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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
BEADS Resource Report Resource Website 10+ mentions |
BEADS (RRID:SCR_013229) | BEADS | software resource | Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:21646344 | OMICS_00466, biotools:beads | https://bio.tools/beads | SCR_013229 | BEADS: Bias Elimination Algorithm for Deep Sequencing, Bias Elimination Algorithm for Deep Sequencing | 2026-02-14 02:02:50 | 37 | ||||||
|
Trans-ABySS Resource Report Resource Website 50+ mentions |
Trans-ABySS (RRID:SCR_013322) | Trans-ABySS | software resource | A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
OMICS_01326, biotools:trans-abyss | https://bio.tools/trans-abyss/ | SCR_013322 | 2026-02-14 02:02:47 | 69 | ||||||||
|
chimerascan Resource Report Resource Website 50+ mentions |
chimerascan (RRID:SCR_013298) | chimerascan | software resource | Software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets. Used for detection of chimeric transcripts in high-throughput sequencing data. | Gene fusion detection, paired-end RNA sequencing data, RNA sequencing data, chimeric transcripts detection, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:chimerascan, OMICS_01343 | https://bio.tools/chimerascan | SCR_013298 | 2026-02-14 02:02:29 | 53 | |||||||
|
Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers Resource Report Resource Website 1+ mentions |
Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers (RRID:SCR_013409) | PCS | software resource | A stand-alone package to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3''-UTRs. | perl, perl script, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Tsinghua University; Beijing; China |
biotools:pcs, nlx_33020 | https://bio.tools/pcs | http://bioinfo.au.tsinghua.edu.cn/member/~gujin/pcs/ | SCR_013409 | Pairwise Conservation Scores | 2026-02-14 02:02:51 | 3 | ||||||
|
CNV-seq Resource Report Resource Website 100+ mentions |
CNV-seq (RRID:SCR_013357) | CNV-seq | software resource | A method for detecting DNA copy number variation (CNV) using high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:cnv-seq, OMICS_00339 | https://bio.tools/cnv-seq | SCR_013357 | 2026-02-14 02:02:51 | 167 | |||||||
|
DISEASES Resource Report Resource Website 500+ mentions |
DISEASES (RRID:SCR_015664) | data or information resource, database | Database that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. It also assigns confidence scores that facilitate comparison of the different types and sources of evidence. | disease, gene, disease-gene association, text-mining, , bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
Novo Nordisk Foundation Center for Protein Research NNF14CC0001; European Union Seventh Framework Programme n259348 |
PMID:25484339 | biotools:diseases | https://bio.tools/diseases | SCR_015664 | 2026-02-14 02:02:52 | 627 | |||||||
|
WebGeSTer DB Resource Report Resource Website 1+ mentions |
WebGeSTer DB (RRID:SCR_002165) | WebGeSTer DB | data or information resource, database | Database of intrinsic terminators of transcription that is comprized of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids. Information about structural parameters of individual terminators such as sequence, length of stem and loop, mismatches and gaps, U-trail, genomic coordinates and gene name and accession number is available in both tabular form and as a composite figure. Summary statistics for terminator profiles of whole genome can be also obtained. Raw data files for individual genomes can be downloaded (.zip files) for detailed investigations. Data is organized into different tiers such that users can fine-tune their search by entering name of the species, or taxon ID or genomes with a certain number of terminators. To visualize the occurrence of the terminators, an interactive map, with the resolution to single gene level, has been developed. | genome, terminator, transcription, plasmid, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20972211 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:webgester_db, OMICS_01862 | https://bio.tools/webgester_db | SCR_002165 | WebGesTer Database, Web Genome Scannner for Terminators Database, WebGeSTer DB - A Transcription Terminator Database | 2026-02-14 02:06:08 | 5 | |||||
|
PubGene Resource Report Resource Website 10+ mentions |
PubGene (RRID:SCR_002119) | data or information resource, database | It helps users retrieve information on genes and proteins. The underlying structure of PubGene can be viewed as a gene-centric database. Gene and protein names are cross-referenced to each other and to terms that are relevant to understanding their biological function, importance in disease and relationship to chemical substances. The result is a literature network organizing information in a form that is easy to navigate. | gene, information, protein, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is parent organization of: Coremine Medical |
Free, Freely Available | biotools:pubgene, nif-0000-20908 | https://bio.tools/pubgene | SCR_002119 | PubGene | 2026-02-14 02:06:07 | 39 | |||||||
|
COSMIC - Catalogue Of Somatic Mutations In Cancer Resource Report Resource Website 1000+ mentions |
COSMIC - Catalogue Of Somatic Mutations In Cancer (RRID:SCR_002260) | COSMIC | data or information resource, database |
Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats. Some key features of COSMIC are: * Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types. * Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines. |
cancer, mutation, somatic mutation, tumor, cancer genome, genome, gene, dna, tissue, histology, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Cancer | Wellcome Trust 077012/Z/05/Z | PMID:20952405 | Free | nif-0000-02690, biotools:cosmic, OMICS_00082 | http://www.sanger.ac.uk/perl/CGP/cosmic https://bio.tools/cosmic |
SCR_002260 | Catalogue Of Somatic Mutations In Cancer | 2026-02-14 02:06:06 | 4486 | |||
|
EchoBASE Resource Report Resource Website 1+ mentions |
EchoBASE (RRID:SCR_002430) | EchoBASE | data or information resource, database | A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. It has been created to integrate information from post-genomic experiments into a single resource with the aim of providing functional predictions for the 1500 or so gene products for which we have no knowledge of their physiological function. While EchoBASE provides a basic annotation of the genome, taken from other databases, its novelty is in the curation of post-genomic experiments and their linkage to genes of unknown function. Experiments published on E. coli are curated to one of two levels. Papers dealing with the determination of function of a single gene are briefly described, while larger dataset are actually included in the database and can be searched and manipulated. This includes data for proteomics studies, protein-protein interaction studies, microarray data, functional genomic approaches (looking at multiple deletion strains for novel phenotypes) and a wide range of predictions that come out of in silico bioinformatic approaches. The aim of the database is to provide hypothesis for the functions of uncharacterized gene products that may be used by the E. coli research community to further our knowledge of this model bacterium. | gene, bio.tools |
is listed by: bio.tools is listed by: Debian |
GlaxoSmithKline ; BBSRC |
PMID:15608209 | nif-0000-02781, biotools:echobase, r3d100011646 | https://bio.tools/echobase https://doi.org/10.17616/R38W6H |
SCR_002430 | EchoBASE: an integrated post-genomic database for Escherichia coli | 2026-02-14 02:06:10 | 6 | |||||
|
Autophagy Database Resource Report Resource Website 10+ mentions |
Autophagy Database (RRID:SCR_002671) | Autophagy DB, AutophagyDB | data or information resource, database | Database that provides basic, up-to-date information on relevant literature, and a list of autophagy-related proteins and their homologs in eukaryotes. | autophagy, protein, homolog, ortholog, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:20972215 | Free, Available for download, Freely available | OMICS_03306, biotools:the_autophagy_database, r3d100012565 | https://bio.tools/the_autophagy_database https://doi.org/10.17616/R3J786 |
SCR_002671 | 2026-02-14 02:05:48 | 17 | |||||
|
DOMINE: Database of Protein Interactions Resource Report Resource Website 1+ mentions |
DOMINE: Database of Protein Interactions (RRID:SCR_002399) | DOMINE | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Database of known and predicted protein domain (domain-domain) interactions containing interactions inferred from PDB entries, and those that are predicted by 8 different computational approaches using Pfam domain definitions. DOMINE contains a total of 26,219 domain-domain interactions (among 5,410 domains) out of which 6,634 are inferred from PDB entries, and 21,620 are predicted by at least one computational approach. Of the 21,620 computational predictions, 2,989 interactions are high-confidence predictions (HCPs), 2,537 interactions are medium-confidence predictions (MCPs), and the remaining 16,094 are low-confidence predictions (LCPs). (May 2014) | domain-domain interaction, prediction, protein domain, interaction, protein domain interaction, protein, domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Pfam has parent organization: University of Texas at Dallas; Texas; USA |
PMID:21113022 PMID:17913741 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01906, nif-0000-02758, biotools:domine | https://bio.tools/domine | SCR_002399 | Database of Protein Domain Interactions | 2026-02-14 02:06:07 | 1 | |||||
|
Nucleic Acid Database Resource Report Resource Website 10+ mentions |
Nucleic Acid Database (RRID:SCR_003255) | NDB | data or information resource, database | A database of three-dimensional structural information about nucleic acids and their complexes. In addition to primary data, it contains derived geometric data, classifications of structures and motifs, standards for describing nucleic acid features, as well as tools and software for the analysis of nucleic acids. A variety of search capabilities are available, as are many different types of reports. NDB maintains the macromolecular Crystallographic Information File (mmCIF). | nucleic acid, dna, nucleopeptide, nucleoprotein, nucleotide, rna, transfection, sequence, structure, function, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: MINAS - Metal Ions in Nucleic AcidS is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Jenalib: Jena Library of Biological Macromolecules has parent organization: Rutgers University; New Jersey; USA |
NSF ; DOE ; NIH |
PMID:24185695 PMID:1384741 |
Free, Available for download, Freely available | nif-0000-03184, biotools:ndb, r3d100010415 | https://bio.tools/ndb https://doi.org/10.17616/R3531R |
SCR_003255 | 2026-02-14 02:05:49 | 36 | |||||
|
RefSeq Resource Report Resource Website 10000+ mentions |
RefSeq (RRID:SCR_003496) | data or information resource, database | Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases. | reference sequence, transcript, protein, dna, rna, plasmid, organelle, virus, genome, nucleic acid, ortholog, paralog, haplotype, nucleotide sequence, gene expression, blast, gold standard, bio.tools |
is listed by: OMICtools is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: BeetleBase is related to: EcoGene is related to: INSDC is related to: HFV Database is related to: RefSeqGene is related to: NCBI Protein Database is related to: RefSeqGene is related to: UniParc at the EBI is related to: NCBI Nucleotide is related to: UniParc is related to: ProRepeat is related to: NCBI Virus is related to: Codon and Codon-Pair Usage Tables is related to: RefSeq non-redundant proteins has parent organization: NCBI |
PMID:24316578 PMID:24259432 PMID:22121212 PMID:18927115 PMID:17130148 PMID:15608248 |
Free, Available for download, Freely available | SCR_016579, nif-0000-03397, OMICS_01659, biotools:refseq, r3d100011306 | ftp://ftp.ncbi.nlm.nih.gov/refseq https://bio.tools/refseq https://doi.org/10.17616/R3HP70 |
SCR_003496 | RefSeq, , Reference Sequence Database, Reference Sequence, Reference Sequences, NCBI | 2026-02-14 02:05:50 | 18049 | ||||||
|
MutDB Resource Report Resource Website 10+ mentions |
MutDB (RRID:SCR_003251) | data or information resource, database | Database with annotations for human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene. | web database, annotation database, human genome, human protein, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Buck Institute; California; USA |
PMID:15980479 | Free, Freely available | biotools:mutdb, nif-0000-03173 | https://bio.tools/mutdb | SCR_003251 | 2026-02-14 02:06:11 | 10 | |||||||
|
PolymiRTS Resource Report Resource Website 100+ mentions |
PolymiRTS (RRID:SCR_003389) | PolymiRTS | data or information resource, database | Database of naturally occurring DNA variations in microRNA (miRNA) seed regions and miRNA target sites. MicroRNAs pair to the transcripts of protein-coding genes and cause translational repression or mRNA destabilization. SNPs and INDELs in miRNAs and their target sites may affect miRNA-mRNA interaction, and hence affect miRNA-mediated gene repression. The PolymiRTS database was created by scanning 3'UTRs of mRNAs in human and mouse for SNPs and INDELs in miRNA target sites. Then, the potential downstream effects of these polymorphisms on gene expression and higher-order phenotypes are identified. Specifically, genes containing PolymiRTSs, cis-acting expression QTLs, and physiological QTLs in mouse and the results of genome-wide association studies (GWAS) of human traits and diseases are linked in the database. The PolymiRTS database also includes polymorphisms in target sites that have been supported by a variety of experimental methods and polymorphisms in miRNA seed regions. | polymorphism, microrna, human, disease, trait, snp, indel, pathway, genetic variant, gene expression, phenotype, chromosome, chromosome location, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
PhRMA Foundation ; UT Center for Integrative and Translational Genomics ; NICHD HD052472; NIAAA AA014425; NIDA DA021131; NINR NR009270; NIAID AI081050; NIAID AI019782; American Heart Association 0830134N; United States Department of Defense W81XHW-05-01-0227 |
PMID:24163105 PMID:22080514 |
Free, Available for download, Freely available | nif-0000-03324, biotools:polymirts, OMICS_00391 | https://bio.tools/polymirts | http://compbio.utmem.edu/miRSNP/ | SCR_003389 | Polymorphism in microRNA Target Site, PolymiRTS Database, Polymorphism in microRNAs and their TargetSites | 2026-02-14 02:06:12 | 149 | |||
|
PHI-base Resource Report Resource Website 100+ mentions |
PHI-base (RRID:SCR_003331) | PHI-base | data or information resource, database | Database that catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. It is an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, it also includes antifungal compounds and their target genes. Each entry is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes have been annotated using controlled vocabularies and links to external sources (Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC). | gene expression, pathogenic bacteria, virulence, infection, target site, gene, pathogen-host interaction, interaction, phenotype, pathogen, disease, host, anti-infective, nucleotide sequence, amino acid sequence, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian |
BBSRC BB/1000488/1 | PMID:17942425 PMID:17153929 PMID:16381911 |
Free, Freely available | nif-0000-03276, r3d100011301, biotools:phi-base | https://bio.tools/phi-base https://doi.org/10.17616/R35D1V |
http://www4.rothamsted.bbsrc.ac.uk/phibase/ | SCR_003331 | Pathogen Host Interaction base, Pathogen Host Interaction, Pathogen Host Interaction-Base | 2026-02-14 02:05:43 | 198 | |||
|
MiST - Microbial Signal Transduction database Resource Report Resource Website 10+ mentions |
MiST - Microbial Signal Transduction database (RRID:SCR_003166) | MiST | data or information resource, database | Database which contains the signal transduction proteins for complete and draft bacterial and archaeal genomes. The MiST2 database identifies and catalogs the repertoire of signal transduction proteins in microbial genomes. | signal transduction proteins, bacterial genome, archaeal genome, microbial genome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Tennessee Knoxville; Tennessee; USA |
South Carolina Research Association ; DOE Office of Science ; NIH ; NIGMS GM083177 |
PMID:19900966 | Free, Freely available | biotools:mist, nif-0000-03140 | https://bio.tools/mist | SCR_003166 | MiST 2.2, Microbial Signal Transduction Database, Microbial Signal Transduction database (MiST), MiST2 | 2026-02-14 02:06:11 | 31 | ||||
|
SIDER Resource Report Resource Website 100+ mentions |
SIDER (RRID:SCR_004321) | SIDER | data or information resource, database | Database containing information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect frequency, drug and side effect classifications as well as links to further information, for example drug-target relations. The SIDER Side Effect Resource represents an effort to aggregate dispersed public information on side effects. To our knowledge, no such resource exist in machine-readable form despite the importance of research on drugs and their effects. The creation of this resource was motivated by the many requests for data that we received related to our paper (Campillos, Kuhn et al., Science, 2008, 321(5886):263-6.) on the utilization of side effects for drug target prediction. Inclusion of side effects as readouts for drug treatment should have many applications and we hope to be able to enhance the respective research with this resource. You may browse the drugs by name, browse the side effects by name, download the current version of SIDER, or use the search interface. | medicine, drug, side effect, adverse drug reaction, drug-target, phenotype, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Allen Institute Neurowiki has parent organization: European Molecular Biology Laboratory |
PMID:20087340 | Except as otherwise noted, Creative Commons Attribution-NonCommercial-ShareAlike License, v3, Commercial use requires permission | r3d100012791, nlx_33359, OMICS_01588, biotools:sider | https://bio.tools/sider https://doi.org/10.17616/R3J226 |
SCR_004321 | Side Effect Resource, SIDER: Side Effect Resource | 2026-02-14 02:05:51 | 372 | |||||
|
SGD Resource Report Resource Website 1000+ mentions |
SGD (RRID:SCR_004694) | SGD, SGD LOCUS, SGD REF | data or information resource, database | A curated database that provides comprehensive integrated biological information for Saccharomyces cerevisiae along with search and analysis tools to explore these data. SGD allows researchers to discover functional relationships between sequence and gene products in fungi and higher organisms. The SGD also maintains the S. cerevisiae Gene Name Registry, a complete list of all gene names used in S. cerevisiae which includes a set of general guidelines to gene naming. Protein Page provides basic protein information calculated from the predicted sequence and contains links to a variety of secondary structure and tertiary structure resources. Yeast Biochemical Pathways allows users to view and search for biochemical reactions and pathways that occur in S. cerevisiae as well as map expression data onto the biochemical pathways. Literature citations are provided where available. | database, yeast, pathway, analysis, gene, nomenclature, predicted sequence, fungi, functional relationship, protein structure, bio.tools, FASEB list |
uses: InterMOD is used by: NIF Data Federation is used by: PhenoGO is listed by: re3data.org is listed by: OMICtools is listed by: InterMOD is listed by: bio.tools is listed by: Debian is affiliated with: InterMOD is related to: AmiGO is related to: Yeast Search for Transcriptional Regulators And Consensus Tracking is related to: HomoloGene is related to: TXTGate is related to: PhenoGO has parent organization: Stanford University School of Medicine; California; USA has parent organization: Stanford University; Stanford; California is parent organization of: Ascomycete Phenotype Ontology is parent organization of: SGD Gene Ontology Slim Mapper |
NHGRI 5P41HG001315-11; NHGRI 5P41HG002273-05; NHGRI 5U41HG001315-18; NHGRI 2U41HG002273-13; NHGRI 5R01HG004834-04 |
PMID:24265222 PMID:12519985 PMID:9399804 |
Free for academic use, The community can contribute to this resource, Non-commercial | nif-0000-03456, biotools:sgd, r3d100010419, OMICS_01661 | https://bio.tools/sgd https://doi.org/10.17616/R3N313 |
http://genome-www.stanford.edu/Saccharomyces/ | SCR_004694 | SGD LOCUS, Saccharomyces Genome Database, SGD REF | 2026-02-14 02:06:21 | 1920 |
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