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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SVA Resource Report Resource Website 10+ mentions |
SVA (RRID:SCR_002155) | SVA | software application, commercial organization, software resource | Software package to annotate, visualize, and analyze the genetic variants identified through next-generation sequencing studies, including whole-genome sequencing (WGS) and exome sequencing studies. SVA aims to provide the research community with a user-friendly and efficient tool to analyze large amount of genetic variants, and to facilitate the identification of the genetic causes of human diseases and related traits. | gene, genetic, genomic, annotate, visualize, genetic variant, next-generation sequencing, whole-genome sequencing, exome, sequencing, genome, disease, trait, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Duke University School of Medicine; North Carolina; USA |
PMID:21624899 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154666, OMICS_00190, biotools:sequencevariantanalyzer | http://www.svaproject.org/, https://bio.tools/sequencevariantanalyzer | SCR_002155 | Sequence Variant Analyzer, SVA: Sequence Variant Analyzer | 2026-08-04 09:40:34 | 16 | |||||
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Ensembl Protists Resource Report Resource Website 10+ mentions |
Ensembl Protists (RRID:SCR_013154) | database, data or information resource | The Ensembl Genomes project produces genome databases for important species from across the taxonomic range, using the Ensembl software system. Five sites are now available, one of which is Ensembl Protists, which houses protists species. Sponsors: EnsembProtists is a project run by EMBL - EBI to maintain annotation on selected genomes, based on the software developed in the Ensembl project developed jointly by the EBI and the Wellcome Trust Sanger Institute. | database, genome, protist, software, specie, taxonomic | has parent organization: Ensembl | r3d100011200, nif-0000-33712 | SCR_013154 | EnsemblProtists | 2026-08-04 09:43:09 | 44 | |||||||||
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Mouse Genome Database Resource Report Resource Website 500+ mentions |
Mouse Genome Database (RRID:SCR_012953) | MGD | database, data or information resource | Community model organism database for laboratory mouse and authoritative source for phenotype and functional annotations of mouse genes. MGD includes complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics.Contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology. | gene, genome, genetic, chromosome, clone, cytogenetic, dna, genomic, inbred, mammalian, mouse, mutant, ortholog, phenotype, primer, protein, reagent, sequence, strain, bio.tools |
is used by: DisGeNET is listed by: Debian is listed by: bio.tools is related to: Mouse Genome Informatics (MGI) has parent organization: Jackson Laboratory |
NHGRI HG000330 | PMID:21051359 | biotools:mgi, biotools:mgd, nif-0000-10301 | http://www.informatics.jax.org/mgihome/projects/overview.shtml, https://bio.tools/mgd, https://bio.tools/mgi | SCR_012953 | Mouse Genome Informatics: Mouse Genome Database, MGID, Mouse Genome Informatics Database | 2026-08-04 09:43:06 | 502 | |||||
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Cube-DB Resource Report Resource Website 1+ mentions |
Cube-DB (RRID:SCR_013233) | Cube-DB | database, data or information resource | Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family classification follows (largely) the classification suggested by HUGO Gene Nomenclature Committee. Sets of orhtologous protein sequences were generated by mutual-best-hit strategy using full vertebrate genomes available in Ensembl. The scores, described on documentation page, are assigned to each individual residue in a protein, and presented in the form of a table (html or downloadable xls formats) and mapped, when appropriate, onto the related structure (Jmol, Pymol, Chimera). | protein, functional divergence, vertebrate, genome, ortholog, protein sequence, data set, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Bioinformatics Institute; Singapore; Singapore |
PMID:22139934 | nlx_149432, biotools:cube-db | https://bio.tools/cube-db | SCR_013233 | Cube-DB: Detection of Functional Divergence in Human Protein Families | 2026-08-04 09:43:10 | 3 | ||||||
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Baylor College of Medicine Human Genome Sequencing Center Resource Report Resource Website 50+ mentions |
Baylor College of Medicine Human Genome Sequencing Center (RRID:SCR_013605) | BCM-HGSC | analysis service resource, production service resource, service resource | Center for high-throughput DNA sequence generation and the accompanying analysis. The sequence data generated by the center's machines are analyzed in a complex bioinformatics pipeline, and the data are deposited regularly in the public databases at the National Center for Biotechnology Information (NCBI). | next-generation sequencing, genetic variation, genome, dna sequence, FASEB list |
has parent organization: Baylor University; Texas; USA is parent organization of: Mercury is parent organization of: xAtlas |
NIH Office of the Director R24 OD011173 | nif-0000-10162 | SCR_013605 | Human Genome Sequencing Center, BCM HGSC | 2026-08-04 09:43:14 | 65 | |||||||
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GiardiaDB Resource Report Resource Website 100+ mentions |
GiardiaDB (RRID:SCR_013377) | database, data or information resource | GiardiaDB is a resource for information on Giardia lamblia. It contains gene information, including genomic attributes, protein expression patterns, evolution, and EST sequence information. The website provides tools for BLASTing, sequence retrieval, graphic visualization, and PubMed information. | genome, giardia lamblia, protein expression, FASEB list | nif-0000-02908, r3d100012458 | SCR_013377 | GiardiaDB | 2026-08-04 09:43:12 | 100 | ||||||||||
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Planteome Resource Report Resource Website 10+ mentions |
Planteome (RRID:SCR_014411) | database, data or information resource | An international collaborative effort to develop and enrich new and existing reference ontologies for plants, improve ontology use and cross-references, and to develop data annotation standards. Users can search for ontology terms and bioentities and submit the ontology-related term requests by visiting the following GitHub request trackers. | database, ontology, plant, genome | NSF IOS:1340112 | Available to the research community, Only registered users of the GitHub website are allowed to submit requests and make suggestions or comments | SCR_014411 | 2026-08-04 09:43:25 | 26 | ||||||||||
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RiceGE Resource Report Resource Website 50+ mentions |
RiceGE (RRID:SCR_015061) | database, data or information resource | Gene database for Japonica rice. RiceGE is associated with SIGnAL at the Salk Institute. | japonica rice, rice, gene, genome | has parent organization: SIGnAL Salk Institute Genomic Analysis Laboratory | Freely available | http://signal.salk.edu/cgi-bin/RiceGE5 | SCR_015061 | RiceGE: Genome Express Database, Rice Functional Genomic Express Database | 2026-08-04 09:43:34 | 73 | ||||||||
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Genome Aggregation Database Resource Report Resource Website 1000+ mentions |
Genome Aggregation Database (RRID:SCR_014964) | gnomAD | database, data or information resource | Database that aggregates exome and genome sequencing data from large-scale sequencing projects. The gnomAD data set contains individuals sequenced using multiple exome capture methods and sequencing chemistries. Raw data from the projects have been reprocessed through the same pipeline, and jointly variant-called to increase consistency across projects. | database, genome, , bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: Broad Institute Genomics Platform has parent organization: Broad Institute has parent organization: Broad Institute of MIT and Harvard |
Broad Institute | Open source, Available to the biomedical community, The community can contribute to this resource | biotools:gnomad | https://github.com/macarthur-lab/gnomad_browser/issues, https://bio.tools/gnomad | SCR_014964 | gnomAD 2.0, gnomAD Browser, gnomAD version 2.0, Exome Aggregation Consortium | 2026-08-04 09:43:33 | 4229 | |||||
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RegulomeDB Resource Report Resource Website 100+ mentions |
RegulomeDB (RRID:SCR_017905) | database, data or information resource, service resource | Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature. | Annotate, SNP, regulatory, DNA, element, intergenic, region, human, genome, sequence, DNAase, hypersensitivity, binding, site, transcription, factor, promoter, region, data, FASEB list | NHGRI U54 HG 004558; Beta Cell Consortium |
PMID:22955989 | Free, Freely available | SCR_017905 | 2026-08-04 09:44:15 | 123 | |||||||||
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HumanBase Resource Report Resource Website 50+ mentions |
HumanBase (RRID:SCR_016145) | database, data or information resource | Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations. | genome, analysis, tissue, network, gene, machine, learning, biology | NIGMS R01 GM071966; NHGRI R01 HG005998; NHLBI U54 HL117798; NIGMS P20 GM103534; NHGRI T32 HG003284; NCI T32 CA009528; NIGMS P50 GM071508; US Department Of Health And Human Services HHSN272201000054C |
PMID:25915600 | Free, Public | SCR_016145 | GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), GIANT | 2026-08-04 09:43:50 | 74 | ||||||||
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ABA Mouse Brain: Atlas Resource Report Resource Website 100+ mentions |
ABA Mouse Brain: Atlas (RRID:SCR_017479) | database, data or information resource, service resource | Genome wide database of gene expression in mouse brain. Genome-wide atlas of gene expression in the adult mouse brain. | Genome, data, gene, expression, mouse, brain |
has parent organization: Allen Institute for Brain Science is provided by: Allen Brain Atlas |
PMID:17151600 | Free, Freely available | SCR_017479 | Allen Brain Atlas: Mouse Brain, , Allen Brain Atlas Mouse Brain: Atlas | 2026-08-04 09:44:10 | 328 | ||||||||
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Molecular Signatures Database Resource Report Resource Website 500+ mentions |
Molecular Signatures Database (RRID:SCR_016863) | MSigDB | database, data or information resource | Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software. | collection, annotated, gene, set, GSEA, enrichment, analysis, genome, RNA, expression, data, FASEB list, DRKB |
uses: GSEA uses: Gene Set Enrichment Analysis has parent organization: Broad Institute |
NIH ; NIGMS ; NCI CA295532 |
Free, Freely available, Registration required to download GSEA software | https://www.gsea-msigdb.org/gsea/msigdb/ | SCR_016863 | Molecular Signatures Database, The Molecular Signatures Database, MSigDB, MSigDB database v6.2 | 2026-08-04 09:44:00 | 762 | ||||||
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GTOP - Genomes To Protein structures Resource Report Resource Website 1+ mentions |
GTOP - Genomes To Protein structures (RRID:SCR_007698) | database, data or information resource | GTOP is a database consists of data analyses of proteins identified by various genome projects. This database mainly uses sequence homology analyses and features extensive utilization of information on three-dimensional structures. GTOP is built by the Laboratory of Gene-Product Informatics at the National Institute of Genetics. This research is supported by the Japan Science and Technology Corporation and Grants-in-Aid for Scientific Research (Genomes in category C) from the Ministry of Education, Science, Sports and Culture of Japan. We use the following methods: Prediction of 3D structure Sequence homology search of PDB, using REVERSE PSI-BLAST. Functional predictions (family classifications) Sequence homology search of Swiss-Prot, a well-annotated sequence database, with the use of BLAST. Other analytical methods We are also carrying out the following analyses: Motif Analysis(PROSITE) Family classification(Pfam) Prediction of transmembrane helix domains(SOSUI) Prediction of coiled-coil regions(Multicoil) Repetitive sequence analysis(RepAlign) | genome, protein, sequence homology | has parent organization: National Institute of Genetics; Shizuoka; Japan | nif-0000-02931 | SCR_007698 | GTOP | 2026-08-04 09:41:58 | 6 | |||||||||
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LEGER: the post-genome Database for Listeria Research Resource Report Resource Website 1+ mentions |
LEGER: the post-genome Database for Listeria Research (RRID:SCR_007760) | database, data or information resource | Knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species.Provides information on gene functions (as annotated or supposed by literature from homologous organisms) , protein expression levels under defined experimental conditions ,subcellular localization of proteins (expected and/or experimentally validated) , biological meaning of genes and proteins based on KEGG, InterPro and Gene Ontology. | Proteome, functional, genome, data, protein, expression, subcellular, localization | German Bundesministerium für Bildung und Forschung (BMBF) | PMID:16381897 | Free, Freely available | nif-0000-03077 | SCR_007760 | Proteome Database LEGER | 2026-08-04 09:41:56 | 2 | |||||||
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PhylomeDB Resource Report Resource Website 50+ mentions |
PhylomeDB (RRID:SCR_007850) | database, data or information resource | Database for phylomes, that is, complete collections of phylogenetic trees for all proteins encoded in a given genome. It aims at providing a repository of high-quality phylogenies and alignments for proteins encoded in model species. To derive a phylome, each protein encoded in a given genome is used as a seed to retrieve its homologs in other complete genomes. These sequences are aligned and processed to derive reliable phylogenies using several phylogenetic methods. Besides providing the evolutionary history of the gene families, phylomeDB includes phylogeny based predictions of orthology and paralogy relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Genome-wide collections, gene phylogenies, phylogenetic trees collection, proteins encoded, genome, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:17962297 PMID:21075798 PMID:24275491 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03281, biotools:PhylomeDb | https://bio.tools/PhylomeDB | SCR_007850 | PhylomeDB | 2026-08-04 09:41:58 | 52 | ||||||
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Cytokine Family Database Resource Report Resource Website 1+ mentions |
Cytokine Family Database (RRID:SCR_008134) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. A collection of cDNA, gene and protein records of cytokines deposited in public databases provides various information about the cytokine members of vertebrates in other databases including NCBI GenBank, Swiss-Prot, UniGene, TIGR (The Institute for Genomic Research) Gene Indices, Ensembl, Entrez Gene, Mouse Genome Informatics (MGI) and Rat Genome Database (RGD). It also provides orthologous relationship of cytokine members and includes novel members identified in the databases. | family, fish, gene, amphibian, bird, cdna, chemokine, cow, cytokine, genome, human, mammalian, mouse, oncogene, phylogenetic, protein, rat, receptor, reptile, virus |
is listed by: 3DVC has parent organization: Kumamoto University; Kumamoto; Japan |
Japan Society for the Promotion of Science | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20948 | http://cytokine.medic.kumamoto-u.ac.jp/ | SCR_008134 | dbCFC | 2026-08-04 09:42:03 | 1 | ||||||
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Animal Genome Database Resource Report Resource Website 1+ mentions |
Animal Genome Database (RRID:SCR_008165) | database, data or information resource | Database of comparative gene mapping between species to assist the mapping of the genes related to phenotypic traits in livestock. The linkage maps, cytogenetic maps, polymerase chain reaction primers of pig, cattle, mouse and human, and their references have been included in the database, and the correspondence among species have been stipulated in the database. AGP is an animal genome database developed on a Unix workstation and maintained by a relational database management system. It is a joint project of National Institute of Agrobiological Sciences (NIAS) and Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF-Institute), under cooperation with other related research institutes. AGP also contains the Pig Expression Data Explorer (PEDE), a database of porcine EST collections derived from full-length cDNA libraries and full-length sequences of the cDNA clones picked from the EST collection. The EST sequences have been clustered and assembled, and their similarity to sequences in RefSeq, and UniGene determined. The PEDE database system was constructed to store sequences and similarity data of swine full-length cDNA libraries and to make them available to users. It provides interfaces for keyword and ID searches of BLAST results and enables users to obtain sequence data and names of clones of interest. Putative SNPs in EST assemblies have been classified according to breed specificity and their effect on coding amino acids, and the assemblies are equipped with an SNP search interface. The database contains porcine nucleotide sequences and cDNA clones that are ready for analyses such as expression in mammalian cells, because of their high likelihood of containing full-length CDS. PEDE will be useful for researchers who want to explore genes that may be responsible for traits such as disease susceptibility. The database also offers information regarding major and minor porcine-specific antigens, which might be investigated in regard to the use of pigs as models in various medical research applications. | est, expression, gene, amino acid, animal, antigen, breed, cattle, cdna, cell, chain, clone, coding, cytogenetic, genome, human, linkage, livestock, mammalian, map, mouse, nucleotide, organism, phenotypic, pig, polymerase, porcine, primer, reaction, sequence, snp, specie, swine, trait | has parent organization: National Institute of Agrobiological Sciences; Ibaraki; Japan | nif-0000-21029 | SCR_008165 | AGP | 2026-08-04 09:42:03 | 1 | |||||||||
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Silkworm Genome Database Resource Report Resource Website 1+ mentions |
Silkworm Genome Database (RRID:SCR_008242) | database, data or information resource | Silkbase''s objective is to build a foundation for the complete genome analysis of Bombyx mori. | anopheles gambiae, bombyx mori, drosophila, genome, moth, samia cynthia invertebrate databases | has parent organization: University of Tokyo; Tokyo; Japan | nif-0000-21370 | SCR_008242 | Silkworm Genome Database | 2026-08-04 09:42:05 | 3 | |||||||||
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Peroxisome Database Resource Report Resource Website 10+ mentions |
Peroxisome Database (RRID:SCR_008352) | database, data or information resource | The aim of the PEROXISOME database (PeroxisomeDB) is to gather, organize and integrate curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders. PeroxisomeDB contains the complete peroxisomal proteome of Homo sapiens (encoded by 85 genes) and Saccharomyces cerevisiae (encoded by 61 genes). Now, we have included 34 new organism genomes with the acquisition of 2426 new peroxisomal homolog proteins. PeroxisomeDB 2.0 integrates the peroxisomal metabolome of whole microbody family by the new incorporation of the glycosome proteomes of trypanosomatids and the glyoxysome proteome of Arabidopsis thaliana. The site also provides a Peroxisome Metabolome of peroxisomal genes and proteins, their molecular interactions and metabolic pathways, tools for comparative genomics, predictive tools. Sponsors: Preoxisome Database is funded by Institut de Gntique et deBiologie Molculaire et Cellulaire. | family, function, gene, arabidopsis thaliana, disorder, genome, genomic, glycosome, glyoxysome, homolog, homo sapiens, interaction, metabolic, metabolome, microbody, molecular, organism, pathway, peroxisome, protein, proteome, saccharomyces cerevisiae, trypanosomatid | nif-0000-25216 | SCR_008352 | Preoxisomedb | 2026-08-04 09:42:06 | 27 |
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