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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Autosomal Recessive Polycystic Kidney Disease Mutation Database Resource Report Resource Website 10+ mentions |
Autosomal Recessive Polycystic Kidney Disease Mutation Database (RRID:SCR_002290) | data or information resource, data repository, database, service resource, storage service resource | Catalog of all changes detected in PKHD1 (Polycystic Kidney and Hepatic Disease 1) in a locus specific database. Investigators are invited to submit their novel data to this database. These data should be meaningful for clinical practice as well as of relevance for the reader interested in molecular aspects of polycystic kidney disease (PKD). There are also some links and information for ARPKD patients and their parents. Autosomal recessive polycystic kidney disease (ARPKD/PKHD1) is an important cause of renal-related and liver-related morbidity and mortality in childhood. This study reports mutation screening in 90 ARPKD patients and identifies mutations in 110 alleles making up a detection rate of 61%. Thirty-four of the detected mutations have not been reported previously. Two underlying mutations in 40 patients and one mutation in 30 cases are disclosed, and no mutation was detected on the remaining chromosomes. Mutations were found to be scattered throughout the gene without evidence of clustering at specific sites. PKHD1 mutation analysis is a powerful tool to establish the molecular cause of ARPKD in a given family. Direct identification of mutations allows an unequivocal diagnosis and accurate genetic counseling even in families displaying diagnostic challenges. | clinical, gene, genetic, mutation, protein, recessive, renal | has parent organization: RWTH Aachen University; Aachen; Germany | Autosomal recessive polycystic kidney disease, Polycystic kidney disease | PMID:16199545 PMID:11919560 |
Permission required, Terms of use | nif-0000-21038 | http://www.humgen.rwth-aachen.de/index.asp?subform=database.html&nav=database_nav.html | SCR_002290 | Mutation Database Autosomal Recessive Polycystic Kidney Disease (ARPKD/PKHD1) | 2026-08-10 09:31:40 | 14 | |||||
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Kidney and Urinary Pathway Knowledge Base Resource Report Resource Website 1+ mentions |
Kidney and Urinary Pathway Knowledge Base (RRID:SCR_001746) | KUPKB | data or information resource, analysis service resource, data repository, production service resource, data set, service resource, data analysis service, storage service resource | A collection of omics datasets (mRNA, proteins and miRNA) that have been extracted from PubMed and other related renal databases, all related to kidney physiology and pathology giving KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. Some microarray raw datasets have also been downloaded from the Gene Expression Omnibus and analyzed by the open-source software GeneArmada. The Semantic Web technologies, together with the background knowledge from the domain's ontologies, allows both rapid conversion and integration of this knowledge base. SPARQL endpoint http://sparql.kupkb.org/sparql The KUPKB Network Explorer will help you visualize the relationships among molecules stored in the KUPKB. A simple spreadsheet template is available for users to submit data to the KUPKB. It aims to capture a minimal amount of information about the experiment and the observations made. | kidney, urinary, urine, pathway, molecule, visualizer, gene, protein, mirna, metabolite, mrna, microarray, ortholog, rdf, renal cell, anatomy, animal model, disease, sparql, proteomics, ontology, biomarker, gene expression, physiology, pathology |
is related to: NIDDK Information Network (dkNET) is related to: Gene Expression Omnibus is related to: Gene Ontology is related to: KEGG has parent organization: University of Manchester; Manchester; United Kingdom has parent organization: National Institute of Health and Medical Research; Rennes; France |
Kidney disease | European Union ; FP7 ; ICT-2007.4.4 e-LICO project |
PMID:21624162 | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_154134 | http://www.e-lico.eu/kupkb | SCR_001746 | Kidney & Urinary Pathway Knowledge Base | 2026-08-10 09:31:31 | 2 | |||
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Capital Biosciences Resource Report Resource Website 1+ mentions |
Capital Biosciences (RRID:SCR_004879) | commercial organization | Biological products including Cell Immortalization Products, Clinically Defined Human Tissue, cDNA ORF Clones, Premade Adenoviruses, Purified Proteins, Viral Expression Systems and others as well as services like Custom Recombinant Adenovirus Production, Custom Recombinant Lentivirus Production, Protein Detection and Quantification and Stable Cell Line Production for academic and governmental research institutes, pharmaceutical and biotechnology industry. Capital Biosciences offers most types of human tissues, normal and diseased, with extensive clinical history and follow up information. Standard specimen format: Snap-frozen(flash-frozen), Formalin fixed and paraffin embedded (FFPE) tissues, Blood and blood products, Bone marrow, Total RNA, Genomic DNA, Total Proteins, Primary cell cultures, Viable frozen tissue. Tumor tissue samples include: Bladder cancer, Glioblastoma, Medulloblastoma, Breast Carcinoma, Cervical Cancer, Colorectal Cancer, Endometrial Cancer, Esophageal Cancer, Head and Neck (H&N) Carcinoma, Hepatocellular Carcinoma (HCC), Hodgkin's lymphoma, Kidney, Renal Cell Carcinoma, Lung Cancer, Non-Small Cell (NCSLC), Lung Cancer, Small Cell (SCLC), Melanoma, Mesothelioma, non-Hodgkin's Lymphoma, Ovarian Adenocarcinoma, Pancreatic Cancer, Prostate Cancer, Stomach Cancer. | cell immortalization, clinical, tissue, cdna orf clone, premade adenovirus, purified protein, viral expression, recombinant adenovirus, recombinant lentivirus, protein, detection, quantification, cell line, disease, formalin fixed and paraffin embedded, frozen, tissue, blood, blood product, bone marrow, rna, dna, protein, cell culture, tumor tissue | is listed by: One Mind Biospecimen Bank Listing | Normal, Cancer, Tumor, Bladder cancer, Glioblastoma, Medulloblastoma, Breast Carcinoma, Cervical Cancer, Colorectal Cancer, Endometrial Cancer, Esophageal Cancer, Head Carcinoma, Neck Carcinoma, Hepatocellular Carcinoma, Hodgkin's lymphoma, Kidney, Renal Cell Carcinoma, Lung Cancer, Non-Small Cell, Lung Cancer, Small Cell, Melanoma, Mesothelioma, Non-Hodgkin's Lymphoma, Ovarian Adenocarcinoma, Pancreatic Cancer, Prostate Cancer, Stomach Cancer | nlx_85333 | http://www.capitalbiosciences.com/category/show/tissue-human-clinically-defined.html | SCR_004879 | Capital Biosciences: innovative solutions for life sciences, Capital Biosciences Inc. | 2026-08-08 11:58:28 | 2 | |||||||
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CellFinder Resource Report Resource Website 10+ mentions |
CellFinder (RRID:SCR_006598) | CellFinder | data or information resource, analysis service resource, production service resource, database, service resource, data analysis service | Database of mapped validated gene and protein expression, phenotype and images related to cell types. The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells are related to more complex systems such as tissues, organs and organisms and arranged according to their position in development. CellFinder provides long-term data storage for validated and curated primary research data and provides additional expert-validation through relevant information extracted from text. Operated under the Open Source/Access model, community and scientific networking applications will allow users to store and retrieve their data and to explore cells and their interactions on singular and complex resolution levels. The involvement of stem cell registries and banks will allow direct access to selected cells. The set up the stem cell data repository will involve three lines of action: * the acquisition of scientific data and contents * the standardized description of this data, its organization with the help of ontologies and technical implementation * the integration of existing sources/logistics and to ensure sustainable long-term operation | cell, gene expression, protein expression, phenotype, image, gene, stem cell, cellome, metadata standard, stem cell therapy, differential expression, protein, cell type, development, adrenal gland, gall bladder, intestine, inferior vena cava, kidney, liver, spleen |
is related to: Allen Institute for Brain Science has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany is parent organization of: CELDA Ontology |
BMBF ; DFG |
PMID:23599415 | nlx_153857 | SCR_006598 | Cell Finder | 2026-08-10 09:32:53 | 31 | ||||||
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TissueNet - The Database of Human Tissue Protein-Protein Interactions Resource Report Resource Website 10+ mentions |
TissueNet - The Database of Human Tissue Protein-Protein Interactions (RRID:SCR_002052) | TissueNet | data or information resource, database | Database of human tissue protein-protein interactions (PPIs) that associates each interaction with human tissues that express both pair mates. This was achieved by integrating current data of experimentally detected PPIs with extensive data of gene and protein expression across 16 main human tissues. Users can query TissueNet using a protein and retrieve its PPI partners per tissue, or using a PPI and retrieve the tissues expressing both pair mates. The graphical representation of the output highlights tissue-specific and tissue-wide PPIs. Thus, TissueNet provides a unique platform for assessing the roles of human proteins and their interactions across tissues. | protein-protein interaction, protein, tissue, adipose, adrenal, brain, breast, colon, heart, kidney, liver, lung, lymph node, ovary, prostate, skeletal muscle, testis, thyroid, white blood cell, protein expression, dna-microarray |
is listed by: OMICtools is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: Database of Interacting Proteins (DIP) is related to: IntAct is related to: MINT has parent organization: Ben-Gurion University of the Negev; Beer-Sheva; Israel |
PMID:23193266 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01913 | SCR_002052 | 2026-08-10 09:31:36 | 27 | |||||||
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GenitoUrinary Development Molecular Anatomy Project Resource Report Resource Website 100+ mentions |
GenitoUrinary Development Molecular Anatomy Project (RRID:SCR_001554) | GUDMAP | material resource, organism supplier, biomaterial supply resource | Project aggregates and provides experimental gene expression data from genito-urinary system. International consortium providing molecular atlas of gene expression for developing organs of GenitoUrinary (GU) tract. Mouse strains to facilitate developmental and functional studies within GU system. Experimental protocols and standard specifications. Tutorials describing GU organogenesis and primary data via database. Data are from large-scale in situ hybridization screens (wholemount and section) and microarray gene expression data of microdissected, laser-captured and FACS-sorted components of developing mouse genitourinary (GU) system. | gene expression, genitourinary tract, molecular anatomy, genitourinary system, organogenesis, genitourinary, in situ hybridization, immunohistochemistry, microarray, mutant mouse strain, development, rna, protein, theiler stage, gene, anatomy, male, female, embryonic mouse, kidney, urogenital tract, urinary, reproductive, disease, molecule, cell, gene, phenotype, functional annotation, protein interaction, transgenic transgene, image, rna extraction, sample preparation, fluorescent immunohistochemistry, rna isolation, rna amplification, labeling, fluorescent in situ-hybridization, riboprobe synthesis, cellular localization, tissue isolation, embedding, cryostat sectioning, laser capture microdissection, paraffin, whole mount, optimal cutting temperature, riboprobe synthesis, target amplification, sectioning, FASEB list |
is used by: NIDDK Information Network (dkNET) is listed by: One Mind Biospecimen Bank Listing is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology is related to: ToppCluster is related to: One Mind Biospecimen Bank Listing is parent organization of: GUDMAP Ontology is parent organization of: GATACA GUDMAP Gene Explorer |
NIDDK DK070136; NIDDK DK070200; NIDDK DK070181 |
PMID:21652655 PMID:18287559 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152871, nif-0000-33426 | SCR_001554 | Murine Atlas for Genitourinary Development | 2026-08-10 09:31:27 | 289 | |||||
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Collecting Duct Database Resource Report Resource Website |
Collecting Duct Database (RRID:SCR_000759) | CDDB | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. This database is intended to serve as a learning tool to obtain curated information for the design of microarray targets to scan collecting duct tissues (human, rat, mouse). The database focuses on regulatory and transporter proteins expressed in the collecting duct, but when collecting duct proteins are a member of a larger family of proteins, common additional members of the family are included even if they have not been demonstrated to be expressed in the collecting duct. An Internet-accessible database has been devised for major collecting duct proteins involved in transport and regulation of cellular processes. The individual proteins included in this database are those culled from literature searches and from previously published studies involving cDNA arrays and serial analysis of gene expression (SAGE). Design of microarray targets for the study of kidney collecting duct tissues is facilitated by the database, which includes links to curated base pair and amino acid sequence data, relevant literature, and related databases. Use of the database is illustrated by a search for water channel proteins, aquaporins, and by a subsequent search for vasopressin receptors. Links are shown to the literature and to sequence data for human, rat, and mouse, as well as to relevant web-based resources. Extension of the database is dynamic and is done through a maintenance interface. This permits creation of new categories, updating of existing entries, and addition of new ones. CDDB is a database that organizes lists of genes found in collecting duct tissues from three mammalian species: human, rat, and mouse. Proteins are divided into categories by family relationships and functional classification, and each category is assigned a section in the database. Each section includes links to the literature and to sequence information for genes, proteins, expressed sequence tags, and related information. The user can peruse a section or use a search engine at the bottom of the web page to search the database for a name or abbreviation or for a link to a sequence. Each entry in the database includes links to relevant papers in the kidney and collecting duct literature. It uses links to PubMed to generate MEDLINE searches for retrieval of references. In addition, each entry includes links to curated sequence data available in LocusLink. Individual links are made to sequence and protein data for human, rat, and mouse. Links are then added as curated sequences become available for proteins identified in the renal collecting duct and for proteins identified in kidney and similar in function or homologous to proteins identified in the collecting duct. | expressed sequence tag, expression, family, functional, gene, aquaporin, array, cdna, classification, collecting duct, homologous, human, kidney, literature, mammal, mammalian, microarray, mouse, protein, protein localization and targeting databases, rat, receptor, regulatory, relationship, scan, serial analysis, specie, target, tissue, transporter, vasopressin, water channel protein | has parent organization: National Institutes of Health | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21078 | SCR_000759 | Collecting Duct Database | 2026-08-10 09:31:15 | 0 | |||||||
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Hopkins Conte Digestive Diseases Basic and Translational Research Core Center Proteomics Core Resource Report Resource Website |
Hopkins Conte Digestive Diseases Basic and Translational Research Core Center Proteomics Core (RRID:SCR_015597) | core facility, access service resource, service resource | Core facility that uses mass spectrometry coupled to one (1D) and two (2D) dimensional separations by column chromatography or gel electrophoresis to identify, quantify or characterize proteins and their post-translational modifications, that are expressed in well characterized protein fractions from the small intestine, colon, kidney, liver and pancreas. Techniques such as difference gel electrophoresis (DIGE), isobaric tag for relative and absolute quantitation (iTRAQ), tandem mass tags (TMT) and stable isotope labeling of amino acids in cell culture (SILAC) as well as non-labeling methods (MudPIT, multi-dimensional protein identification technology) are available for quantifying relative differences in protein expression and post-translational modifications, such as acetylation, glycosylation, phosphorylation, nitrosation, ubiquitination and novel cleavage sites. | proteomics, mass spectrometry, digestive disease, protein, HDDBTRCC |
is listed by: NIDDK Information Network (dkNET) has parent organization: Hopkins Conte Digestive Diseases Basic and Translational Research Core Center is organization facet of: Hopkins Conte Digestive Diseases Basic and Translational Research Core Center |
digestive disease | NIDDK P30 DK089502 | Available to affiliated researchers, Available to John Hopkins University | SCR_015597 | 2026-08-10 09:35:24 | 0 | ||||||||
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SpecimenCentral.com Resource Report Resource Website 1+ mentions |
SpecimenCentral.com (RRID:SCR_003536) | SpecimenCentral.com | material resource, biomaterial supply resource | World's open biospecimen research database where biobanks and biomedical researchers meet to exchange human biospecimen needs and supply: whole blood, serum, plasma, solid tissue samples and more. The connection is accelerated so researchers save valuable time and money and tissue banks utilize inventory. The pace of specimen procurement remains unacceptably slow to the biomedical research community. Specimen Central is the foremost global resource to aid biomedical researchers in expediting their search for high quality human biospecimens, tissues, samples and specimens. They facilitate your search for blood, whole blood, buccal swab, DNA, RNA, protein, cell lines, plasma, serum, RBC, white cells, buffy coat, fluid, marrow, urine, stem cells, and solid tissue such as tumor, tumor and biopsy materials spanning all manner of common and rare pathologies and indications including Alzheimer's, basal cell carcinoma, bladder cancer, bone cancer, brain cancer, breast cancer, cerebrospinal fluid, amniotic fluid, colorectal cancer, colon cancer, hodgkins and non-hodgkins lymphoma, kidney/renal cancer, leukemia, liver cancer, lung cancer, melanoma, multiple sclerosis, myeloma neuroblastoma, neurodegenerative diseases, ovarian cancer, pancreatic cancer, prostate cancer, urinary cancer. This includes adult and pediatric indications. Specimen Central users specify a number of variables in their Specimen Requests, including preparation, preservation and handling requirements such as cryo-preserved, FFPE (Formalin-fixed paraffin-embedded), formalin, frozen, refrigerated, OCT, snap frozen, paraffin block, fresh, prospective, autopsy or cadaveric, etc. Many users require clinically annotated date associated with their specimens, as well as documentation of IRB or ethics committee approval and informed consents. For Researchers Most specimen databases require researchers to waste time and effort entering lengthy registrations and search queries that yield poor results, if anything. Specimen Central solves this problem by having tissue banks search for you. From years to months, months to weeks, and weeks to days, Specimen Central seeks to reduce delays and costs in the research & development life cycle by expediting connections between demand and supply. For Biobanks The capital costs of maintaining a biobank infrastructure are substantial and growing. Biobanks use Specimen Central as a marketing tool to augment their business development efforts. By routinely checking Specimen Central's Specimen Requests, biobanks can uncover market demand for their inventories and develop new connections and revenue streams to defray costs. Specimen Central supplements - not displaces - the efforts of your sales representatives, agents, brokers and commercial partners. | blood, tissue, cell, dna, rna, protein, body fluid, whole blood, buccal swab, cell line, plasma, serum, red blood cell, white cell, buffy coat, marrow, urine, stem cell, solid tissue, tumor, adult, pediatric, biopsy material, child, clinically annotated, clinical, annotated, tissue | is listed by: One Mind Biospecimen Bank Listing | All | The community can contribute to this resource | nlx_10317 | SCR_003536 | Specimen Central, SpecimenCentral | 2026-08-09 09:03:49 | 1 | ||||||
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Binding Site Resource Report Resource Website 1+ mentions |
Binding Site (RRID:SCR_004051) | commercial organization | Company provides specialist diagnostic products to clinicians and laboratory professionals worldwide. Specialist protein company committed to research, development, manufacture and distribution of immunodiagnostic assays for global laboratory market. Specialized in antibody specificity technology, Binding Site gives clinicians and laboratory staff tools to significantly improve diagnosis and management of those patients with specific cancers and immune disorders. Binding Site manufactures wide range of products for plasma protein analysis including Freelite, Hevylite and SPAplus. | Diagnostic products, protein, diagnosis, monitoring, assay, immunodiagnostic assays | is related to: Kidney Health Initiative | Cancer, Immune disorder, Multiple Myeloma, Primary immunodeficiency disease | nlx_158482 | SCR_004051 | The Binding Site, The Binding Site Group Ltd, Binding Site Inc, The Specialist Protein Company, Binding Site Group Ltd | 2026-08-08 11:58:13 | 2 | ||||||||
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European Nucleotide Archive (ENA) Resource Report Resource Website 1000+ mentions |
European Nucleotide Archive (ENA) (RRID:SCR_006515) | ENA | data or information resource, data repository, database, service resource, storage service resource | Public archive providing a comprehensive record of the world''''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource. | analysis, bioinformatics, dna, nucleotide, sequencing, web service, rna, molecular biology, nucleotide sequence, protein, gene expression, gene, genome, biochemistry, molecular structure, metabolite, protein binding, chemogenomics, gold standard |
is used by: BioSample Database at EBI 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: 3DVC is listed by: re3data.org is listed by: OMICtools is related to: NCBI Sequence Read Archive (SRA) is related to: ENA Sequence Version Archive is related to: VBASE2 is related to: DDBJ Sequence Read Archive is related to: ISA Infrastructure for Managing Experimental Metadata is related to: DNA DataBank of Japan (DDBJ) is related to: DNA DataBank of Japan (DDBJ) is related to: NCBI is related to: INSDC is related to: INSDC is related to: NCBI Assembly Archive Viewer has parent organization: European Bioinformatics Institute is parent organization of: ENA Sequence Search works with: Eutherian comparative genomic analysis protocol |
EMBL ; Wellcome Trust ; European Union |
PMID:20972220 | Public, The community can contribute to this resource, Acknowledgement requested | OMICS_01029, r3d100010527, nif-0000-32981 | http://www.ebi.ac.uk/embl/, https://doi.org/10.17616/R3HW3J | SCR_006515 | ENA, European Nucleotide Archive | 2026-08-10 09:32:54 | 1344 | ||||
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IntAct Resource Report Resource Website 1000+ mentions |
IntAct (RRID:SCR_006944) | IntAct | data or information resource, data repository, database, service resource, storage service resource | Open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. Direct user submissions of molecular interaction data are encouraged, which may be deposited prior to publication in a peer-reviewed journal. The IntAct Database contains (Jun. 2014): * 447368 Interactions * 33021 experiments * 12698 publications * 82745 Interactors IntAct provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows "zooming in" on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available. | protein domain, motif, protein interaction, molecular interaction, interaction, protein, binary interaction, complex, data set, protein-protein interaction, pathway, small molecule-protein, nucleic acid-protein, small molecule, nucleic acid, protein binding, chromatin, cancer, apoptosis, molecular biology, virus, source code, isoform, gold standard |
is used by: ChannelPedia is used by: MINT is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: 3DVC is listed by: re3data.org is listed by: OMICtools is related to: 3D-Interologs is related to: IMEx - The International Molecular Exchange Consortium is related to: MPIDB is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: InteroPorc is related to: Interaction Reference Index is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: Integrated Molecular Interaction Database is related to: VirHostNet: Virus-Host Network is related to: PSICQUIC Registry is related to: UniProt is related to: SIB Swiss Institute of Bioinformatics is related to: I2D is related to: InnateDB is related to: MatrixDB is related to: MBInfo is related to: AgBase is related to: Cardiovascular Gene Ontology Annotation Initiative is related to: PSI-MI is related to: Agile Protein Interactomes DataServer has parent organization: European Bioinformatics Institute works with: IMEx - The International Molecular Exchange Consortium |
European Union contract FP7-HEALTH-2007-223411; European Union contract FP7-HEALTH-2007-200767 |
PMID:24234451 PMID:22121220 PMID:19850723 PMID:17145710 PMID:14681455 |
Apache License, v2, (software), Creative Commons Attribution License, (data), The community can contribute to this resource | OMICS_01918, r3d100010671, nif-0000-03026 | https://doi.org/10.17616/R3QS4R | SCR_006944 | IntAct | 2026-08-10 09:32:59 | 1955 | ||||
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PDBe - Protein Data Bank in Europe Resource Report Resource Website 50+ mentions |
PDBe - Protein Data Bank in Europe (RRID:SCR_004312) | PDBe | data or information resource, data repository, database, service resource, storage service resource | The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules. | x-ray, nmr, cryo-em, hybrid method, dna, protein, rna, sugar, ligand, virus, compound, fold, enzyme, 3d spatial image, structure, macromolecule, protein-protein interaction, gold standard, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DNA DataBank of Japan (DDBJ) is related to: EMDataResource.org is related to: Worldwide Protein Data Bank (wwPDB) is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: DNA DataBank of Japan (DDBJ) is related to: Worldwide Protein Data Bank (wwPDB) is related to: PDBj - Protein Data Bank Japan is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: European Bioinformatics Institute is parent organization of: Electron Microscopy Data Bank at PDBe (MSD-EBI) works with: MOLEonline |
European Molecular Biology Laboratory; Heidelberg; Germany ; Wellcome Trust ; BBSRC ; NIH ; European Union ; MRC ; CCP4 |
PMID:21045060 PMID:21460450 PMID:19858099 |
r3d100012791, biotools:pdbe, nlx_32372 | https://bio.tools/pdbe, https://doi.org/10.17616/R3J226 | SCR_004312 | Protein DataBank Europe, Protein DataBank in Europe, PDBe, Protein Data Bank in Europe, Protein Data Bank Europe, Macromolecular Structure Database | 2026-08-10 09:32:14 | 55 | |||||
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Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) Resource Report Resource Website 10000+ mentions |
Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) | RCSB PDB | data or information resource, data repository, database, service resource, storage service resource | Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results. | 3-dimensional, annotation, molecule, nucleic acid, protein, visualization, sequence, function, macromolecule, ligand, model, dna, x-ray crystallography, ribosome, structure, oncogene, nucleic acids, molecular structure, cryomicroscopy, gold standard, FASEB list |
is used by: Structural Genomics Consortium is used by: Ligand Expo is used by: DARC - Database for Aligned Ribosomal Complexes is used by: FireDB is used by: Protein Data Bank Bind Database is used by: Protein Data Bank Site is used by: NIF Data Federation is used by: ChannelPedia is used by: MobiDB is used by: BALBES is used by: Structural Antibody Database is used by: BioLiP 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: re3data.org is affiliated with: EMDataResource.org is affiliated with: ConSurf Database is related to: pdb-data is related to: PDB2MultiGif is related to: GlyProt is related to: pdb-care is related to: pdb2linucs is related to: GlyVicinity is related to: GlyTorsion is related to: GlySeq is related to: AffinDB is related to: StatAlign is related to: Community Structure-Activity Resource is related to: Binding MOAD is related to: ConSurf Database is related to: glycosciences.de is related to: DOMINE: Database of Protein Interactions is related to: Jenalib: Jena Library of Biological Macromolecules is related to: SynSysNet is related to: EMDataResource.org is related to: PDBe - Protein Data Bank in Europe is related to: TFinDIT is related to: HOLLOW is related to: ccPDB - Compilation and Creation of datasets from PDB is related to: DOMMINO - Database Of MacroMolecular INteractiOns is related to: InterEvol database is related to: Polbase is related to: PoSSuM is related to: ProtChemSI is related to: RNA CoSSMos is related to: PDBsum is related to: Worldwide Protein Data Bank (wwPDB) is related to: canSAR is related to: CAPS Database is related to: Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING is related to: Combinatorial Extension (CE) is related to: Metalloprotein Site Database is related to: PDBj - Protein Data Bank Japan is related to: Statistical Torsional Angles Potentials of NMR Refinement Database is related to: Metalloprotein Ligand Interaction Database is related to: CARP is related to: PDBTM is related to: RNA FRABASE - RNA FRAgments search engine and dataBASE is related to: AmiGO is related to: ConsensusPathDB is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: DNA DataBank of Japan (DDBJ) is related to: FlyMine is related to: NCBI Protein Database is related to: NCBI Nucleotide is related to: FunTree is related to: IndelFR - Indel Flanking Region Database is related to: NMR Restraints Grid is related to: Enzyme Structures Database is related to: Electron Microscopy Data Bank at PDBe (MSD-EBI) is related to: Worldwide Protein Data Bank (wwPDB) is related to: DNA DataBank of Japan (DDBJ) is related to: PDBe - Protein Data Bank in Europe is related to: MINAS - Metal Ions in Nucleic AcidS is related to: PDBj - Protein Data Bank Japan has parent organization: University of California at San Diego; California; USA has parent organization: Rutgers University; New Jersey; USA is parent organization of: RCSB PDB Software Tools is parent organization of: Protein Data Bank Markup Language is parent organization of: Ligand Expo works with: CellPhoneDB |
NIH ; DOE ; NSF DBI-1338415 |
PMID:12037327 | Public, Acknowledgement requested | nif-0000-00135, SCR_017379, r3d100010327 | http://www.rcsb.org, http://www.pdb.org, | http://www.rcsb.org/pdb/ | SCR_012820 | RCSB, Research Collaboratory for Structural Bioinformatics Protein Data Bank, The Protein Data Bank, PDB, Protein Databank, RCSB Protein Data Bank, Protein Data Bank | 2026-08-10 09:34:45 | 12459 | |||
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KEGG Resource Report Resource Website 10000+ mentions |
KEGG (RRID:SCR_012773) | KEGG | data or information resource, analysis service resource, data access protocol, production service resource, database, portal, web service, topical portal, service resource, software resource, data analysis service | Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies. | model, pathway, functional hierarchy, module, cancer, disease, drug, drug classification, orthology, ortholog, genome, gene, protein, compound, classification, biochemical reaction, pathway, ligand, biosynthesis, pathway prediction, sequence, chemical structure, human, enzyme, database, molecular interaction, metabolism, metabolomics, cellular process, structure, drug development, reaction, cell |
is used by: NIF Data Federation is used by: Arabidopsis Reactome is used by: LIPID MAPS Proteome Database is used by: globaltest is used by: MitoMiner is used by: Database for Annotation Visualization and Integrated Discovery is used by: Biochemical Pathways Reaction Kinetics Database is used by: Ultimate Rough Aggregation of Metabolic Map is used by: GEMINI is used by: In vivo - In silico Metabolite Database is listed by: 3DVC is listed by: OMICtools is affiliated with: Kyoto Encyclopedia of Genes and Genomes Expression Database is related to: PathCase Pathways Database System is related to: ExplorEnz is related to: NCBI BioSystems Database is related to: Allen Institute Neurowiki is related to: eQuilibrator is related to: GeneTrail is related to: KegTools is related to: PRODORIC is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: METLIN is related to: Kidney and Urinary Pathway Knowledge Base is related to: DAVID is related to: ConsensusPathDB is related to: ENZYME is related to: FlyMine is related to: Babelomics is related to: SynSysNet is related to: Cotton EST Database is related to: Integrated Molecular Interaction Database is related to: SEGS is related to: INMEX is related to: BioExtract is related to: ClueGO is related to: MalaCards is related to: TrED is related to: FunTree is related to: MOPED - Model Organism Protein Expression Database is related to: ProOpDB is related to: KOBAS is related to: GeneTerm Linker is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: GeneCodis is related to: FunNet - Transcriptional Networks Analysis is related to: LegumeIP is related to: Algal Functional Annotation Tool is related to: aGEM is related to: DINIES is related to: KEGG PATHWAY Database is related to: ShinyGO is related to: KEGGREST has parent organization: Kyoto University; Kyoto; Japan has parent organization: University of Tokyo; Tokyo; Japan is parent organization of: KegTools works with: DIANA-mirPath works with: MiMeDB |
Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japan Science and Technology Agency |
PMID:22700311 PMID:22130871 PMID:22080510 PMID:19880382 PMID:19172790 PMID:18428742 PMID:18287706 PMID:18077471 PMID:16381885 PMID:16014746 PMID:14681412 PMID:12539951 PMID:11752249 PMID:10928937 PMID:10592173 PMID:9847135 |
Restricted | nlx_31015, OMICS_01583, OMICS_03010, OMICS_01582, OMICS_03974, OMICS_05434, OMICS_05360 | http://www.genome.jp/kegg/ | SCR_012773 | KEGG - Kyoto Encyclopedia of Genes and Genomes, Kyoto Encyclopedia of Genes and Genomes | 2026-08-10 09:34:44 | 81488 | ||||
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Database of Interacting Proteins (DIP) Resource Report Resource Website 100+ mentions |
Database of Interacting Proteins (DIP) (RRID:SCR_003167) | DIP | data or information resource, analysis service resource, data repository, production service resource, database, service resource, data analysis service, storage service resource | Database to catalog experimentally determined interactions between proteins combining information from a variety of sources to create a single, consistent set of protein-protein interactions that can be downloaded in a variety of formats. The data were curated, both, manually and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks. Tools are available to analyze, visualize and integrate user's own experimental data with the information about protein-protein interactions available in the DIP database. The DIP database lists protein pairs that are known to interact with each other. By interact they mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organization and complexity of the protein interaction network at the cellular level. Registration is required to gain access to most of the DIP features. Registration is free to the members of the academic community. Trial accounts for the commercial users are also available. | blast, cellular network, ligand-receptor complex, ligand, network, protein, protein interaction, protein ligand, protein-protein interaction, protein receptor, receptor, sequence, interaction, regulatory pathway, signaling pathway, protein binding, bio.tools, FASEB list |
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: re3data.org is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: IMEx - The International Molecular Exchange Consortium is related to: IMEx - The International Molecular Exchange Consortium is related to: MPIDB is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: InteroPorc is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: NIH Data Sharing Repositories is related to: PSICQUIC Registry is related to: Agile Protein Interactomes DataServer has parent organization: University of California at Los Angeles; California; USA |
NIGMS | PMID:14681454 | Free, Available for download, Freely available | OMICS_01905, nif-0000-00569, r3d100010882, biotools:dip | https://dip.doe-mbi.ucla.edu/dip/Main.cgi, https://bio.tools/dip, https://doi.org/10.17616/R3431F | SCR_003167 | , Database of Interacting Proteins, DIP, Database of Interacting Proteins (DIP) | 2026-08-10 09:31:56 | 167 | ||||
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Electron Microscopy Data Bank at PDBe (MSD-EBI) Resource Report Resource Website 100+ mentions |
Electron Microscopy Data Bank at PDBe (MSD-EBI) (RRID:SCR_006506) | EMDB at PDBe | data or information resource, analysis service resource, data repository, production service resource, database, service resource, data analysis service, storage service resource | Repository for electron microscopy density maps of macromolecular complexes and subcellular structures at Protein Data Bank in Europe. Covers techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. | electron microscopy, density map, macromolecule, complex, subcellular structure, single-particle analysis, electron tomography, electron crystallography, macromolecular complex, structure, protein, protein binding, electron, electron configuration, tomography, microscopy, gold standard |
is used by: DARC - Database for Aligned Ribosomal Complexes is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is related to: EMDataResource.org is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: PDBe - Protein Data Bank in Europe |
NIH | Public | r3d100010562, nlx_149453 | https://doi.org/10.17616/R3HP57 | SCR_006506 | MSD-EBI, Electron Microscopy Data Bank at Protein Data Bank in Europe, Electron Microscopy DataBank, Electron Microscopy Data Bank at PDBe (MSD-EBI), Electron Microscopy Data Bank at PDBe | 2026-08-10 09:32:51 | 153 | |||||
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Global Proteome Machine Database (GPM DB) Resource Report Resource Website 100+ mentions |
Global Proteome Machine Database (GPM DB) (RRID:SCR_006617) | The GPM | data or information resource, data analysis software, data repository, software application, database, service resource, software resource, storage service resource, data processing software | The Global Proteome Machine Organization was set up so that scientists involved in proteomics using tandem mass spectrometry could use that data to analyze proteomes. The projects supported by the GPMO have been selected to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results. The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. This database has been integrated into GPM server pages, allowing users to quickly compare their experimental results with the best results that have been previously observed by other scientists. | mass spectrometry, pattern, peptide, protein, proteome, scientist, spectra, tandem, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
r3d100010883, nif-0000-10455 | https://www.thegpm.org/GPMDB/index.html, https://researchdata.ands.org.au/gpm-global-proteome-machine-database/11342, https://doi.org/10.17616/R30C90 | SCR_006617 | GPM, The Global Proteome Machine Organization: Proteomics Database and Open Source Software, Global Proteome Machine Database, GPM DB, The Global Proteome Machine Database, The Global Proteome Machine, Global Proteome Machine Database (GPM DB), The Global Proteome Machine Organization | 2026-08-10 09:32:53 | 282 | |||||||
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PeptideAtlas Resource Report Resource Website 500+ mentions |
PeptideAtlas (RRID:SCR_006783) | PeptideAtlas | data or information resource, data repository, database, service resource, storage service resource | Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. All results of sequence and spectral library searching are subsequently processed through the Trans Proteomic Pipeline to derive a probability of correct identification for all results in a uniform manner to insure a high quality database, along with false discovery rates at the whole atlas level. The raw data, search results, and full builds can be downloaded for other uses. All results of sequence searching are processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner ensuring a high quality database. All peptides are mapped to Ensembl and can be viewed as custom tracks on the Ensembl genome browser. The long term goal of the project is full annotation of eukaryotic genomes through a thorough validation of expressed proteins. The PeptideAtlas provides a method and a framework to accommodate proteome information coming from high-throughput proteomics technologies. The online database administers experimental data in the public domain. You are encouraged to contribute to the database. | proteomics, peptide, mass spectrometry, annotation, eukaryotic, genome, peptide sequence, high-throughput mass spectrometry, ensembl, peptideprophet, protein sequence, blood plasma, protein, eukaryotic cell, dna, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: ProteomeXchange 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: Biositemaps is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: ProteomeXchange is related to: NIH Data Sharing Repositories is related to: Integrated Manually Extracted Annotation has parent organization: Institute for Systems Biology; Washington; USA |
NCI ; NHGRI ; NIGMS |
PMID:20013378 PMID:23215161 PMID:16381952 PMID:15642101 |
Public, The community can contribute to this resource, Acknowledgement requested | nif-0000-03266, r3d100010889, biotools:peptideatlas | https://bio.tools/peptideatlas, https://doi.org/10.17616/R3BK61 | SCR_006783 | Peptide Atlas, PeptideAtlas | 2026-08-10 09:33:01 | 511 | ||||
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DNA DataBank of Japan (DDBJ) Resource Report Resource Website 500+ mentions |
DNA DataBank of Japan (DDBJ) (RRID:SCR_002359) | DDBJ | data or information resource, data repository, database, service resource, storage service resource | Maintains and provides archival, retrieval and analytical resources for biological information. Central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: DDBJ Omics Archive and BioProject. DOR is archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides organizational framework to access metadata about research projects and data from projects that are deposited into different databases. | nucleotide sequence, genome, dna, dna database, dna research, nucleotide, phylogenetics, protein, sequence, protein binding, gene expression, gene, genetics, nucleoid, genomics, protein binding, gold standard, bio.tools, FASEB list |
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: re3data.org is listed by: Debian is listed by: bio.tools is related to: INSDC is related to: GenBank is related to: INSDC is related to: European Nucleotide Archive (ENA) is related to: GenBank is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Worldwide Protein Data Bank (wwPDB) is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: PDBe - Protein Data Bank in Europe is related to: PDBe - Protein Data Bank in Europe is related to: European Nucleotide Archive (ENA) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: NCBI Assembly Archive Viewer has parent organization: National Institute of Genetics; Shizuoka; Japan is parent organization of: DDBJ Omics Archive is parent organization of: BodyMap-Xs is parent organization of: DDBJ Sequence Read Archive is parent organization of: CIBEX: Center for Information Biology gene EXpression database is parent organization of: Japanese Genotype-phenotype Archive (JGA) |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:26578571 PMID:25477381 |
Free, Freely available, | OMICS_01644, biotools:ddbj, nif-0000-02740, r3d100010218 | https://bio.tools/ddbj, https://doi.org/10.17616/R3M01R | SCR_002359 | DNA DataBank of Japan (DDBJ), DNA DataBank of Japan, DDBJ, DNA Data Bank of Japan, DDBJ - DNA Data Bank of Japan | 2026-08-10 09:31:42 | 709 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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