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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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KI Biobank - TwinGene Resource Report Resource Website 10+ mentions |
KI Biobank - TwinGene (RRID:SCR_006006) | TwinGene | biomaterial supply resource, material resource | In collaboration with GenomeEUtwin, the TwinGene project investigates the importance of quantitative trait loci and environmental factors for cardiovascular disease. It is well known that genetic factors are of considerable importance for some familial lipid syndromes and that Type A Behavior pattern and increased lipid levels infer increased risk for cardiovascular disease. It is furthermore known that genetic factors are of importance levels of blood lipid biomarkers. The interplay of genetic and environmental effects for these risk factors in a normal population is less well understood and virtually unknown for the elderly. In the TwinGene project twins born before 1958 are contacted to participate. Health and medication data are collected from self-reported questionnaires, and blood sampling material is mailed to the subject who then contacts a local health care center for blood sampling and a health check-up. In the simple health check-up, height, weight, circumference of waist and hip, and blood pressure are measured. Blood is sampled for DNA extraction, serum collection and clinical chemistry tests of C-reactive protein, total cholesterol, triglycerides, HDL and LDL cholesterol, apolipo��protein A1 and B, glucose and HbA1C. The TwinGene cohort contains more than 10000 of the expected final number of 16000 individuals. Molecular genetic techniques are being used to identify Quantitative Trait Loci (QTLs) for cardiovascular disease and biomarkers in the TwinGene participants. Genome-wide linkage and association studies are ongoing. DZ twins have been genome-scanned with 1000 STS markers and a subset of 300 MZ twins have been genome-scanned with Illumina 317K SNP platform. Association of positional candidate SNPs arising from these genomscans are planned. The TwinGene project is associated with the large European collaboration denoted GenomEUtwin (www.genomeutwin.org, see below) which since 2002 has aimed at gathering genetic data on twins in Europe and setting up the infrastructure needed to enable pooling of data and joint analyses. It has been the funding source for obtaining the genome scan data. Types of samples: * EDTA whole blood * DNA * Serum Number of sample donors: 12 044 (sample collection completed) | quantitative trait loci, environmental factor, cardiovascular disease, environment, genetic, gene, lipid syndrome, lipid, health, medication, questionnaire, c-reactive protein, total cholesterol, triglyceride, hdl, ldl, cholesterol, apolipo-protein a1, apolipo-protein b, glucose, hba1c, genome-wide linkage study, genome-wide association study, genome |
is listed by: One Mind Biospecimen Bank Listing is related to: GenomEUtwin is related to: Swedish Twin Registry has parent organization: Karolisnka Biobank |
Twin | NIH ; European Union ; VR ; SSF |
nlx_151387 | http://ki.se/ki/jsp/polopoly.jsp?d=29354&a=31600&l=en | SCR_006006 | 2026-09-12 01:02:35 | 19 | ||||||
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Ensembl Protists Resource Report Resource Website 10+ mentions |
Ensembl Protists (RRID:SCR_013154) | data or information resource, database | 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 | 2026-09-12 01:02:09 | 48 | |||||||||
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GiardiaDB Resource Report Resource Website 100+ mentions |
GiardiaDB (RRID:SCR_013377) | data or information resource, database | 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 | 2026-09-12 01:02:11 | 108 | ||||||||||
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Cube-DB Resource Report Resource Website 1+ mentions |
Cube-DB (RRID:SCR_013233) | Cube-DB | data or information resource, database | 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 | 2026-09-12 01:02:10 | 3 | ||||||
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Planteome Resource Report Resource Website 10+ mentions |
Planteome (RRID:SCR_014411) | data or information resource, database | 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 | 2026-09-12 01:02:14 | 28 | ||||||||||
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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 | 2026-09-12 01:02:13 | 65 | |||||||
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RiceGE Resource Report Resource Website 50+ mentions |
RiceGE (RRID:SCR_015061) | data or information resource, database | 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 | 2026-09-12 01:02:15 | 87 | ||||||||
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HumanBase Resource Report Resource Website 50+ mentions |
HumanBase (RRID:SCR_016145) | data or information resource, database | 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 | NCI T32 CA009528; NHGRI R01 HG005998; NHGRI T32 HG003284; NHLBI U54 HL117798; NIGMS P20 GM103534; NIGMS P50 GM071508; NIGMS R01 GM071966; 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 | 2026-09-12 01:02:16 | 95 | ||||||||
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Genome Aggregation Database Resource Report Resource Website 5000+ mentions |
Genome Aggregation Database (RRID:SCR_014964) | gnomAD | data or information resource, database | 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 | 2026-09-12 01:02:15 | 5310 | |||||
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RegulomeDB Resource Report Resource Website 100+ mentions |
RegulomeDB (RRID:SCR_017905) | data or information resource, database, 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 | Beta Cell Consortium ; NHGRI U54 HG 004558 |
PMID:22955989 | Free, Freely available | SCR_017905 | 2026-09-12 01:02:18 | 161 | |||||||||
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ABA Mouse Brain: Atlas Resource Report Resource Website 100+ mentions |
ABA Mouse Brain: Atlas (RRID:SCR_017479) | data or information resource, database, 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 | 2026-09-12 01:02:18 | 405 | ||||||||
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Molecular Signatures Database Resource Report Resource Website 1000+ mentions |
Molecular Signatures Database (RRID:SCR_016863) | MSigDB | data or information resource, database | 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 |
NCI CA295532; NIGMS ; NIH |
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 | 2026-09-12 01:02:17 | 1702 | ||||||
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GENCODE Resource Report Resource Website 5000+ mentions Rating or validation data |
GENCODE (RRID:SCR_014966) | data or information resource, dataset, portal, project portal | Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation. | human, mouse, genome, annotation, sequence, gene features, bio.tools |
is listed by: Debian is listed by: bio.tools is affiliated with: ENCODE |
NHGRI 5U54HG004555; Wellcome Trust WT098051 |
PMID:22955987 | Free | biotools:GENCODE | https://bio.tools/GENCODE | SCR_014966 | ENCODE | 2026-09-12 01:01:03 | 8811 | |||||
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EASE: the Expression Analysis Systematic Explorer Resource Report Resource Website 50+ mentions |
EASE: the Expression Analysis Systematic Explorer (RRID:SCR_013361) | EASE | data processing software, software application, software resource | Windows(c) desktop software application, customizable and standalone, that facilitates the biological interpretation of gene lists derived from the results of microarray, proteomic, and SAGE experiments. Provides statistical methods for discovering enriched biological themes within gene lists, generates gene annotation tables, and enables automated linking to online analysis tools. Offers statistical models to deal with multi-test comparison problem. Platform: Windows compatible | gene, microarray, genome, gene ontology, statistical analysis, enrichment analysis, FASEB list |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Database for Annotation Visualization and Integrated Discovery |
NIAID | PMID:12734009 PMID:19131956 PMID:19033363 |
Free for academic use | nlx_149218 | SCR_013361 | Expression Analysis Systematic Explorer | 2026-09-12 01:01:01 | 94 | |||||
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Saccharomyces Genome Deletion Project Resource Report Resource Website 10+ mentions |
Saccharomyces Genome Deletion Project (RRID:SCR_014961) | data or information resource, database, portal, project portal | Database and project to reveal open reading frames (ORFs) in the yeast genome in order to discover their functions. A PCR-based gene deletion strategy is used to assign functions through phenotypic analysis of mutants. | yeast, open reading frames, ORF, genome, deletion, Saccharomyces cerevisiae | Free | SCR_014961 | 2026-09-12 01:01:03 | 19 | |||||||||||
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4D Nucleome Resource Report Resource Website 10+ mentions |
4D Nucleome (RRID:SCR_016925) | data or information resource, portal, project portal | Research project to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development and diseases. Portal provides free access to datasets, software packages, and protocols to advance biomedical research of nuclear architecture. Aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes. | nuclear, organization, gene, expression, cellular, function, normal, development, disease, map, structure, human, mouse, genome |
is listed by: NIDDK Information Network (dkNET) is related to: International Human Epigenome Consortium |
NIH Common Fund | PMID:28905911 | Public | SCR_016925 | 4D Nucleome Network; 4DN Web Portal, The 4D nucleome project, 4DN Portal | 2026-09-12 01:01:04 | 30 | |||||||
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rnaQUAST Resource Report Resource Website 1+ mentions |
rnaQUAST (RRID:SCR_016994) | data processing software, software application, software resource | Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software. | evaluation, quality, RNA-Seq, assembly, data, transcriptome, assembler, reference, genome, gene, database, raw, read, , bio.tools |
uses: BUSCO is listed by: Debian is listed by: bio.tools is related to: rnaSPAdes is related to: Python Programming Language is related to: SPAdes |
EMC Research and Development Department ; St. Petersburg State University ; Russia |
PMID:27153654 | Free, Available for download, Freely available | biotools:rnaQUASt | https://bio.tools/rnaQUAST | SCR_016994 | 2026-09-12 01:01:05 | 4 | ||||||
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Whole Genome Shotgun (WGS) Project Resource Report Resource Website 1+ mentions |
Whole Genome Shotgun (WGS) Project (RRID:SCR_016637) | WGS | data processing software, software application, software resource | Project for assemblies of incomplete genomes or incomplete chromosomes of prokaryotes or eukaryotes that are being sequenced by a whole genome shotgun strategy. WGS projects may be annotated, but annotation is not required. The nucleotide and protein data from all WGS projects go into the BLAST database. | assembly, incomplete, chromosome, prokaryote, eukaryote, sequenced, whole, genome, shot, gun, strategy, data |
has parent organization: NCBI works with: NCBI BLAST |
National Library of Medicine | SCR_016637 | Whole Genome Shotgun WGS Project, Whole Genome Shotgun WGS, WGS Projects, Whole Genome Shotgun | 2026-09-12 01:01:04 | 9 | ||||||||
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Gene-conservation-informed-contig-alignment Resource Report Resource Website 1+ mentions |
Gene-conservation-informed-contig-alignment (RRID:SCR_017617) | GCICA | data processing software, software application, software resource | Software tool for separation haplotigs from genome assembly. Method to separate haplotigs based on sequence similarity. | Separation, haplotig, genome, assembly, sequence, similarity | Free, Available for download, Freely available | SCR_017617 | 2026-09-12 01:01:06 | 1 | ||||||||||
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TGS-GapCloser Resource Report Resource Website 10+ mentions |
TGS-GapCloser (RRID:SCR_017633) | data processing software, software application, software resource | Software tool that uses long reads to enhance genome assembly. Fast and accurate gap closing software tool that uses low coverage of error-prone long reads generated by third generation sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs for large genomes. | Error, prone, third, generation, sequencing, long, read, gap, closing, genome, assembly, contig, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:tGS-GapCloser | https://bio.tools/TGS-GapCloser | SCR_017633 | 2026-09-12 01:01:06 | 45 |
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