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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Distant Regulatory Elements Resource Report Resource Website 10+ mentions |
Distant Regulatory Elements (RRID:SCR_003058) | DiRE | data analysis service, analysis service resource, production service resource, service resource | Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data. | regulatory element, enhancer identification, genome, prediction, transcription factor binding site, gene, co-expression, co-function, function, transcription factor, comparative genomics, regulatory function, gene locus, chromosome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
NLM ; Intramural Research Program |
PMID:18487623 | Free, Freely available | nif-0000-30448, biotools:dire | https://bio.tools/dire | SCR_003058 | Distant Regulatory Elements of co-regulated genes | 2026-08-04 09:40:48 | 25 | ||||
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MiST - Microbial Signal Transduction database Resource Report Resource Website 10+ mentions |
MiST - Microbial Signal Transduction database (RRID:SCR_003166) | MiST | database, data or information resource | 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 | 2026-08-04 09:40:50 | 31 | ||||
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Identifiers.org Resource Report Resource Website 50+ mentions |
Identifiers.org (RRID:SCR_003735) | Identifiers.org | production service resource, service resource, identifier resolution | A system providing resolvable persistent Uniform Resource Identifiers (URIs) used to identify data for the scientific community, with a current focus on the Life Sciences domain. The provision of resolvable identifiers (URLs) fits well with the Semantic Web vision, and the Linked Data initiative. It provides direct access to the identified data using one chosen physical location (or resource). If more than one physical locations providing the data are recorded in the Registry, then you can access them via the top banner or by using a profile. | identifier, life sciences, bio.tools |
uses: MIRIAM Resources is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
Free | nlx_157931, biotools:identifiers.org | https://bio.tools/identifiers.org | SCR_003735 | 2026-08-04 09:40:58 | 50 | |||||||
|
RefSeq Resource Report Resource Website 10000+ mentions |
RefSeq (RRID:SCR_003496) | database, data or information resource | 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 | 2026-08-04 09:40:55 | 18049 | ||||||
|
INMEX Resource Report Resource Website 10+ mentions |
INMEX (RRID:SCR_004173) | INMEX | data analysis service, analysis service resource, production service resource, service resource | A web-based tool to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments. INMEX contains three functional modules. The data preparation module supports flexible data processing, annotation and visualization of individual data sets. The statistical analysis module allows researchers to combine multiple data sets based on P-values, effect sizes, rank orders and other features. The significant genes can be examined in functional analysis module for enriched Gene Ontology terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, or expression profile visualization. INMEX has built-in support for common gene/metabolite identifiers (IDs), as well as 45 popular microarray platforms for human, mouse and rat. Complex operations are performed through a user-friendly web interface in a step-by-step manner. | gene expression, meta-analysis, metabolomics, pathway, gene, metabolite, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: KEGG is related to: Human Metabolome Database has parent organization: University of British Columbia; British Columbia; Canada |
Killam Trust ; Canadian Institutes of Health Research |
PMID:23766290 | Acknowledgement requested | biotools:inmex, OMICS_01546 | https://bio.tools/inmex | SCR_004173 | INtegrative Meta-analysis of EXpression data, INMEX - INtegrative Meta-analysis of EXpression data | 2026-08-04 09:41:04 | 19 | ||||
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PolymiRTS Resource Report Resource Website 100+ mentions |
PolymiRTS (RRID:SCR_003389) | PolymiRTS | database, data or information resource | 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 | 2026-08-04 09:40:54 | 149 | |||
|
PHI-base Resource Report Resource Website 100+ mentions |
PHI-base (RRID:SCR_003331) | PHI-base | database, data or information resource | 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 | 2026-08-04 09:40:53 | 198 | |||
|
T-profiler Resource Report Resource Website 10+ mentions |
T-profiler (RRID:SCR_003452) | T-profiler | data analysis service, analysis service resource, production service resource, service resource | One of the key challenges in the analysis of gene expression data is how to relate the expression level of individual genes to the underlying transcriptional programs and cellular state. The T-profiler tool hosted on this website uses the t-test to score changes in the average activity of pre-defined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif, and location on the same chromosome, respectively. If desired, an iterative procedure can be used to select a single, optimal representative from sets of overlapping gene groups. A jack-knife procedure is used to make calculations more robust against outliers. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters. Currently, gene expression data from Saccharomyces cerevisiae and Candida albicans are supported. Users can submit their microarray data for analysis by clicking on one of the two organism-specific tabs above. Platform: Online tool | expression, gene, binding, cellular, transcriptional, gene expression, microarray, gene ontology, transcription factor, binding motif, chip-chip, chip, motif, t-test, statistical analysis, transcriptome, bio.tools |
is listed by: Biositemaps is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Columbia University; New York; USA has parent organization: University of Amsterdam; Amsterdam; Netherlands |
Netherlands Foundation for Technical Research APB.5504; NHGRI R01HG003008 |
PMID:15980543 | Free for academic use | nif-0000-33354, biotools:t-profiler | https://bio.tools/t-profiler | SCR_003452 | T-profiler: Scoring the Activity of Pre-defined Groups of Genes Using Gene Expression Data | 2026-08-04 09:40:54 | 11 | ||||
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SIDER Resource Report Resource Website 100+ mentions |
SIDER (RRID:SCR_004321) | SIDER | database, data or information resource | 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 | 2026-08-04 09:41:06 | 372 | |||||
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NEWT Resource Report Resource Website 10+ mentions |
NEWT (RRID:SCR_004477) | NEWT | database, data or information resource | NEWT is the taxonomy database maintained by the UniProt group. It integrates taxonomy data compiled in the NCBI database and data specific to the UniProt Knowledgebase. Browse by hierarchy, List all, or Complete proteomes. Organisms are classified in a hierarchical tree structure. Our taxonomy database contains every node (taxon) of the tree. UniProtKB taxonomy data is manually curated: next to manually verified organism names, we provide a selection of external links, organism strains and viral host information. Species with protein sequences stored in the UniProt Knowledgebase are named according to UniProt nomenclature. We endeavour to maintain a list of manually curated species names for which protein sequence data is available. In particular, we have adopted a systematic convention for naming viral and bacterial strains and isolates. Links to external sites are chosen by the UniProt taxonomy team and show pictures and various scientific data of interest (taxonomy, biology, physiology,...). | archaea, bacteria, eukaryota, viruses, cellular organism, sequence, viroid, gold standard, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: NCBI Taxonomy has parent organization: UniProt |
PMID:12824428 | nlx_46189, biotools:newt | https://bio.tools/newt | http://www.ebi.ac.uk/newt/ | SCR_004477 | UniProtKB taxonomy database, UniProt Taxonomy Database, UniProt Taxonomy | 2026-08-04 09:41:09 | 23 | |||||
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Ancestrymap Resource Report Resource Website 10+ mentions |
Ancestrymap (RRID:SCR_004353) | ANCESTRYMAP | software application, software resource, source code | Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux. | disease gene, ancestry, gene, genomic, unix, linux, admixture mapping, admixture, genome, linkage disequilibrium, population |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools has parent organization: Harvard Medical School; Massachusetts; USA |
Burroughs Wellcome Fund ; NHGRI K-01 HG002758-01 |
PMID:15088269 | Restricted | nlx_39116, biotools:ancestrymap, OMICS_02083 | https://reich.hms.harvard.edu/software, https://bio.tools/ancestrymap | http://genepath.med.harvard.edu/~reich/Software.htm, http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html | SCR_004353 | 2026-08-04 09:41:07 | 12 | ||||
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Selectome: a Database of Positive Selection Resource Report Resource Website 1+ mentions |
Selectome: a Database of Positive Selection (RRID:SCR_004542) | database, data or information resource | Database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML on all branches of animal gene trees. | duplication, events, gene, animal, positive selection, speciation, p-value, speciation, duplication, selectome, phylogenetic, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Lausanne; Lausanne; Switzerland |
PMID:24225318 | nif-0000-03451, biotools:selectome | https://bio.tools/selectome | SCR_004542 | Selectome | 2026-08-04 09:41:10 | 8 | |||||||
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cpnDB: A Chaperonin Database Resource Report Resource Website 1+ mentions |
cpnDB: A Chaperonin Database (RRID:SCR_002263) | cpnDB | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences. | chaperonin sequence, microbial ecology, phylogenetics, chaperonin, plastid, mitochondria, cytoplasm, sequence, blast, fasta, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Canadian Biotechnology Strategy ; National Research Council Genomics and Health Initiative |
PMID:15289485 | Free, Freely available | biotools:cpndb, OMICS_01511, nif-0000-02694 | https://bio.tools/cpndb | http://www.cpndb.ca/cpnDB/home.php | SCR_002263 | 2026-08-04 09:40:36 | 3 | ||||
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ToppCluster Resource Report Resource Website 100+ mentions |
ToppCluster (RRID:SCR_001503) | ToppCluster | data analysis service, resource, analysis service resource, production service resource, service resource | A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene. | term enrichment, gene, analysis, gene enrichment analysis, connectivity, heatmap, ortholog, microarray, function, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GenitoUrinary Development Molecular Anatomy Project is related to: ToppGene Suite |
NIDDK 1U01DK70219; NIDDK P30DK078392; NCRR U54 RR025216; NIDCR U01DE020049 |
PMID:20484371 | Free | OMICS_02225, nlx_152801, biotools:toppcluster | https://bio.tools/toppcluster | SCR_001503 | ToppCluster: A multiple gene list feature analyzer for the dissection of biological systems | 2026-08-04 09:40:24 | 144 | ||||
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StatAlign Resource Report Resource Website 1+ mentions |
StatAlign (RRID:SCR_001892) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software package for Bayesian analysis of protein, DNA and RNA sequences. It utilizes multiple alignments, phylogenetic trees and evolutionary parameters to quantify uncertainty in these analyses. It is written in Java. | software package, bayesian, protein, dna, rna, sequencing, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
PMID:23335014 | Free, Available for download, Freely available | biotools:StatAlign, OMICS_03743 | https://bio.tools/StatAlign | SCR_001892 | StatAlign 2.0 | 2026-08-04 09:40:30 | 1 | ||||||
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FACTA+. Resource Report Resource Website 1+ mentions |
FACTA+. (RRID:SCR_001767) | FACTA+ | data access protocol, software resource, service resource, web service | Text mining tool to discover associations between biomedical concepts from MEDLINE articles. Use the service from your browser or via a Web Service. The whole MEDLINE corpus containing more than 20 million articles is indexed with an efficient text search engine, and it allows you to navigate such associations and their textual evidence in a highly interactive manner - the system accepts arbitrary query terms and displays relevant concepts immediately. A broad range of important biomedical concepts are covered by the combination of a machine learning-based term recognizer and large-scale dictionaries for genes, proteins, diseases, and chemical compounds. There is also a FACTA+ visualization service that can be found here: http://www.nactem.ac.uk/facta-visualizer/ | text mining, gene, protein, disease, symptom, drug, enzyme, compound, biomedical, association, machine learning, chemical, text-mining software, bio.tools |
is listed by: OMICtools is listed by: FORCE11 is listed by: bio.tools is listed by: Debian is related to: MEDLINE has parent organization: National Centre for Text Mining |
JISC | PMID:18772154 | Free, Freely available | biotools:facta_plus, nif-0000-10272, OMICS_01181 | http://refine1-nactem.mc.man.ac.uk/facta/, https://bio.tools/facta_plus | SCR_001767 | Finding Associated Concepts with Text Analysis | 2026-08-04 09:40:28 | 2 | ||||
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ImaGene Resource Report Resource Website 100+ mentions |
ImaGene (RRID:SCR_002178) | data processing software, software application, software resource, data analysis software | Software tool as convolutional neural network to quantify natural selection from genomic data.Supervised machine learning algorithm to predict natural selection and estimate selection coefficients from population genomic data. Can be used to estimate any parameter of interest from evolutionary population genetics model., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microarray analysis, machine vision, convolutional neural network, quantify natural selection, genomic data, population genomic data, evolutionary population, genetics model, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Imperial College London ; Politecnico di Milano |
PMID:31757205 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:ImaGene, OMICS_00841 | https://github.com/mfumagalli/ImaGene, https://bio.tools/ImaGene | http://www.biodiscovery.com/software/imagene/ | SCR_002178 | 2026-08-04 09:40:34 | 405 | |||||
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FusionCatcher Resource Report Resource Website 1+ mentions |
FusionCatcher (RRID:SCR_000060) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software that searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples. | fusion gene, known fusion gene, translocation, chimera, rna-seq data, hiseq, solexa, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/011650 | Free, Available for download, Freely available | biotools:fusioncatcher, OMICS_01348 | https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md, https://bio.tools/fusioncatcher | http://code.google.com/p/fusioncatcher/ | SCR_000060 | 2026-08-04 09:40:03 | 7 | ||||||
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Dissect Resource Report Resource Website |
Dissect (RRID:SCR_000058) | Dissect | data processing software, alignment software, software resource, software application, image analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions. | Structural events containing transcripts, transcriptome-to-genome alignment, identify and characterize transcriptomic events, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Simon Fraser University; British Columbia; Canada |
PMID:22689759 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01346, biotools:dissect | https://bio.tools/dissect | SCR_000058 | Dissect: DIScovery of Structural Events Containing Transcripts, DIScovery of Structural Events Containing Transcripts | 2026-08-04 09:40:03 | 0 | |||||
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SoyBase Resource Report Resource Website 500+ mentions |
SoyBase (RRID:SCR_005096) | SoyBase | data analysis service, analysis service resource, storage service resource, controlled vocabulary, production service resource, service resource, data repository, ontology, database, data or information resource | Professionally curated repository for genetics, genomics and related data resources for soybean that contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. SoyBase includes annotated Williams 82 genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. The repository maintains controlled vocabularies for soybean growth, development, and traits that are linked to more general plant ontologies. Contributions to SoyBase or the Breeder''s Toolbox are welcome. | soybean, gene, genetic map, genome, data set, trait, phenotype, molecular biology, sequence, chromosome, quantitative trait locus, php, genetics, genomics, legume, bio.tools, FASEB list |
is listed by: 3DVC is listed by: re3data.org is listed by: Debian is listed by: bio.tools has parent organization: Iowa State University; Iowa; USA is parent organization of: Soybean Ontologies is parent organization of: Soy Ontology |
USDA Agricultural Research Service | PMID:20008513 | The community can contribute to this resource | nif-0000-03483, r3d100010846, biotools:soybase | https://bio.tools/soybase, https://doi.org/10.17616/R3S032 | SCR_005096 | SoyBase and the Soybean Breeder''s Toolbox, SoyBase and the Soybean Breeder''s Toolbox: Integrating Genetics and Molecular Biology for Soybean Researchers | 2026-08-04 09:41:17 | 646 |
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