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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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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Africa Centre for Health and Population Studies Resource Report Resource Website 1+ mentions |
Africa Centre for Health and Population Studies (RRID:SCR_008964) | Africa Centre Datasets, Africa Center Datasets, AfricaCentre Datasets | data or information resource, data set | Longitudinal datasets of demographic, social, medical and economic information from a rural demographic in northern KwaZulu-Natal, South Africa where HIV prevalence is extremely high. The data may be filtered by demographics, years, or by individuals questionnaires. The datasets may be used by other researchers but the Africa Centre requests notification that anyone contact them when downloading their data. The datasets are provided in three formats: Stata11 .dta; tables in a MS-Access .accdb database; and worksheets in a MS-Excel .xlsx workbook. Datasets are generated approximately every six months containing information spanning the whole period of surveillance from 1/1/2000 to present. | medicine, hiv infection, economic, demography, biology, social, longitudinal |
is listed by: re3data.org is listed by: DataCite has parent organization: University of KwaZulu-Natal; Durban; South Africa |
HIV | Wellcome Trust ; Agence Nationale de Recherches sur le Sida et les Hepatites Virales ; Department for International Development ; USAID ; EDCTP ; South African MRC ; National Research Foundation ; CSIR ; UNFPA ; CIDA |
Open unspecified license, Data Use Agreement, Approval required | nlx_152006 | SCR_008964 | Africa Centre for Health and Population Studies Datasets, Africa Center for Health and Population Studies | 2026-09-19 12:58:41 | 4 |
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