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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SOURCE Resource Report Resource Website 50+ mentions |
SOURCE (RRID:SCR_005799) | SOURCE | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches Platform: Online tool | genomic, functional annotation, ontology, gene expression, gene, genome, statistical analysis, bio.tools, FASEB list |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: SMD |
NIGMS ; NCI CA85129-04; NIGMS GM07365 |
PMID:12519986 | Restricted | biotools:source, nlx_149287 | https://login.stanford.edu/idp/profile/SAML2/Redirect/SSO?execution=e1s1 https://bio.tools/source |
SCR_005799 | 2026-02-13 10:55:42 | 69 | |||||
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JCVI CMR Resource Report Resource Website 10+ mentions |
JCVI CMR (RRID:SCR_005398) | JCVI_CMR, JCVI CMR, TIGR_CMR, TIGR CMR | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Database of all of the publicly available, complete prokaryotic genomes. In addition to having all of the organisms on a single website, common data types across all genomes in the CMR make searches more meaningful, and cross genome analysis highlight differences and similarities between the genomes. CMR offers a wide variety of tools and resources, all of which are available off of our menu bar at the top of each page. Below is an explanation and link for each of these menu options. * Genome Tools: Find organism lists as well as summary information and analyses for selected genomes. * Searches: Search CMR for genes, genomes, sequence regions, and evidence. * Comparative Tools: Compare multiple genomes based on a variety of criteria, including sequence homology and gene attributes. SNP data is also found under this menu. * Lists: Select and download gene, evidence, and genomic element lists. * Downloads: Download gene sequences or attributes for CMR organisms, or go to our FTP site. * Carts: Select genome preferences from our Genome Cart or download your Gene Cart genes. The Omniome is the relational database underlying the CMR and it holds all of the annotation for each of the CMR genomes, including DNA sequences, proteins, RNA genes and many other types of features. Associated with each of these DNA features in the Omniome are the feature coordinates, nucleotide and protein sequences (where appropriate), and the DNA molecule and organism with which the feature is associated. Also available are evidence types associated with annotation such as HMMs, BLAST, InterPro, COG, and Prosite, as well as individual gene attributes. In addition, the database stores identifiers from other centers such as GenBank and SwissProt, as well as manually curated information on each genome or each DNA molecule including website links. Also stored in the Omniome are precomputed homology data, called All vs All searches, used throughout the CMR for comparative analysis. | microbial, prokaryotic, genome, annotation, dna sequence, protein, rna gene, blast, FASEB list |
is used by: NIF Data Federation is related to: AmiGO has parent organization: J. Craig Venter Institute is parent organization of: JCVI GenProp |
NSF ; NIAID ; DOE |
Free | nif-0000-03555 | SCR_005398 | JCVI Comprehensive Microbial Resource, J. Craig Venter Institute Comprehensive Microbial Resource, CMR, Comprehensive Microbial Resource | 2026-02-13 10:55:37 | 37 | ||||||
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VMD Resource Report Resource Website 1+ mentions |
VMD (RRID:SCR_004905) | PAMGO_VMD, VMD | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Database covering a range of plant pathogenic oomycetes, fungi and bacteria primarily those under study at Virginia Bioinformatics Institute. The data comes from different sources and has genomes of 3 oomycetes pathogens: Phytophthora sojae, Phytophthora ramorum and Hyaloperonospora arabidopsidis. The genome sequences (95 MB for P.sojae and 65 MB for P.ramorum) were annotated with approximately 19,000 and approximately 16,000 gene models, respectively. Two different statistical methods were used to validate these gene models, Fickett''''s and a log-likelihood method. Functional annotation of the gene models is based on results from BlastX and InterProScan screens. From the InterProScan results, putative functions to 17,694 genes in P.sojae and 14,700 genes in P.ramorum could be assigned. An easy-to-use genome browser was created to view the genome sequence data, which opens to detailed annotation pages for each gene model. A community annotation interface is available for registered community members to add or edit annotations. There are approximately 1600 gene models for P.sojae and approximately 700 models for P.ramorum that have already been manually curated. A toolkit is provided as an additional resource for users to perform a variety of sequence analysis jobs. | microbial genome sequence, genome, genome sequence, genome model, gene, image, oomycete, fungus, bacteria, phytophthora sojae, phytophthora ramorum, hyaloperonospora arabidopsidis, plant |
is used by: NIF Data Federation is related to: AmiGO has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA |
USDA Cooperative State Research Education and Extension Service 2002-35600-12747; USDA Cooperative State Research Education and Extension Service 2004-35600-15055; NSF MCB-0242131; NSF EF-0412213; NSF DBI-0211863 |
PMID:16381891 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_87328 | http://phytophthora.vbi.vt.edu | SCR_004905 | VBI Microbial Database, Virginia Bioinformatics Institute Microbial Database | 2026-02-13 10:55:32 | 8 | ||||
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PLEXdb - Plant Expression Database Resource Report Resource Website 10+ mentions |
PLEXdb - Plant Expression Database (RRID:SCR_006963) | PLEXdb | data repository, storage service resource, data analysis service, portal, analysis service resource, data or information resource, production service resource, service resource, topical portal, database | PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data. The integrated tools of PLEXdb allow investigators to use commonalities in plant biology for a comparative approach to functional genomics through use of large-scale expression profiling data sets. | gene expression, plant, plant pathogen, genotype, phenotype, genetic, physical, pathway, plant biology, compare, functional genomics, expression profiling, expression atlas, pathogen, genome, anova, cluster, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: FuncExpression has parent organization: Iowa State University; Iowa; USA |
UniNSF DBI-0543441; NSF IOS-0922746; USDA 3625-21000-049-00D |
PMID:22084198 | biotools:plexdb, r3d100011516, nlx_149236 | https://bio.tools/plexdb https://doi.org/10.17616/R39D13 |
SCR_006963 | PLEXdb - Gene expression resources for plants and plant pathogens, Plant Expression Database | 2026-02-13 10:55:57 | 21 | |||||
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Pig Genome Mapping Resource Report Resource Website |
Pig Genome Mapping (RRID:SCR_012884) | PiGMaP | data or information resource, image collection, atlas, database | Map of identifyied genes controlling traits of economic and welfare significance in the pig. The project objectives were to produce a genetic map with markers spaced at approximately 20 centiMorgan intervals over at least 90% of the pig genome; to produce a physical map with at least one distal and one proximal landmark locus mapped on each porcine chromosome arm and also genetically mapped; to develop a flow karyotype for the pig based on FACS sorted chromosomes; to develop PCR based techniques to enable rapid genotyping for polymorphic markers; to evaluate synteny conservation between pigs, man, mice and cattle; to develop and evaluate the statistical techniques required to analyze data from QTL mapping experiments and to plan and initiate the mapping of QTLs in the pig; to map loci affecting traits of economic and biological significance in the pig; and to develop the molecular tools to allow the future identification and cloning of mapped loci. Animal breeders currently assume that economically important traits such as growth, carcass composition and reproductive performance are controlled by an infinite number of genes each of infinitessimal effect. Although this model is known to be unrealistic, it has successfully underpinned the genetic improvement of livestock, including pigs, over recent decades. A map of the pig genome would allow the development of more realistic models of the genetic control of economic traits and the ultimately the identification of the major trait genes. This would allow the development of more efficient marker assisted selection which may be of particular value for traits such as disease resistance and meat quality. | gene, genetic, artificial chromosome, bacteriophage, biological, carcass, cattle, cdna, comparative, disease, genome, genotype, growth, human, karyotpe, linkage, livestock, locus, map, mapping, marker, mice, molecular, p1, pig, quality, quantitative, sus scrofa, trait, yeast | has parent organization: Roslin Institute | PMID:7749223 | nif-0000-20987 | http://www.projects.roslin.ac.uk/pigmap/pigmap.html | SCR_012884 | PGM | 2026-02-13 10:57:02 | 0 | ||||||
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Ascidian Network for InSitu Expression and Embryological Data Resource Report Resource Website 50+ mentions |
Ascidian Network for InSitu Expression and Embryological Data (RRID:SCR_013030) | ANISEED | data repository, storage service resource, data or information resource, service resource, software resource, database |
Database of ascidian embryonic development at the level of the genome (cis-regulatory sequences, gene expression, protein annotation), of the cell (morphology, fate, induction, lineage) or of the whole embryo (anatomy, morphogenesis). Currently, four organism models are described in Aniseed: Ciona intestinalis, Ciona savignyi, Halocynthia roretzi and Phallusia mammillata. This version supports four sets of Ciona intestinalis transcript models: JGI v1.0, KyotoGrail 2005, KH and ENSEMBL, all functionally annotated, and grouped into Aniseedv3.0 gene models. Users can explore their expression profiles during normal or manipulated development, access validated cis-regulatory regions, get the molecular tools used to assay gene function, or all articles related to the function, or regulation of a given gene. Known transcriptional regulators and targets are listed for each gene, as are the gene regulatory networks acting in individual anatomical territories. ANISEED is a community tool, and the direct involvement of external contributors is important to optimize the quality of the submitted data. Virtual embryo: The 3D Virtual embryo is available to download in the download section of the website. |
embryology, embryo, gene, genome, anatomy, cis-regulatory, development, morphogenesis, morphology, protein, molecular neuroanatomy resource, cis-regulatory sequence, gene expression, protein annotation, cell, expression profile, function, regulation, blast, visualization, data analysis service, clone, FASEB list | CNRS ; French Ministry of Research ; Marseille-Nice Genopole ; ARC ; European Network QLK3-CT-2001-01890 |
PMID:20647237 | nif-0000-10155 | http://crfb.univ-mrs.fr/aniseed/index.php | SCR_013030 | Aniseed database | 2026-02-13 10:57:03 | 60 | ||||||
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Genetic and Rare Diseases Information Center Resource Report Resource Website 10+ mentions |
Genetic and Rare Diseases Information Center (RRID:SCR_008695) | GARD | disease-related portal, data or information resource, portal, topical portal | Genetic and Rare Diseases Information Center (GARD) is a collaborative effort of two agencies of the National Institutes of Health, The Office of Rare Diseases Research (ORDR) and the National Human Genome Research Institute (NHGRI) to help people find useful information about genetic conditions and rare diseases. GARD provides timely access to experienced information specialists who can furnish current and accurate information about genetic and rare diseases. So far, GARD has responded to 27,635 inquiries on about 7,147 rare and genetic diseases. Requests come not only from patients and their families, but also from physicians, nurses and other health-care professionals. GARD also has proved useful to genetic counselors, occupational and physical therapists, social workers, and teachers who work with people with a genetic or rare disease. Even scientists who are studying a genetic or rare disease and who need information for their research have contacted GARD, as have people who are taking part in a clinical study. Community leaders looking to help people find resources for those with genetic or rare diseases and advocacy groups who want up-to-date disease information for their members have contacted GARD. And members of the media who are writing stories about genetic or rare diseases have found the information GARD has on hand useful, accurate and complete. GARD has information on: :- What is known about a genetic or rare disease. :- What research studies are being conducted. :- What genetic testing and genetic services are available. :- Which advocacy groups to contact for a specific genetic or rare disease. :- What has been written recently about a genetic or rare disease in medical journals. GARD information specialists get their information from: :- NIH resources. :- Medical textbooks. :- Journal articles. :- Web sites. :- Advocacy groups, and their literature and services. :- Medical databases. | genetic, disease, information, genome, human, rare disease, health, physician, counselor, gene, journal, medical | has parent organization: National Institutes of Health | Office of Rare Diseases Research ; NHGRI |
nif-0000-37627 | SCR_008695 | Genetic Rare Diseases Information Center | 2026-02-13 10:56:14 | 14 | |||||||
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BECA Resource Report Resource Website 1+ mentions |
BECA (RRID:SCR_015846) | BECA | data visualization software, data processing software, software application, software resource, image analysis software | Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version. | visual exploration, brain, neuroscience, network, genetic determinant, fmri, neuroimaging, genome | has parent organization: Indiana University School of Medicine; Indiana; USA | NLM R01 LM011360; NIA U01 AG024904; NIA RC2 AG036535; NIA R01 AG19771; NIA P30 AG10133; NSF IIS-1117335; NIBIB R01 EB022574 |
PMID:27171688 | Free, Available for download | SCR_015846 | Brain Explorer for Connectome Analysis (BECA), BECA - Brain Explorer for Connectome Analysis | 2026-02-13 10:57:37 | 5 | ||||||
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Alliance of Genome Resources Resource Report Resource Website 50+ mentions |
Alliance of Genome Resources (RRID:SCR_015850) | portal, consortium, data or information resource, organization portal, service resource, access service resource | Organization that aims to develop and maintain sustainable genome information resources to promote understanding of the genetic and genomic basis of human biology, health, and disease. The Alliance is composed of FlyBase, Mouse Genome Database (MGD), the Gene Ontology Consortium (GOC), Saccharomyces Genome Database (SGD), Rat Genome Database (RGD), WormBase, and the Zebrafish Information Network (ZFIN). | gene ontology, human biology, genome, organism model, gene ontology consortium, FASEB list | NHGRI U41HG02223E | SCR_015850 | The Alliance | 2026-02-13 10:57:37 | 69 | ||||||||||
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MetaNetX Resource Report Resource Website 50+ mentions |
MetaNetX (RRID:SCR_015882) | data access protocol, software resource, web service | Web application to perform automated model construction and genome annotation for large-scale metabolic networks. Platform for accessing, analyzing and manipulating genome-scale metabolic networks (GSM) as well as biochemical pathways. | automated model construction, genome annotation, model, construction, genome, annotation, metabolic network, repository, gsm, biochemical, pathway | Swiss National Science Foundation ; Swiss Federal Government ; SIB Swiss Institute of Bioinformatics |
PMID:26527720 PMID:23357920 PMID:23172809 |
Free, Freely available | SCR_015882 | MNXref, MetaNetX: Automated Model Construction and Genome Annotation for Large-Scale Metabolic Networks | 2026-02-13 10:57:41 | 82 | ||||||||
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Barrnap Resource Report Resource Website 500+ mentions |
Barrnap (RRID:SCR_015995) | sequence analysis software, data processing software, data analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | multithreading, fasta, sequencing, software, predict, location, ribosomal, gene, genome, RNA, prediction, bacteria, archaea, mitochondria, eukaryote, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:barrnap, OMICS_13988 | https://github.com/tseemann/barrnap https://bio.tools/barrnap https://sources.debian.org/src/barrnap/ |
SCR_015995 | Barrnap: Basic rapid ribosomal RNA predictor | 2026-02-13 10:57:42 | 568 | |||||||
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Aegean Resource Report Resource Website 1+ mentions |
Aegean (RRID:SCR_015965) | sequence analysis software, data processing software, data analysis software, software toolkit, software application, software resource | Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more. | genome, evaluation, annotation, structure, loci |
is listed by: Debian is listed by: OMICtools |
National Science Foundation 1126267 | PMID:22852583 | Free, Available for download, Freely available, | OMICS_19721 | https://github.com/BrendelGroup/AEGeAn https://sources.debian.org/src/aegean/ |
SCR_015965 | AEGeAn: analysis and evaluation of genome annotations, Aegean Toolkit | 2026-02-13 10:57:38 | 6 | |||||
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andi Resource Report Resource Website 10+ mentions |
andi (RRID:SCR_015971) | data processing software, image analysis software, alignment software, software application, software resource, algorithm resource | Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes. | algorithm, computing, estimate, analysis, genome, alignment, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Deutsche Forschungsgemeinschaft Pf672/3-1 | PMID:25504847 | Free, Freely available, Available for download | OMICS_09287, biotools:andi | https://bio.tools/andi https://sources.debian.org/src/andi/ |
SCR_015971 | 2026-02-13 10:57:36 | 41 | ||||||
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Cross-species scaffolding Resource Report Resource Website 1+ mentions |
Cross-species scaffolding (RRID:SCR_015932) | sequence analysis software, data processing software, data analysis software, source code, software application, software resource | Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Super-scaffolding of draft genome assemblies with in silico mate-pair libraries derived from (closely) related references. | mate, pair, end, reference, genome | Free, Available for download, Freely available | SCR_016125 | SCR_015932 | cross-species-scaffolding | 2026-02-13 10:57:41 | 1 | |||||||||
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Piggy Resource Report Resource Website 10+ mentions |
Piggy (RRID:SCR_015941) | data analysis software, software resource, data processing software, software application | Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary). | intergenic, region, bacterial, analysis, gene, genome, assembly | Medical Research Council | Free, Available for download | SCR_015941 | 2026-02-13 10:57:41 | 31 | ||||||||||
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Falcon Resource Report Resource Website 100+ mentions |
Falcon (RRID:SCR_016089) | data processing software, alignment software, software application, software resource, image analysis software | Software package for aligning long sequencing reads as a diploid-aware genome assembler. Used for assembling non-inbred or rearranged heterozygous genomes. | fast, aligner, sequencing, diploid, genome, assembly, non-inbred, rearranged, heterozygous, single-molecule |
is listed by: Debian is listed by: OMICtools is related to: Howard Hughes Medical Institute |
National Science Foundation DBI-1350041; National Science Foundation IOS-1237880; National Science Foundation MCB 0929402; National Science Foundation MCB 1122246; Gordon and Betty Moore Foundation GBMF 3034; NHGRI R01 HG006677 |
PMID:27749838 | Free, Available for download, Freely available | OMICS_13514 | https://sources.debian.org/src/falcon/ | SCR_016089 | 2026-02-13 10:57:43 | 279 | ||||||
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EnrichmentMap Resource Report Resource Website 500+ mentions |
EnrichmentMap (RRID:SCR_016052) | data visualization software, data processing software, source code, software application, software resource | Source code of a Cytoscape plugin for functional enrichment visualization. It organizes gene-sets, such as pathways and Gene Ontology terms, into a network to reveal which mutually overlapping gene-sets cluster together. | cytoscape, functional, visualization, enrichment, gene, mapping, genome, pathway, network, cluster, bio.tools |
is listed by: Debian is listed by: bio.tools is a plug in for: Cytoscape |
NHGRI P41 HG04118; Ontario Genomics Institute ; Heart and Stroke Foundation of Canada ; Canada Foundation for Innovation ; Ontario Research Fund (ORF) |
PMID:21085593 | biotools:enrichmentmap | https://github.com/BaderLab/EnrichmentMapApp https://bio.tools/enrichmentmap |
SCR_016052 | 2026-02-13 10:57:42 | 545 | |||||||
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Clonalframe Resource Report Resource Website 100+ mentions |
Clonalframe (RRID:SCR_016060) | sequence analysis software, data processing software, data analysis software, software application, software resource | Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance. | analysis, sequence, inference, bacteria, microevolution, multilocus, clonal, sample, chromosome, homologuous, recombination, disrupted, inheritance, DNA, genome |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust | DOI:10.1534/genetics.106.063305 | Free, Available for download | OMICS_14623 | https://github.com/xavierdidelot/ClonalFrameML https://sources.debian.org/src/clonalframe/ |
SCR_016060 | ClonalFrameML | 2026-02-13 10:57:42 | 379 | |||||
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BLINK Resource Report Resource Website 1+ mentions |
BLINK (RRID:SCR_016288) | data processing software, data analysis software, software application, software resource, algorithm resource | Software for next level of genome wide association studies with both individuals and markers in millions. The method releases the requirement that causative genes are evenly distributed on genome and consequently boosts statistical power. | GWAS, SNP, dataset, r, genome, bayesian, linkage, nested, keyway, statistic, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Tutorial available | biotools:BLINK | https://bio.tools/BLINK | SCR_016288 | BLINK (Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway) | 2026-02-13 10:57:43 | 1 | |||||||
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Gubbins Resource Report Resource Website 500+ mentions |
Gubbins (RRID:SCR_016131) | sequence analysis software, data processing software, data analysis software, software application, software resource | Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | rapid, phylogenetic, analysis, large, sample, recombinant, bacteria, whole, genome, sequence, loci, elevated, densities, base, substitiution, mutatiion, outside, region, evolution, alignment |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust 098051 | PMID:25414349 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_14386 | https://sources.debian.org/src/gubbins/ | SCR_016131 | Gubbins: Genealogies Unbiased By recomBinations In Nucleotide Sequences | 2026-02-13 10:57:45 | 602 |
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