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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SUPFAM Resource Report Resource Website 10+ mentions |
SUPFAM (RRID:SCR_005304) | SUPFAM | data or information resource, database | SUPFAM is a database that consists of clusters of potentially related homologous protein domain families, with and without three-dimensional structural information, forming superfamilies. The present release (Release 3.0) of SUPFAM uses homologous families in Pfam (Version 23.0) and SCOP (Release 1.69) which are examples of sequence -alignment and structure classification databases respectively. The two steps involved in setting up of SUPFAM database are * Relating Pfam and SCOP families using a new profile-profile alignment algorithm AlignHUSH. This results in identifying many Pfam families which could be related to a family or superfamily of known structural information. * An all-against-all match among Pfam families with yet unknown structure resulting in identification of related Pfam families forming new potential superfamilies. The SUPFAM database can be used in either the Browse mode or Search mode. In Browse mode you can browse through the Superfamilies, Pfam families or SCOP families. In each of these modes you will be presented with a full list which can be easily browsed. In Search mode, you can search for Pfam families, SCOP families or Superfamilies based on keywords or SCOP/Pfam identifiers of families and superfamilies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | duf/upf connections, 3-d structure, alignment, amino acid sequence, bioinformatics, clustering, homologous protein family, multiple sequence alignment, nmr, pali, pfam, phylogeny, protein classification, protein domain database, protein families, protein sequence database, rps_blast, scop, structural genomics, structure determination, superfamily, three-dimensional, x-ray crystalography |
is related to: Pfam is related to: SCOP: Structural Classification of Proteins has parent organization: Indian Institute of Science; Bangalore; India |
Council of Scientific and Industrial Research New Delhi ; Wellcome Trust |
PMID:15113407 PMID:11752317 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03517 | http://pauling.mbu.iisc.ernet.in/~supfam | SCR_005304 | 2026-02-14 02:06:23 | 13 | |||||
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Major depressive disorder neuroimaging database Resource Report Resource Website 1+ mentions |
Major depressive disorder neuroimaging database (RRID:SCR_005835) | MaND | data or information resource, database | The Major Depressive Disorder Neuroimaging Database (MaND) contains information of 225 studies which have investigated brain structure (using MRI and CT scans) in patients with major depressive disorder compared to a control group. 143 studies and 63 brain structures are included in the meta-analysis. The database and meta-analysis are contained in an Excel spreadsheet file which may be freely downloaded from this website. | mri, brain, ct, neuroimaging, image, normal control | has parent organization: King's College London; London; United Kingdom | Major depressive disorder | Wellcome Trust ; National Institute for Health Research ; EPSRC |
PMID:21727252 | nlx_149353 | SCR_005835 | Major Depressive Disorder Neuroimaging Database (MaND) | 2026-02-14 02:06:25 | 2 | |||||
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DECIPHER Resource Report Resource Website 1000+ mentions |
DECIPHER (RRID:SCR_006552) | DECIPHER | data or information resource, database | Interactive database which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance. Used to enhance clinical diagnosis by retrieving information from bioinformatics resources relevant to the imbalance found in the patient. Contributing to the DECIPHER database is a Consortium, comprising an international community of academic departments of clinical genetics. Each center maintains control of its own patient data (which are password protected within the center''''s own DECIPHER project) until patient consent is given to allow anonymous genomic and phenotypic data to become freely viewable within Ensembl and other genome browsers. Once data are shared, consortium members are able to gain access to the patient report and contact each other to discuss patients of mutual interest, thus facilitating the delineation of new microdeletion and microduplication syndromes. | chromosomal imbalance, phenotype, chromosome, gene, genome, deletion, duplication, copy number, genotype, polymorphism, FASEB list |
is used by: MARRVEL is listed by: OMICtools is related to: Deciphering Developmental Disorders is related to: Ensembl has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Developmental disorder, Microdeletion Syndrome, Overgrowth syndrome, Microduplication syndrome, Deletion syndrome, Duplication syndrome, Wolf-Hirschhorn Syndrome, Williams-Beuren Syndrome, Smith-Magenis Syndrome, Etc | Wellcome Trust WT077008 | PMID:19344873 | Acknowledgement required | nlx_151653, OMICS_00265 | SCR_006552 | Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources, DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources, Database of Chromosomal Imbalance Phenotype in Humans using Ensembl Resources, Decipher | 2026-02-14 02:05:56 | 1797 | ||||
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Wellcome-CTC Mouse Strain SNP Genotype Set Resource Report Resource Website 1+ mentions |
Wellcome-CTC Mouse Strain SNP Genotype Set (RRID:SCR_003216) | Wellcome-CTC Mouse Strain SNP Genotype Set | data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Data set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34. | genome, genotype, snp, chromosome, haplotype, haplotype structure, recombinant inbred mouse strain | has parent organization: Wellcome Trust Centre for Human Genetics | Wellcome Trust ; NCRR R24RR015116; NIGMS R01GM072863; NIAAA U01AA014425; NINDS R01NS049445; NIMH P20-MH 62009; NIAAA U24AA13513 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156947 | SCR_003216 | 2026-02-14 02:07:20 | 3 | |||||||
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Africa Centre for Health and Population Studies Resource Report Resource Website 1+ mentions |
Africa Centre for Health and Population Studies (RRID:SCR_008964) | Africa Centre Datasets, Africa Center Datasets, AfricaCentre Datasets | data or information resource, data set | Longitudinal datasets of demographic, social, medical and economic information from a rural demographic in northern KwaZulu-Natal, South Africa where HIV prevalence is extremely high. The data may be filtered by demographics, years, or by individuals questionnaires. The datasets may be used by other researchers but the Africa Centre requests notification that anyone contact them when downloading their data. The datasets are provided in three formats: Stata11 .dta; tables in a MS-Access .accdb database; and worksheets in a MS-Excel .xlsx workbook. Datasets are generated approximately every six months containing information spanning the whole period of surveillance from 1/1/2000 to present. | medicine, hiv infection, economic, demography, biology, social, longitudinal |
is listed by: re3data.org is listed by: DataCite has parent organization: University of KwaZulu-Natal; Durban; South Africa |
HIV | Wellcome Trust ; Agence Nationale de Recherches sur le Sida et les Hepatites Virales ; Department for International Development ; USAID ; EDCTP ; South African MRC ; National Research Foundation ; CSIR ; UNFPA ; CIDA |
Open unspecified license, Data Use Agreement, Approval required | nlx_152006 | SCR_008964 | Africa Centre for Health and Population Studies Datasets, Africa Center for Health and Population Studies | 2026-02-14 02:07:24 | 4 | |||||
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Eagle Resource Report Resource Website 50+ mentions |
Eagle (RRID:SCR_015991) | software resource, software toolkit | Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. | hmm, hidden markov model, statistic, estimation, haplotype, phase, reference, panel, sequencing, algorithm, analysis, probability |
is listed by: Debian is listed by: OMICtools has parent organization: Broad Institute |
NHGRI R01 HG006399; NIMH R01 MH101244; NHGRI F32HG007805; Wellcome Trust WT098051; Austrian Science Fund J-3401; NHGRI HG007022; NHLBI HL117626; Fannie and John Hertz Foundation ; NCRR S10 RR028832; NWO 480-05-003; Dutch Brain Foundation |
PMID:27694958 PMID:27270109 |
Free, Available for download, Freely available | OMICS_14099, SCR_017262 | https://sources.debian.org/src/bio-eagle/ https://github.com/poruloh/Eagle https://data.broadinstitute.org/alkesgroup/Eagle/downloads/ |
SCR_015991 | Bio-eagle, Eagle1, Eagle2 | 2026-02-14 02:07:27 | 51 | |||||
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fragon Resource Report Resource Website |
fragon (RRID:SCR_019158) | software resource, software toolkit | Software tool for rapid high resolution structure determination from ideal protein fragments. Pipeline to determine crystal structures using molecular replacement with small fragments followed by density modification. It is available through CCP4. | Density modification, molecular replacement, protein fragments, crystal structure determination | is related to: CCP4 | Wellcome Trust | PMID:29533228 | Free, Freely available | SCR_019158 | 2026-02-14 02:07:19 | 0 | ||||||||
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MLST Resource Report Resource Website 1000+ mentions |
MLST (RRID:SCR_010245) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms via the internet. The aim of MLST is to provide a portable, accurate, and highly discriminating typing system that can be used for most bacteria and some other organisms. It is envisaged that this approach will be particularly helpful for the typing of bacterial pathogens. To achieve this aim we have taken the proven concepts of multilocus enzyme electrophoresis (MLEE) and have adapted them so that alleles at each locus are defined directly, by nucleotide sequencing, rather than indirectly from the electrophoretic moblity of their gene products. MLST was developed in the laboratories of Martin Maiden, Dominique Caugant, Ian Feavers, Mark Achtman and Brian Spratt. This site is hosted at Imperial College with funding from the Wellcome Trust. The location of the subsites for the individual species are shown on their respective front pages. | has parent organization: Imperial College London; London; United Kingdom | Wellcome Trust | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_156883 | SCR_010245 | 2026-02-14 02:06:11 | 1230 | |||||||||
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Open Trials Resource Report Resource Website 1+ mentions |
Open Trials (RRID:SCR_015570) | data or information resource, database | Database that contains data such as registry entries, portions of regulatory documents describing individual trials, structured data on methods and results, and researchers and papers from and/or related to clinical trials. The initiative aims to locate, match, and share all publicly accessible data and documents, on all trials conducted, on all medicines and other treatments, globally. | clinical trial, clinical trial database, clinical trial data, open database, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Oxford; Oxford; United Kingdom |
Laura and John Arnold Foundation ; Wellcome Trust ; World Health Organisation ; West of England Academic Health Science Network |
Open source | biotools:opentrials | https://bio.tools/opentrials | SCR_015570 | 2026-02-14 02:06:46 | 3 | |||||||
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mousebrain.org Resource Report Resource Website 100+ mentions |
mousebrain.org (RRID:SCR_016999) | data or information resource, atlas | Atlas of brain cell types, derived from single cell RNA-Seq data from Linnarsson Lab. Can be browsed by taxon, cell type, tissue, and gene, with information on enriched genes, specific markers, anatomical location and more. Single cell gene expression atlas of mouse nervous system. | Atlas, brain cell, cell type, single cell RNA seq data, taxon, tissue, gene, marker, anatomical location, data | has parent organization: Karolinska Institute; Stockholm; Sweden | Knut and Alice Wallenberg Foundation ; Swedish Foundation for Strategic Research ; Wellcome Trust ; Swedish Research Council ; SSF ; Cancerfonden ; EU ; Hjärnfonden ; SFO Strat Regen ; European Research Council ; Ollie and Elof Ericssons Foundation ; Åke Wiberg Foundation |
PMID:30096314 | Free, Available for download, Freely available | SCR_018356 | SCR_016999 | Linnarsson lab Mouse Brain Atlas | 2026-02-14 02:06:31 | 111 | ||||||
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GEROprotectors Resource Report Resource Website 10+ mentions |
GEROprotectors (RRID:SCR_016737) | data or information resource, database | Collection of structured and manually curated data of current therapeutic interventions in aging and age-related disease. Describes compounds and mechanisms using multiple chemical and biological databases. | geroprotector, data, collection, current, thearpeutic, prevention, aging, disease, geriatic |
uses: PubChem uses: ChemSpider uses: DrugBank uses: ChEMBL uses: CHEBI uses: UniProt uses: GenAge |
Wellcome Trust ; Israel Ministry of Science and Technology ; Fund in Memory of Dr. Amir Abramovich |
PMID:26342919 | Public, Free, Freely available | SCR_016737 | Geroprotectors | 2026-02-14 02:06:24 | 11 | |||||||
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BIGSdb Resource Report Resource Website 1+ mentions |
BIGSdb (RRID:SCR_023551) | data or information resource, database | Platform for gene-by-gene bacterial population annotation and analysis. Designed to store and analyse sequence data for bacterial isolates. Used for scalable analysis of bacterial genome variation at population level. | sequence data, bacterial isolates, gene-by-gene bacterial population, annotation and analysis, bacterial genome variation, | Wellcome Trust | PMID:21143983 | Free, Freely available | https://bigsdb.readthedocs.io/en/latest/ | SCR_023551 | Bacterial Isolate Genome Sequence Database | 2026-02-14 02:06:35 | 1 | |||||||
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Human Developmental Biology Resource Resource Report Resource Website 100+ mentions |
Human Developmental Biology Resource (RRID:SCR_006326) | HDBR | biomaterial supply resource, material resource | Collection of human embryonic and fetal material (Tissue and RNA) ranging from 3 to 20 weeks of development available to the international scientific community. Material can either be sent to registered users or our In House Gene Expression Service (IHGES) can carry out projects on user''''s behalf, providing high quality images and interpretation of gene expression patterns. Gene expression data emerging from HDBR material is added to our gene expression database which is accessible via our HUDSEN (Human Developmental Studies Network) website. A significant proportion of the material has been cytogenetically karyotyped, and normal karyotyped material is provided for research. | development, fetal material, fetus, embryonic human, fetus human, karyotype, gene expression, image, imaging, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is related to: HUDSEN Human Gene Expression Spatial Database has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom has parent organization: University College London; London; United Kingdom |
Normal | MRC ; Wellcome Trust |
Public: Intended for use primarily by academic researchers. Every effort is made to ensure that optimal use is made of donated tissue, Both in terms of the aims and quality of the research for which it is used and avoidance of duplication/wastage. Applications by pharmaceutical or biotechnology companies for access to the Resource are considered, Provided that the tissue itself is not used directly for financial gain. | nlx_152030 | SCR_006326 | MRC-Wellcome Trust Human Developmental Biology Resource | 2026-02-14 02:06:39 | 284 | |||||
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Genes to Cognition Database Resource Report Resource Website |
Genes to Cognition Database (RRID:SCR_002735) | G2Cdb | data or information resource, database | Database of protein complexes, protocols, mouse lines, and other research products generated from the Genes to Cognition project, a project focused on understanding molecular complexes involved in synaptic transmission in the brain. | allele, gene list, mouse line, human disease, phenotyping, plasticity, behavior, proteonomics, brain, cognition, cognition disorder, learning, memory, neuroscience, experimental protocol, synapse proteomics, synapse | Wellcome Trust ; MRC ; BBSRC ; Gatsby Charitable Foundation ; Human Frontiers Science Programme ; European Union ; Framework Programme ; EPSRC ; NSF |
PMID:18984621 | Free, Freely available | nif-0000-02864 | http://www.genes2cognition.org/cgi-bin/SearchView | SCR_002735 | Genes-to-Cognition Database | 2026-02-14 02:06:11 | 0 | |||||
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PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees Resource Report Resource Website 1+ mentions |
PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees (RRID:SCR_003321) | PANDIT | data or information resource, database | PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains: * the seed protein sequence alignments from the Pfam-A (curated families) database (version 17.0) * nucleotide sequence alignments derived from sequences available for the above and using the protein alignments as "templates"; * protein sequence alignments restricted to the family members for which nucleotide sequences are available * inferred phylogenetic trees for each alignment The data in PANDIT and the dataset's development have been frozen owing to a lack of funding support. The existing data, version 17.0 corresponding to Pfam 17.0, remain stable and, we hope, useful. The entire database is also available for download as a flatfile from this website. | gold standard, database, protein, associated nucleotide domain | has parent organization: European Bioinformatics Institute | Wellcome Trust | PMID:16381879 PMID:12912837 |
Free, Available for download, Freely available | r3d100010570, nif-0000-03241 | https://doi.org/10.17616/R3GP69 | SCR_003321 | Protein and Associated Nucleotide Domains with Inferred Trees | 2026-02-14 02:06:11 | 4 | ||||
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GeneDB Gmorsitans Resource Report Resource Website 1+ mentions |
GeneDB Gmorsitans (RRID:SCR_004310) | GeneDB Gmorsitans, GeneDB G. morsitans | data or information resource, database | As of 12th March 2009, GeneDB provides access to the transcriptome of the Tsetse fly Glossina morsitans morsitans, the biological vector of African trypanosomiases. The current data set includes: >>7,015 contigs comprised of ESTs from Trypanosoma brucei infected midgut tissue (Lehane et al, Genome Biol. 2003;4(10):R63) >>7,493 contigs comprised of ESTs from salivary gland tissue >>18,404 contigs comprised of EST pooled from a range of different tissue- and developmental stage-specific libraries: head (2,700 ESTs), midgut (21,662 ESTs), reproductive organs (3, 438 ESTs), salivary gland (27,426 ESTs), larvae (2,304 ESTs), pupae (2,304 ESTs), fatbody (20,257 ESTs) (Attardo et al, Insect Molecular Biology 2006, 15(4):411-424), male and female whole bodies (19,968 ESTs). These data include the midgut and salivary gland ESTs used in the library specific clustering for the contig sets listed above. Initial automated annotations of product descriptions were manually revised by participants in two community annotation jamborees held under the auspice of the International Glossina Genome Initiative (IGGI) with funding by TDR. A Glossina morsitans morsitans genome project is currently also underway. To date, 2.4M capillary shotgun reads have been produced and the initial assembly is available to download via the ftp server and for blast analysis. | has parent organization: GeneDB | Wellcome Trust ; TDR |
nlx_32209 | SCR_004310 | Glossina morsitans GeneDB | 2026-02-14 02:05:51 | 2 | ||||||||
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Brain Intensity AbNormality Classification Algorithm Resource Report Resource Website 1+ mentions |
Brain Intensity AbNormality Classification Algorithm (RRID:SCR_024928) | BIANCA | data processing software, software application, segmentation software, software resource, image analysis software | Software tool for automated segmentation of white matter hyperintensities. Classifies image’s voxels based on their intensity and spatial features, and the output image represents the probability per voxel of being WMH. Flexible in terms of MRI modalities to use and offers different options for weighting spatial information, local spatial intensity averaging, and different options for choice of number and location of training points. | images voxels classification, automated segmentation of white matter hyperintensities, white matter hyperintensities, | is a plug in for: FSL | Wellcome Trust ; Wolfson Foundation ; UK Stroke Association ; NIHR Oxford Biomedical Research Centre |
PMID:27402600 | Free, Freely available | SCR_024928 | BIANKA:Brain Intensity AbNormality Classification Algorithm | 2026-02-14 02:08:49 | 3 | ||||||
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IBEX Knowledge Base Resource Report Resource Website 1+ mentions |
IBEX Knowledge Base (RRID:SCR_025296) | knowledge base | Open, global repository as central resource for reagents, protocols, panels, publications, software, and datasets. In addition to IBEX, we support standard, single cycle multiplexed imaging (Multiplexed 2D imaging), volume imaging of cleared tissues with clearing enhanced 3D (Ce3D), highly multiplexed 3D imaging (Ce3D-IBEX), and extension of the IBEX dye inactivation protocol to the Leica Cell DIVE (Cell DIVE-IBEX). Committed to sharing knowledge related to multiplexed imaging. Antibody validation community knowledgebase. | Antibody, validation, multiplexed imaging, | NCI ; NIAID ; Schroeder Allergy and Immunology Research Institute ; McMaster University ; CA ; Chan Zuckerberg Initiative ; Wellcome Trust |
Free, Freely available | https://zenodo.org/records/7693279 | SCR_025296 | Iterative Bleaching Extends Multiplexity (IBEX) Knowledge-Base | 2026-02-14 02:09:01 | 3 | ||||||||
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Retinal wave repository Resource Report Resource Website |
Retinal wave repository (RRID:SCR_010462) | Retinal wave repository | data or information resource, data set | A subset of the CARMEN repository, a curated set of data and code of multielectrode array recordings of spontaneous activity in developing mouse and ferret retina. The data have been annotated with minimal metadata and converted into HDF5 (Hierarchical data format, version 5) including the essential features of the recordings, such as developmental age, and genotype. All code and tools used in the analyses are also fully available for reuse, giving the ability to regenerate each figure and table and know exactly how the results were calculated, adding confidence in the research output and allowing others to easily build upon previous work. The addition of published data to the repository is encouraged. | hdf5, development, neural circuit, retina, eye, multielectrode, array recording, spontaneous activity, reproducible research, retinal wave, electrophysiology, multielectrode array, developmental age, genotype |
has parent organization: GigaScience has parent organization: Code Analysis Repository and Modelling for e-Neuroscience has parent organization: University of Cambridge; Cambridge; United Kingdom |
Developing retina, Aging | EPSRC EP/E002331/1; BBSRC BB/H023577/1; BBSRC BB/I000984/1; Wellcome Trust 083205/B/07/Z |
PMID:24666584 | Registration required, (CARMEN), Acknowledgement required, The community can contribute to this resource | nlx_157664 | http://www.damtp.cam.ac.uk/user/eglen/waverepo/ | SCR_010462 | A data repository and analysis framework for spontaneous neural activity recordings in developing retina | 2026-02-14 02:08:15 | 0 | |||
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HumanIslets Resource Report Resource Website 1+ mentions |
HumanIslets (RRID:SCR_025719) | data or information resource, portal, project portal | Data visualization portal for HumanIslets project. Integrated platform for human islet data access and analysis. Includes data on human islet donors, allows users to access linked datasets describing molecular profiles, islet function and donor phenotypes, and to perform various statistical and functional analyses at donor, islet and single-cell levels. Provides set of resources and tools to support metabolism and diabetes research community. | human islet data, data access and analysis, molecular profiles, islet function, donor phenotypes, metabolism, diabetes | Canadian Institutes of Health Research ; BCCHRI Child Health Integrative Partnership Strategy Funding ; NIDDK U01 DK 120447; NIDDK U01-DK-123716; NIDDK U01-DK105535; NIDDK U01-DK085545; NIDDK UM-1DK126185; Wellcome Trust ; UBC Life Sciences Institute ; Canada Foundation for Innovation ; BC Knowledge Development Fund ; Genome Canada |
PMID:38948734 | Free, Freely available | SCR_025719 | 2026-02-14 02:09:17 | 9 |
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