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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NCBI Protein Database Resource Report Resource Website 1000+ mentions |
NCBI Protein Database (RRID:SCR_003257) | NCBI_GP, NCBI Protein, NCBI GP | data or information resource, database | Databases of protein sequences and 3D structures of proteins. Collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. | amino acid sequence, nucleotide, dna sequence, protein, sequence, sequence data, structure, function, dna, nucleotide sequence, genomics, protein binding, gold standard |
is used by: NIF Data Federation is listed by: re3data.org is related to: AmiGO is related to: GenBank is related to: RefSeq is related to: TPA is related to: UniProtKB is related to: Protein Information Resource is related to: Protein Research Foundation is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: BioExtract is related to: DIG IT - Database of Immunoglobulins and Integrated Tools has parent organization: NCBI |
Free, Freely available | SCR_017486, r3d100011331, nif-0000-03178 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=protein, https://doi.org/10.17616/R3JH0X | SCR_003257 | Entrez Protein, Protein Database, NCBI Protein Database, Protein sequence database, Entrez Protein Database | 2026-09-19 12:56:39 | 1025 | ||||||
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Influenza Virus Resource Resource Report Resource Website 50+ mentions |
Influenza Virus Resource (RRID:SCR_002984) | Influenza Virus Resource | data or information resource, database | Database of data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis and annotation. In addition, it provides links to other resources that contain flu sequences, publications and general information about flu viruses. Users can search the Flu database, build queries, retrieve sequences, and apply analysis tools. This includes selecting influenza sequences by virus, subtype, host, and other criteria, finding complete genome sets, aligning sequence and others in the database (up to 1000 sequences), viewing clustering and phylogenetic trees, BLAST searching a flu sequence against the database, and more. | genomics, genome, flu, variation, annotation, blast, cluster, phylogenetic tree, align, data analysis service |
is listed by: re3data.org is related to: GenBank is related to: Virus Variation has parent organization: NCBI |
Influenza virus | PMID:17942553 | Free, Available for download, Freely available | nif-0000-03023, r3d100011004 | https://doi.org/10.17616/R3S61C | SCR_002984 | NCBI Influenza Virus Resource | 2026-09-19 12:56:38 | 83 | ||||
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TPA Resource Report Resource Website 1+ mentions |
TPA (RRID:SCR_003593) | TPA | data or information resource, database | Database designed to capture experimental or inferential results that support submitter-provided annotation for sequence data that the submitter did not directly determine but derived from GenBank primary data. Records are divided into two categories: * TPA:experimental: Annotation of sequence data is supported by peer-reviewed wet-lab experimental evidence. * TPA:inferential: Annotation of sequence data by inference (where the source molecule or its product(s) have not been the subject of direct experimentation) TPA records are retrieved through the Nucleotide Database and feature information on the sequence, how it was cataloged, and proper way to cite the sequence information. | gene, gene expression, nucleotide sequence, annotation, sequence |
is listed by: re3data.org is related to: GenBank is related to: NCBI Protein Database is related to: NCBI Nucleotide has parent organization: NCBI |
PMID:16901214 | nlx_157738, r3d100010506 | https://doi.org/10.17616/R3KS4H | SCR_003593 | Third Party Annotation, NCBI TPA, NCBI Third Party Annotation | 2026-09-19 12:56:40 | 4 | ||||||
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NCBI Structure Resource Report Resource Website 10+ mentions |
NCBI Structure (RRID:SCR_004218) | NCBI Structure | data or information resource, database | Database of three-dimensional structures of macromolecules that allows the user to retrieve structures for specific molecule types as well as structures for genes and proteins of interest. Three main databases comprise Structure-The Molecular Modeling Database; Conserved Domains and Protein Classification; and the BioSystems Database. Structure also links to the PubChem databases to connect biological activity data to the macromolecular structures. Users can locate structural templates for proteins and interactively view structures and sequence data to closely examine sequence-structure relationships. * Macromolecular structures: The three-dimensional structures of biomolecules provide a wealth of information on their biological function and evolutionary relationships. The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more. It is possible, for example, to find 3D structures for homologs of a protein of interest by following the Related Structure link in an Entrez Protein sequence record. * Conserved domains and protein classification: Conserved domains are functional units within a protein that act as building blocks in molecular evolution and recombine in various arrangements to make proteins with different functions. The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, in addition to NCBI-curated domains that use 3D-structure information explicitly to define domain boundaries and provide insights into sequence/structure/function relationships. * Small molecules and their biological activity: The PubChem project provides information on the biological activities of small molecules and is a component of NIH''''s Molecular Libraries Roadmap Initiative. PubChem includes three databases: PCSubstance, PCBioAssay, and PCCompound. The PubChem data are linked to other data types (illustrated example) in the Entrez system, making it possible, for example, to retrieve information about a compound and then Link to its biological activity data, retrieve 3D protein structures bound to the compound and interactively view their active sites, and find biosystems that include the compound as a component. * Biological Systems: A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. The NCBI BioSystems Database provides centralized access to biological pathways from several source databases and connects the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system. BioSystem records list and categorize components (illustrated example), such as the genes, proteins, and small molecules involved in a biological system. The companion FLink icon FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. | macromolecule, conserved domain, protein classification, protein, small molecule, biological activity, molecule, biosystem, biological system, structure, gene, alignment, biomolecule, interaction, function, evolution, 3d spatial image, visualization, gold standard |
is listed by: re3data.org is related to: PubChem is related to: NCBI BioSystems Database is related to: Conserved Domain Database is related to: Molecular Modeling DataBase is related to: CBLAST is related to: NCBI Structure: Cn3D is related to: IBIS: Inferred Biomolecular Interactions Server is related to: Vector Alignment Search Tool is related to: PubMed has parent organization: NCBI |
Free, Public, Acknowledgement requested | nlx_23947, r3d100010927 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure, https://doi.org/10.17616/R3PP7J | SCR_004218 | 2026-09-19 12:56:42 | 26 | |||||||
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FAIRsharing Resource Report Resource Website 50+ mentions |
FAIRsharing (RRID:SCR_004177) | data or information resource, database | Web-based, searchable portal of three interlinked registries, containing both in-house and crowdsourced manually curated descriptions of standards, databases and data policies, combined with integrated view across all three types of resource. By registering your resource on FAIRsharing, you gain credit for your work, increase its visibility outside of your direct domain, reduce potential for unnecessary reinvention and proliferation of standards and databases. | Metadata standard, ontology, data sharing, data policy, data standard |
is used by: Integrated Datasets lists: Brain Imaging Data Structure (BIDs) lists: EBRAINS lists: Code Ocean lists: Distributed Archives for Neurophysiology Data Integration lists: CaltechDATA lists: DataONE lists: GBIF - Global Biodiversity Information Facility lists: Incorporated Research Institutions for Seismology lists: Mendeley Data lists: Open Science Framework lists: MorphoBank lists: PhysioNet lists: GigaDB lists: INPTDAT lists: OpenNeuro lists: Cancer Imaging Archive (TCIA) lists: Qualitative Data Repository lists: UK Data Archive lists: Dryad Digital Repository lists: BOLD lists: ZENODO lists: Vivli lists: FigShare lists: Influenza Research Database (IRD) lists: Cambridge Structural Data Base lists: National Snow and Ice Data Center lists: Virus Pathogen Resource (ViPR) lists: 4TU.ResearchData lists: Australian Data Archive lists: Atlas of Living Australia lists: Australian Ocean Data Network lists: Arch lists: Bolin Centre Database lists: B2SHARE Eudat lists: Connectome Workbench is listed by: FORCE11 is listed by: re3data.org is related to: bioDBcore is related to: Standards-based Infrastructure with Distributed Resources is related to: Genomic Standards Consortium is related to: ELIXIR Tools and Data Services Registry is related to: NCI Imaging Data Commons is related to: Cancer Research Data Commons is related to: SciLifeLab Data Platform is related to: NiPoppy has parent organization: University of Oxford; Oxford; United Kingdom is parent organization of: Minimum Information for Biological and Biomedical Investigations is parent organization of: FAIRSharing Catalogue of Standards |
Free, freely available | r3d100011250, nlx_143602, SCR_017615 | http://www.force11.org/node/4701, https://fairsharing.org/, https://doi.org/10.17616/R3C621 | http://www.biosharing.org/ | SCR_004177 | BioSharing | 2026-09-19 12:56:42 | 74 | ||||||
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UniGene Resource Report Resource Website 1000+ mentions |
UniGene (RRID:SCR_004405) | UniGene | data or information resource, database, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Web tool for an organized view of the transcriptome. Collection of the computationally identified transcripts from the same locus. Information on protein similarities, gene expression, cDNA clones, and genomic location. System for automatically partitioning GenBank sequences into a non redundant set of gene oriented clusters. | colleciton, data, information, organized, view, transcriptome, locus, protein, similarity, gene, expression, |
is used by: Rank Rank Hypergeometric Overlap is listed by: OMICtools is listed by: re3data.org is related to: ProbeMatchDB 2.0 is related to: Bgee: dataBase for Gene Expression Evolution is related to: GeneSpeed- A Database of Unigene Domain Organization has parent organization: NCBI works with: Digital Differential Display (DDD) |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_41571, OMICS_01663, r3d100010774 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene, https://doi.org/10.17616/R35G7T | SCR_004405 | NCBI UniGene, Organized View of the Transcriptome, UniGene | 2026-09-19 12:56:44 | 1153 | ||||||
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NCBI Nucleotide Resource Report Resource Website 100+ mentions |
NCBI Nucleotide (RRID:SCR_004860) | NCBI Nucleotide, NCBI gi | data or information resource, database | Database of nucleotide sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery. | gene expression, genomics, nucleic acid, biological assay, nucleotide, gold standard |
is listed by: re3data.org is related to: GenBank is related to: BioExtract is related to: DIG IT - Database of Immunoglobulins and Integrated Tools is related to: RefSeq is related to: TPA is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: NCBI |
nlx_84100, r3d100010778 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore, http://www.ncbi.nlm.nih.gov/nuccore, https://doi.org/10.17616/R3NG8J | SCR_004860 | Nucleotide Database, Entrez Nucleotide, CoreNucleotide, Nucleotide | 2026-09-19 12:56:47 | 378 | |||||||
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NCBI BioProject Resource Report Resource Website 10000+ mentions |
NCBI BioProject (RRID:SCR_004801) | data or information resource, database | Database of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. It is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. Submissions are supported by a web-based Submission Portal. The database facilitates organization and classification of project data submitted to NCBI, EBI and DDBJ databases that captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. BioProject records link to corresponding data stored in archival repositories. The BioProject resource is a redesigned, expanded, replacement of the NCBI Genome Project resource. The redesign adds tracking of several data elements including more precise information about a project''''s scope, material, and objectives. Genome Project identifiers are retained in the BioProject as the ID value for a record, and an Accession number has been added. Database content is exchanged with other members of the International Nucleotide Sequence Database Collaboration (INSDC). BioProject is accessible via FTP. | genome sequencing, sequencing, genotype, phenotype, sequence variant, epigenetic, data set, genome, assembly, annotation, mapping, cellular organism, gene mapping, gene expression, biological tag, gene rearrangement, genetic algorithm, genetic code, genetic genealogy, gold standard, bio.tools |
is listed by: 3DVC is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: INSDC has parent organization: NCBI |
NLM | PMID:22139929 | Free, Freely available | r3d100013330, nlx_143909, biotools:bioproject | http://www.ncbi.nlm.nih.gov/genomeprj, https://bio.tools/bioproject, https://doi.org/10.17616/R31NJMS2 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=genomeprj | SCR_004801 | NCBI BioProject Database, BioProject | 2026-09-19 12:56:47 | 14025 | ||||
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Tuberculosis Database Resource Report Resource Website 50+ mentions |
Tuberculosis Database (RRID:SCR_006619) | TBDB | data or information resource, database | Database providing integrated access to genome sequence, expression data and literature curation for Tuberculosis (TB) that houses genome assemblies for numerous strains of Mycobacterium tuberculosis (MTB) as well assemblies for over 20 strains related to MTB and useful for comparative analysis. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives, including over 3000 MTB microarrays, 95 RT-PCR datasets, 2700 microarrays for human and mouse TB related experiments, and 260 arrays for Streptomyces coelicolor. (July 2010) To enable wide use of these data, TBDB provides a suite of tools for searching, browsing, analyzing, and downloading the data. | genomic, protein, blast, genome, gene, systems biology, gene expression, microarray, comparative analysis, regulatory network, metabolic network, epitope, expression profile, rt-pcr, gene regulation, genome browser, FASEB list |
is listed by: re3data.org is related to: SMD is related to: BioCyc has parent organization: Broad Institute has parent organization: Stanford University School of Medicine; California; USA |
Tuberculosis | Bill and Melinda Gates Foundation | PMID:20488753 PMID:18835847 |
Acknowledgement requested, Public, (Published data) | nif-0000-03537, r3d100010930 | https://doi.org/10.17616/R39G8F | SCR_006619 | TB Database, TBDatabase | 2026-09-19 12:56:59 | 64 | |||
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HIstome: The Histone Infobase Resource Report Resource Website 1+ mentions |
HIstome: The Histone Infobase (RRID:SCR_006972) | HIstome | data or information resource, database | Database of human histone variants, sites of their post-translational modifications and various histone modifying enzymes. The database covers 5 types of histones, 8 types of their post-translational modifications and 13 classes of modifying enzymes. Many data fields are hyperlinked to other databases (e.g. UnprotKB/Swiss-Prot, HGNC, OMIM, Unigene etc.). Additionally, this database also provides sequences of promoter regions (-700 TSS +300) for all gene entries. These sequences were extracted from the UCSC genome browser. Sites of post-translational modifications of histones were manually searched from PubMed listed literature. Current version contains information for about ~50 histone proteins and ~150 histone modifying enzymes. HIstome is a combined effort of researchers from two institutions, Advanced Center for Treatment, Research and Education in Cancer (ACTREC), Navi Mumbai and Center of Excellence in Epigenetics (CoEE), Indian Institute of Science Education and Research (IISER), Pune. | histone, protein, enzyme, modifying enzyme, post-translational modification, variant, promoter region, gene, epigenetic regulation, india, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools has parent organization: ACTREC - Advanced Centre for Treatment Research and Education in Cancer |
Cancer | ACTREuropean Union - Advanced Centre for Treatment Research and Education in Cancer ; Government of India |
PMID:22140112 | Free, Public, Acknowledgement requested | biotools:histome, r3d100010977, nlx_151419 | http://www.actrec.gov.in/histome/, https://bio.tools/histome, https://doi.org/10.17616/R3RD0R | http://www.histome.net/ | SCR_006972 | 2026-09-19 12:57:01 | 1 | |||
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HPRD - Human Protein Reference Database Resource Report Resource Website 1000+ mentions |
HPRD - Human Protein Reference Database (RRID:SCR_007027) | HPRD | data or information resource, database | Database that represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data. | protein, disease, network, post-translational, proteome, protein binding, protein s, protein c, pathway, protein-protein interaction, protein expression, subcellular localization, phosphorylation motif, signaling pathway, protein sequence, blast, molecule, domain, motif, post-translational modification, protein isoform, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: GEMINI is listed by: re3data.org is related to: Human Proteinpedia is related to: MatrixDB is related to: Interaction Reference Index is related to: Pathway Commons is related to: ConsensusPathDB is related to: Gene Ontology is related to: Agile Protein Interactomes DataServer has parent organization: Johns Hopkins University; Maryland; USA has parent organization: Institute of Bioinformatics; Bangalore; India |
PMID:18988627 PMID:16381900 PMID:14525934 |
Acknowledgement requested, Free, Non-commercial, Commercial requires license | nif-0000-00137, r3d100010978 | https://doi.org/10.17616/R3MK9N | SCR_007027 | Human Protein Reference Database | 2026-09-19 12:57:01 | 1311 | |||||
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FAOSTAT Resource Report Resource Website 500+ mentions |
FAOSTAT (RRID:SCR_006914) | FAOSTAT | data or information resource, database | A multilingual database that provides large time-series and cross sectional data relating to hunger, food, agriculture, nutrition, fisheries, forestry and food aid by country and region from 1961 to present. Data can be searched, browsed, analyzed and downloaded. | agriculture, agricultural productivity, food supply, economic, forest, hunger, malnutrition, web service, food, trade, price, emission, investment, environment, FASEB list | is listed by: re3data.org | Free | r3d100010847, nif-0000-30554 | http://faostat.fao.org/site/368/DesktopDefault.aspx?PageID=368#ancor, http://faostat3.fao.org/faostat-gateway/go/to/home/E, https://doi.org/10.17616/R3N614 | SCR_006914 | 2026-09-19 12:57:00 | 973 | |||||||
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German Collection of Microorganisms and Cell Cultures Resource Report Resource Website 100+ mentions |
German Collection of Microorganisms and Cell Cultures (RRID:SCR_001711) | DSMZ | data or information resource, database | The DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganisms and Cell Cultures) is the most comprehensive biological resource center in Europe. With more than 18.000 microorganisms, 1.200 plant viruses, 600 human and animal cell lines, 770 plant cell cultures and more than 7.100 cultures deposited for the purposes of patenting, DSMZ has demonstrated their obligation to serve science for decades. Main functions of DSMZ are: - to collect, maintain and store microorganisms and cell lines, as well as other biological material of relevance for applied biology, biotechnology, microbiology, teaching and other areas of research and general application; - to keep the scientific and industrial community informed on the contents of the collections by the means of catalogs, special lists, databases or electronic media; - to supply scientists and institutions with DSMZ cultures, in accordance with national and international laws such as the Infektionsschutzgesetz (Act dealing with protection against infection), the Genetic Engineering Act, the Foreign Trade Laws, the Convention on Biological Diversity as well as the DSMZ terms of supply; - to function as an internationally recognized collection center for the deposit of microorganisms, cell lines, and other biological material which have been cited in scientific literature or which are used in national or international test procedures (e.g. type strains, reference strains for national and international quality control regulations or susceptibility tests, strains with special properties, such as the production of enzymes, degradation of pollutants, host strains for plasmids, etc.); - to act as an International Depositary Authority (IDA) for the deposit of biological material for patent purposes according to the Budapest Treaty; - to act, in a confidential manner, as a center for the safe deposit of biological material; - to act as an advisory center for the scientific community and to offer teaching and service facilities. The DSMZ collections contain over 26 000 cultures (including 6500 patent deposits) representing more than 16 000 cultures of microorganisms (Archaea, Bacteria, plasmids, phages, yeasts, fungi), 750 plant cell cultures, 600 plant viruses, 700 antisera and 580 human and animal cell lines. Unique subcollections are held in the prokaryotes groups of acidophiles, alkaliphiles, halophiles, methanogens, phototrophs, thermophiles, and sulfate reducers. The research is focused on collection related fields which include: - Taxonomy - Evolution - Phylogeny - Microbial diversity and molecular assessment of diversity - Molecular systematics - Research on pathobiological aspects of leukemia-lymphoma cell lines applying classical and molecular genetics, immunological and cell biological methods * Development of cultivation and preservation methods for biological material * Characterization and identification of biological material | enzyme, europe, evolution, fungus, genetic, acidophile, alkaliphile, animal, antisera, archaea, bacteria, biological, biology, biotechnology, cell, cell culture, culture, degradation, diversity, halophile, host, human, human cell line, immunological, leukemia, literature, lymphoma, methanogen, microbial, microbiology, microorganism, molecular, pathobiological, phage, phototroph, phylogeny, plant, plant virus, plasmid, pollutant, prokaryote, reducer, research, science, scientific, strain, sulfate, systematic, taxonomy, thermophile, virus, yeast, FASEB list |
is listed by: DataCite is listed by: re3data.org is parent organization of: SILVA works with: Cellosaurus |
PMID:18080463 | Free, Freely Available | DOI:10.17616/R3G88X, nif-0000-10209, r3d100010219, DOI:10.13145 | https://doi.org/10.17616/R3G88X, https://doi.org/10.17616/r3G88X, https://doi.org/10.13145/, https://dx.doi.org/10.13145/, https://doi.org/10.17616/R3G88X | SCR_001711 | Leibniz Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures | 2026-09-19 12:56:31 | 424 | |||||
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MPIDB Resource Report Resource Website 1+ mentions |
MPIDB (RRID:SCR_001898) | MPIDB | data or information resource, database | Database that collects and provides all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, co-purification, and 3D domain contacts (iPfam, 3did). (spoke/matrix) binary interactions inferred from pull-down experiments are not included. | 3d domain, conservation, co-purification, interaction, microbial, protein, microbial interaction, protein interaction, interaction conservation, interaction co-purification, 3d domain contact, protein-protein interaction, microbial protein, microbiology |
is listed by: re3data.org is related to: IMEx - The International Molecular Exchange Consortium is related to: IntAct is related to: Database of Interacting Proteins (DIP) is related to: BIND is related to: MINT is related to: Interaction Reference Index is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry has parent organization: J. Craig Venter Institute |
J. Craig Venter Institute ; Indgen Life Technologies ; NIH ; NIMH R01GM79710 |
PMID:18556668 | THIS RESOURCE IS NO LONGER IN SERVICE | r3d100010673, nif-0000-10467 | http://jcvi.org/mpidb/ | SCR_001898 | The Microbial Protein Interaction Database, Microbial Protein Interaction Database | 2026-09-19 12:56:32 | 5 | ||||
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American FactFinder Resource Report Resource Website 50+ mentions |
American FactFinder (RRID:SCR_002932) | American FactFinder | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2025. Database that provides access to population, housing, economic, and geographic data from several censuses and surveys about the United States, Puerto Rico and the Island Areas. Census data may be compiled into tables, maps and downloadable files, which can be viewed or printed. A large selection of pre-made tables and maps satisfies many information requests. By law, no one is permitted to reveal information from these censuses and surveys that could identify any person, household, or business. The following data are available: * American Community Survey * ACS Content Review * American Housing Survey * Annual Economic Surveys * Annual Surveys of Governments * Census of Governments * Decennial Census * Economic Census * Equal Employment Opportunity (EEO) Tabulation * Population Estimates Program * Puerto Rico Community Survey | population, household survey, income, census, community, housing, economic, government, industry, map, FASEB list |
is listed by: re3data.org has parent organization: U.S. Census Bureau |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30094, r3d100010768 | https://doi.org/10.17616/R3PG7G | http://factfinder.census.gov/ | SCR_002932 | 2026-09-19 12:56:37 | 58 | ||||||
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Ligand-Gated Ion Channel Database Resource Report Resource Website 1+ mentions |
Ligand-Gated Ion Channel Database (RRID:SCR_002418) | LGICdb | data or information resource, database | Database providing access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamate activated cationic channels superfamily. Due to the lack of evolutionary relationship, these three superfamilies are treated separately. It currently contains 554 entries of ligand-activated ion channel subunits. In this database one may find: the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Additionally, the atomic coordinates of subunits, or portion of subunits, are provided when available. Redundancy is kept to a minimum, i.e. one entry per gene. Each entry in the database has been manually constructed and checked by a researcher of the field in order to reduce the inaccuracies to a minimum. NOTE: This database is not actively maintained anymore. People should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc. | equilibrium, extracellular, gabaa, gated, gene, genetics, 3d model, alignment, anionic, atomic, atp, cationic, cellular, molecular, channel, compartment, computation, conformation, coordinate, cys-loop, glutamate, glycine, histamine, homologous, ion, ion channel, ligand, membrane, nicotinic, nucleic acid, phylogenetic, pore, portion, proteic, nucleic acid, protein, phylogeny, receptor, segment, sequence, sequence data, serotonin, subunit, superfamily, transmembrane |
is listed by: re3data.org has parent organization: European Bioinformatics Institute |
College of France; Paris; France ; Centre National de la Recherche Scientifique ; European Union ; Biotech and Biomed contracts ; French Ministry of Higher Education and Research ; Institut Pasteur |
PMID:16381861 PMID:11125117 |
nif-0000-00037, r3d100010796 | https://doi.org/10.17616/R3Q90D | SCR_002418 | LGIC Database | 2026-09-19 12:56:35 | 1 | |||||
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GermOnline Resource Report Resource Website 10+ mentions |
GermOnline (RRID:SCR_002807) | GermOnline | data or information resource, database | Cross-species microarray expression database focusing on high-throughput expression data relevant for germline development, meiosis and gametogenesis as well as the mitotic cell cycle. The database contains a unique combination of information: 1) High-throughput expression data obtained with whole-genome high-density oligonucleotide microarrays (GeneChips). 2) Sample annotation (mouse over the sample name and click on it) using the Multiomics Information Management and Annotation System (MIMAS 3.0). 3) In vivo protein-DNA binding data and protein-protein interaction data (available for selected species). 4) Genome annotation information from Ensembl version 50. 5) Orthologs are identified using data from Ensembl and OMA and linked to each other via a section in the report pages. The portal provides access to the Saccharomyces Genomics Viewer (SGV) which facilitates online interpretation of complex data from experiments with high-density oligonucleotide tiling microarrays that cover the entire yeast genome. The database displays only expression data obtained with high-density oligonucleotide microarrays (GeneChips)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | fertility, development, germline, microarray, annotation, in vivo, protein-dna binding, protein-protein interaction, genome, ortholog, high-density oligonucleotide microarray, gene expression, genome annotation, gene orthology, genechip, tiling array, development, meiosis, gametogenesis, mitotic cell cycle, data set, data repository, bio.tools |
is listed by: 3DVC is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: OMA Browser has parent organization: National Institute of Health and Medical Research; Rennes; France |
Swiss Institute of Bioinformatics ; bioinformatics platform of Biogenouest ; National Institute of Health and Medical Research; Rennes; France ; University of Rennes 1; Rennes; France |
PMID:21149299 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:germonline, nif-0000-02906, r3d100010248 | https://bio.tools/germonline, https://doi.org/10.17616/R37K5Q | SCR_002807 | 2026-09-19 12:56:37 | 17 | |||||
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HomoloGene Resource Report Resource Website 100+ mentions |
HomoloGene (RRID:SCR_002924) | HomoloGene | data or information resource, database, service resource | Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase. | homolog, paralog, ortholog, genome, gene, protein, protein alignment, phenotype, conserved domain, homology, amino acid sequence, cell, dna, gold standard |
is used by: NIF Data Federation is used by: Nowomics is used by: MitoMiner is listed by: OMICtools is listed by: re3data.org is related to: OMIM is related to: Mouse Genome Informatics (MGI) is related to: Zebrafish Information Network (ZFIN) is related to: SGD is related to: FlyBase is related to: ProbeMatchDB 2.0 is related to: Biomine is related to: Consensus CDS has parent organization: NCBI |
PMID:23193264 | Free, Freely availalbe | nif-0000-02975, r3d100010781, OMICS_01544 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene, https://doi.org/10.17616/R3889F | SCR_002924 | NCBI HomoloGene | 2026-09-19 12:56:37 | 459 | |||||
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Zebrafish Information Network (ZFIN) Resource Report Resource Website 500+ mentions |
Zebrafish Information Network (ZFIN) (RRID:SCR_002560) | ZFIN | data or information resource, database | Model organism database that serves as central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations.Serves as primary community database resource for laboratory use of zebrafish. Developed and supports integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases. | expression, gene, anatomy, development, disease, genomic, model, molecular, mutant, neuronal, organism, phenotype, physiological, synteny, zebrafish, gene expression, genome sequence, molecular neuroanatomy resource, genotype, anatomical structure, publication, genome, image collection, gold standard, bio.tools, FASEB list, RRID Community Authority |
uses: InterMOD is used by: NIF Data Federation is used by: Resource Identification Portal is used by: Morpholino Database is used by: Integrated Animals is used by: NIH Heal Project is recommended by: Resource Identification Portal is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: InterMOD is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: Phenoscape Knowledgebase is related to: MONARCH Initiative is related to: Bgee: dataBase for Gene Expression Evolution is related to: NIH Data Sharing Repositories is related to: HomoloGene is related to: Zebrafish International Resource Center is related to: Integrated Manually Extracted Annotation is related to: Zebrafish Genome Project has parent organization: University of Oregon; Oregon; USA is parent organization of: ZFIN Antibody Database is parent organization of: Zebrafish Anatomical Ontology is parent organization of: ZFIN Protocol Wiki is parent organization of: ZFIN Antibody Wiki is organization facet of: Alliance of Genome Resources |
NHGRI P41 HG002659; NHGRI R01 HG004834 |
PMID:23074187 PMID:21036866 PMID:16381936 |
Free, Available for download, Freely available | OMICS_01666, nif-0000-21427, biotools:zfin, r3d100010421, SCR_017504 | http://zfin.org/ZFIN/misc_html/tips.html#newrecord, https://wiki.zfin.org/display/general/ZFIN+Data+Submissions, https://bio.tools/zfin, https://doi.org/10.17616/R3CK5Z | SCR_002560 | Zebrafish Database, The Zebrafish Model Organism Database, Zebra Model Organism Database, ZebraFish Information Network, ZFIN | 2026-09-19 12:56:36 | 978 | ||||
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EcoGene Resource Report Resource Website 50+ mentions |
EcoGene (RRID:SCR_002437) | ECK, ECOGENE, ECOGENE G | data or information resource, database | Database that contains updated information about the Escherichia coli K-12 genome and proteome sequences, including extensive gene bibliographies. Users are able to download customized tables, perform Boolean query comparisons, generate sets of paired DNA sequences, and download any E. coli K-12 genomic DNA sub-sequence. BLAST functions, microarray data, an alphabetical index of genes, and gene overlap queries are also available. The Database Table Downloads Page provides a full list of EG numbers cross-referenced to the new cross-database ECK numbers and other common accession numbers, as well as gene names and synonyms. Monthly release archival downloads are available, but the live, daily updated version of EcoGene is the default mysql database for download queries. | life sciences, genomics, proteomics, gene, gene expression, genetics, protein, protein binding, protein-protein interaction, membrane, rna, dna, structure, function, functional annotation, annotation, blast, FASEB list |
is listed by: re3data.org is related to: RefSeq is related to: Colibri has parent organization: University of Miami Miller School of Medicine; Florida; USA |
NIH ; Lucille P. Markey Foundation ; NIGMS 5-R01-GM58560-05 |
PMID:23197660 PMID:10592181 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02784, r3d100010546 | https://doi.org/10.17616/R3KP5V | http://bmb.med.miami.edu/ http://bmb.med.miami.edu/EcoGene/EcoWeb/ http://www.ecogene.org/old/ | SCR_002437 | EcoGene Database of Escherichia coli Sequence and Function | 2026-09-19 12:56:36 | 58 |
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