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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Bgee: dataBase for Gene Expression Evolution Resource Report Resource Website 50+ mentions |
Bgee: dataBase for Gene Expression Evolution (RRID:SCR_002028) | Bgee | database, data or information resource | Database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data) to anatomy and development of different species. Bgee is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of gene expression. | gene expression, scrna-seq, rna-seq, affymetrix, in situ hybridization, expressed sequence tag, cross specie, comparison, homology, anatomy, developmental stage, gene expression pattern, development, genome, function, chordate, fish, transcriptiome, embryo, adult, mirna, protein coding, prenatal, immature, post-embryonic development, alimentary system, cardiovascular system, nervous system, renal system, reproductive system, respiratory system, skeletal system, ortholog, ontology, FASEB list |
is related to: Gene Expression Omnibus is related to: NCBI Sequence Read Archive (SRA) is related to: ArrayExpress is related to: Zebrafish Information Network (ZFIN) is related to: Xenbase is related to: Mouse Genome Informatics (MGI) is related to: Berkeley Drosophila Genome Project is related to: UniGene is related to: Zebrafish Anatomical Ontology is related to: eVOC is related to: Adult Mouse Anatomy Ontology is related to: Xenopus Anatomy Ontology is related to: Drosophila anatomy and development ontologies is related to: Ensembl has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: University of Lausanne; Lausanne; Switzerland |
Free, Freely available | nif-0000-11819, r3d100014596 | https://doi.org/10.17616/R31NJNR8 | SCR_002028 | Bgee: dataBase Gene Expression Evolution, dataBase Gene Expression Evolution | 2026-08-04 09:40:32 | 54 | ||||||
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Primate Orthologous Exon Database Resource Report Resource Website 1+ mentions |
Primate Orthologous Exon Database (RRID:SCR_002065) | Primate Orthologous Exon Database | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of orthologous exon regions in the genomes of human, chimpanzee, and rhesus macaque. It can be used in analysis of multi-species RNA-seq expression data, allowing for comparisons of exon-level expression across primates, as well as comparative examination of alternative splicing and transcript isoforms. | alternative splicing, transcript isoform, ortholog, exon, gene, rna-seq, primate, genome |
is listed by: OMICtools has parent organization: University of Chicago; Illinois; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01895 | SCR_002065 | 2026-08-04 09:40:33 | 1 | ||||||||
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NIH Rat Genomics and Genetics Resource Report Resource Website |
NIH Rat Genomics and Genetics (RRID:SCR_002267) | database, data or information resource | The Rat Genome Program was launched after the National Institutes of Health (NIH) realized the potential of rat models in understanding basic biology and human health and disease. The purpose of this NIH Rat Genomics and Genetics web site is to serve as a central point for information on NIH sponsored and related rat genetic and genomic activities and resources. It will provide information on: the follow up to recommendations made to the NIH; funding opportunities for rat genomic and genetic tools and resources; major rat genomic resources available and/or produced in response to the NIH Rat Program; courses and meetings related to rat genomics and genetics; and selected reports and publications. These programs have produced a wide variety of resources and a way to link and capitalize upon the data and resources of other model organisms and the human. In conjunction with and in addition to these programs, the NIH, through the RGWG, has convened advisory groups and workshops to discuss the opportunities that rat models offer and provide recommendations on the investments that are needed to capitalize on these opportunities. | biology, disease, genome, human health, model, rat | nif-0000-20991 | SCR_002267 | RGS | 2026-08-04 09:40:36 | 0 | ||||||||||
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COSMIC - Catalogue Of Somatic Mutations In Cancer Resource Report Resource Website 1000+ mentions |
COSMIC - Catalogue Of Somatic Mutations In Cancer (RRID:SCR_002260) | COSMIC | database, data or information resource |
Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats. Some key features of COSMIC are: * Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types. * Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines. |
cancer, mutation, somatic mutation, tumor, cancer genome, genome, gene, dna, tissue, histology, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Cancer | Wellcome Trust 077012/Z/05/Z | PMID:20952405 | Free | nif-0000-02690, biotools:cosmic, OMICS_00082 | http://www.sanger.ac.uk/perl/CGP/cosmic, https://bio.tools/cosmic | SCR_002260 | Catalogue Of Somatic Mutations In Cancer | 2026-08-04 09:40:36 | 4486 | |||
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ProTISA Resource Report Resource Website 1+ mentions |
ProTISA (RRID:SCR_002138) | ProTISA | database, data or information resource | Database of confirmed translation initiation sites (TISs) for prokaryotic genomes. The confirmed data has supporting evidence from different sources, including experiments records in the public protein database Swiss-Prot, literature, conserved domain search and sequence alignment among orthologous genes. Combing with predictions from the-state-of-the-art TIS predictor MED-Start/MED-StartPlus (in release 1.0 & 1.2) and TriTISA (since release 1.4) and annotations on potential regulatory signals, the database can serve as a refined annotation resource for the public database RefSeq. | translation initiation site, annotation, genome |
is listed by: OMICtools has parent organization: Peking University; Beijing; China |
PMID:17942412 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01871 | SCR_002138 | 2026-08-04 09:40:34 | 1 | |||||||
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Human Proteomics Initiative Resource Report Resource Website |
Human Proteomics Initiative (RRID:SCR_002373) | HPI | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 03, 2011. IT HAS BEEN REPLACED BY A NEW UniProtKB/Swiss-Prot ANNOTATION PROGRAM CALLED UniProt Chordata protein annotation program. The Human Proteome Initiative (HPI) aims to annotate all known human protein sequences, as well as their orthologous sequences in other mammals, according to the quality standards of UniProtKB/Swiss-Prot. In addition to accurate sequences, we strive to provide, for each protein, a wealth of information that includes the description of its function, domain structure, subcellular location, similarities to other proteins, etc. Although as complete as currently possible, the human protein set they provide is still imperfect, it will have to be reviewed and updated with future research results. They will also create entries for newly discovered human proteins, increase the number of splice variants, explore the full range of post-translational modifications (PTMs) and continue to build a comprehensive view of protein variation in the human population. The availability of the human genome sequence has enabled the exploration and exploitation of the human genome and proteome to begin. Research has now focused on the annotation of the genome and in particular of the proteome. With expert annotation extracted from the literature by biologists as the foundation, it has been possible to expand into the areas of data mining and automatic annotation. With further development and integration of pattern recognition methods and the application of alignments clustering, proteome analysis can now be provided in a meaningful way. These various approaches have been integrated to attach, extract and combine as much relevant information as possible to the proteome. This resource should be valuable to users from both research and industry. We maintain a file containing all human UniProtKB/Swiss-Prot entries. This file is updated at every biweekly release of UniProt and can be downloaded by FTP download, HTTP download or by using a mirroring program which automatically retrieves the file at regular intervals. | function, gene, alignment, biologist, clustering, coding, development, genome, human, location, mammalian, modification, ortholog, population, post-translational, protein, proteome, proteomic, proteomics, sequence, splice, structure, subcellular, variant, variation, gold standard |
is related to: UniProt Chordata protein annotation program has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:11301130 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21199 | SCR_002373 | Human Proteome Initiative, UniProtKB/Swiss-Prot Human Proteome Initiative | 2026-08-04 09:40:37 | 0 | ||||||
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Organelle Genomics Resource Report Resource Website 1+ mentions |
Organelle Genomics (RRID:SCR_002137) | OGMP | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. It investigates mitochondrial genome diversity and evolution by systematically determining the complete mitochondrial DNA (mtDNA) sequences of a phylogenetically broad selection of protists. The mtDNAs of lower fungi and choanoflagellates are being analyzed by the Fungal Mitochondrial Genome Project (FMGP), a sister project to the OGMP. | genome, mitochondrial dna, mitochondrial genome, organelle | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20928, r3d100010926 | https://doi.org/10.17616/R3TG9G | SCR_002137 | Organelle Genome Megasequencing Program | 2026-08-04 09:40:34 | 1 | |||||||
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WebGeSTer DB Resource Report Resource Website 1+ mentions |
WebGeSTer DB (RRID:SCR_002165) | WebGeSTer DB | database, data or information resource | Database of intrinsic terminators of transcription that is comprized of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids. Information about structural parameters of individual terminators such as sequence, length of stem and loop, mismatches and gaps, U-trail, genomic coordinates and gene name and accession number is available in both tabular form and as a composite figure. Summary statistics for terminator profiles of whole genome can be also obtained. Raw data files for individual genomes can be downloaded (.zip files) for detailed investigations. Data is organized into different tiers such that users can fine-tune their search by entering name of the species, or taxon ID or genomes with a certain number of terminators. To visualize the occurrence of the terminators, an interactive map, with the resolution to single gene level, has been developed. | genome, terminator, transcription, plasmid, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20972211 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:webgester_db, OMICS_01862 | https://bio.tools/webgester_db | SCR_002165 | WebGesTer Database, Web Genome Scannner for Terminators Database, WebGeSTer DB - A Transcription Terminator Database | 2026-08-04 09:40:34 | 5 | |||||
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Automatic Generated Test-Sets Database for Protein-Protein Docking Resource Report Resource Website |
Automatic Generated Test-Sets Database for Protein-Protein Docking (RRID:SCR_002281) | AGT-SDP | database, data or information resource | Database providing automatic test cases for protein-protein docking. A consensus-type approach is proposed processing the whole PDB and classifying protein structures into complexes and unbound proteins by combining information from three different approaches. Out of this classification test cases are generated automatically. All calculations were run on the database. The information stored is available via a web interface. The user can choose several criteria for generating his own subset out of the test cases, e.g. for testing docking algorithms. In unbound protein--protein docking, the complex of two proteins is predicted using the unbound conformations of the proteins (Halperin et al.,2002). For testing of docking algorithms, two unbound proteins which form a known complex have to be identified, so that the result of the docking algorithm can be compared to the known complex. For the identification of test cases, the structures taken from the PDB have to be classified as unbound proteins or complexes and unbound proteins with a 100% sequence identity to one complex part have to be searched. By now, most groups use handpicked test sets. The largest collection of test cases used so far is described by Chen et al. (Chen et al.,2003) and contains 31 test cases for unbound docking. Because of the exponential growth of available protein structures in the PDB, automatic generation of test cases will become more and more important in the future. | algorithm, alignment, classification, comparison, complex, conformation, design, docking, genome, primer, protein, rna, structure, unbound, protein domain, protein classification, protein-protein docking | has parent organization: Bielefeld University; North Rhine-Westphalia; Germany | DFG | PMID:15479711 | Acknowledgement requested, The community can contribute to this resource | nif-0000-21012 | SCR_002281 | 2026-08-04 09:40:37 | 0 | ||||||
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AceView Resource Report Resource Website 100+ mentions |
AceView (RRID:SCR_002277) | AceView/WormGenes | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes and their functions and to stimulate further validating experiments at the bench. AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals' transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer an up-to-date resource on the genes, in the hope to stimulate further experiments at the bench, or to help medical research. AceView can be queried by meaningful words or groups of words as well as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID, GenBank accessions. | est, exon, expression, function, gene, alignment, arabidopsis, cdna, co-alignment, coding, disease, genome, genomic, human, intron, localization, mammal, mouse, mrna, nematode, pathway, phenotype, plant, polyadenylation, promoter, rat, sequence, signal, tissue, transcript, transcriptome, worm, blast, gold standard | has parent organization: NCBI | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21007, r3d100010651 | https://doi.org/10.17616/R3260G | http://www.ncbi.nih.gov/IEB/Research/Acembly/ | SCR_002277 | AceView genes, AceView/WormGenes, The AceView Genes | 2026-08-04 09:40:36 | 186 | |||||
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RegPrecise Resource Report Resource Website 50+ mentions |
RegPrecise (RRID:SCR_002149) | RegPrecise | database, data or information resource | Collection of manually curated inferences of regulons in prokaryotic genomes. Database for capturing, visualization and analysis of transcription factor regulons that were reconstructed by comparative genomic approach in wide variety of prokaryotic genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | regulon, genome, transcription factor, gene, operon, transcription factor binding site, taxonomy, rna, effector, pathway, ortholog, function, FASEB list |
is listed by: OMICtools has parent organization: Lawrence Berkeley National Laboratory |
Department of Energy ; NSF DBI-0850546 |
PMID:24175918 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01869 | SCR_002149 | 2026-08-04 09:40:34 | 80 | ||||||
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Full-Malaria: Malaria Full-Length cDNA Database Resource Report Resource Website 1+ mentions |
Full-Malaria: Malaria Full-Length cDNA Database (RRID:SCR_002348) | database, data or information resource | FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum. Because of its medical importance, this organism is the first target for genome sequencing of a eukaryotic pathogen; the sequences of two of its 14 chromosomes have already been determined. However, for the full exploitation of this rapidly accumulating information, correct identification of the genes and study of their expression are essential. Using the oligo-capping method, this database has produced a full-length-enriched cDNA library from erythrocytic stage parasites and performed one-pass reading. The database consists of nucleotide sequences of 2490 random clones that include 390 (16%) known malaria genes according to BLASTN analysis of the nr-nt database in GenBank; these represent 98 genes, and the clones for 48 of these genes contain the complete protein-coding sequence (49%). On the other hand, comparisons with the complete chromosome 2 sequence revealed that 35 of 210 predicted genes are expressed, and in addition led to detection of three new gene candidates that were not previously known. In total, 19 of these 38 clones (50%) were full-length. From these observations, it is expected that the database contains approximately 1000 genes, including 500 full-length clones. It should be an invaluable resource for the development of vaccines and novel drugs. Full-malaria has been updated in at least three points. (i) 8934 sequences generated from the addition of new libraries added so that the database collection of 11,424 full-length cDNAs covers 1375 (25%) of the estimated number of the entire 5409 parasite genes. (ii) All of its full-length cDNAs and GenBank EST sequences were mapped to genomic sequences together with publicly available annotated genes and other predictions. This precisely determined the gene structures and positions of the transcriptional start sites, which are indispensable for the identification of the promoter regions. (iii) A total of 4257 cDNA sequences were newly generated from murine malaria parasites, Plasmodium yoelii yoelii. The genome/cDNA sequences were compared at both nucleotide and amino acid levels, with those of P.falciparum, and the sequence alignment for each gene is presented graphically. This part of the database serves as a versatile platform to elucidate the function(s) of malaria genes by a comparative genomic approach. It should also be noted that all of the cDNAs represented in this database are supported by physical cDNA clones, which are publicly and freely available, and should serve as indispensable resources to explore functional analyses of malaria genomes. Sponsors: This database has been constructed and maintained by a Grant-in-Aid for Publication of Scientific Research Results from the Japan Society for the Promotion of Science (JSPS). This work was also supported by a Special Coordination Funds for Promoting Science and Technology from the Science and Technology Agency of Japan (STA) and a Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports and Culture of Japan. | drug, eukaryotic, expression, function, gene, alignment, amino acid, cdna, chromosome, clone, coding, comparative, genome, genomic, human, malaria, medical, nucleotide, oligo-capping, organism, parasite, pathogen, physical, plasmodium falciparum, promoter, protein, region, sequence, sequencing, unicellular eukaryote genome databases, vaccine | has parent organization: University of Tokyo; Tokyo; Japan | PMID:18987005 PMID:14681428 |
nif-0000-21157 | SCR_002348 | Full-Malaria | 2026-08-04 09:40:38 | 2 | ||||||||
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Human Gene Connectome Server Resource Report Resource Website 1+ mentions |
Human Gene Connectome Server (RRID:SCR_002627) | HGCS | data analysis service, analysis service resource, production service resource, service resource | An interactive web server that enables researchers to prioritize any list of genes by their biological proximity to defined core genes (i.e. genes that are known to be associated with the phenotype), and to predict novel gene pathways. | gene, disease, phenotype, genome, connectome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Human Gene Connectome |
PMID:23509278 | Free | nlx_156049, biotools:hgcs | https://bio.tools/hgcs | SCR_002627 | 2026-08-04 09:40:42 | 5 | ||||||
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Interrupted CoDing Sequence Database Resource Report Resource Website |
Interrupted CoDing Sequence Database (RRID:SCR_002949) | ICDS Database | database, data or information resource | Database of interrupted coding sequences detected by a similarity-based approach in complete prokaryotic genomes. The definition of each interrupted gene is provided as well as the ICDS genomic localization with the surrounding sequence. To facilitate the experimental characterization of ICDS, optimized primers are proposed for re-sequencing purposes. The database is accessible by BLAST search or by genome. 118 Genomes are available in the database. | genome, blast, interrupted coding sequence, gene | has parent organization: University of Strasbourg; Strasbourg; France | PMID:16381882 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03036 | SCR_002949 | 2026-08-04 09:40:46 | 0 | |||||||
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NBDC - National Bioscience Database Center Resource Report Resource Website 1+ mentions |
NBDC - National Bioscience Database Center (RRID:SCR_000814) | NBDC | portal, organization portal, database, data or information resource | The National Bioscience Database Center (NBDC) intends to integrate all databases for life sciences in Japan, by linking each database with expediency to maximize convenience and make the entire system more user-friendly. We aim to focus our attention on the needs of the users of these databases who have all too often been neglected in the past, rather than the needs of the people tasked with the creation of databases. It is important to note that we will continue to honor the independent integrity of each database that will contribute to our endeavor, as we are fully aware that each database was originally crafted for specific purposes and divergent goals. Services: * Database Catalog - A catalog of life science related databases constructed in Japan that are also available in English. Information such as URL, status of the database site (active vs. inactive), database provider, type of data and subjects of the study are contained for each database record. * Life Science Database Cross Search - A service for simultaneous searching across scattered life-science databases, ranging from molecular data to patents and literature. * Life Science Database Archive - maintains and stores the datasets generated by life scientists in Japan in a long-term and stable state as national public goods. The Archive makes it easier for many people to search datasets by metadata in a unified format, and to access and download the datasets with clear terms of use. * Taxonomy Icon - A collection of icons (illustrations) of biological species that is free to use and distribute. There are more than 200 icons of various species including Bacteria, Fungi, Protista, Plantae and Animalia. * GenLibi (Gene Linker to bibliography) - an integrated database of human, mouse and rat genes that includes automatically integrated gene, protein, polymorphism, pathway, phenotype, ortholog/protein sequence information, and manually curated gene function and gene-related or co-occurred Disease/Phenotype and bibliography information. * Allie - A search service for abbreviations and long forms utilized in life sciences. It provides a solution to the issue that many abbreviations are used in the literature, and polysemous or synonymous abbreviations appear frequently, making it difficult to read and understand scientific papers that are not relevant to the reader's expertise. * inMeXes - A search service for English expressions (multiple words) that appear no less than 10 times in PubMed/MEDLINE titles or abstracts. In addition, you can easily access the sentences where the expression was used or other related information by clicking one of the search results. * HOWDY - (Human Organized Whole genome Database) is a database system for retrieving human genome information from 14 public databases by using official symbols and aliases. The information is daily updated by extracting data automatically from the genetic databases and shown with all data having the identifiers in common and linking to one another. * MDeR (the MetaData Element Repository in life sciences) - a web-based tool designed to let you search, compare and view Data Elements. MDeR is based on the ISO/IEC 11179 Part3 (Registry metamodel and basic attributes). * Human Genome Variation Database - A database for accumulating all kinds of human genome variations detected by various experimental techniques. * MEDALS - A portal site that provides information about databases, analysis tools, and the relevant projects, that were conducted with the financial support from the Ministry of Economy, Trade and Industry of Japan. | life science, research, database, catalog, tool, gene, service, molecule, patent, literature, taxonomy, image, bacteria, fungus, protist, plant, animal, human, mouse, rat, gene, protein, polymorphism, pathway, phenotype, ortholog, protein sequence, gene function, disease, phenotype, bibliography, english expression, human genome, genome, human genome variation, variation, analysis tool |
has parent organization: Japan Science and Technology Agency is parent organization of: Human Variation DB is parent organization of: Japanese Genotype-phenotype Archive (JGA) is parent organization of: ChIP-Atlas |
Japan Science and Technology Agency | nlx_151485 | SCR_000814 | National Bioscience Database Center, National Bioscience Database Center (NBDC) | 2026-08-04 09:40:14 | 3 | |||||||
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SPAdes Resource Report Resource Website 100+ mentions |
SPAdes (RRID:SCR_000131) | SPAdes | software resource, software toolkit | Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | assembler, single, cell, small, genome, short, read, data |
is used by: shovill is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: rnaSPAdes is related to: rnaQUAST has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia works with: Illumina: iSeq 100 Sequencing System |
Government of the Russian Federation ; NCRR P41 RR024851 |
PMID:24093227 PMID:22506599 DOI:10.1089/cmb.2012.0021 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01502 | https://sources.debian.org/src/spades/ | http://bioinf.spbau.ru/spades/ | SCR_000131 | SPAdes Genome Assembler | 2026-08-04 09:40:03 | 101 | |||
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Plant Metabolic Network Resource Report Resource Website 100+ mentions |
Plant Metabolic Network (RRID:SCR_002888) | portal, project portal, data or information resource | Collaborative project to bring together biochemical pathway databases and research communities focused on plant metabolism. Used to build broad network of plant metabolic pathway databases. Central feature of PMN is PlantCyc, comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism. | e. coli, gene, arabidopsis, barley, coffee, database, genome, grass, homolog, maize, medicago, oats, pathway, pepper, plant, potato, rice, rye, sorghum, species, taxonomy, tomato, wheat, ontology | lists: PlantCyc | nif-0000-25602, SCR_003778, nlx_15806 | SCR_002888 | Plant Biochemical Pathway Databases | 2026-08-04 09:40:45 | 149 | |||||||||
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International Gene Trap Consortium Resource Report Resource Website 10+ mentions |
International Gene Trap Consortium (RRID:SCR_002305) | IGTC | cell repository, material resource, biomaterial supply resource | Consortium represents all publicly available gene trap cell lines, which are available on non-collaborative basis for nominal handling fees. Researchers can search and browse IGTC database for cell lines of interest using accession numbers or IDs, keywords, sequence data, tissue expression profiles and biological pathways, can find trapped genes of interest on IGTC website, and order cell lines for generation of mutant mice through blastocyst injection. Consortium members include: BayGenomics (USA), Centre for Modelling Human Disease (Toronto, Canada), Embryonic Stem Cell Database (University of Manitoba, Canada), Exchangeable Gene Trap Clones (Kumamoto University, Japan), German Gene Trap Consortium provider (Germany), Sanger Institute Gene Trap Resource (Cambridge, UK), Soriano Lab Gene Trap Resource (Mount Sinai School of Medicine, New York, USA), Texas Institute for Genomic Medicine - TIGM (USA), TIGEM-IRBM Gene Trap (Naples, Italy). | embryo, embryonic, gene, genome, allele, analysis, assay, bioinformatics, blastocyst, cell, colony, consortium, genotyping, hybridization, in situ, international, knockout, murine, mutant, mutation, probe, qpcr, researcher, scientist, sequence, stem cell, tagging, trap, vector, cell line, embryonic stem cell line, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is related to: Centre for Modeling Human Disease Gene Trap Resource has parent organization: University of California at San Francisco; California; USA is parent organization of: International Gene Trap Consortium Pathways |
NCRR P41 RR01081 | PMID:16381950 | Restricted | nif-0000-00036 | https://igtc.org/ | SCR_002305 | International Gene Trap Consortium | 2026-08-04 09:40:36 | 43 | ||||
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IMG System Resource Report Resource Website 100+ mentions |
IMG System (RRID:SCR_002965) | IMG, IMG/M | portal, data or information resource | Resource for analysis and annotation of genome and metagenome datasets in comprehensive comparative context. IMG provides users with tools for analyzing publicly available genome datasets and metagenome datasets. | microbiome, microbial genetics, genome and metagenome datasets analysis, genome and metagenome datasets, genome, metagenomics, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: Human Microbiome Project has parent organization: DOE Joint Genome Institute |
PMID:17932063 PMID:22086953 |
Free, Freely available | nif-0000-03010, OMICS_01478, SCR_014605, biotools:img_m | http://img.jgi.doe.gov/m, https://bio.tools/img_m | SCR_002965 | Integrated Microbial Genomes System | 2026-08-04 09:40:46 | 199 | |||||
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DOE Joint Genome Institute Resource Report Resource Website 500+ mentions |
DOE Joint Genome Institute (RRID:SCR_003045) | DOE JGI, JGI, | portal, organization portal, data or information resource | Institute to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. Supported by the DOE Office of Science, the DOE JGI unites the expertise at Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory, and the HudsonAlpha Institute for Biotechnology. The facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. | genomics, sequencing, computational analysis, clean energy, environment, biotechnology, nucleotide sequence, protein, genome, bacteria, microorganism, fungal colony, fungal community, dna, phenotype, molecular biology, life science, genomics, genetics, nature, nurture, ecology, bioenergetics, high-throughput sequencing |
is listed by: re3data.org has parent organization: University of California; California; USA is parent organization of: Microbial Genetics Resource at JGI is parent organization of: JGI Genome Portal is parent organization of: Genomes Online Database is parent organization of: IMG System is parent organization of: Classifier for Metagenomic Sequences is parent organization of: MycoCosm is parent organization of: Plant Genome Resource at JGI is parent organization of: Classifier for Metagenomic Sequences is parent organization of: Phytozome is parent organization of: IMG is parent organization of: Metagenomics Program at JGI is parent organization of: Assembly Likelihood Estimator is parent organization of: 1000 Fungal Genome Project is parent organization of: Bestus Bioinformaticus Tools is parent organization of: Bestus Bioinformaticus Duk is parent organization of: Bestus Bioinformaticus Merge is parent organization of: Reformat |
DOE | Free, Freely available | nif-0000-30425 | SCR_003045 | DOE Joint Genome Institute - Enabling Advances in Bioenergy & Environmental Research, Department of Energy Joint Genome Institute, Joint Genome Institute | 2026-08-04 09:40:48 | 689 |
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