China 863 program 2011BAD23B05-3; Ministry of Science and Technology China ; Ministry of Education China NCET-10-0572; Shanghai Jiaotong University ; Shanghai Municipality ; Action Medical Research SP4255; Innovation Fellowship ; East Midlands Development Agency |
PMID:22009673 | nlx_151424, biotools:iceberg | https://bio.tools/iceberg | SCR_006026 | ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria | 2026-02-17 10:00:43 | 77 | |||||
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NCBI dbRBC Resource Report Resource Website 1+ mentions |
NCBI dbRBC (RRID:SCR_005959) | dbRBC | data or information resource, topical portal, portal, database | The dbRBC database provides an open, publicly accessible platform for DNA and clinical data related to the human Red Blood Cells (RBC). A new bioinformatics resource, dbRBC, has been installed at the National Center of Biotechnology Information (NCBI). This resource combines the well established Blood Group Antigen Gene Mutation Database (BGMUT) with tools and interlinked resources developed at the NCBI. The main task of dbRBC is to provide access to publicly available genomic, protein and structural information linked to the red blood cell antigens. The site offers a number of resources: * BGMUT Database * Alignment Viewer * SBT Tool * Probe/Primer Resource * Typing Kit Interface * Obstacle | red blood cell, dna, clinical data, allele, anitgen, genome, protein, structure, gold standard |
has parent organization: NCBI has parent organization: Medical University of Graz; Graz; Austria is parent organization of: Blood Group Antigen Gene Mutation Database |
nlx_151317 | SCR_005959 | dbRBC Database | 2026-02-17 10:00:42 | 1 | ||||||||
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modENCODE Resource Report Resource Website 100+ mentions |
modENCODE (RRID:SCR_006206) | modENCODE | data or information resource, production service resource, analysis service resource, service resource, data analysis service, data set | A comprehensive encyclopedia of genomic functional elements in the model organisms C. elegans and D. melanogaster. modENCODE is run as a Research Network and the consortium is formed by 11 primary projects, divided between worm and fly, spanning the domains of gene structure, mRNA and ncRNA expression profiling, transcription factor binding sites, histone modifications and replacement, chromatin structure, DNA replication initiation and timing, and copy number variation. The raw and interpreted data from this project is vetted by a data coordinating center (DCC) to ensure consistency and completeness. The entire modENCODE data corpus is now available on the Amazon Web Services EC2 cloud. What this means is that virtual machines and virtual compute clusters that you run within the EC2 cloud can mount the modENCODE data set in whole or in part. Your software can run analyses against the data files directly without experiencing the long waits and logistics associated with copying the datasets over to your local hardware. You may also view the data using GBrowse, Dataset Search, or download the data via FTP, as well as download pre-release datasets. | epigenomics, epigenetics, genomics, functional element, model organism, genome, copy number variation, gene structure, genome sequence, histone modification, histone replacement, chromatin binding site, expression profiling, replication, transcription factor binding site, transcription factor, binding site, chromatin, rna, expression profiling, regulatory network, mrna, ncrna, dna replication, genotype |
is related to: ENCODE is related to: Encode |
NHGRI | PMID:19536255 | Public, With some restrictions on its use for 9 months following publication, Acknowledgement requested | nlx_151752 | SCR_006206 | NHGRI model organism ENCyclopedia Of DNA Elements, National Human Genome Research Institute model organism ENCyclopedia Of DNA Elements, model organism ENCyclopedia Of DNA Elements | 2026-02-17 10:00:53 | 255 | |||||
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Spark Resource Report Resource Website 100+ mentions |
Spark (RRID:SCR_006207) | Spark | software application, data processing software, data analysis software, software resource, data visualization software | A clustering and visualization tool that enables the interactive exploration of genome-wide data, with a specialization in epigenomics data. Spark is also available as a service within the Epigenome toolset of the Genboree Workbench. The approach utilizes data clusters as a high-level visual guide and supports interactive inspection of individual regions within each cluster. The cluster view links to gene ontology analysis tools and the detailed region view connects to existing genome browser displays taking advantage of their wealth of annotation and functionality. | epigenomics, genome browser, clustering, visualization, genome, computation, pattern discovery, cluster |
is related to: Genboree Discovery System is related to: Roadmap Epigenomics Project has parent organization: BC Cancer Agency |
Canadian Institutes of Health Research ; Michael Smith Foundation for Health Research ; Natural Sciences and Engineering Research Council of Canada ; NIDA U01 DA025956; NIEHS 5U01ES017154-02; NHGRI HG004558 |
PMID:22960372 | Available for download without charge. Please cite. | nlx_151753 | SCR_006207 | Sparkinsight | 2026-02-17 10:01:01 | 403 | |||||
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CSHL - Hannon Lab Resource Report Resource Website 50+ mentions |
CSHL - Hannon Lab (RRID:SCR_005982) | Hannon Lab | data or information resource, portal, laboratory portal, organization portal | The Hannon laboratory comprises a broad spectrum of programs in small RNA biology, mammalian genetics and genomics. We study RNAi and related pathways in a wide variety of organisms to extract common themes that define both the mechanisms by which small RNAs act and the biological processes which they impact. Currently, we focus on microRNAs, endogenous siRNAs and piRNAs and their roles in gene regulation, cancer biology, stem cell biology and in defense of the genome against transposons. In collaboration with Steve Elledge (Harvard) and Scott Lowe (CSHL), we develop genome-wide shRNA tools for RNAi-based genetics in mammalian cells, and we are now producing similar collections of artificial microRNAs for Arabidopsis with Detlef Weigel (MPI), Dick McCombie (CSHL) and Rob Martienssen (CSHL) as part of the 2010 project (see 2010.cshl.edu). Our genomic efforts include the application of RNAi-based genetic screens to cancer biology and stem cells. We also make heavy use of next generation sequencing methodologies for probing small RNA populations, in part as a member of the ENCODE consortium (with Tom Gingeras, CSHL). Finally, we develop (with Dick McCombie) and apply focal re-sequencing methods for identifying disease relevant mutations, for probing the epigenetic landscape and for the study of human evolution. | rnai, rna, mammal, genetics, genomics, microrna, sirna, pirna, gene regulation, cancer biology, stem cell biology, defense, genome, transposon, cancer, stem cell | has parent organization: Cold Spring Harbor Laboratory | nlx_151354 | SCR_005982 | Cold Spring Harbor Laboratory - Hannon Lab | 2026-02-17 10:01:03 | 66 | ||||||||
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ErmineJ Resource Report Resource Website 50+ mentions |
ErmineJ (RRID:SCR_006450) | ermineJ | data analysis software, software application, data processing software, software resource | Data analysis software for gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are doing something interesting in the data. The software is designed to be used by biologists with little or no informatics background. A command-line interface is available for users who wish to script the use of ermineJ. Major features include: * Implementation of multiple methods for gene set analysis: ** Over-representation analysis ** A resampling-based method that uses gene scores ** A rank-based method that uses gene scores ** A resampling-based method that uses correlation between gene expression profiles (a type of cluster-enrichment analysis). * Gene sets receive statistical scores (p-values), and multiple test correction is supported. * Support of the Gene Ontology terminology; users can choose which aspects to analyze. * User files use simple text formats. * Users can modify gene sets or create new ones. * The results can be visualized within the software. * It is simple to compare multiple analyses of the same data set with different settings. * User-definable hyperlinks are provided to external sites to allow more efficient browsing of the results. * For programmers, there is a command line interface as well as a simple application programming interface that can be used to plug ermineJ functionality into your own code Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | microarray, gene ontology, analysis, high-throughput, gene, gene expression, statistical analysis, term enrichment, genome |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of British Columbia; British Columbia; Canada has parent organization: Columbia University; New York; USA |
PMID:16280084 | Free for academic use | nif-0000-07758 | SCR_006450 | ermineJ: Gene Ontology analysis for high-throughput data | 2026-02-17 10:00:52 | 50 | ||||||
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InterSpecies Analysing Application using Containers Resource Report Resource Website 10+ mentions |
InterSpecies Analysing Application using Containers (RRID:SCR_006243) | ISAAC | production service resource, analysis service resource, service resource, software resource, data analysis service | Web based tool to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. One can switch back to previous states and perform new analyses. Sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. Sets as well as results of analyses can be exchanged between members of groups. | protein function, protein interaction, pathway, mirna, disease, drug, gene, genome, transcript, protein, regulation |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University of Wurzburg; Bavaria; Germany |
PMID:24428905 | OMICS_02237 | SCR_006243 | ISAAC (Interspecies Analysing Application using Containers), ISAAC - InterSpecies Analysing Application using Containers, Interspecies Analysing Application using Containers - ISAAC | 2026-02-17 10:01:05 | 35 | |||||||
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Rat Genome Database (RGD) Resource Report Resource Website 100+ mentions |
Rat Genome Database (RGD) (RRID:SCR_006444) | RGD | storage service resource, data or information resource, database, service resource, data repository | Database for genetic, genomic, phenotype, and disease data generated from rat research. Centralized database that collects, manages, and distributes data generated from rat genetic and genomic research and makes these data available to scientific community. Curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data is provided. Facilitates investigators research efforts by providing tools to search, mine, and analyze this data. Strain reports include description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain sources. | RIN, Resource Information Network, mouse, rat, human, gene, qtl, marker, map, strain, sequence, est, genome, ontology, pathway, comparative genomics, physiology, phenotype, disease, model organism, proteomics, function, genetic, genomic, variation, immunology, behavior, knockout, inbred rat strain, mutant, congenic rat, recombinant inbred rat, data analysis service, organism supplier, genotype, gold standard, FASEB list, RRID Community Authority |
uses: InterMOD is used by: ChannelPedia is used by: Resource Identification Portal is used by: DisGeNET is used by: Integrated Animals is used by: NIH Heal Project is recommended by: Resource Identification Portal is listed by: re3data.org is listed by: InterMOD is listed by: Resource Information Network is affiliated with: InterMOD is related to: Rat Gene Symbol Tracker is related to: MPO is related to: NIF Data Federation is related to: MONARCH Initiative is related to: Vertebrate Trait Ontology is related to: Biositemaps is related to: One Mind Biospecimen Bank Listing is related to: AmiGO is related to: OMICtools is related to: re3data.org is related to: Integrated Manually Extracted Annotation is related to: OntoMate has parent organization: Medical College of Wisconsin; Wisconsin; USA is parent organization of: Diabetes Disease Portal is parent organization of: Rat Strain Ontology is parent organization of: Rat Strain Ontology is parent organization of: Renal Disease Portal |
NHLBI | PMID:23434633 PMID:18996890 PMID:17151068 |
Free, Freely available | nif-0000-00134, r3d100010417, OMICS_01660 | https://doi.org/10.17616/R3WK60 | SCR_006444 | , Rat Genome Database, RGD | 2026-02-17 10:00:52 | 272 | ||||
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Genomic Standards Consortium Resource Report Resource Website 10+ mentions |
Genomic Standards Consortium (RRID:SCR_006273) | GSC | narrative resource, international standard specification, data or information resource, standard specification, knowledge environment | An open-membership International community to promote mechanisms that standardize the description of genomes and the exchange and integration of genomic data. Community-driven standards have the best chance of success if developed within the auspices of international working groups. Participants in the GSC include biologists, computer scientists, those building genomic databases and conducting large-scale comparative genomic analyses, and those with experience of building community-based standards. The mission of the GSC is to work with the wider community towards: * the implementation of new genomic standards * methods of capturing and exchanging metadata * harmonization of metadata collection and analysis efforts across the wider genomics community | genome, genomics, standards |
is listed by: OMICtools is related to: Minimum Information for Biological and Biomedical Investigations is related to: FAIRsharing is related to: Ontology for Biomedical Investigations is related to: OBO is related to: ISA Infrastructure for Managing Experimental Metadata is parent organization of: Gazetteer |
National Institute for Environmental eScience ; NERC NE/3521773/1 |
nlx_151884, OMICS_01780 | http://gensc.org/gc_wiki/index.php/Main_Page | SCR_006273 | 2026-02-17 10:00:49 | 29 | |||||||
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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 | 2026-02-17 10:01:58 | 4 | |||||
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Genome Projector Resource Report Resource Website 1+ mentions |
Genome Projector (RRID:SCR_011790) | Genome Projector | data or information resource, production service resource, analysis service resource, database, service resource, software resource, data analysis service | A searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk. | genome, plasmid, pathway, dna, map, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Japan Society for the Promotion of Science | GNU General Public License, V.2 | OMICS_00912, biotools:genome_projector | https://bio.tools/genome_projector | SCR_011790 | 2026-02-17 10:01:57 | 3 | ||||||
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BVSim Resource Report Resource Website 1+ mentions |
BVSim (RRID:SCR_026926) | BVSim | software development tool, software application, code profiler, software resource, simulation software | Software package provides several functions and parameters for simulating genetic variations. Benchmarking variation simulator mimicking human variation spectrum. | genome, structural alteration, simulating genetic variations, | Free, Available for download, Freely available | SCR_026926 | Benchmarking Variation Simulator | 2026-02-16 09:51:16 | 1 | |||||||||
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Cistrome Resource Report Resource Website 10+ mentions |
Cistrome (RRID:SCR_000242) | data access protocol, web service, software resource | Web based integrative platform for transcriptional regulation studies. | Transcriptional, regulation, Chip, data, analysis, genome, gene, expression, motif, mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy has parent organization: Harvard University; Cambridge; United States |
Dana-Farber Cancer Institute High Tech and Campaign Technology Fund ; National Basic Research Program of China ; NHGRI HG004069; NIDDK DK074967; NIDDK DK062434 |
PMID:21859476 | Free, Freely available | SCR_017663, biotools:cistrome, OMICS_02173 | http://cistrome.org/ap/root https://bio.tools/cistrome |
SCR_000242 | Galaxy Cistrome | 2026-02-17 09:59:25 | 16 |
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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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
