Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Human Disease Ontology Resource Report Resource Website 1+ mentions |
Human Disease Ontology (RRID:SCR_000476) | DO | data or information resource, ontology, controlled vocabulary, database | Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases. | obo, pathological, organismal, cellular, disease, biomedical, health, neurologic disease, neurological disorder, phenotype, bio.tools, |
is used by: DOAF is listed by: BioPortal is listed by: OBO is listed by: bio.tools is listed by: Debian is related to: PharmGKB Ontology is related to: GWASdb is related to: NUgene Project is related to: FunDO is related to: Neurocarta has parent organization: University of Maryland School of Medicine; Maryland; USA |
NHGRI U24 HG012557 | PMID:22080554 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-35926, nlx_157432, SCR_003491, biotools:disease_ontology | http://disease-ontology.org/ https://bio.tools/disease_ontology http://purl.obolibrary.org/obo/doid.obo |
http://do-wiki.nubic.northwestern.edu/index.php/Main_Page | SCR_000476 | Human Disease Ontology Knowledgebase, Disease Ontology | 2026-02-14 01:59:45 | 5 | |||
|
SiPhy Resource Report Resource Website 1+ mentions |
SiPhy (RRID:SCR_000564) | SiPhy | sequence analysis resource | Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions. | java, mutation, phylogeny, substitution pattern, mutation rate |
is listed by: OMICtools has parent organization: Broad Institute |
NHGRI ; NSF |
PMID:19478016 | Free, Available for download, Freely available, | OMICS_00183 | SCR_000564 | 2026-02-14 01:59:46 | 6 | ||||||
|
forqs Resource Report Resource Website |
forqs (RRID:SCR_000643) | forqs | software resource, simulation software, software application | Software for forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. It also also models quantitative traits and selection on those traits. | c++, linux, osx, windows, command line, simulation, recombination, quantitative trait, selection, haplotype pattern |
is listed by: OMICtools has parent organization: University of California at Los Angeles; California; USA has parent organization: Bitbucket |
NHGRI HG002536; NHGRI R01 HG007089; NSF EF-0928690 |
PMID:24336146 | Free, Available for download, Freely available | OMICS_02196 | SCR_000643 | Forward-in-time simulation of Recombination, and Selection, Quantitative traits | 2026-02-14 01:59:46 | 0 | |||||
|
STAR Resource Report Resource Website 10000+ mentions |
STAR (RRID:SCR_004463) | data processing software, alignment software, software application, software resource, image analysis software | Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays. | RNA-seq data, alignment, RNA-seq reads alignment, reference genome, using uncompressed suffix arrays, bio.tools |
is used by: STARsolo is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
NHGRI U54 HG004557 | PMID:23104886 DOI:10.1093/bioinformatics/bts635 |
biotools:star, OMICS_01254, SCR_015899 | https://github.com/alexdobin/STAR https://bio.tools/star https://sources.debian.org/src/rna-star/ |
SCR_004463 | Spliced Transcripts Alignment to Reference, Spliced Transcripts Alignment to a Reference (STAR), rna-star, ultrafast universal RNA-seq aligner | 2026-02-14 02:00:44 | 22809 | ||||||
|
Gene Ontology Resource Report Resource Website 10000+ mentions |
Gene Ontology (RRID:SCR_002811) | GO | knowledge environment resource, portal, consortium, data or information resource, organization portal, project portal | Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases. | gene, product, annotation, molecular, function, cellular, biological, role, database, query, obo, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: GreenPhylDB is used by: LIPID MAPS Proteome Database is used by: Aging Portal is used by: ChannelPedia is used by: Open PHACTS is used by: CoPub is used by: PhenoGO is used by: Database for Annotation Visualization and Integrated Discovery is used by: MitoMiner is used by: dcGO is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: barleyGO is used by: SynGO is used by: Functional Annotation is used by: SwissLipids is listed by: BioPortal is listed by: OBO is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: Mouse Genome Informatics: The Gene Ontology Project is related to: GenNav is related to: SynaptomeDB is related to: High-Throughput GoMiner is related to: Onto-Design is related to: OnEx - Ontology Evolution Explorer is related to: Avadis is related to: GONUTS is related to: PiNGO is related to: Automated Microarray Pipeline is related to: categoryCompare is related to: globaltest is related to: Semantic Measures Library is related to: WegoLoc is related to: AnimalTFDB is related to: MEME Suite - Motif-based sequence analysis tools is related to: Arabidopsis Hormone Database is related to: DAVID is related to: Arabidopsis thaliana Protein Interactome Database is related to: TM4 Microarray Software Suite - TIGR MultiExperiment Viewer is related to: pSTIING is related to: GoMiner is related to: FunSimMat is related to: GeneSpeed- A Database of Unigene Domain Organization is related to: Centre for Modeling Human Disease Gene Trap Resource is related to: Patterns of Gene Expression in Drosophila Embryogenesis is related to: Babelomics is related to: BioPerl is related to: GeneCruiser is related to: GOLEM An interactive, graphical gene-ontology visualization, navigation, and analysis tool is related to: GOToolBox Functional Investigation of Gene Datasets is related to: Cotton EST Database is related to: MouseNET is related to: PLANTTFDB is related to: T-profiler is related to: Physico-Chemical Process is related to: Integrated Molecular Interaction Database is related to: SEGS is related to: GOCat is related to: Quantitative Enrichment of Sequence Tags is related to: Neural-Immune Gene Ontology is related to: INMEX is related to: StRAnGER is related to: QuickGO is related to: Repository of molecular brain neoplasia data is related to: Cardiovascular Gene Ontology Annotation Initiative is related to: PANTHER is related to: Short Time-series Expression Miner (STEM) is related to: DATFAP is related to: GORetriever is related to: Gene Ontology Browsing Utility (GOBU) is related to: GeneTools is related to: GOSlimViewer is related to: go-moose is related to: Network Ontology Analysis is related to: Onto-Compare is related to: Onto-Express is related to: OntoVisT is related to: STRAP is related to: CGAP GO Browser is related to: COBrA is related to: Gene Class Expression is related to: GeneInfoViz is related to: GOfetcher is related to: GoFish is related to: GOProfiler is related to: GOanna is related to: Manatee is related to: Pandora - Protein ANnotation Diagram ORiented Analysis is related to: TAIR Keyword Browser is related to: Wandora is related to: GOTaxExplorer is related to: Onto-Miner is related to: Onto-Translate is related to: ToppGene Suite is related to: DBD - Slim Gene Ontology is related to: ONTO-PERL is related to: Blip: Biomedical Logic Programming is related to: OWL API is related to: CLENCH is related to: BiNGO: A Biological Networks Gene Ontology tool is related to: CateGOrizer is related to: FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products is related to: ProteInOn is related to: GeneMerge is related to: GraphWeb is related to: ClueGO is related to: CLASSIFI - Cluster Assignment for Biological Inference is related to: GOHyperGAll is related to: FuncAssociate: The Gene Set Functionator is related to: GOdist is related to: FuncExpression is related to: FunCluster is related to: FIVA - Functional Information Viewer and Analyzer is related to: GARBAN is related to: GOEx - Gene Ontology Explorer is related to: SGD Gene Ontology Slim Mapper is related to: GOArray is related to: SNPsandGO is related to: GoSurfer is related to: GOtcha is related to: MAPPFinder is related to: GoAnnotator is related to: MetaGeneProfiler is related to: OntoGate is related to: ProfCom - Profiling of complex functionality is related to: SerbGO is related to: SOURCE is related to: Ontologizer is related to: THEA - Tools for High-throughput Experiments Analysis is related to: Generic GO Term Mapper is related to: GREAT: Genomic Regions Enrichment of Annotations Tool is related to: GoBean - a Java application for Gene Ontology enrichment analysis is related to: TXTGate is related to: GO-Module is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures is related to: G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools is related to: MalaCards is related to: FSST - Functional Similarity Search Tool is related to: Expression Profiler is related to: GOChase is related to: GoPubMed is related to: Whatizit is related to: REViGO is related to: WEGO - Web Gene Ontology Annotation Plot is related to: Blast2GO is related to: InterProScan is related to: PubSearch is related to: TrED is related to: CharProtDB: Characterized Protein Database is related to: VirHostNet: Virus-Host Network is related to: Pathbase is related to: GO Online SQL Environment (GOOSE) is related to: Neurobehavior Ontology is related to: InterSpecies Analysing Application using Containers is related to: KOBAS is related to: ConceptWiki is related to: GeneTerm Linker is related to: Bioconductor is related to: ErmineJ is related to: Gene Ontology For Functional Analysis (GOFFA) is related to: MGI GO Browser is related to: Comparative Toxicogenomics Database (CTD) is related to: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit is related to: Ontology Lookup Service is related to: LexGrid is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: g:Profiler is related to: OwlSim is related to: GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool is related to: YeTFaSCo is related to: FastSemSim is related to: RamiGO is related to: AutismKB is related to: GeneCodis is related to: FunSpec is related to: FunNet - Transcriptional Networks Analysis is related to: PhenoM - Phenomics of yeast Mutants is related to: agriGO is related to: GOblet is related to: DynGO is related to: SeqExpress is related to: ProbeExplorer is related to: ECgene: Gene Modeling with Alternative Splicing is related to: Organelle DB is related to: Gemma is related to: Candidate Genes to Inherited Diseases is related to: Proteome Analyst PA-GOSUB is related to: Network Analysis, Visualization and Graphing TORonto is related to: GOstat is related to: Onto-Express To Go (OE2GO) is related to: Tk-GO is related to: EGAN: Exploratory Gene Association Networks is related to: Spotfire is related to: GOMO - Gene Ontology for Motifs is related to: GFINDer: Genome Function INtegrated Discoverer is related to: Generic GO Term Finder is related to: Agile Protein Interactomes DataServer is related to: AgingDB is related to: UBERON is related to: Algal Functional Annotation Tool is related to: gsGator is related to: Flash Gviewer is related to: Cerebellar Development Transcriptome Database is related to: PlantNATsDB - Plant Natural Antisense Transcripts DataBase is related to: EASE: the Expression Analysis Systematic Explorer is related to: PiGenome is related to: L2L Microarray Analysis Tool is related to: MeGO is related to: CELDA Ontology is related to: Diabetes Disease Portal is related to: MatrixDB is related to: Kidney and Urinary Pathway Knowledge Base is related to: MouseCyc is related to: Candida Genome Database is related to: Honey Bee Brain EST Project is related to: ECO is related to: FlyMine is related to: Gramene is related to: 3D-Interologs is related to: Biomine is related to: UniProtKB is related to: NCBI BioSystems Database is related to: EBIMed is related to: Coremine Medical is related to: EMAGE Gene Expression Database is related to: GeneMANIA is related to: Yeast Search for Transcriptional Regulators And Consensus Tracking is related to: GeneTrail is related to: Magic is related to: Mouse Genome Informatics (MGI) is related to: FlyBase is related to: InterPro is related to: InnateDB is related to: canSAR is related to: HPRD - Human Protein Reference Database is related to: CRCView is related to: Integrated Manually Extracted Annotation is related to: LegumeIP is related to: Renal Disease Portal is related to: PhenoGO is related to: DOAF is related to: OBO is related to: biomaRt is related to: OncoboxPD is parent organization of: AmiGO is parent organization of: GOlr is parent organization of: RefGenome is parent organization of: OBO-Edit is parent organization of: OWLTools is parent organization of: Gene Ontology Tools is parent organization of: Gene Ontology Extension is parent organization of: SO is parent organization of: go-db-perl is parent organization of: go-perl works with: topGO works with: DIANA-mirPath works with: GOnet |
European Union QLRI-CT-2001-0098; European Union QLRI-CT-2001-00015; NHGRI P41 HG002273 |
PMID:23161678 PMID:10802651 |
Free, Freely available, Available for download | biotools:go, OMICS_02278, nif-0000-02915 | http://bioportal.bioontology.org/ontologies/GO https://bio.tools/go |
SCR_002811 | the Gene Ontology, GO, Gene Ontology Resource, Gene Ontology | 2026-02-14 02:00:32 | 10623 | ||||
|
ArrayExpress Resource Report Resource Website 5000+ mentions |
ArrayExpress (RRID:SCR_002964) | ArrayExpress | data repository, storage service resource, catalog, data or information resource, service resource, database | International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus. | gold, standard, functional, genomics, data, collection, microarray, next, generation, sequencing, NGS, repository |
uses: MIAME uses: MINSEQE uses: Gene Expression Omnibus is used by: NIF Data Federation is used by: BioSample Database at EBI is used by: Integrated Datasets is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: OMICtools is listed by: re3data.org is related to: DDBJ Omics Archive is related to: MIAME is related to: Gene Expression Atlas is related to: Experimental Factor Ontology is related to: Bgee: dataBase for Gene Expression Evolution is related to: ISA Infrastructure for Managing Experimental Metadata is related to: FlyMine is related to: MAGE-TAB is related to: Experimental Factor Ontology is related to: Magic is related to: ArrayExpress (R) is related to: CancerMIRNome has parent organization: European Bioinformatics Institute |
European Union ; SLING 226073; European Commission ; Gen2Phen 200754; NHGRI P41 HG003619 |
PMID:23193272 PMID:21071405 |
Available Public or Private, Free, Available for download, The community can contribute to this resource, Acknowledgement requested, to access private data registration required | OMICS_01023, nif-0000-30123, r3d100010222 | http://www.ebi.ac.uk/microarray-as/ae https://doi.org/10.17616/R3302G |
SCR_002964 | , ArrayExpress, ArrayExpress - functional genomics data, ArrayExpress Archive | 2026-02-14 02:00:28 | 7529 | ||||
|
SNPHunter Resource Report Resource Website |
SNPHunter (RRID:SCR_002968) | sequence analysis software, data processing software, resource, data analysis software, software application, software resource | A tool for SNP Search and downloading with local management. It also offers flanking sequence downloading and automatic SNP filtering. It requires Windows and .NET Framework. | population, genetics, software, management, single nucleotide polymorphism, population genetics, training tools, data acquisition |
is listed by: 3DVC has parent organization: Harvard University; Cambridge; United States |
NIH ; NHGRI R01HG002518; NIDDK R01DK062290; NIDDK R01DK066401; NHLBI R01HL073882 |
DOI:10.1186/1471-2105-6-60 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30137 | http://www.hsph.harvard.edu/ppg/software.htm | SCR_002968 | SNPHunter - dbSNP Search & Management, Program for Population Genetics Software | 2026-02-14 02:00:21 | 0 | |||||
|
Lowes Syndrome Mutation Database Resource Report Resource Website 1+ mentions |
Lowes Syndrome Mutation Database (RRID:SCR_002907) | data repository, storage service resource, data or information resource, service resource, database | The Lowe Syndrome Mutation Database is now being maintained by the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. A database of mutations causing Lowe syndrome. Information on new mutations may be submitted online. Lowe oculocerebrorenal syndrome is an X-linked disorder caused by mutations in the OCRL1 gene, which encodes a 105-kDa Golgi protein with phosphatidylinositol (4,5) bisphosphate 5-phosphatase activity. genetics | mutation | has parent organization: NCBI | Lowe syndrome | NHGRI | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00155 | http://research.nhgri.nih.gov/lowe/ | SCR_002907 | Lowe Syndrome Mutation Database | 2026-02-14 02:00:34 | 1 | |||||
|
Patterns of Gene Expression in Drosophila Embryogenesis Resource Report Resource Website 50+ mentions |
Patterns of Gene Expression in Drosophila Embryogenesis (RRID:SCR_002868) | BDGP insitu | image collection, data or information resource, source code, software resource, database | Database of embryonic expression patterns using a high throughput RNA in situ hybridization of the protein-coding genes identified in the Drosophila melanogaster genome with images and controlled vocabulary annotations. At the end of production pipeline gene expression patterns are documented by taking a large number of digital images of individual embryos. The quality and identity of the captured image data are verified by independently derived microarray time-course analysis of gene expression using Affymetrix GeneChip technology. Gene expression patterns are annotated with controlled vocabulary for developmental anatomy of Drosophila embryogenesis. Image, microarray and annotation data are stored in a modified version of Gene Ontology database and the entire dataset is available on the web in browsable and searchable form or MySQL dump can be downloaded. So far, they have examined expression of 7507 genes and documented them with 111184 digital photographs. | embryo, embryogenesis, gene, anatomy, microarray, pattern, protocol, rna, gene expression, expression pattern, embryonic drosophila, in situ hybridization, annotation, est, FASEB list |
is related to: Gene Ontology has parent organization: Berkeley Drosophila Genome Project |
Howard Hughes Medical Institute ; NIH ; NIGMS R01 GM076655; NHGRI HG00750; NHGRI P41 HG00739 |
PMID:17645804 PMID:12537577 |
Free, Freely available, Available for download | nif-0000-25550, r3d100011327 | https://doi.org/10.17616/R32H0K | http://www.fruitfly.org/cgi-bin/ex/insitu.pl | SCR_002868 | BDGP Embryonic Expression Patterns | 2026-02-14 02:00:34 | 64 | |||
|
Primer3Plus Resource Report Resource Website 1000+ mentions |
Primer3Plus (RRID:SCR_003081) | Primer3Plus | data analysis service, analysis service resource, production service resource, source code, service resource, software resource | A web interface to the Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. | primer, dna sequence, primer design, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Primer3 has parent organization: Wageningen University and Research Centre; Gelderland; Netherlands |
Howard Hughes Medical Institute ; NHGRI R01-HG00257; NHGRI P50-HG00098 |
PMID:17485472 | Free, Freely available | biotools:primer3plus, OMICS_02347 | https://bio.tools/primer3plus | SCR_003081 | Primer3Plus - pick primers from a DNA sequence | 2026-02-14 02:00:29 | 1673 | ||||
|
LUMPY Resource Report Resource Website 100+ mentions |
LUMPY (RRID:SCR_003253) | data processing software, data analysis software, software application, software resource, simulation software, standalone software | Software package as probabilistic framework for structural variant discovery. Capable of integrating any number of SV detection signals including those generated from read alignments or prior evidence. Simplified wrapper for standard analyses, LUMPY Express, can also be executed. | probabilistic, framework, structural, variant, discovery |
is listed by: OMICtools is listed by: Debian has parent organization: University of Virginia; Virginia; USA |
NHGRI R01 HG006693; NIH Office of the Director DP2 OD006493; Burroughs Wellcome Fund Career Award |
PMID:24970577 | Free, Available for download, Freely available | OMICS_04674 | https://sources.debian.org/src/lumpy-sv/ | SCR_003253 | lumpy-sv, LUMPY Express | 2026-02-14 02:00:24 | 447 | |||||
|
Primer3 Resource Report Resource Website 10000+ mentions |
Primer3 (RRID:SCR_003139) | Primer3 | data analysis service, analysis service resource, production service resource, service resource, software resource | Tool used to design PCR primers from DNA sequence - often in high-throughput genomics applications. It does everything from mispriming libraries to sequence quality data to the generation of internal oligos. | primer, primer design, polymerase chain reaction, pcr primer, dna sequence, c, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Primer3Plus is related to: Primer-BLAST has parent organization: University of Tartu; Tartu; Estonia |
NHGRI R01-HG00257; NHGRI P50-HG00098 |
PMID:22730293 PMID:17379693 DOI:10.1385/1-59259-192-2:365 DOI:10.1385/1-59259-192-2:365 |
Free, Freely available | nlx_156833, OMICS_02325, biotools:primer3 | http://bioinfo.ut.ee/primer3-0.4.0/ http://sourceforge.net/projects/primer3/ http://frodo.wi.mit.edu/primer3 https://bio.tools/primer3 https://sources.debian.org/src/primer3/ https://sources.debian.org/src/primer3/ |
SCR_003139 | Primer3web - Pick primers from a DNA sequence, Primer3 - PCR primer design tool, Primer3web | 2026-02-14 02:00:41 | 10957 | ||||
|
Talking Glossary of Genetic Terms Resource Report Resource Website |
Talking Glossary of Genetic Terms (RRID:SCR_003215) | Talking Glossary | data or information resource, narrative resource, training material, database | Glossary of Genetic Terms to help everyone understand the terms and concepts used in genetic research. In addition to definitions, specialists in the field of genetics share their descriptions of terms, and many terms include images, animation and links to related terms. | glossary, image, genetic, gene, education |
is listed by: OMICtools has parent organization: National Human Genome Research Institute |
NHGRI | The community can contribute to this resource | nlx_156942, OMICS_01555 | SCR_003215 | NHGRI Talking Glossary, NHGRI Talking Glossary of Genetic Terms | 2026-02-14 02:00:24 | 0 | ||||||
|
Mouse Phenome Database (MPD) Resource Report Resource Website 100+ mentions |
Mouse Phenome Database (MPD) (RRID:SCR_003212) | MPD | experimental protocol, data repository, storage service resource, data or information resource, service resource, narrative resource, database | Database enables integration of genomic and phenomic data by providing access to primary experimental data, data collection protocols and analysis tools. Data represent behavioral, morphological and physiological disease-related characteristics in naive mice and those exposed to drugs, environmental agents or other treatments. Collaborative standardized collection of measured data on laboratory mouse strains to characterize them in order to facilitate translational discoveries and to assist in selection of strains for experimental studies. Includes baseline phenotype data sets as well as studies of drug, diet, disease and aging effect., protocols, projects and publications, and SNP, variation and gene expression studies. Provides tools for online analysis. Data sets are voluntarily contributed by researchers from variety of institutions and settings, or retrieved by MPD staff from open public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys. MPD collects data on classical inbred strains as well as any fixed-genotype strains and derivatives that are openly acquirable by the research community. New panels include Collaborative Cross (CC) lines and Diversity Outbred (DO) populations. Phenotype data include measurements of behavior, hematology, bone mineral density, cholesterol levels, endocrine function, aging processes, addiction, neurosensory functions, and other biomedically relevant areas. Genotype data are primarily in the form of single-nucleotide polymorphisms (SNPs). MPD curates data into a common framework by standardizing mouse strain nomenclature, standardizing units (SI where feasible), evaluating data (completeness, statistical power, quality), categorizing phenotype data and linking to ontologies, conforming to internal style guides for titles, tags, and descriptions, and creating comprehensive protocol documentation including environmental parameters of the test animals. These elements are critical for experimental reproducibility. | female, genomic location, genotype, inbred strain, male, mouse strain, phenome, phenotype, qtl, reference data, single-nucleotide polymorphism, strain allele, strain characteristic, strain, trait, gene expression, variation, hypothesis testing, data set, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: Integrated Datasets is used by: NIH Heal Project is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Special Mouse Strains Resource is related to: Vertebrate Trait Ontology is related to: GenomeMUSter has parent organization: Jackson Laboratory |
NIDA ; NHGRI HG003057; NHLBI HL66611; NIA AG025707; NIA AG038070; NIMH MH071984; NIDA DA028420 |
PMID:24243846 PMID:22102583 PMID:18987003 PMID:17151079 |
Free, Freely available | biotools:mpd, nif-0000-03160, r3d100010101 | https://bio.tools/mpd https://doi.org/10.17616/R3PC7F |
http://www.jax.org/phenome | SCR_003212 | Mouse Phenome Database | 2026-02-14 02:00:42 | 221 | |||
|
PIRSF Resource Report Resource Website 10+ mentions |
PIRSF (RRID:SCR_003352) | PIRSF | data or information resource, narrative resource, database, standard specification | A SuperFamily classification system, with rules for functional site and protein name, to facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors. The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains; therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains. There are different PIRSF classification levels. The primary level is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). At a lower level are the subfamilies which are clusters representing functional specialization and/or domain architecture variation within the family. Above the homeomorphic level there may be parent superfamilies that connect distantly related families and orphan proteins based on common domains. Because proteins can belong to more than one domain superfamily, the PIRSF structure is formally a network. The FTP site provides free download for PIRSF. | protein annotation, classification, protein, superfamily, functional site, protein name, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: UniProtKB has parent organization: Protein Information Resource |
NHGRI U01-HG02712; NSF DBI-0138188; NSF ITR-0205470 |
PMID:19455212 PMID:14681371 |
Free, Freely available | biotools:pirsf, nif-0000-03294, OMICS_01697 | https://bio.tools/pirsf | http://pir.georgetown.edu/pirsf/ | SCR_003352 | PIR SuperFamily, Protein Information Resource SuperFamily | 2026-02-14 02:00:46 | 28 | |||
|
eDoctoring Resource Report Resource Website 1+ mentions |
eDoctoring (RRID:SCR_003336) | eDoctoring | training service resource, training resource, data or information resource, service resource, continuing medical education, narrative resource, training material | Online educational tool that brings challenging clinical practice to your computer, providing medical education that is engaging, challenging and interactive. While there is no substitute for real-life direct contact with patients or colleagues, research has shown that interactive online education can be a highly effective and enjoyable method of learning many components of clinical medicine, including ethics, clinical management, epidemiology and communication skills. eDoctoring offers 25 simulated clinical cases, 15 interactive tutorials and a virtual library containing numerous articles, fast facts and video clips. Their learning material is arranged in the following content areas: * Ethical, Legal and Social Implications of Genetic Testing * Palliative and End-of-Life Care * Prostate Cancer Screening and Shared Decision-Making | clinical, medical education, medical, clinical medicine, ethics, clinical management, epidemiology, communication, legal, social, implication, genetic testing, palliative care, end-of-life care, prostate cancer screening, decision-making, prostate cancer, medicine, tutorial, article, video, fact, training material |
has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom has parent organization: University of California; California; USA |
NCI ; NIH ; CDC ; NHGRI ; Health Resources and Services Administration ; Paul G. Allen Family Foundation ; Robert Wood Johnson Foundation |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31964 | http://edoctoring.ncl.ac.uk/System_Check/psa_detect_html;clickonRouletteWheels | SCR_003336 | 2026-02-14 02:00:32 | 1 | ||||||
|
Reactome Resource Report Resource Website 1000+ mentions |
Reactome (RRID:SCR_003485) | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. | pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: DisGeNET is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: WikiPathways is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: AmiGO is related to: PSICQUIC Registry is related to: Integrated Molecular Interaction Database is related to: NCBI BioSystems Database is related to: MOPED - Model Organism Protein Expression Database is related to: KOBAS is related to: PSICQUIC Registry is related to: Pathway Interaction Database is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: Algal Functional Annotation Tool has parent organization: Ontario Institute for Cancer Research has parent organization: Cold Spring Harbor Laboratory has parent organization: European Bioinformatics Institute has parent organization: New York University School of Medicine; New York; USA works with: PathwayMatcher |
Ontario Research Fund ; European Molecular Biology Laboratory ; NHGRI P41 HG003751; European Union FP6 ENFIN LSHG-CT-2005-518254; NIGMS GM080223; NIGMS R01 GM100039 |
PMID:21082427 PMID:21067998 |
Open source, Public, Freely available | r3d100010285, nif-0000-03390, biotools:reactome | https://bio.tools/reactome https://doi.org/10.17616/R3V59P |
SCR_003485 | Reactome Functional Interaction Network | 2026-02-14 02:00:50 | 4282 | |||||
|
AmiGO Resource Report Resource Website 1000+ mentions |
AmiGO (RRID:SCR_002143) | AmiGO | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Web tool to search, sort, analyze, visualize and download data of interest. Along with providing details of the ontologies, gene products and annotations, features a BLAST search, Term Enrichment and GO Slimmer tools, the GO Online SQL Environment and a user help guide.Used at the Gene Ontology (GO) website to access the data provided by the GO Consortium. Developed and maintained by the GO Consortium. | search, sort, analyze, visualize, data, ontology, gene, annotation, FASEB list |
uses: GOlr is used by: NIF Data Federation is listed by: OMICtools is listed by: Gene Ontology Tools is related to: ASAP is related to: Candida Genome Database is related to: Berkeley Bioinformatics Open-Source Projects is related to: ECO is related to: Zebrafish Information Network (ZFIN) is related to: Gramene is related to: WormBase is related to: NCBI Protein Database is related to: UniProtKB is related to: GeneDB Lmajor is related to: TAIR is related to: SGD is related to: GeneDB Tbrucei is related to: VMD is related to: JCVI CMR is related to: go-db-perl is related to: Mouse Genome Informatics (MGI) is related to: NCBI is related to: FlyBase is related to: GeneDB Pfalciparum is related to: PomBase is related to: Pseudomonas Genome Database is related to: Dictyostelium discoideum genome database is related to: Plant Ontology is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: MeGO is related to: ASPGD is related to: EcoCyc is related to: Reactome is related to: SGN is related to: GO-Module is related to: Songbird Brain Transcriptome Database is related to: Rat Genome Database (RGD) is related to: RamiGO has parent organization: Gene Ontology |
NHGRI P41 HG002273 | PMID:19033274 | Free, Available for download, Freely available | nif-0000-20935, OMICS_02266 | http://sourceforge.net/projects/geneontology/ | SCR_002143 | GO Consortium, AmiGO, AmiGO 2, AmiGene Ontology, Gene Ontology Database, Gene Ontology Consortium, GO Database, The Gene Ontology Consortium | 2026-02-14 02:00:15 | 1242 | ||||
|
Pathway Commons Resource Report Resource Website 10+ mentions |
Pathway Commons (RRID:SCR_002103) | PC | web service, data or information resource, data access protocol, software resource, database | Database of publicly available pathways from multiple organisms and multiple sources represented in a common language. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathways were downloaded directly from source databases. Each source pathway database has been created differently, some by manual extraction of pathway information from the literature and some by computational prediction. Pathway Commons provides a filtering mechanism to allow the user to view only chosen subsets of information, such as only the manually curated subset. The quality of Pathway Commons pathways is dependent on the quality of the pathways from source databases. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. It currently contains data from nine databases with over 1,668 pathways, 442,182 interactions,414 organisms and will be continually expanded and updated. (April 2013) | biological pathway, pathway, molecule, biopax, standard exchange format, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: cPath is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: IntAct is related to: Reactome is related to: MINT is related to: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is related to: Cancer Cell Map is related to: HPRD - Human Protein Reference Database is related to: Integrated Molecular Interaction Database is related to: Pathway Interaction Database is related to: CHEBI is related to: UniProt is related to: PANTHER is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit has parent organization: University of Toronto; Ontario; Canada |
NHGRI P41HG004118; NIGMS 2R01GM070743-06; NIGMS 1T32 GM083937; Cancer Biomedical Informatics Grid |
PMID:21071392 | Free, Freely available | nif-0000-20884, biotools:PathwayCommons_web_service_API | https://bio.tools/PathwayCommons_web_service_API | SCR_002103 | 2026-02-14 02:00:22 | 14 | |||||
|
SAMTOOLS Resource Report Resource Website 10000+ mentions |
SAMTOOLS (RRID:SCR_002105) | SAMtools | sequence analysis software, data processing software, data analysis software, software toolkit, software application, software resource | Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data. | Samtools, BCFtools, HTSlib, next generation sequencing, nucleotide alignments, sequence variant, genomic, c, perl, read, alignment, nucleotide, sequence, data, process, sam, bam, cram, vcf, bcf, bio.tools |
is used by: deFuse is used by: Short Read Sequence Typing for Bacterial Pathogens is used by: ROSE is used by: Fcirc is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SNVer is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Platypus is related to: shovill is related to: pysam has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: SAMtools/BCFtools is required by: RelocaTE is required by: Wessim is required by: SL-quant is required by: smMIPfil |
Wellcome Trust ; NHGRI U54 HG002750 |
PMID:19505943 PMID:21903627 DOI:10.1093/bioinformatics/btp352 |
Free, Available for download, Freely available | SCR_018682, biotools:samtools, OMICS_01074, nlx_154607, OMICS_00090 | https://github.com/samtools/samtools https://github.com/samtools/htslib https://bio.tools/samtools https://sources.debian.org/src/samtools/ |
http://samtools.sourceforge.net/ | SCR_002105 | samtools, Samtools, Sequence Alignment Map TOOLS, SAMtools, SAM tools | 2026-02-14 02:00:18 | 30156 |
Can't find your Tool?
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 dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET 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 dkNET then you can log in from here to get additional features in dkNET 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 dkNET 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.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
Email: info_at_ dknet.org
