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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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HVSeeker Resource Report Resource Website 1+ mentions |
HVSeeker (RRID:SCR_026120) | software application, software resource | Software tool for distinguishing between bacterial and phage sequences. Consists of two separate models: one analyzing DNA sequences and the other focusing on proteins. | genome, bacteria, phage, sequence, distinguishing between bacterial and phage sequences, | German Research Foundation INST 37/935-1 FUGG; King Fahd University of Petroleum and Minerals |
Free, Available for download, Freely available, | SCR_026120 | 2026-02-15 09:24:05 | 1 | ||||||||||
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MPscan Resource Report Resource Website |
MPscan (RRID:SCR_000587) | MPscan | data access protocol, software resource, web service | Web tool for index free mapping of multiple short reads on a genome. | linux, macos, next-generation sequencing, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: ATGC: Montpellier bioinformatics platform |
Free, Available for download, Freely available | biotools:mpscan, OMICS_00670 | https://bio.tools/mpscan | SCR_000587 | MPscan: index free mapping of multiple short reads on a genome | 2026-02-16 09:45:17 | 0 | ||||||
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GDC Resource Report Resource Website 1+ mentions |
GDC (RRID:SCR_001007) | GDC | software application, data processing software, data analysis software, data management software, software resource | A C++ application designed for compression of genome collections from the same species. | compression, genome collection, c++, genome, software |
is listed by: OMICtools is hosted by: GitHub |
DOI:10.1038/srep11565 | Source code available for download | OMICS_00958 | https://github.com/refresh-bio/GDC2 | SCR_001007 | GDC 2, Genome Differential Compressor, Genome Differential Compressor (GDC) | 2026-02-16 09:45:23 | 1 | |||||
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Functional Annotation of the Mammalian Genome Resource Report Resource Website 10+ mentions |
Functional Annotation of the Mammalian Genome (RRID:SCR_000788) | FANTOM | organization portal, database, consortium, portal, data or information resource | International collaborative research project and database of annotated mammalian genome. Used to improve estimates of total number of genes and their alternative transcript isoforms in both human and mouse. Consortium to assign functional annotations to full length cDNAs that were collected during Mouse Encyclopedia Project at RIKEN. | mammal, genome, isoform, human, gene, transcriptome, regulatory network, FASEB list |
is related to: CAGE Basic Viewer for Mus musculus is related to: RIKEN integrated database of mammals has parent organization: RIKEN Brain Science Institute |
NIMH MH062261 | PMID:20211142 PMID:33211864 |
nif-0000-30552 | http://fantom.gsc.riken.jp | SCR_000788 | Functional Annotation of the Mammalian Genome, FANTOM, Functional Annotation of the Mammalian Genome (FANTOM) | 2026-02-16 09:45:20 | 43 | |||||
|
USP Molecular Genetics and Bioinformatics Laboratory Resource Report Resource Website 1+ mentions |
USP Molecular Genetics and Bioinformatics Laboratory (RRID:SCR_000605) | USP Molecular Genetics and Bioinformatics Laboratory | data or information resource, laboratory portal, organization portal, portal | Laboratory portal of the University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory. | genetics, bioinformatics, data mining, genome, gene | has parent organization: University of Sao Paulo; Sao Paulo; Brazil | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149158 | SCR_000605 | University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory, USP Laboratorio de Genetica Molecular e Bioinformatica, University of Sao Paulo Molecular Genetics and Bioinformatics Laboratory, USP Molecular Genetics Bioinformatics Laboratory, USP Molecular Genetics and Bioinformatic Laboratory | 2026-02-16 09:45:18 | 1 | |||||||
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WiggleTools Resource Report Resource Website 1+ mentions |
WiggleTools (RRID:SCR_001170) | WiggleTools | software application, data processing software, software toolkit, software library, software resource | A multithreaded software library that computes statistics on large numbers of datasets, generating statistical summaries within minutes with limited memory requirements, whether on the whole genome or on selected regions. | visualization, statistical analysis, parallel processing, genome |
is listed by: OMICtools has parent organization: European Bioinformatics Institute |
PMID:24363377 | Apache License, v2 | OMICS_02188 | SCR_001170 | 2026-02-16 09:45:25 | 1 | |||||||
|
R453Plus1Toolbox Resource Report Resource Website 1+ mentions |
R453Plus1Toolbox (RRID:SCR_001105) | software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource | R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided. | genome, sequence, visualization, structural variants, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:21349869 | Free, Available for download, Freely available | OMICS_01354 | SCR_001105 | 2026-02-16 09:45:25 | 4 | ||||||||
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Morpholino Database Resource Report Resource Website 1+ mentions |
Morpholino Database (RRID:SCR_001378) | MODB | data repository, database, storage service resource, service resource, data or information resource | Central database to house data on morpholino screens currently containing over 700 morpholinos including control and multiple morpholinos against the same target. A publicly accessible sequence-based search opens this database for morpholinos against a particular target for the zebrafish community. Morpholino Screens: They set out to identify all cotranslationally translocated genes in the zebrafish genome (Secretome/CTT-ome). Morpholinos were designed against putative secreted/CTT targets and injected into 1-4 cell stage zebrafish embryos. The embryos were observed over a 5 day period for defects in several different systems. The first screen examined 184 gene targets of which 26 demonstrated defects of interest (Pickart et al. 2006). A collaboration with the Verfaillie laboratory examined the knockdown of targets identified in a comparative microarray analysis of hematopoietic stem cells demonstrating how microarray and morpholino technologies can be used in conjunction to enrich for defects in specific developmental processes. Currently, many collaborations are underway to identify genes involved in morphological, kidney, skin, eye, pigment, vascular and hematopoietic development, lipid metabolism and more. The screen types referred to in the search functions are the specific areas of development that were examined during the various screens, which include behavior, general morphology, pigmentation, toxicity, Pax2 expression, and development of the craniofacial structures, eyes, kidneys, pituitary, and skin. Only data pertaining to specific tests performed are presented. Due to the complexity of this international collaboration and time constraints, not all morpholinos were subjected to all screen types. They are currently expanding public access to the database. In the future we will provide: * Mortality curves and dose range for each morpholino * Preliminary data regarding the effectiveness of each morpholino * Expanded annotation for each morpholino * External linkage of our morpholino sequences to ZFIN and Ensembl. To submit morpholino-knockdown results to MODB please contact the administrator for a user name and password. | morpholino, target mrna, embryonic zebrafish, sequence, target, blast, phenotype, anatomy, development, behavior, morphology, pigmentation, toxicity, pax2 expression, craniofacial structure, eye, kidney, pituitary, skin, name, target name, target sequence, gene target, genetic, mortality, toxicity, defect, function, gene annotation, genome, data analysis service |
uses: Zebrafish Information Network (ZFIN) uses: PATO has parent organization: Mayo Clinic Minnesota; Minnesota; USA |
NIGMS GM63904; NIA CA65493 |
PMID:18179718 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152566 | SCR_001378 | MODB (MOprholino DataBase) | 2026-02-16 09:45:28 | 1 | |||||
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AutoAssemblyD Resource Report Resource Website |
AutoAssemblyD (RRID:SCR_001087) | software application, data processing software, sequence analysis software, data analysis software, software resource | Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers. | genome, genome assembly, xml, sequence analysis software, local genome assembly, remote genome assembly, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24143057 | Free, Available for download, Freely available | biotools:autoassemblyd, OMICS_00874 | https://bio.tools/autoassemblyd | SCR_001087 | 2026-02-16 09:45:25 | 0 | |||||||
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Kyoto Encyclopedia of Genes and Genomes Expression Database Resource Report Resource Website 1000+ mentions |
Kyoto Encyclopedia of Genes and Genomes Expression Database (RRID:SCR_001120) | KEGG Expression Database | data repository, database, storage service resource, service resource, data or information resource | Database for mapping gene expression profiles to pathways and genomes. Repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community. | encyclopedia, endogenous, environment, enzyme, escherichia coli, exogenous, expression, family, functional, gene, genetic, anabaena, bacillus subtilis, biological system, biology, building block, cell, cellular, chemical, community, complex, genome, genomic, hierarchy, interaction, japanese, mapping, metabolic, metabolic pathway databases, microarray, molecular, molecular wiring, nomenclature, order, organism, ortholog, pathway, process, protein, reaction, research, sequence, specie, substance, synechocystis, FASEB list |
is listed by: LabWorm is affiliated with: KEGG has parent organization: Kyoto University; Kyoto; Japan |
PMID:9847135 PMID:10592173 |
Free, Available for download, Freely available | r3d100011570, nif-0000-21234 | https://doi.org/10.17616/R3792T | SCR_001120 | Kyoto Encyclopedia of Genes and Genomes Expression Database | 2026-02-16 09:45:25 | 1274 | |||||
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Globin Gene Server Resource Report Resource Website 10+ mentions |
Globin Gene Server (RRID:SCR_001480) | Globin Gene Server | narrative resource, training material, data analysis service, analysis service resource, resource, database, software resource, source code, production service resource, service resource, data or information resource | Data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences with one another to discover regions that are likely to play significant roles. | dna sequence, hemoglobin, mutation, globin gene cluster, sequence comparison, functional genomics, gene, alignment, genetic analysis, variant, gene expression, protein, thalassemia, globin gene, genome, pairwise alignment, multiple alignment, annotation, sequence analysis, dna |
is listed by: NIDDK Information Network (dkNET) has parent organization: Pennsylvania State University |
NLM R01LM05773; NLM R01LM05110; NIDDK DK27635 |
PMID:11857738 PMID:11480780 PMID:9799599 PMID:9576329 PMID:8088828 |
Free, Freely available | nlx_152723 | SCR_001480 | 2026-02-16 09:45:29 | 27 | ||||||
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Mugsy Resource Report Resource Website 50+ mentions |
Mugsy (RRID:SCR_001414) | software application, data processing software, sequence analysis software, data analysis software, software resource | Software resource for multiple whole genome alignment. It uses Nucmer, a custom graph-based segmentation procedure, for pairwise alignment, and the Seqan:TCoffee's multiple alignment strategy. | software, genome, genome alignment, segmentation, pairwise alignment, sequence analysis software |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:21148543 DOI:10.1093/bioinformatics/btq665 |
Free, Available for download, Freely available | OMICS_03606 | https://sources.debian.org/src/mugsy/ | SCR_001414 | 2026-02-16 09:45:28 | 71 | |||||||
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Ensembl Variation Resource Report Resource Website 1+ mentions |
Ensembl Variation (RRID:SCR_001630) | Ensembl Variation | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | Public database that stores areas of genome that differ between individual genomes (variants) and, where available, associated disease and phenotype information. Different types of variants for several species: single nucleotide polymorphisms (SNPs), short nucleotide insertions and/or deletions, and longer variants classified as structural variants (including CNVs). Effects of variants on the Ensembl transcripts and regulatory features for each species are predicted. You can run same analysis on your own data using Variant Effect Predictor. These data are integrated with other data sources in Ensembl, and can be accessed using the API or website. For several different species in Ensembl, they import variation data (SNPs, CNVs, allele frequencies, genotypes, etc) from a variety of sources (e.g. dbSNP). Imported variants and alleles are subjected to quality control process to flag suspect data. In human, they calculate linkage disequilibrium for each variant, by population. | genome, disease, phenotype, genomic variant, single nucleotide polymorphism nucleotide, insertion, deletion, structural variant, copy number variation, inversion, translocation, somatic variant, allele frequency, genotype, disease phenotype, inherited disease |
is used by: MONARCH Initiative is related to: dbSNP is related to: Database of Genomic Variants Archive (DGVa) is related to: PubMed is related to: Animal QTLdb is related to: OMIA - Online Mendelian Inheritance in Animals has parent organization: Ensembl |
PMID:23203987 PMID:20562413 PMID:20459810 PMID:20459805 |
Free, Available for download, Freely available | nlx_153897 | SCR_001630 | ensembl variation | 2026-02-16 09:45:32 | 4 | ||||||
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BLASTN Resource Report Resource Website 10000+ mentions |
BLASTN (RRID:SCR_001598) | BLASTn | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | Web application to search nucleotide databases using a nucleotide query. Algorithms: blastn, megablast, discontiguous megablast. | nucleotide, alignment, compare, sequence, genome, blast, transcript, dna sequence |
is listed by: OMICtools is listed by: SoftCite has parent organization: NCBI works with: Seek and Blastn works with: RMBlast |
PMID:17666756 PMID:18567917 |
Free, Freely available | nlx_153932, OMICS_00990 | http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome | SCR_001598 | NCBI BLASTN, Nucleotide Blast, Standard Nucleotide BLAST | 2026-02-16 09:45:32 | 19679 | |||||
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Ancora Resource Report Resource Website 10+ mentions |
Ancora (RRID:SCR_001623) | Ancora | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | Web resource that provides data and tools for exploring genomic organization of highly conserved noncoding elements (HCNEs) for multiple genomes. It includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains. They identify HCNEs as non-exonic regions of high similarity between genome sequences from distantly related organisms, such as human and fish, and provide tools for studying the distribution of HCNEs along chromosomes. Major peaks of HCNE density along chromosomes most often coincide with developmental regulatory genes. Their aim with this site is to aid discovery of developmental regulatory genes, their regulatory domains and their fundamental regulatory elements. | genome, highly conserved noncoding element, noncoding element, regulatory gene, regulatory domain, regulatory element, developmental regulatory gene, evolution, enhancer |
is related to: MONARCH Initiative has parent organization: University of Bergen; Bergen; Norway |
Research Council of Norway ; Bergen Research Foundation ; Sars Centre |
PMID:18279518 | Free, Freely available | nlx_153891 | SCR_001623 | Atlas of Noncoding Conserved Regions in Animals | 2026-02-16 09:45:32 | 19 | |||||
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PhenoGen Informatics Resource Report Resource Website 10+ mentions |
PhenoGen Informatics (RRID:SCR_001613) | PhenoGen | application programming interface, data set, data analysis service, analysis service resource, data access protocol, data repository, software resource, storage service resource, source code, production service resource, service resource, data or information resource | Website for analyzing microarray data. Software toolbox for storing, analyzing and integrating microarray data and related genotype and phenotype data. The site is particularly suited for combining QTL and microarray data to search for candidate genes contributing to complex traits. In addition, the site allows, if desired by the investigators, sharing of the data. Investigators can conduct in-silico microarray experiments using their own and/or shared data. There are five major sections of the site: Genome/Transcriptome Data Browser, Microarray Analysis Tools, Gene List Analysis Tools, QTL Tools, and Downloads. The genome/transcriptome data browser combines a genome browser with all the microarray, RNA-Seq, and Genomic Sequencing data. This provides an effective platform to view all of this data side by side. Source code is available on GitHub. | genome, transcription, microarray, gene, quantitative trait loci, analysis, complex trait, genotype, phenotype, high-throughput, rna-seq, snp, genomic marker, region, data sharing, normalize, statistics, gene list, pathway, expression value, expression, correlation, exon, annotation, promoter, homolog, brain, heart, liver, adipose, candidate gene, genetics, transcriptome, eqtl, genome browser, inbred panel |
is related to: MONARCH Initiative has parent organization: University of Colorado Denver; Colorado; USA |
NIAAA R24 AA013162; NIAAA R01 AA13162; NIAAA U01 AA013524 |
PMID:17760997 | Free, Freely available | rid_000093, nlx_153879, r3d100011596 | https://github.com/TabakoffLab/PhenogenCloud https://doi.org/10.17616/R3WS7F |
http://phenogen.ucdenver.edu, http://phenogen.uchsc.edu | SCR_001613 | PhenoGen Informatics - The site for quantitative genetics of the transcriptome. | 2026-02-16 09:45:32 | 22 | |||
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North American Conditional Mouse Mutagenesis Project Resource Report Resource Website 1+ mentions |
North American Conditional Mouse Mutagenesis Project (RRID:SCR_001614) | NorCOMM | production service resource, material service resource, biomaterial manufacture, service resource | Large-scale research initiative focused on developing and distributing a library of mouse embryonic stem (ES) cell lines carrying single gene trapped or targeted mutations across the mouse genome. NorCOMM's large and growing archive of ES cells is publicly available on a cost-recovery basis from the Canadian Mouse Mutant Repository. As an international public resource, access to clones is unrestricted and nonexclusive. Through NorCOMM's affiliation with the Canadian Mouse Consortium (CMC), NorCOMM also provides clients with a single point of access to regional mouse derivation, phenotyping, genetic and archiving services across Canada. These value-added services can help your company harness NorCOMM's resources for drug discovery, target discovery and preclinical validation. | gene, target, embryonic stem cell line, gene trap, targeted mutation, mouse genome, mutation, genome, derivation, phenotype, genetic, archive, phenotyping, archiving, gene target, clone |
is related to: CMMR - Canadian Mouse Mutant Repository is related to: CMMR - Canadian Mouse Mutant Repository has parent organization: International Knockout Mouse Consortium |
Genome Canada | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153880 | SCR_001614 | 2026-02-16 09:45:32 | 4 | |||||||
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Sea Urchin Genome Project Resource Report Resource Website 1+ mentions |
Sea Urchin Genome Project (RRID:SCR_001735) | data or information resource, project portal, portal | Provides informationa about Genome of California Purple Sea Urchin, one species (Strongylocentrotus purpuratus) of which has been sequenced and annotated by Sea Urchin Genome Sequencing Consortium led by HGSC. Reports sequence and analysis of genome of sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. | echinoderm, evolutionary, fragile urchin, gene, genome, allocentrotus fragilis, bacterial artificial chromosome (bac), biology, chromosome, clone, core facility, deuterostome, developmental biology, heterozygosity, metabase, model, sea urchin, sequence, shotgun, strongylocentrotus franciscanus, strongylocentrotus purpuratus, systems biology, vertebrate | has parent organization: Baylor University; Texas; USA | Free, Freely Available | nif-0000-25606, SCR_002841, nif-0000-10253 | http://www.hgsc.bcm.tmc.edu/project-species-o-Strongylocentrotus%20purpuratus.hgsc?pageLocation=Strongylocentrotus%20purpuratus | SCR_001735 | Sea Urchin, HGSC Sea Urchin Genome Project | 2026-02-16 09:45:34 | 1 | |||||||
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Animal QTLdb Resource Report Resource Website 50+ mentions |
Animal QTLdb (RRID:SCR_001748) | Animal QTLdb | data repository, database, storage service resource, service resource, data or information resource | Database of trait mapping data, i.e. QTL (phenotype / expression, eQTL), candidate gene and association data (GWAS) and copy number variations (CNV) mapped to livestock animal genomes, to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features, such as annotated genes. QTLdb is open to house QTL/association date from other animal species where feasible. Most scientific journals require that any original QTL/association data be deposited into public databases before paper may be accepted for publication. User curator accounts are provided for direct data deposit. Users can download QTLdb data from each species or individual chromosome. | chromosome, comparative genomics, dna sequence, genome, livestock, quantitative trait locus, non-human animal, structural genomics, single-nucleotide polymorphism, gene association, genomics, trait, copy number variation, trait, phenotype, expression, eqtl, genome wide association study, candidate gene, genotype |
uses: Entrez Gene uses: Ensembl is used by: NIF Data Federation is used by: MONARCH Initiative is listed by: re3data.org is related to: Ensembl Variation is related to: Vertebrate Trait Ontology has parent organization: Iowa State University; Iowa; USA has parent organization: NAGRP Bioinformatics Coordination Program |
USDA NRSP-8; USDA 2007-04187 |
PMID:23180796 PMID:17245610 |
Free, Freely available | nif-0000-02550 | http://www.animalgenome.org/QTLdb/ | SCR_001748 | Animal QTL database, Animal Quantitative Trait Loci database, AnimalQTLdb, Animal Quantitative Trait Loci (QTL) database | 2026-02-16 09:45:34 | 50 | ||||
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South African National Bioinformatics Institute: Resources Resource Report Resource Website |
South African National Bioinformatics Institute: Resources (RRID:SCR_001867) | software application, data processing software, data analysis software, organization portal, software resource, database, portal, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. The South African National Bioinformatics Institute delivers biomedical discovery appropriate to both international and African context. Researchers at SANBI perform the highest level of research and provide excellence in education. Research at SANBI has set well recognized milestones in the field of computational biology. The tools and techniques used have not only been developed but also implemented across heterogeneous domains of advanced research. Local and international efforts have driven our discoveries. Until recently, the core of SANBIs research has focused upon gene expression biology. Methods developed and applied at SANBI revolve around a greater understanding of the underlying causes of diseases. SANBI approaches the problem by comparison of genes, genomes and transcriptomes. It uses computational gene expression biology to create novel biological insights and to provide biomarkers for experimental validation. It also performs analysis of human genome variation, transcriptional diversity on both the expression and splicing level and the unravelling of transcriptional regulatory networks. Resources - Hinv, STACKdb, Malaria resources and Trypanosome databases are available for on-line seaching. - SANBI offers WCD, STACKdb, stackPACK and eVOC and the eVOKE viewer as tools that can be downloaded. Sponsors: SANBI receives funding and support from a range of organisations in South Africa and Internationally. Organisations currently supporting SANBI include: South Africa * South African Medical Research Council * South African AIDS Vaccine Initiative * National Bioinformatics Network * National Research Foundation * Claude Leon Foundation * International Business Machines Inc. Europe * European Unions 6th Framework Programme * World Health Organization USA * US National Institutes of Health * Fogarty International Centre * Ludwig Institute for Cancer Research | expression, gene, gene expression, bioinformatics, biological, biology, biomaker, biomedical, computational biology, disease, genome, heterogeneous domain, human, splicing, transcriptional diversity, transcriptional regulatory network, transcriptome, variation | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10432 | SCR_001867 | SANBI | 2026-02-16 09:45:36 | 0 |
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