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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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KEGG Resource Report Resource Website 10000+ mentions |
KEGG (RRID:SCR_012773) | KEGG | analysis service resource, data access protocol, data analysis service, data or information resource, database, portal, production service resource, service resource, software resource, topical portal, web service | Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies. | model, pathway, functional hierarchy, module, cancer, disease, drug, drug classification, orthology, ortholog, genome, gene, protein, compound, classification, biochemical reaction, pathway, ligand, biosynthesis, pathway prediction, sequence, chemical structure, human, enzyme, database, molecular interaction, metabolism, metabolomics, cellular process, structure, drug development, reaction, cell |
is used by: NIF Data Federation is used by: Arabidopsis Reactome is used by: LIPID MAPS Proteome Database is used by: globaltest is used by: MitoMiner is used by: Database for Annotation Visualization and Integrated Discovery is used by: Biochemical Pathways Reaction Kinetics Database is used by: Ultimate Rough Aggregation of Metabolic Map is used by: GEMINI is used by: In vivo - In silico Metabolite Database is listed by: 3DVC is listed by: OMICtools is affiliated with: Kyoto Encyclopedia of Genes and Genomes Expression Database is related to: PathCase Pathways Database System is related to: ExplorEnz is related to: NCBI BioSystems Database is related to: Allen Institute Neurowiki is related to: eQuilibrator is related to: GeneTrail is related to: KegTools is related to: PRODORIC is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: METLIN is related to: Kidney and Urinary Pathway Knowledge Base is related to: DAVID is related to: ConsensusPathDB is related to: ENZYME is related to: FlyMine is related to: Babelomics is related to: SynSysNet is related to: Cotton EST Database is related to: Integrated Molecular Interaction Database is related to: SEGS is related to: INMEX is related to: BioExtract is related to: ClueGO is related to: MalaCards is related to: TrED is related to: FunTree is related to: MOPED - Model Organism Protein Expression Database is related to: ProOpDB is related to: KOBAS is related to: GeneTerm Linker is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: GeneCodis is related to: FunNet - Transcriptional Networks Analysis is related to: LegumeIP is related to: Algal Functional Annotation Tool is related to: aGEM is related to: DINIES is related to: KEGG PATHWAY Database is related to: ShinyGO is related to: KEGGREST has parent organization: Kyoto University; Kyoto; Japan has parent organization: University of Tokyo; Tokyo; Japan is parent organization of: KegTools works with: DIANA-mirPath works with: MiMeDB |
Japan Science and Technology Agency ; Japanese Ministry of Education Culture Sports Science and Technology MEXT |
PMID:22700311 PMID:22130871 PMID:22080510 PMID:19880382 PMID:19172790 PMID:18428742 PMID:18287706 PMID:18077471 PMID:16381885 PMID:16014746 PMID:14681412 PMID:12539951 PMID:11752249 PMID:10928937 PMID:10592173 PMID:9847135 |
Restricted | nlx_31015, OMICS_01583, OMICS_03010, OMICS_01582, OMICS_03974, OMICS_05434, OMICS_05360 | http://www.genome.jp/kegg/ | SCR_012773 | KEGG - Kyoto Encyclopedia of Genes and Genomes, Kyoto Encyclopedia of Genes and Genomes | 2026-09-12 12:57:52 | 81488 | ||||
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IMGT - the international ImMunoGeneTics information system Resource Report Resource Website 500+ mentions |
IMGT - the international ImMunoGeneTics information system (RRID:SCR_012780) | IMGT | analysis service resource, data analysis service, data or information resource, database, portal, production service resource, service resource, topical portal | A high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates, serving as the global reference in immunogenetics and immunoinformatics. IMGT provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools. | immunogenetics, immunoinformatics, immunoglobulin, antibody, t cell receptor, major histocompatibility complex, immunoglobulin superfamily, major histocompatibility complex superfamily, protein, immune system, sequence, genome, structure, monoclonal antibody, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: IMGT Repertoire has parent organization: Montpellier 2 University; Montpellier; France is parent organization of: IMGT/LIGM-DB is parent organization of: IMGT/GENE-DB is parent organization of: IMGT-ONTOLOGY is parent organization of: IMGT/V-QUEST is parent organization of: IMGT/HLA |
CNRS ; MESR ; Reseau National des Genopoles ; Region Languedoc-Roussillon ; European Union BIOMED1 BIOCT930038; European Union Biotechnology BIOTECH2 BIO4CT960037; European Union 5th PCRDT Quality of Life and Management of Living Resources QLG2-2000-01287; Agence Nationale de la recherche ANR BIOSYS06_135457; EU ImmunoGrid IST-028069 |
PMID:18978023 | nif-0000-03011, biotools:imgt | https://bio.tools/imgt | http://imgt.cines.fr | SCR_012780 | ImMunoGeneTics Information System, IMGT/LIGM, ImMunoGeneTics | 2026-09-12 12:57:52 | 779 | ||||
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Flash Gviewer Resource Report Resource Website 1+ mentions |
Flash Gviewer (RRID:SCR_012870) | Flash GViewer | software resource | Flash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes and QTLs associated with a specific phenotype, etc. rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. In addition the bands on the chromosomes can link to defineable URL and new region selection sliders can be used to select a specific chromosome region and then link out to a genome browser for higher resolution information. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts. This tool is not GO-specific, but was built for the purpose of viewing GO annotation data. Platform: Online tool | visualization, chromosome, video, gene, qtl, genome, navitgation, phenotype, ontology or annotation visualization |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Medical College of Wisconsin; Wisconsin; USA |
Free for academic use | nlx_149333 | http://gmod.org/flashgviewer | SCR_012870 | 2026-09-12 12:57:54 | 2 | |||||||
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Sequencing of Candida Albicans Resource Report Resource Website 10+ mentions |
Sequencing of Candida Albicans (RRID:SCR_013437) | data or information resource, portal, topical portal | The Stanford Genome Technology Center began a whole genome shotgun sequencing of strain SC5314 of Candida albicans. After reaching its original goal of 1.5X mean coverage of the haploid genome (16Mb) in summer, 1998, Stanford was awarded a supplemental grant to continue sequencing up to a coverage of 10X, performing as much assembly of the sequence as possible, using recognizable genes as nucleation points. Candida albicans is one of the most commonly encountered human pathogens, causing a wide variety of infections ranging from mucosal infections in generally healthy persons to life-threatening systemic infections in individuals with impaired immunity. Oral and esophogeal Candida infections are frequently seen in AIDS patients. Few classes of drugs are effective against these fungal infections, and all of them have limitations with regard to efficacy and side-effects. | stanford, genome, technology, shotgun, sequencing, strain, haploid, gene, nucleation, health, life, aids, drug, patient | has parent organization: Stanford University; Stanford; California | Burroughs Wellcome Fund ; NIDCR DE12302-02S2; NIAID RO1AI16567; NIAID RO1AI46351; NIAID NO1AI05406; NIDCR R01DE12940; NIDCR P01DE07946 |
nif-0000-30294 | SCR_013437 | Candida Albicans | 2026-09-12 12:58:03 | 21 | ||||||||
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PlasmoDB Resource Report Resource Website 1000+ mentions |
PlasmoDB (RRID:SCR_013331) | analysis service resource, data access protocol, data analysis service, data or information resource, data repository, database, production service resource, service resource, software resource, storage service resource, web service | Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene. | Functional, genomic, database, malaria, parasite, data, analysis, visualization, gene, genome, annotation, transcription, proteomics, protein, evolution, FASEB list |
uses: SynView is related to: GeneDB Pfalciparum has parent organization: Eukaryotic Pathogen Database Resources has parent organization: Pennsylvania State University has parent organization: University of Georgia; Georgia; USA |
malaria | NIAID | PMID:18957442 | nif-0000-03314, SCR_017665, r3d100011569 | SCR_013331 | PlasmoDB, Plasmodium Genomics Resource, PlasmoDB 5.5, Plasmodium genome-resource | 2026-09-12 12:58:02 | 1324 | ||||||
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PiGenome Resource Report Resource Website |
PiGenome (RRID:SCR_013394) | PiGenome | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database for ESTs (Expressed Sequence Tags), consensus sequences, bacterial artificial chromosome (BAC) clones, BES (BAC End Sequences). They have generated 69,545 ESTs from 6 full-length cDNA libraries (Porcine Abdominal Fat, Porcine Fat Cell, Porcine Loin Muscle, Liver and Pituitary gland). They have also identified a total of 182 BAC contigs from chromosome 6. It is very valuable resources to study porcine quantitative trait loci (QTL) mapping and genome study. Users can explore genomic alignment of various data types, including expressed sequence tags (ESTs), consensus sequences, singletons, QTL, Marker, UniGene and BAC clones by several options. To estimate the genomic location of sequence dataset, their data aligned BES (BAC End Sequences) instead of genomic sequence because Pig Genome has low-coverage sequencing data. Sus scrofa Genome Database mainly provide comparative map of four species (pig, cattle, dog and mouse) in chromosome 6. | gene expression, genome, sequence, gene, expressed sequence tag, consensus sequence, bac clone, bac end sequence, bac contig, quantitative trait loci, singleton, marker, unigene, chromosome 6, blast, transcript, bacterial artificial chromosome, snp, alignment |
is related to: Gene Ontology has parent organization: National Institute of Animal Science; Gyeonggi-do; South Korea |
National Institute of Animal Science; Gyeonggi-do; Korea ; Korean Rural Development Administration ; Biogreen21 Project 20050301034467 |
PMID:19082661 | nlx_153888 | http://pigenome.nabc.go.kr/ | SCR_013394 | Sus scrofa Genome database, Pig Genome Database, Pigenome database | 2026-09-12 12:58:02 | 0 | |||||
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ENIGMA Resource Report Resource Website 100+ mentions |
ENIGMA (RRID:SCR_013400) | data analysis software, data processing software, software application, software resource | A software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering. The modules are further characterized by incorporating other data types, e.g. GO annotation, protein interactions and transcription factor binding information, and by suggesting regulators that might have an effect on the expression of (some of) the genes in the module. Version : ENIGMA 1.1 used GO annotation version : Aug 29th 2007 | genome, gene, genetic software, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium is parent organization of: ENIGMA-DTI Pipeline |
PMID:18402676 | biotools:enigma, nlx_144365 | https://bio.tools/enigma | SCR_013400 | 2026-09-12 12:58:02 | 133 | ||||||||
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Genetic Association Information Network (GAIN) Resource Report Resource Website 1+ mentions |
Genetic Association Information Network (GAIN) (RRID:SCR_013703) | GAIN | consortium, data or information resource, organization portal, portal | The Genetic Association Information Network (GAIN) supports a series of Genome-Wide Association Studies (GWAS) designed to identify specific points of DNA variation associated with the occurrence of a particular common disease. Initially focusing on six major common diseases, GAIN focused on combining the results with clinical data to create a significant new resource for genetic researchers. | tool development, biomarker research, data-sharing enabler, genome, genome wide association studies, FNIH, | has parent organization: Foundation for the National Institutes of Health | Pfizer Inc ; Affymetrix Inc |
SCR_013703 | 2026-09-12 12:58:07 | 9 | |||||||||
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RAST Server Resource Report Resource Website 1000+ mentions |
RAST Server (RRID:SCR_014606) | RAST | production service resource, service resource | A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes. | microbiome, seed, annotate, genome, bacteria, archaea, service, bio.tools |
is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools |
National Science Foundation 0850546; NIAID contract HHSN272200900040C |
PMID:18261238 | Free for the scientific community, Login required | biotools:theseed | https://bio.tools/theseed | SCR_014606 | Rapid Annotation using Subsystem Technology, Rapid Annotation using Subsystem Technology Server | 2026-09-12 12:58:19 | 1198 | ||||
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Prokka Resource Report Resource Website 1000+ mentions |
Prokka (RRID:SCR_014732) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | annotation, prokaryote, genome, prokaryotic genome, sequence analysis software, annotation software, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btu153 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04220, biotools:prokka | https://bio.tools/prokka, https://sources.debian.org/src/prokka/, https://sources.debian.org/src/prokka/ | SCR_014732 | 2026-09-12 12:58:21 | 4882 | |||||||
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EnteroBase Resource Report Resource Website 100+ mentions |
EnteroBase (RRID:SCR_019019) | data access protocol, data or information resource, database, software resource, web service | Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella. | Bacteria, pathogen, genome, Illumina short read, genotype, core genome multilocus, sequence typing, cgMLST, cgMLST sequence, bacterial strain mapping, visualizing genomic variation, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: University of Warwick; Coventry; United Kingdom |
Biotechnology and Biological Sciences Research Council ; Wellcome Trust |
Restricted | biotools:Enterobase | https://bio.tools/EnteroBase | SCR_019019 | 2026-09-12 12:59:08 | 317 | |||||||
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Differential Methylation Analysis Package Resource Report Resource Website |
Differential Methylation Analysis Package (RRID:SCR_019148) | DMAP | data analysis software, data processing software, software application, software resource, software toolkit | Software package for large scale genomic DNA methylation analysis. Filters and processes aligned bisulphite sequenced data to generate comprehensive reference methylomes in different units for any genome. Processes aligned SAM files of multiple samples to provide reliable and statistically significant differentially methylated regions, then relate them to proximal genes and CpG features with reasonable rapidity. | Genomic DNA methylation, DNA methylation analysis, bisulphite sequenced data, reference methylomes generation, genome, aligned SAM files processing, differentially methylated regions | has parent organization: University of Otago; Dunedin; New Zealand | National Centre for Growth and Development and Health Research Council ; New Zealand |
PMID:24608764 | Free, Freely available | SCR_019148 | 2026-09-12 12:59:10 | 0 | |||||||
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IGB Resource Report Resource Website 100+ mentions |
IGB (RRID:SCR_011792) | IGB | software resource | An easy-to-use, highly customizable genome browser you can use to visualize and explore genomic data and annotations, including RNA-Seq, ChIP-Seq, tiling array data, and more. | genome, rna-seq, chip-seq, tiling array, browser |
is listed by: OMICtools has parent organization: University of North Carolina at Charlotte; North Carolina; USA |
PMID:19654113 | Free, Acknowledgement requested | OMICS_00916 | SCR_011792 | Integrated Genome Browser | 2026-09-12 12:57:39 | 354 | ||||||
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GenomeCloud Resource Report Resource Website |
GenomeCloud (RRID:SCR_011886) | GenomeCloud | data repository, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 29, 2019. A cloud platform for next-generation sequencing analysis and storage. Services include: * g-Analysis: Automated genome analysis pipelines at your fingertips * g-Cluster: Easy-of-use and cost-effective genome research infrastructure * g-Storage: A simple way to store, share and protect data * g-Insight: Accurate analysis and interpretation of biological meaning of genome data | genome | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01219 | SCR_011886 | 2026-09-12 12:57:41 | 0 | ||||||||
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JiffyNet Resource Report Resource Website 1+ mentions |
JiffyNet (RRID:SCR_011954) | analysis service resource, data analysis service, production service resource, service resource, simulation software, software application, software resource | Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species. | protein network, protein, network, genome, sequence, pathway annotation, network visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Yonsei University; Seoul; South Korea |
National Research Foundation of Korea ; Next-Generation BioGreen 21 Program |
PMID:23685435 | Free, Freely available | OMICS_01548, biotools:jiffynet | https://bio.tools/jiffynet | SCR_011954 | 2026-09-12 12:57:42 | 1 | ||||||
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GenomeJack Resource Report Resource Website 10+ mentions |
GenomeJack (RRID:SCR_012026) | GenomeJack | software resource | A genome browser specialized in next-generation sequencing data. | next-generation sequencing, genome, browser, analysis | is listed by: OMICtools | Free, Public | OMICS_02143 | SCR_012026 | 2026-09-12 12:57:43 | 35 | ||||||||
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BECA Resource Report Resource Website 1+ mentions |
BECA (RRID:SCR_015846) | BECA | data processing software, data visualization software, image analysis software, software application, software resource | Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version. | visual exploration, brain, neuroscience, network, genetic determinant, fmri, neuroimaging, genome | has parent organization: Indiana University School of Medicine; Indiana; USA | NIA P30 AG10133; NIA R01 AG19771; NIA RC2 AG036535; NIA U01 AG024904; NIBIB R01 EB022574; NLM R01 LM011360; NSF IIS-1117335 |
PMID:27171688 | Free, Available for download | SCR_015846 | Brain Explorer for Connectome Analysis (BECA), BECA - Brain Explorer for Connectome Analysis | 2026-09-12 12:58:31 | 5 | ||||||
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Alliance of Genome Resources Resource Report Resource Website 50+ mentions |
Alliance of Genome Resources (RRID:SCR_015850) | access service resource, consortium, data or information resource, organization portal, portal, service resource | Organization that aims to develop and maintain sustainable genome information resources to promote understanding of the genetic and genomic basis of human biology, health, and disease. The Alliance is composed of FlyBase, Mouse Genome Database (MGD), the Gene Ontology Consortium (GOC), Saccharomyces Genome Database (SGD), Rat Genome Database (RGD), WormBase, and the Zebrafish Information Network (ZFIN). | gene ontology, human biology, genome, organism model, gene ontology consortium, FASEB list, DRKB |
has organization facet: WormBase has organization facet: Mouse Genome Databases has organization facet: FlyBase has organization facet: Gene Ontology has organization facet: SGD has organization facet: Rat Genome Database (RGD) has organization facet: Zebrafish Information Network (ZFIN) |
NHGRI U41HG02223E; NIH HG010859 |
SCR_015850 | The Alliance | 2026-09-12 12:58:31 | 87 | |||||||||
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Cross-species scaffolding Resource Report Resource Website 1+ mentions |
Cross-species scaffolding (RRID:SCR_015932) | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Super-scaffolding of draft genome assemblies with in silico mate-pair libraries derived from (closely) related references. | mate, pair, end, reference, genome | Free, Available for download, Freely available | SCR_016125 | SCR_015932 | cross-species-scaffolding | 2026-09-12 12:58:32 | 1 | |||||||||
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Piggy Resource Report Resource Website 10+ mentions |
Piggy (RRID:SCR_015941) | data analysis software, data processing software, software application, software resource | Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary). | intergenic, region, bacterial, analysis, gene, genome, assembly | Medical Research Council | Free, Available for download | SCR_015941 | 2026-09-12 12:58:32 | 32 |
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