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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Electronic Cell Project Resource Report Resource Website 10+ mentions |
Electronic Cell Project (RRID:SCR_007381) | simulation software, modeling software, software resource, software application | Software platform, general technologies and theoretical supports for computational biology with the grand aim to make precise whole cell simulation at the molecular level possible.Technologies include formalisms and techniques, including technologies to predict, obtain or estimate parameters such as reaction rates and concentrations of molecules in the cell. The E-Cell System is a software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale system like the cell. The E-Cell Project is open to anyone who shares the view with u that development of cell simulation technology, and, even if such ultimate goal might not be within ten years of reach yet, solving various conceptual, computational and experimental problems that will continue to arise in the course of pursuing it, may have a multitude of eminent scientific, medical and engineering impacts on our society. | gene, protein, ontology, binary executable; software development tool, cell | is listed by: Debian | nif-0000-00378 | https://sources.debian.org/src/ecell/ | SCR_007381 | E-Cell | 2026-08-03 09:33:21 | 15 | ||||||||
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HPID - Human Protein Interaction database Resource Report Resource Website 1+ mentions |
HPID - Human Protein Interaction database (RRID:SCR_007724) | HPID | data repository, data or information resource, database, storage service resource, service resource | Database that provides human protein interaction information and integrated interaction and also finds proteins from databases that can potentially react with proteins submitted by users. The human protein interaction information was pre-computed by a statistical method from existing structural and experimental data, while the integrated human protein interactions are derived from BIND, DIP and HPRD. A score composed of three parts is assigned to the predicted interaction data, and those interactions with high scores were found reliable. HPID allows the user to use the protein IDs in EMBL, Ensembl, MIM, RefSeq, HPRD and NCBI to search protein interactions of interest. A set of web-based software tools has also been developed so that users can visualize and analyze protein interaction networks. | human protein, protein, interaction, protein superfamily, yeast, visualize, analyze, protein interaction network | has parent organization: Inha University; Incheon; South Korea | Ministry of Information and Communication of Korea IMT2000-C3-4 | PMID:15117749 | nif-0000-02984 | http://www.hpid.org | SCR_007724 | 2026-08-03 09:33:29 | 2 | ||||||
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GeneNetWorks Resource Report Resource Website 1+ mentions |
GeneNetWorks (RRID:SCR_008034) | data acquisition software, software application, database, data processing software, data analysis software, data or information resource, software resource, data visualization software | GeneNetWorks is designed for accumulation of experimental data, data navigation, data analysis, and analysis of dependencies in the field of gene expression regulation. It integrates the databases and programs for processing the data about structure and function of DNA, RNA, and proteins, together with the other information resources important for gene expression description. The unique property of above described system is that all the resources within the system GeneNetWorks are divided according to the natural hierarchy of molecular genetic systems and has the following levels: (1) DNA; (2) RNA; (3) proteins; and (4) gene networks. Each module contains: 1) experimental data represented as a database or some sample; 2) program for data analysis; 3) results of an automated data processing; 4) tools for the graphical representation of these data and the results of the data analyses. | experimental, expression, gene, gene regulation, genetic, analysis, data, dna, graphical, molecular, navigation, network, program, protein, rna, software, system | nif-0000-10232 | SCR_008034 | GNW | 2026-08-03 09:33:51 | 1 | ||||||||||
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Gene Regulation Databases Resource Report Resource Website 100+ mentions |
Gene Regulation Databases (RRID:SCR_008033) | Gene Regulation Public Databases | topical portal, data or information resource, portal | In an effort to strongly support the collaborative nature of scientific research, BIOBASE offers academic and non-profit organizations free access to reduced functionality versions of their products. TRANSFAC Professional provides gene regulation analysis solutions, offering the most comprehensive collection of eukaryotic gene regulation data. The professional paid subscription gives customers access to up-to-date data and tools not available in the free version. The public databases currently available for academic and non-profit organizations are: * TRANSFAC: contains data on transcription factors, their experimentally-proven binding sites, and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. * TRANSPATH: provides data about molecules participating in signal transduction pathways and the reactions they are involved in, resulting in a complex network of interconnected signaling components.TRANSPATH focuses on signaling cascades that change the activities of transcription factors and thus alter the gene expression profile of a given cell. * PathoDB: is a database on pathologically relevant mutated forms of transcription factors and their binding sites. It comprises numerous cases of defective transcription factors or mutated transcription factor binding sites, which are known to cause pathological defects. * S/MARt DB: presents data on scaffold or matrix attached regions (S/MARs) of eukaryotic genomes, as well as about the proteins that bind to them. S/MARs organize the chromatin in the form of functionally independent loop domains gained increasing support. Scaffold or Matrix Attached Regions (S/MARs) are genomic DNA sequences through which the chromatin is tightly attached to the proteinaceous scaffold of the nucleus. * TRANSCompel: is a database on composite regulatory elements affecting gene transcription in eukaryotes. Composite regulatory elements consist of two closely situated binding sites for distinct transcription factors, and provide cross-coupling of different signaling pathways. * PathoSign Public: is a database which collects information about defective cell signaling molecules causing human diseases. While constituting a useful data repository in itself, PathoSign is also aimed at being a foundational part of a platform for modeling human disease processes. | element, eukaryote, eukaryotic, expression, functionally, gene, genome, alignment, bind, binding site, cell, chromatin, collaborative, component, coupling, disease, dna, domain, human, matrix, molecular weight, molecule, mononucleotide, network, nucleotide, nucleus, pathological, protein, region, regulated, regulatory, scientific research, sequence, signaling, signal pathway, transcription factor, molecular neuroanatomy resource |
lists: TRANSFAC has parent organization: BIOBASE Corporation |
BIOBASE | nif-0000-10230 | SCR_008033 | gene-regulation.com: Public Databases for Academic and Non-profit Organizations | 2026-08-03 09:33:38 | 130 | |||||||
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Genomatix Software: Understanding Gene Regulation Resource Report Resource Website 500+ mentions |
Genomatix Software: Understanding Gene Regulation (RRID:SCR_008036) | portal, software application, database, data processing software, short course material, narrative resource, topical portal, data analysis software, data or information resource, software resource, training material | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 13,2026. Genomatix is a privately held company that offers software, databases, and services aimed at understanding gene regulation at the molecular level representing a central part of systems biology. Its multilayer integrative approach is a working implementation of systems biology principles. Genomatix combines sequence analysis, functional promoter analysis, proprietary genome annotation, promoter sequence databases, comparative genomics, scientific literature data mining, pathway databases, biological network databases, pathway analysis, network analysis, and expression profiling into working solutions and pipelines. It also enables better understanding of biological mechanisms under different conditions and stimuli in the biological context of your data. Some of Genomatix'' most valuable assets are the strong scientific background and the years of experience in research & discovery as well as in development & application of scientific software. Their firsthand knowledge of all the complexities involved in the in-silico analysis of biological data makes them a first-rate partner for all scientific projects involving the evaluation of gene regulatory mechanisms. The Genomatix team has more than a decade of scientific expertise in the successful application of computer aided analysis of gene regulatory networks, which is reflected by more than 150 peer reviewed scientific publications from Genomatix'' scientists More than 35,000 researchers in industry and academia around the world use this technology. The software available in Genomatix are: - GenomatixSuite: GenomatixSuite is our comprehensive software bundle including ElDorado, Gene2Promoter, GEMS Launcher, MatInspector and MatBase. GenomatixSuite PE also includes BiblioSphere Pathway Edition. Chromatin IP Software - RegionMiner: Fast, extensive analysis of genomic regions. - ChipInspector: Discover the real power of your microarray data. Genome Annotation Software - ElDorado: Extended Genome Annotation. - Gene2Promoter: Retrieve & analyze promoters - GPD: The Genomatix Promoter Database, which is now included with Gene2Promoter. Knowledge Mining Software - BiblioSpere : The next level of pathway/genomics analysis. - LitInspector: Literature and pathway analysis for free. Sequence Analysis Software - GEMS Launcher: Our integrated collection of sequence analysis tools. - MalInspector: Search transcription factor binding sites - MatBase: The transcription factor knowledge base. Other (no registration required) Software - DiAlign: Multiple alignment of DNA/protein sequence. - Genomatix tools: Various small tools for sequence statistics, extraction, formatting, etc. | effect, expression, functional, gene, genome, alignment, analysis, annotation, biological, cascade, cell, data, dna, in-silico analysis, mechanism, metabolic pathway, microarray, mining, molecular, network, pathway, promoter, protein, region, regulation, scientific, sequence, signaling, software, stimulus, systems biology, technology, text mining, transcription, FASEB list | has parent organization: Genomatix Solutions | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10236 | http://www.genomatix.de/products/index.html | SCR_008036 | Genomatix | 2026-08-03 09:33:38 | 868 | |||||||
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INFEVERS Resource Report Resource Website 10+ mentions |
INFEVERS (RRID:SCR_007738) | Infevers | data repository, data or information resource, storage service resource, service resource, data set | Registry for Familial Mediterranean Fever (FMF) and hereditary inflammatory disorders mutations. As of 2014, it includes twenty genes including: MEFV, MVK, TNFRSF1A, NLRP3, NOD2, PSTPIP1, LPIN2 and NLRP7, and contains over 1338 sequence variants. Confidential data, simple and complex alleles are accepted. For each gene, a menu offers: 1) a tabular list of the variants that can be sorted by several parameters; 2) a gene graph providing a schematic representation of the variants along the gene; 3) statistical analysis of the data according to the phenotype, alteration type, and location of the mutation in the gene; 4) the cDNA and gDNA sequences of each gene, showing the nucleotide changes along the sequence, with a color-based code highlighting the gene domains, the first ATG, and the termination codon; and 5) a download menu making all tables and figures available for the users, which, except for the gene graphs, are all automatically generated and updated upon submission of the variants. The entire database was curated to comply with the HUGO Gene Nomenclature Committee (HGNC) and HGVS nomenclature guidelines, and wherever necessary, an informative note was provided. | sequence variant, mutation, allele, genetics, dna, rna, protein, disease, heredity, inflammation, gene, function, phenotype, complex allele, simple allele, exon, intron, cdna sequence, genomic sequence, gdna, FASEB list |
is listed by: re3data.org is related to: Human Genome Variation Society is related to: HGNC |
Familial Mediterranean Fever, Auto-inflammatory Disorder, Hereditary Auto-inflammatory Disorder | European Union | PMID:18409191 PMID:15300846 PMID:12520003 |
Acknowledgement required, Free, Public | nif-0000-03022, r3d100010548 | http://fmf.igh.cnrs.fr/infevers, https://doi.org/10.17616/R3B61B | SCR_007738 | Internet Fevers | 2026-08-03 09:33:40 | 37 | |||
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MetaCore Resource Report Resource Website 1000+ mentions |
MetaCore (RRID:SCR_008125) | software resource, data processing software, software application, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. An integrated software suite for functional analysis of experimental data. The scope of data types includes microarray and SAGE gene expression, SNPs and CGH arrays, proteomics, metabolomics, pathway analysis, Y2H and other custom interactions. MetaCore is based on a proprietary manually curated database of human protein-protein, protein-DNA and protein compound interactions, metabolic and signaling pathways and the effects of bioactive molecules in gene expression. | expression, gene, dna, interaction, metabolomics, microarray, pathway, protein, proteomic, software | is listed by: Metabolomics Workbench | THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-20874 | http://www.genego.com/metacore.php | SCR_008125 | 2026-08-03 09:33:53 | 1182 | ||||||||
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RIKEN Omics Science Center Resource Report Resource Website |
RIKEN Omics Science Center (RRID:SCR_008241) | portal, disease-related portal, topical portal, research forum portal, data or information resource | Omics Science Center is aiming to develop a comprehensive system called Life Science Accelerator(LSA) for the advancement of omics research. The LSA is a comprehensive system consists of biological resources, human resources, technologies, know-how, and essential administrative ability. Ultimate goal of LSA is to support and accelerate the advancement in life science research. Omics is the comprehensive study of molecules in living organisms. The complete sequencing of genomes (the complete set of genes in an organism) has enabled rapid developments in the collection and analysis of various types of comprehensive molecular data such as transcriptomes (the complete set of gene expression data) and proteomes (the complete set of intracellular proteins). Fundamental omics research aims to link these omics data to molecular networks and pathways in order to advance the understanding of biological phenomena as systems at the molecular level. | expression, gene, genome, human, intracellular, life, living, model organisms and comparative genomics databases, molecule, omics, organism, pathway, protein, proteome, science, sequence, technology, transcriptome | is parent organization of: FANTOM DB | RIKEN Yokohama Institute Yokohama Research Promotion Division of Japan | nif-0000-21361 | SCR_008241 | RIKEN OSC | 2026-08-03 09:33:44 | 0 | ||||||||
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Algal Functional Annotation Tool Resource Report Resource Website |
Algal Functional Annotation Tool (RRID:SCR_012034) | Algal Functional Annotation Tool | production service resource, data analysis service, data or information resource, database, analysis service resource, service resource | Tools to search gene lists for functional term enrichment as well as to dynamically visualize proteins onto pathway maps. Additionally, integrated expression data may be used to discover similarly expressed genes based on a starting gene of interest. | gene, pathway, visualization, annotation, function, protein family, ontology, protein, genomics |
is listed by: OMICtools is related to: Gene Ontology is related to: KEGG is related to: MetaCyc is related to: Reactome is related to: Pfam is related to: InterPro has parent organization: University of California at Los Angeles; California; USA |
DOE ; NAABB ; IGP ; Air Force Office of Scientific Research |
PMID:21749710 | OMICS_02226 | SCR_012034 | 2026-08-03 09:34:47 | 0 | |||||||
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JiffyNet Resource Report Resource Website 1+ mentions |
JiffyNet (RRID:SCR_011954) | production service resource, data analysis service, software application, analysis service resource, simulation software, service resource, software resource | Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species. | protein network, protein, network, genome, sequence, pathway annotation, network visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Yonsei University; Seoul; South Korea |
National Research Foundation of Korea ; Next-Generation BioGreen 21 Program |
PMID:23685435 | Free, Freely available | OMICS_01548, biotools:jiffynet | https://bio.tools/jiffynet | SCR_011954 | 2026-08-03 09:35:01 | 1 | ||||||
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Virus Pathogen Resource (ViPR) Resource Report Resource Website 100+ mentions |
Virus Pathogen Resource (ViPR) (RRID:SCR_012983) | ViPR | data repository, data or information resource, database, software application, data processing software, storage service resource, service resource, software resource, data visualization software | Provides searchable public repository of genomic, proteomic and other research data for different strains of pathogenic viruses along with suite of tools for analyzing data. Data can be shared, aggregated, analyzed using ViPR tools, and downloaded for local analysis. ViPR is an NIAID-funded resource that support the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases. It provides a dedicated gateway to SARS-CoV-2 data that integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank), direct submissions, analysis pipelines and expert curation, and provides a suite of bioinformatics analysis and visualization tools for virology research. | flu, gene, bioinformatic, database, diagnostic, genomic, health, human, influenza, pathogen, protein, research, strain, therapeutic, tool, vaccine, virus, visualization, FASEB list |
is recommended by: National Library of Medicine is listed by: Data and Computational Resources to Address COVID-19 is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing has parent organization: University of Texas Southwestern Medical Center; Texas; USA |
COVID-19 | NIAID | Restricted | nif-0000-25312, DOI:10.35083, DOI:10.35084, DOI:10.17616/R30P93, DOI:10.25504/FAIRsharing.2qx8n8 | http://www.viprbrc.org/, https://doi.org/10.17616/r30p93, https://doi.org/10.35083/, https://doi.org/10.35084/, https://dx.doi.org/10.35083/, https://dx.doi.org/10.35084/, https://fairsharing.org/10.25504/FAIRsharing.2qx8n8 | SCR_012983 | Virus Pathogen Resource, ViPR | 2026-08-03 09:35:17 | 140 | ||||
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Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) Resource Report Resource Website 5000+ mentions |
Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) | RCSB PDB | data repository, data or information resource, database, storage service resource, 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 | 2026-08-03 09:35:04 | 9870 | |||
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KEGG Resource Report Resource Website 10000+ mentions |
KEGG (RRID:SCR_012773) | KEGG | portal, production service resource, data analysis service, web service, service resource, database, topical portal, analysis service resource, data access protocol, data or information resource, software resource | 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 | 2026-08-03 09:35:05 | 75877 | ||||
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IMGT - the international ImMunoGeneTics information system Resource Report Resource Website 500+ mentions |
IMGT - the international ImMunoGeneTics information system (RRID:SCR_012780) | IMGT | portal, production service resource, data analysis service, service resource, database, topical portal, analysis service resource, data or information resource | A high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates, serving as the global reference in immunogenetics and immunoinformatics. IMGT provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools. | immunogenetics, immunoinformatics, immunoglobulin, antibody, t cell receptor, major histocompatibility complex, immunoglobulin superfamily, major histocompatibility complex superfamily, protein, immune system, sequence, genome, structure, monoclonal antibody, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: IMGT Repertoire has parent organization: Montpellier 2 University; Montpellier; France is parent organization of: IMGT/LIGM-DB is parent organization of: IMGT/GENE-DB is parent organization of: IMGT-ONTOLOGY is parent organization of: IMGT/V-QUEST is parent organization of: IMGT/HLA |
CNRS ; MESR ; Reseau National des Genopoles ; Region Languedoc-Roussillon ; European Union BIOMED1 BIOCT930038; European Union Biotechnology BIOTECH2 BIO4CT960037; European Union 5th PCRDT Quality of Life and Management of Living Resources QLG2-2000-01287; Agence Nationale de la recherche ANR BIOSYS06_135457; EU ImmunoGrid IST-028069 |
PMID:18978023 | nif-0000-03011, biotools:imgt | https://bio.tools/imgt | http://imgt.cines.fr | SCR_012780 | ImMunoGeneTics Information System, IMGT/LIGM, ImMunoGeneTics | 2026-08-03 09:35:14 | 746 | ||||
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PlasmoDB Resource Report Resource Website 1000+ mentions |
PlasmoDB (RRID:SCR_013331) | data repository, production service resource, data analysis service, web service, service resource, database, storage service resource, analysis service resource, data access protocol, data or information resource, software resource | Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene. | Functional, genomic, database, malaria, parasite, data, analysis, visualization, gene, genome, annotation, transcription, proteomics, protein, evolution, FASEB list |
uses: SynView is related to: GeneDB Pfalciparum has parent organization: Eukaryotic Pathogen Database Resources has parent organization: Pennsylvania State University has parent organization: University of Georgia; Georgia; USA |
malaria | NIAID | PMID:18957442 | nif-0000-03314, SCR_017665, r3d100011569 | SCR_013331 | PlasmoDB, Plasmodium Genomics Resource, PlasmoDB 5.5, Plasmodium genome-resource | 2026-08-03 09:35:13 | 1239 | ||||||
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BioIE: Extracting Informative Sentences From the Biomedical Literature Resource Report Resource Website 1+ mentions |
BioIE: Extracting Informative Sentences From the Biomedical Literature (RRID:SCR_013464) | software toolkit, data or information resource, software resource, database | BioIE is a rule-based system that extracts informative sentences relating to protein families, their structures, functions and diseases from the biomedical literature. Based on manual definition of templates and rules, it aims at precise sentence extraction rather than wide recall. After uploading source text or retrieving abstracts from MEDLINE, users can extract sentences based on predefined or user-defined template categories. BioIE also provides a brief insight into the syntactic and semantic context of the source-text by looking at word, N-gram and MeSH-term distributions. Important Applications of BioIE are in, for example, annotation of microarray data and of protein databases. | family, function, biomedical, context, disease, distribution, literature, medline interfaces, mesh-term, microarray, n-gram, protein, semantic, structure, syntactic | has parent organization: University of Manchester; Manchester; United Kingdom | nif-0000-21055 | SCR_013464 | BioIE | 2026-08-03 09:35:14 | 2 | |||||||||
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Wnt homepage Resource Report Resource Website 10+ mentions |
Wnt homepage (RRID:SCR_000662) | Wnt homepage | topical portal, data or information resource, portal | A resource for members of the Wnt community, providing information on progress in the field, maps on signaling pathways, and methods. The page on reagents lists many resources generously made available to and by the Wnt community. Wnt signaling is discussed in many reviews and in a recent book. There are usually several Wnt meetings per year. | wnt signaling, wnt, wnt protein, wnt pathway, signaling, pathway, method, protein, reagent, bibliography | has parent organization: Stanford University; Stanford; California | Cancer | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156863 | SCR_000662 | the Wnt homepage | 2026-08-03 09:31:07 | 13 | ||||||
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Cardiovascular Proteomics Center Resource Report Resource Website |
Cardiovascular Proteomics Center (RRID:SCR_000603) | CPC, BUSM CPC | topical portal, data or information resource, portal | The Cardiovascular Proteomics Center is a research center funded by the NIH/NHLBI to analyze and identify proteins that may be modified or created by oxidative stress. The CPC is developing and applying new proteomics methodology and instrumentation to the analysis of known proteins and those yet to be discovered. | protein, cardiovascular, proteomics, heart, oxidative stress, mass spectrometry, biology, clinical | has parent organization: Boston University School of Medicine; Massachusetts; USA | NHLBI N01HV28178-12-0-1 | nlx_149148 | SCR_000603 | BUSM Cardiovascular Proteomics Center, Boston University School of Medicine Cardiovascular Proteomics Center, BU Cardiovascular Proteomics Center | 2026-08-03 09:31:06 | 0 | |||||||
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Kyoto Encyclopedia of Genes and Genomes Expression Database Resource Report Resource Website 1000+ mentions |
Kyoto Encyclopedia of Genes and Genomes Expression Database (RRID:SCR_001120) | KEGG Expression Database | data repository, data or information resource, database, storage service resource, service resource | Database for mapping gene expression profiles to pathways and genomes. Repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community. | encyclopedia, endogenous, environment, enzyme, escherichia coli, exogenous, expression, family, functional, gene, genetic, anabaena, bacillus subtilis, biological system, biology, building block, cell, cellular, chemical, community, complex, genome, genomic, hierarchy, interaction, japanese, mapping, metabolic, metabolic pathway databases, microarray, molecular, molecular wiring, nomenclature, order, organism, ortholog, pathway, process, protein, reaction, research, sequence, specie, substance, synechocystis, FASEB list |
is listed by: LabWorm is affiliated with: KEGG has parent organization: Kyoto University; Kyoto; Japan |
PMID:9847135 PMID:10592173 |
Free, Available for download, Freely available | r3d100011570, nif-0000-21234 | https://doi.org/10.17616/R3792T | SCR_001120 | Kyoto Encyclopedia of Genes and Genomes Expression Database | 2026-08-03 09:31:14 | 1274 | |||||
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Enrichr Resource Report Resource Website 1000+ mentions |
Enrichr (RRID:SCR_001575) | Enrichr | production service resource, data analysis service, software application, analysis service resource, service resource, software resource | A web-based gene list enrichment analysis tool that provides various types of visualization summaries of collective functions of gene lists. It includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes / proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries. | bed, gene, software as a service, rna-seq, analyze, protein, function, gene list, visualization, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:23586463 | Free, Freely available | biotools:enrichr, SciRes_000171 | https://bio.tools/enrichr | SCR_001575 | 2026-08-03 09:31:27 | 4351 |
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