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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Picky Resource Report Resource Website 10+ mentions |
Picky (RRID:SCR_010963) | Picky | software resource | A software tool for selecting optimal oligonucleotides (oligos) that allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize. |
is listed by: OMICtools has parent organization: Iowa State University; Iowa; USA |
NSF DBI0850195 | PMID:15180932 PMID:19849862 PMID:20406469 |
Free, Public, Acknowledgement requested | OMICS_00833 | SCR_010963 | Picky: Optimal Oligonucleotide Design and Analysis | 2026-02-07 02:08:08 | 35 | ||||||
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APPRIS Resource Report Resource Website 50+ mentions |
APPRIS (RRID:SCR_012019) | APPRIS | data or information resource, database | A database that houses annotations of human splice isoforms. It adds reliable protein structural and functional data and information from cross-species conservation. A visual representation of the annotations for each gene allows users to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, it also selects a single reference sequence for each gene, termed the principal isoform, based on the annotations of structure, function and conservation for each transcript. | isoform, function, annotation, splice, reference sequence, structure, conservation, transcript, FASEB list |
is listed by: OMICtools has parent organization: Spanish National Cancer Research Center |
PMID:23161672 | Free | OMICS_01881 | SCR_012019 | APPRIS - A system for annotating alternative splice isoforms | 2026-02-11 10:58:27 | 85 | ||||||
|
PolyA DB Resource Report Resource Website 100+ mentions |
PolyA DB (RRID:SCR_007867) | PolyA_DB | data or information resource, database | A database of mRNA polyadenylation sites. PolyA_DB version 1 contains human and mouse poly(A) sites that are mapped by cDNA/EST sequences. PolyA_DB version 2 contains poly(A) sites in human, mouse, rat, chicken and zebrafish that are mapped by cDNA/EST and Trace sequences. Sequence alignments between orthologous sites are available. PolyA_SVM predicts poly(A) sites using 15 cis elements identified for human poly(A) sites. | FASEB list | has parent organization: University of Medicine and Dentistry of New Jersey; New Jersey; USA | SCR_007867 | 2026-02-11 10:57:49 | 101 | ||||||||||
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Gemma Resource Report Resource Website 1000+ mentions |
Gemma (RRID:SCR_008007) | Gemma | data or information resource, database | Resource for reuse, sharing and meta-analysis of expression profiling data. Database and set of tools for meta analysis, reuse and sharing of genomics data. Targeted at analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results. | chip, microarray, functional genomics, gene expression, coexpression, differential expression, FASEB list |
is used by: NIF Data Federation is used by: Integrated Data Annotation is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: Gene Expression Omnibus is related to: Phenocarta has parent organization: University of British Columbia; British Columbia; Canada is parent organization of: Neurocarta |
NIGMS GM076990; Canadian Foundation for Innovation ; Michael Smith Foundation for Health Research ; Canadian Institutes for Health Research |
PMID:22782548 | Free, Freely available | nif-0000-08127, r3d100012747 | https://sources.debian.org/src/gemma/ https://doi.org/10.17616/R36R54 https://doi.org/10.17616/R36R54 |
SCR_008007 | 2026-02-11 10:57:44 | 1112 | |||||
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EID: Exon-Intron Database Resource Report Resource Website 10+ mentions |
EID: Exon-Intron Database (RRID:SCR_002469) | EID | data or information resource, data set | Data sets of protein-coding intron-containing genes that contain gene information from humans, mice, rats, and other eukaryotes, as well as genes from species whose genomes have not been completely sequenced. This is a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The database is derived from GenBank release 112, and it contains protein-coding genes that harbor introns, along with extensive descriptions of each gene and its DNA and protein sequences, as well as splice motif information. They have created subdatabases of genes whose intron positions have been experimentally determined. The collection also contains data on untranslated regions of gene sequences and intron-less genes. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames. | eukaryote genome, exon, exon-intro, gene structure, genome splicing, intron, ortholog, fasta, gene, protein-coding gene, splice, motif, gene prediction, structure, coding region |
is listed by: OMICtools has parent organization: University of Toledo; Ohio; USA |
PMID:16772261 PMID:10592221 |
Free, Available for download, Freely available | OMICS_01886, nif-0000-02793 | http://www.utoledo.edu/med/depts/bioinfo/database.html | http://www.meduohio.edu/bioinfo/eid/, http://mcb.harvard.edu/gilbert/EID | SCR_002469 | The Exon-Intron Database, Exon-Intron Database | 2026-02-11 10:56:28 | 11 | ||||
|
Peptide Sequence Database Resource Report Resource Website |
Peptide Sequence Database (RRID:SCR_005764) | PepSeqDB | data or information resource, database | The Peptide Sequence Database contains putative peptide sequences from human, mouse, rat, and zebrafish. Compressed to eliminate redundancy, these are about 40 fold smaller than a brute force enumeration. Current and old releases are available for download. Each species'' peptide sequence database comprises peptide sequence data from releveant species specific UniGene and IPI clusters, plus all sequences from their consituent EST, mRNA and protein sequence databases, namely RefSeq proteins and mRNAs, UniProt''s SwissProt and TrEMBL, GenBank mRNA, ESTs, and high-throughput cDNAs, HInv-DB, VEGA, EMBL, IPI protein sequences, plus the enumeration of all combinations of UniProt sequence variants, Met loss PTM, and signal peptide cleavages. The README file contains some information about the non amino-acid symbols O (digest site corresponding to a protein N- or C-terminus) and J (no digest sequence join) used in these peptide sequence databases and information about how to configure various search engines to use them. Some search engines handle (very) long sequences badly and in some cases must be patched to use these peptide sequence databases. All search engines supported by the PepArML meta-search engine can (or can be patched to) successfully search these peptide sequence databases. | peptide, sequence | has parent organization: Edwards Lab | nlx_149230 | SCR_005764 | 2026-02-11 10:57:13 | 0 | |||||||||
|
ARNIE Resource Report Resource Website |
ARNIE (RRID:SCR_000514) | ARNIE | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided. | network, orthologue, paralogue, gene, orthologue, protein interaction, protein, blast, extracellular, expression profiling, interaction network, ligand, interaction, signaling |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
MRC ; Wellcome Trust |
PMID:20802085 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01529 | SCR_000514 | AVEXIS Receptor Network with Integrated Expression | 2026-02-11 10:56:03 | 0 | |||||
|
Bgee: dataBase for Gene Expression Evolution Resource Report Resource Website 50+ mentions |
Bgee: dataBase for Gene Expression Evolution (RRID:SCR_002028) | Bgee | data or information resource, database | Database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data) to anatomy and development of different species. Bgee is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of gene expression. | gene expression, scrna-seq, rna-seq, affymetrix, in situ hybridization, expressed sequence tag, cross specie, comparison, homology, anatomy, developmental stage, gene expression pattern, development, genome, function, chordate, fish, transcriptiome, embryo, adult, mirna, protein coding, prenatal, immature, post-embryonic development, alimentary system, cardiovascular system, nervous system, renal system, reproductive system, respiratory system, skeletal system, ortholog, ontology, FASEB list |
is related to: Gene Expression Omnibus is related to: NCBI Sequence Read Archive (SRA) is related to: ArrayExpress is related to: Zebrafish Information Network (ZFIN) is related to: Xenbase is related to: Mouse Genome Informatics (MGI) is related to: Berkeley Drosophila Genome Project is related to: UniGene is related to: Zebrafish Anatomical Ontology is related to: eVOC is related to: Adult Mouse Anatomy Ontology is related to: Xenopus Anatomy Ontology is related to: Drosophila anatomy and development ontologies is related to: Ensembl has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: University of Lausanne; Lausanne; Switzerland |
Free, Freely available | nif-0000-11819, r3d100014596 | https://doi.org/10.17616/R31NJNR8 | SCR_002028 | Bgee: dataBase Gene Expression Evolution, dataBase Gene Expression Evolution | 2026-02-11 10:56:22 | 54 | ||||||
|
Phenoscape Knowledgebase Resource Report Resource Website 10+ mentions |
Phenoscape Knowledgebase (RRID:SCR_002821) | Phenoscape Knowledgebase | data or information resource, database | Knowledgebase that uses ontologies to integrate phenotypic data from genetic studies of zebrafish with evolutionary variable phenotypes from the systematic literature of ostariophysan fishes. Users can explore the data by searching for anatomical terms, taxa, or gene names. The expert system enables the broad scale analysis of phenotypic variation across taxa and the co-analysis of these evolutionarily variable features with the phenotypic mutants of model organisms. The Knowledgebase currently contains 565,158 phenotype statements about 2,527 taxa, sourced from 57 publications, as well as 38,189 phenotype statements about 4,727 genes, retrieved from ZFIN. 2013-01-26. | fish, gene, anatomy, model organism, ostariophysan, phenotype, taxis, ontology, anatomy, variation, taxon, genetic, evolution, development, web service, source code |
uses: Teleost Anatomy Ontology is related to: Zebrafish Information Network (ZFIN) is related to: Catalog of Fishes is related to: FishBase is related to: AmphibiaWeb is related to: NCBI Taxonomy is related to: Catalogue of Life has parent organization: NESCent - National Evolutionary Synthesis Center has parent organization: Phenoscape is parent organization of: Teleost Taxonomy Ontology |
NSF DBI-1062404; NSF DBI-1062542; NSF EF-0905606; NSF BDI-0641025; NSF EF-0423641 |
PMID:22736877 PMID:20505755 |
Free, Freely available | nif-0000-24925 | SCR_002821 | 2026-02-11 10:56:35 | 14 | ||||||
|
miRNAMap Resource Report Resource Website 100+ mentions |
miRNAMap (RRID:SCR_003156) | miRNAMap | data or information resource, database | A database of experimentally verified microRNAs and miRNA target genes in human, mouse, rat, and other metazoan genomes. In addition to known miRNA targets, three computational tools previously developed, such as miRanda, RNAhybrid and TargetScan, were applied for identifying miRNA targets in 3'-UTR of genes. In order to reduce the false positive prediction of miRNA targets, several criteria are supported for filtering the putative miRNA targets. Furthermore, miRNA expression profiles can provide valuable clues for investigating the properties of miRNAs, such tissue specificity and differential expression in cancer/normal cell. Therefore, we performed the Q-PCR experiments for monitoring the expression profiles of 224 human miRNAs in eighteen major normal tissues in human. The cross-reference between the miRNA expression profiles and the expression profiles of its target genes can provide effective viewpoint to understand the regulatory functions of the miRNA. | microrna, genome, FASEB list |
is listed by: OMICtools has parent organization: National Chiao Tung University; Hsinchu; Taiwan |
PMID:18029362 PMID:16381831 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03138, OMICS_00408 | SCR_003156 | 2026-02-11 10:56:41 | 246 | |||||||
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Wnt homepage Resource Report Resource Website 10+ mentions |
Wnt homepage (RRID:SCR_000662) | Wnt homepage | data or information resource, portal, topical portal | A resource for members of the Wnt community, providing information on progress in the field, maps on signaling pathways, and methods. The page on reagents lists many resources generously made available to and by the Wnt community. Wnt signaling is discussed in many reviews and in a recent book. There are usually several Wnt meetings per year. | wnt signaling, wnt, wnt protein, wnt pathway, signaling, pathway, method, protein, reagent, bibliography | has parent organization: Stanford University; Stanford; California | Cancer | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156863 | SCR_000662 | the Wnt homepage | 2026-02-12 09:43:01 | 13 | ||||||
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Teleost Anatomy Ontology Resource Report Resource Website 1+ mentions |
Teleost Anatomy Ontology (RRID:SCR_001610) | TAO | data or information resource, ontology, controlled vocabulary | A multi-species anatomy ontology for teleost fishes. It was originally seeded from ZFA, but covers terms relevant to other taxa. The TAO uses terms from the Common Anatomy Reference Ontology (CARO) as a template for its upper level nodes, and the Vertebrate Skeletal Anatomy Ontology (VSAO) for general skeletal anatomy classes. Growth of the TAO is enabled by contributions from data curators and the ichthyological community. The TAO can be browsed by using the NCBO BioPortal and data annotated using TAO terms can be queried using the Phenoscape Knowedgebase. | homology, anatomy, morphology, fish, obo, organismal, zebrafish anatomy |
uses: Zebrafish Anatomical Ontology uses: Common Anatomy Reference Ontology uses: Vertebrate Skeletal Anatomy Ontology is used by: Phenoscape Knowledgebase is listed by: BioPortal is listed by: OBO has parent organization: Phenoscape |
PMID:20547776 | Free, Freely available | nlx_153876 | http://purl.obolibrary.org/obo/tao.obo http://bioportal.bioontology.org/ontologies/38362?p=terms |
https://www.nescent.org/phenoscape/ | SCR_001610 | 2026-02-12 09:43:12 | 1 | |||||
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Morpholino Database Resource Report Resource Website 1+ mentions |
Morpholino Database (RRID:SCR_001378) | MODB | data repository, service resource, storage service resource, database, 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) | 2026-02-12 09:43:08 | 1 | |||||
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Integrated Animals Resource Report Resource Website |
Integrated Animals (RRID:SCR_001421) | organism supplier, material resource, biomaterial supply resource | Integrated Animals is a virtual database currently indexing available animal strains and mutants from: AGSC (Ambystoma), BCBC (mice), BDSC (flies), CWRU Cystic Fibrosis Mouse Models (mice), DGGR (flies), FlyBase (flies), IMSR (mice), MGI (mice), MMRRC (mice), NSRRC (pig), NXR (Xenopus), RGD (rats), Sperm Stem Cell Libraries for Biological Research (rats), Tetrahymena Stock Center (Tetrahymena), WormBase (worms), XGSC (Xiphophorus), ZFIN (zebrafish), and ZIRC (zebrafish). | non human animal, mutant, database, integrated, nif, FASEB list |
uses: Mouse Genome Informatics (MGI) uses: Beta Cell Biology Consortium uses: Zebrafish Information Network (ZFIN) uses: International Mouse Strain Resource uses: Bloomington Drosophila Stock Center uses: Rat Genome Database (RGD) uses: Zebrafish International Resource Center uses: Ambystoma Genetic Stock Center uses: Kyoto Stock Center uses: FlyBase uses: Mutant Mouse Resource and Research Center uses: National Swine Resource and Research Center uses: National Xenopus Resource uses: CWRU In Vivo Animal Facilities uses: Sperm Stem Cell Libraries for Biological Research uses: Tetrahymena Stock Center uses: WormBase uses: Xiphophorus Genetic Stock Center is used by: NIF Data Federation is used by: NIDDK Information Network (dkNET) has parent organization: Integrated |
Free, Freely Available | nif-0000-08137 | https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_154697-1 http://neuinfo.org/nif/nifgwt.html?query=nif-0000-08137, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nif-0000-08137-1 | SCR_001421 | NIF Animals, NIF Integrated Animals, Integrated Animal | 2026-02-12 09:43:09 | 0 | |||||||
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Cold Spring Harbor Protocols: Collected Resources - Behavioral Assays Resource Report Resource Website 100+ mentions |
Cold Spring Harbor Protocols: Collected Resources - Behavioral Assays (RRID:SCR_001697) | CSH Protocols - Behavioral Assays | data or information resource, bibliography | A bibliography of published Behavioral Assays by Cold Spring Harbor Protocols. Cold Spring Harbor Protocols is an interdisciplinary journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. Each monthly issue details multiple essential methods - a mix of cutting-edge and well-established techniques. Newly commissioned protocols and unsolicited submissions are supplemented with articles based on Cold Spring Harbor Laboratorys renowned courses and manuals. All protocols are up-to-date and presented in a consistent, easy-to-follow format. | genetics, bioinformatics, cell, computational biology, development, imaging, immunology, journal, molecular, neuroscience, protein, research, behavioral assay, behavior, ant, honeybee, learning, courtship, larvae, adult, stress, olfactory, aggression, sleep, movement, locomotor, circadian, feeding | has parent organization: Cold Spring Harbor Laboratory | Free, Freely Available | nif-0000-10198 | SCR_001697 | Cold Spring Harbor Protocols - Behavioral Assays | 2026-02-12 09:43:13 | 108 | |||||||
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Ensembl Variation Resource Report Resource Website 1+ mentions |
Ensembl Variation (RRID:SCR_001630) | Ensembl Variation | analysis service resource, service resource, production service resource, database, data analysis service, 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 | 2026-02-12 09:43:12 | 4 | ||||||
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Ancora Resource Report Resource Website 10+ mentions |
Ancora (RRID:SCR_001623) | Ancora | analysis service resource, service resource, production service resource, database, data analysis service, 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 | 2026-02-12 09:43:12 | 19 | |||||
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Reactome Resource Report Resource Website 1000+ mentions |
Reactome (RRID:SCR_003485) | analysis service resource, service resource, production service resource, database, data analysis service, data or information resource | 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 | 2026-02-12 09:43:37 | 4282 | |||||
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InParanoid: Eukaryotic Ortholog Groups Resource Report Resource Website 100+ mentions |
InParanoid: Eukaryotic Ortholog Groups (RRID:SCR_006801) | InParanoid | analysis service resource, service resource, production service resource, database, data analysis service, data or information resource | Collection of pairwise comparisons between 100 whole genomes generated by a fully automatic method for finding orthologs and in-paralogs between TWO species. Ortholog clusters in the InParanoid are seeded with a two-way best pairwise match, after which an algorithm for adding in-paralogs is applied. The method bypasses multiple alignments and phylogenetic trees, which can be slow and error-prone steps in classical ortholog detection. Still, it robustly detects complex orthologous relationships and assigns confidence values for in-paralogs. The original data sets can be downloaded. | protein, ortholog, genome, drosophila pseudoobscura, duplication, entamoeba histolytica, escherichia colik12, eukaryotic, gasterosteus aculeatus, gene, aedes aegypti, apis mellifera, bos taurus, caenorhabditis remanei, candida glabrata, canis familiaris, ciona intestinalis, cryptococcus neoformans, debaromyces hansenii, dictyostelium discoideum, genomic, homolog, inparalog, kluyveromyces lactis, macaca mulatta, monodelphis domestica, orthology, oryza sativa, outparalog, proteome, tetraodon nigroviridis, xenopus tropicalis, blast, proteome, ortholog cluster, cluster, in-paralog, paralog, automatic clustering, genome comparison, FASEB list | has parent organization: Stockholm University; Stockholm; Sweden | Swedish Research Council ; Karolinska Institutet; Stockholm; Sweden ; Pfizer Corporation |
PMID:19892828 PMID:18055500 PMID:15608241 PMID:11743721 |
Acknowledgement requested | nif-0000-03024 | http://www.cgb.ki.se/inparanoid/ | SCR_006801 | Inparanoid eukaryotic ortholog database | 2026-02-12 09:44:24 | 186 | ||||
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The WWW Virtual Library: Model Organisms Resource Report Resource Website |
The WWW Virtual Library: Model Organisms (RRID:SCR_007007) | data or information resource, portal, topical portal | Catalog of internet resources relating to biological model organisms, and is part of the Biosciences area of the Virtual Library project. The main Model Organisms Library discussed in this website are: * E. coli (bacterium) * Yeasts (Saccharomyces cerevisiae, and other species) * Dictyostelium discoideum (slime mold) * Drosophila melanogaster (fruit fly) * Xenopus laevis (African clawed frog) Many aspects of biology are similar in most or all organisms, but it is frequently much easier to study particular aspects in particular organisms - for instance, genetics is easier in small organisms that breed quickly, and very difficult in humans! The most popular model organisms have strong advantages for experimental research, and become even more useful when other scientists have already worked on them, discovering techniques, genes and other useful information. | bacterium, cerevisiae, model organism, saccharomyces, s. cerevisiae, slime mold, xenopus, catalog, link aggregator | is listed by: 3DVC | nif-0000-20953 | SCR_007007 | VL | 2026-02-12 09:44:27 | 0 |
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