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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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European Bioinformatics Institute Resource Report Resource Website 1000+ mentions |
European Bioinformatics Institute (RRID:SCR_004727) | EMBL-EBI | institution | Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL. | organization, academic, bioinformatics, research, service, data, computational, biology, training, database, DNA, protein |
is used by: Blueprint Epigenome is listed by: re3data.org is related to: AgedBrainSYSBIO is related to: ProteomeXchange is related to: Open PHACTS is related to: RHEA is related to: TraCeR is related to: 3D-Beacons is related to: RNAcentral has parent organization: European Molecular Biology Laboratory is parent organization of: CoGenT++ is parent organization of: ENA Sequence Version Archive is parent organization of: Reaper - Demultiplexing trimming and filtering sequencing data is parent organization of: PeakAnalyzer is parent organization of: Tally is parent organization of: Clustal Omega is parent organization of: Biocatalogue - The Life Science Web Services Registry is parent organization of: Experimental Network for Functional Integration: A European Network of Excellence for Data Integration and Systems Biology is parent organization of: The Alternatve Splicing Database is parent organization of: BioModels is parent organization of: CHEBI is parent organization of: MAGE is parent organization of: Ensembl is parent organization of: MIAME is parent organization of: UniProt is parent organization of: Ligand-Gated Ion Channel Database is parent organization of: EBI Genomes is parent organization of: IMEx - The International Molecular Exchange Consortium is parent organization of: Toolbox at the European Bioinformatics Institute is parent organization of: Clustal W2 is parent organization of: ArrayExpress is parent organization of: IMGT/HLA is parent organization of: IntEnz- Integrated relational Enzyme database is parent organization of: IPD - Immuno Polymorphism Database is parent organization of: IPI is parent organization of: MicroArray and Gene Expression Markup Language is parent organization of: DaliLite Pairwise comparison of protein structures is parent organization of: Chemical Information Ontology is parent organization of: PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees is parent organization of: Proteomics Identifications (PRIDE) is parent organization of: Software Ontology is parent organization of: FSSP - Families of Structurally Similar Proteins is parent organization of: Experimental Factor Ontology is parent organization of: Identifiers.org is parent organization of: HipSci is parent organization of: ProteomeXchange is parent organization of: Taxonomy is parent organization of: PDBe - Protein Data Bank in Europe is parent organization of: EBI Dbfetch is parent organization of: ProFunc is parent organization of: WSDbfetch (SOAP) is parent organization of: QuickGO is parent organization of: SAS - Sequence Annotated by Structure is parent organization of: UniProt DAS is parent organization of: UniParc at the EBI is parent organization of: Patent Abstracts is parent organization of: BioSample Database at EBI is parent organization of: Database of Genomic Variants Archive (DGVa) is parent organization of: European Genome phenome Archive is parent organization of: UniSave is parent organization of: ArchSchema is parent organization of: UniRef at the EBI is parent organization of: EBIMed is parent organization of: Kraken is parent organization of: SIMBioMS is parent organization of: Expression Profiler is parent organization of: Whatizit is parent organization of: InterProScan is parent organization of: VectorBase is parent organization of: DRCAT Resource Catalogue is parent organization of: FunTree is parent organization of: CREATE is parent organization of: BioMedBridges is parent organization of: PSICQUIC Registry is parent organization of: PDBsum is parent organization of: European Nucleotide Archive (ENA) is parent organization of: DrugPort is parent organization of: Ontology Lookup Service is parent organization of: EDAM Ontology is parent organization of: InterPro is parent organization of: MIRIAM Resources is parent organization of: EB-eye Search is parent organization of: SBO is parent organization of: Ensembl Genomes is parent organization of: NeuronVisio is parent organization of: IntAct is parent organization of: WSsas - Web Service for the SAS tool is parent organization of: Enzyme Structures Database is parent organization of: EMBOSS CpGPlot/CpGReport/Isochore is parent organization of: PaperMaker is parent organization of: CluSTr is parent organization of: Genome Reviews is parent organization of: GOA is parent organization of: Integr8 : Access to complete genomes and proteomes is parent organization of: IPD-ESTDAB- The European Searchable Tumour Line Database is parent organization of: IPD-HPA - Human Platelet Antigens is parent organization of: IPD-KIR - Killer-cell Immunoglobulin-like Receptors is parent organization of: IPD-MHC- Major Histocompatibility Complex is parent organization of: HilbertVis is parent organization of: Gene Expression Atlas is parent organization of: Parasite genome databases and genome research resources is parent organization of: Alternative Exon Database is parent organization of: AltExtron Database is parent organization of: Patent Data Resources is parent organization of: Pompep is parent organization of: Mouse finder is parent organization of: Gene Regulation Ontology is parent organization of: CiteXplore literature searching is parent organization of: MaxSprout is parent organization of: SRS is parent organization of: MicroCosm Targets is parent organization of: Kalign is parent organization of: MUSCLE is parent organization of: FASTA is parent organization of: WU-BLAST is parent organization of: Oases is parent organization of: HTS Mappers is parent organization of: CRAM is parent organization of: CSA - Catalytic Site Atlas is parent organization of: ArrayExpress (R) is parent organization of: WiggleTools is parent organization of: vsn is parent organization of: rlsim is parent organization of: ISA Infrastructure for Managing Experimental Metadata is parent organization of: BioMart Project is parent organization of: BioPerl is parent organization of: BioJS is parent organization of: EMDataResource.org is parent organization of: HTqPCR is parent organization of: Reactome is parent organization of: Europe PubMed Central is parent organization of: h5vc is parent organization of: LexGrid is parent organization of: Consensus CDS is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: OrChem is parent organization of: Orphanet Rare Disease Ontology is parent organization of: Reflect is parent organization of: BioLayout Express 3D is parent organization of: Virtual Fly Brain is parent organization of: GeneWise is parent organization of: PhenoMeNal is parent organization of: Ensembl Metazoa is parent organization of: Velvet |
EMBL member states ; European Union ; NIH ; Wellcome Trust ; UK Research Councils ; Industry Programme partners ; BBSRC |
grid.225360.0, Wikidata: Q1341845, ISNI: 0000 0000 9709 7726, nlx_72386 | https://ror.org/02catss52 | SCR_004727 | EBI, European Molecular Biology Laboratory - European Bioinformatics Institute | 2026-02-07 02:06:30 | 3689 | ||||||
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EURORDIS Resource Report Resource Website 10+ mentions |
EURORDIS (RRID:SCR_003814) | EURORDIS | nonprofit organization | EURORDIS is a non-governmental patient-driven alliance of patient organizations and individuals active in the field of rare diseases, dedicated to improving the quality of life of all people living with rare diseases in Europe. It is a not-for-profit organization and represents more than 479 rare disease organizations in 45 different countries (of which 25 are EU Member States), covering more than 4,000 rare diseases. It is therefore the voice of the 30 million patients affected by rare diseases throughout Europe. EURORDIS aims at improving the quality of life of people living with rare diseases in Europe through advocacy at the European level, support for research and drug development, networking patient groups, raising awareness and other actions designed to fight against the impact of rare diseases on the lives of patients and family. EURORDIS' training programs and resources are designed to strengthen the capacity of rare disease patients' representatives. Training empowers patients' representatives to advocate effectively for rare diseases at both the local and EU level. Key issues affecting patients of Rare Diseases on which we actively work: * Sustaining rare diseases as an EU public health priority * Making Rare Diseases A Public Health Priority In All Member States * Rare Diseases: An International Public Health Priority * Improving Access To Orphan Drugs * Improving Access To Quality Care * Promoting cross-border healthcare and patient mobility * Bridging Patients And Research * Genetic testing and newborn screening | French Muscular Dystrophy Association ; European Union ; members ; corporate foundations ; health industry |
Wikidata: Q5412882, grid.433753.5, nlx_143535 | https://ror.org/019w4mg02 | SCR_003814 | EURORDIS - Rare Diseases Europe | 2026-02-07 02:06:08 | 37 | ||||||||
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Eurofungbase Resource Report Resource Website |
Eurofungbase (RRID:SCR_007094) | Eurofung | knowledge environment | The Eurofung project is a Coordination Action with the aim of developing a strategy to build up and maintain an integrated, sustainable European genomic database required for innovative genomics research of filamentous fungal model organisms of interest. This database will become a crystallization point for related systems and then could be integrated and conserved in a central European genomic database. The consortium counts 32 member laboratories, three of which have partner status. A Fungal Industrial Platform (FIP) of 13 members is also associated with the project. The project focuses on several filamentous fungi for different reasons. Aspergillus nidulans has a long record of use as a fungal model organism. Aspergillus niger, Trichoderma reesei and Penicillium chrysogenum are important cell factories used for the production of enzymes and metabolites including compounds such as Beta-lactams with benefits to human health. The human pathogen Aspergillus fumigatus serves not only as a model pathogen, but becomes more and more a serious threat to human health. The project contributes to create the conditions and facilities within Europe to widely apply all genomics technologies in filamentous fungal research. This will greatly expand our knowledge about filamentous fungi. This new genomics information will thus be beneficial to European biotechnology industries and help to improve the prevention and treatment of fungal disease. Expected results: The main results expected from this project are: - The contribution of the community to the manual annotation of important fungal genomes through annotation jamborees. - The realization of an integrated sustainable fungal genomic database through collaboration with bioinformatics centers and incorporation of the community data. - The realization of a fungal genomics knowledge base for the Eurofungbase community and the European fungal biotech industry through meetings, workshops and web-based information. - Intensified collaboration between the members of the network including the participating industries, thus strengthening the infrastructure for high quality fungal genomics research in Europe and furthermore determining joint research targets for the future. -Individualized training of a next generation of young scientists in fungal genomics and biotechnological research. | European Union LSSG-CT-2005-018964 | nlx_20616 | SCR_007094 | Eurofung | 2026-02-07 02:07:37 | 0 | |||||||||
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Workflow4Ever Resource Report Resource Website 1+ mentions |
Workflow4Ever (RRID:SCR_005939) | Wf4Ever | knowledge environment | Project to addresses challenges associated with the preservation of scientific experiments in data-intensive science, including: * The definition of models to describe, in a standard way, scientific experiments by means of workflow-centric Research Objects, which comprise scientific workflows, the provenance of their executions, interconnections between workflows and related resources (e.g., datasets, publications, etc.), and social aspects related to such scientific experiments. * The collection of best practices for the creation and management of Research Objects. * The analysis and management of decay in scientific workflows. To address these challenges they are creating an architecture and tooling for the access, manipulation, sharing, reuse and evolution of Research Objects in a range of disciplines. This will result into the next generation RO-enabled myExperiment. | preservation, workflow, provenance, archive, research object, workflow model, management, experimental method |
is listed by: FORCE11 is related to: myExperiment is related to: RightField |
European Union | nlx_151286 | SCR_005939 | 2026-02-07 02:07:00 | 1 | ||||||||
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Semantic MediaWiki Resource Report Resource Website 1+ mentions |
Semantic MediaWiki (RRID:SCR_006246) | SMW | software resource | A free, open-source extension to MediaWiki - the wiki software that powers Wikipedia - that helps to search, organize, tag, browse, evaluate, and share the wiki''s content. While traditional wikis contain only text which computers can neither understand nor evaluate, SMW adds semantic annotations that allow a wiki to function as a collaborative database. Semantic MediaWiki introduces some additional markup into the wiki-text which allows users to add semantic annotations to the wiki. While this first appears to make things more complex, it can also greatly simplify the structure of the wiki, help users to find more information in less time, and improve the overall quality and consistency of the wiki. A large number of related extensions have been created that extend the ability to edit, display and browse through the data stored by SMW: the term Semantic MediaWiki is sometimes used to refer to this entire family of extensions. | extension, wiki, semantic annotation, authoring tool |
is listed by: FORCE11 has parent organization: MediaWiki |
European Union | Open unspecified license | nif-0000-06677 | SCR_006246 | Semantic Media Wiki | 2026-02-07 02:07:28 | 3 | ||||||
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EPILEPSIE database Resource Report Resource Website 1+ mentions |
EPILEPSIE database (RRID:SCR_003179) | data or information resource, database | A comprehensive database for human surface and intracranial EEG data that is suitable for a broad range of applications e.g. of time series analyses of brain activity. Currently, the EU database contains annotated EEG datasets from more than 200 patients with epilepsy, 50 of them with intracranial recordings with up to 122 channels. Each dataset provides EEG data for a continuous recording time of at least 96 hours (4 days) at a sample rate of up to 2500 Hz. Clinical patient information and MR imaging data supplement the EEG data. The total duration of EEG recordings included execeeds 30000 hours. The database is composed of different modalities: Binary files with EEG recording / MR imaging data and Relational database for supplementary meta data. | seizure, electroencephalography, mri, eeg recording, metadata, intracranial, surface, time series analyses, brain activity, brain, clinical, image collection |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
Epilepsy | Excellence Initiative of the German Federal and State Governments ; European Union 211713; BMBF 01GQ0420; German Science Foundation Ti 315/4-2 |
PMID:22738131 | Free, Freely available | nlx_156892 | http://www.nitrc.org/projects/epilepsiaedb http://epilepsy-database.eu/project/ http://www.epilepsiae.eu http://epilepsy-database.eu | SCR_003179 | EPILEPSIAE Project Database, European Epilepsy Database | 2026-02-11 10:56:39 | 3 | ||||
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Arabidopsis Reactome Resource Report Resource Website 1+ mentions |
Arabidopsis Reactome (RRID:SCR_002063) | data or information resource, database | Curated database of core pathways and reactions in plant biology that covers biological pathways ranging from the basic processes of metabolism to high-level processes such as cell cycle regulation. While it is targeted at Arabidopsis pathways, it also includes many biological events from other plant species. This makes the database relevant to the large number of researchers who work on other plants. Arabidopsis Reactome currently contains both in-house curated pathways as well as imported pathways from AraCyc and KEGG databases. All the curated information is backed up by its provenance: either a literature citation or an electronic inference based on sequence similarity. Their ontology ensures that the various events are linked in an appropriate spatial and temporal context. | pathway, reaction, biological process |
uses: AraCyc uses: KEGG is listed by: 3DVC has parent organization: John Innes Centre; Norwich; United Kingdom |
European Union LSHG-CT-2006-037704 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20812 | SCR_002063 | Arabidopsis Reactome - a curated knowledgebase of plant biological pathways | 2026-02-11 10:56:24 | 3 | |||||||
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MINT Resource Report Resource Website 1000+ mentions |
MINT (RRID:SCR_001523) | MINT | data or information resource, database | A database that focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the MINT Viewer. This collection of molecular interaction databases can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. VirusMINT explores the interactions of viral proteins with human proteins. The MINT connect viewer allows you to enter a list of proteins (e.g. proteins in a pathway) to retrieve, display and download a network with all the interactions connecting them. | protein-protein interaction, protein, interaction, virus, peptide, organelle co-localization, pathway, molecular interaction, papillomavirus, epstein-barr virus, hepatitis b virus, hepatitis c virus, human adenovirus, human herpesvirus, human immunodeficiency virus, influenza a virus, vaccinia virus, simian virus 40, virus strains, virus protein, orthologous protein, network, proteomics, ortholog, FASEB list |
uses: IntAct uses: PSI-MI is listed by: re3data.org is affiliated with: 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: VirusMINT is related to: PSICQUIC Registry is related to: Agile Protein Interactomes DataServer has parent organization: University of Rome Tor Vergata; Rome; Italy works with: IMEx - The International Molecular Exchange Consortium |
European Union ; ENFIN ; Interaction Proteome Project ; IMEx - The International Molecular Exchange Consortium ; HUPO Proteomics Standards Initiative ; AIRC Associazione Italiana per la Ricerca sul Cancro |
PMID:22096227 PMID:24234451 PMID:19897547 PMID:18592188 PMID:18551417 PMID:18428712 PMID:17135203 PMID:11911893 |
nlx_152821, r3d100010414 | https://doi.org/10.17616/R38S3B | SCR_001523 | MINT, the Molecular INTeraction database, Molecular Interactions Database, Molecular INTeraction database, MINT - the Molecular INTeraction database | 2026-02-11 10:56:15 | 1109 | |||||
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ConsensusPathDB Resource Report Resource Website 500+ mentions |
ConsensusPathDB (RRID:SCR_002231) | CPDB | data or information resource, database | An integrative interaction database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With human, yeast and mouse complex functional interactions, it currently constitutes the most comprehensive publicly available interaction repository for these species. Different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways is offered. | gene regulatory network, pathway, gene regulatory network, molecular interaction, interaction, gene regulation, protein interaction, genetic interaction, biochemical reaction, drug-target interaction, molecule, visualization, gene, protein, complex, metabolite, FASEB list |
is listed by: OMICtools is related to: BIND is related to: BioCarta Pathways is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: CORUM is related to: Database of Interacting Proteins (DIP) is related to: DrugBank is related to: HPRD - Human Protein Reference Database is related to: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is related to: Integrating Network Objects with Hierarchies is related to: InnateDB is related to: IntAct is related to: KEGG is related to: MINT is related to: MIPS Mammalian Protein-Protein Interaction Database is related to: MatrixDB is related to: NetPath is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: PDZBase is related to: Pathway Interaction Database is related to: PIG - Pathogen Interaction Gateway is related to: PINdb is related to: PharmGKB is related to: PhosphoPOINT is related to: PhosphoSitePlus: Protein Modification Site is related to: Reactome is related to: Small Molecule Pathway Database is related to: SignaLink is related to: SPIKE is related to: Therapeutic Target Database is related to: WikiPathways has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
European Union HEALTH-F4-2007-200767 | PMID:23143270 PMID:21071422 PMID:20847220 PMID:18940869 |
Free, Freely available | nif-0000-02684, OMICS_01903, r3d100012822 | https://doi.org/10.17616/R3HF8Z | SCR_002231 | ConsensusPathDB, ConsensusPathDB-human | 2026-02-11 10:56:25 | 667 | ||||
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International Knockout Mouse Consortium Resource Report Resource Website 50+ mentions |
International Knockout Mouse Consortium (RRID:SCR_005574) | IKMC | data or information resource, database | Database of the international consortium working together to mutate all protein-coding genes in the mouse using a combination of gene trapping and gene targeting in C57BL/6 mouse embryonic stem (ES) cells. Detailed information on targeted genes is available. The IKMC includes the following programs: * Knockout Mouse Project (KOMP) (USA) ** CSD, a collaborative team at the Children''''s Hospital Oakland Research Institute (CHORI), the Wellcome Trust Sanger Institute and the University of California at Davis School of Veterinary Medicine , led by Pieter deJong, Ph.D., CHORI, along with K. C. Kent Lloyd, D.V.M., Ph.D., UC Davis; and Allan Bradley, Ph.D. FRS, and William Skarnes, Ph.D., at the Wellcome Trust Sanger Institute. ** Regeneron, a team at the VelociGene division of Regeneron Pharmaceuticals, Inc., led by David Valenzuela, Ph.D. and George D. Yancopoulos, M.D., Ph.D. * European Conditional Mouse Mutagenesis Program (EUCOMM) (Europe) * North American Conditional Mouse Mutagenesis Project (NorCOMM) (Canada) * Texas A&M Institute for Genomic Medicine (TIGM) (USA) Products (vectors, mice, ES cell lines) may be ordered from the above programs. | gene, knock out mouse, chromosome, allele, c57bl/6, embryonic stem cell, vector, mutant, es cell, genome, targeting, gene list, FASEB list |
is related to: Texas A and M Institute for Genomic Medicine is related to: European Mouse Mutant Archive is related to: CMMR - Canadian Mouse Mutant Repository is parent organization of: EUCOMMTOOLS is parent organization of: North American Conditional Mouse Mutagenesis Project is parent organization of: European Conditional Mouse Mutagenesis Program is parent organization of: Knockout Mouse Project |
European Union ; NHGRI HG004074 |
PMID:22968824 PMID:21677750 |
nlx_146200 | SCR_005574 | 2026-02-11 10:57:10 | 68 | |||||||
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Worldwide Protein Data Bank (wwPDB) Resource Report Resource Website 1000+ mentions |
Worldwide Protein Data Bank (wwPDB) (RRID:SCR_006555) | wwPDB | data or information resource, database | Public global Protein Data Bank archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by individual member organizations and about projects undertaken by wwPDB. Data available via websites of its member organizations. | 3-dimentional, bioinformatics, protein, research, structure, macromolecule, structural data, 3d spatial image, gold standard |
is used by: Ligand Expo is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Proteopedia - Life in 3D is related to: NRG-CING is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DNA DataBank of Japan (DDBJ) is related to: PDBe - Protein Data Bank in Europe is related to: PDBe - Protein Data Bank in Europe is related to: PDBj - Protein Data Bank Japan is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: PDB Validation Server is related to: Structural Antibody Database is parent organization of: PDB-Dev works with: PDB-REDO |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NINDS ; NIDDK ; European Molecular Biology Laboratory ; Heidelberg; Germany ; Wellcome Trust ; BBSRC ; NIH ; European Union ; NBDC - National Bioscience Database Center ; Japan Science and Technology Agency |
PMID:14634627 | Free, Freely available | nif-0000-23903, r3d100011104 | https://doi.org/10.17616/R3462V | SCR_006555 | World Wide Protein DataBank, wwPDB, Worldwide Protein Data Bank (wwPDB), World Wide Protein Data Bank, Worldwide Protein DataBank | 2026-02-11 10:57:20 | 1215 | ||||
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InnateDB Resource Report Resource Website 100+ mentions |
InnateDB (RRID:SCR_006714) | InnateDB | data or information resource, database | Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response. Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases. InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions. InnateDB Capabilities: * View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly. * Search for genes and proteins of interest. * Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc. * Search genes/interactions belonging to 3,900 pathways. * Visualize interactions using an intuitive subcellular localization-based layout in Cerebral. * Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more. * Access curated interaction data via a dedicated PSICQUIC webservice. | gene, immune response, pathway, protein, signaling pathway, interaction, immune, signaling response, gene, orthology prediction, orthology, ortholg, annotation, interactome, gene expression, molecule, protein-protein interaction, molecular interaction, visualization, nucleic acid-protein, nucleic acid, network, web service, transcription factor binding site, software resource, FASEB list |
is listed by: re3data.org is related to: IMEx - The International Molecular Exchange Consortium is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry is related to: PSICQUIC Registry is related to: Gene Ontology is related to: IntAct has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: University of British Columbia; British Columbia; Canada works with: IMEx - The International Molecular Exchange Consortium |
Microbial infection, Allergy, Asthma | Michael Smith Foundation for Health Research ; AllerGen 12ASI1; AllerGen 12B&B2; Teagasc RMIS6018; European Union PSIMEx project contract FP7-HEALTH-2007-223411 |
PMID:23180781 PMID:18766178 |
Free, Freely available | nif-0000-20808, r3d100010676 | https://doi.org/10.17616/R36S43 | SCR_006714 | A Knowledge Resource for Innate Immunity Interactions and Pathways, InnateDB: Systems Biology of the Innate Immune Response, InnateDB - A Knowledge Resource for Innate Immunity Interactions and Pathways | 2026-02-11 10:57:23 | 496 | |||
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VDJbase Resource Report Resource Website 1+ mentions |
VDJbase (RRID:SCR_022599) | data or information resource, database | Open source adaptive immune receptor genotype and haplotype database. Core collection is inferred from immune receptor repertoire sequences and genomically derived material. Provides customisable reports, which allow users to study gene and allele usage in various ways. | Adaptive immune receptor genes, genotypes and haplotypes, immune receptor repertoire sequences, customisable reports, gene and allele | European Union ; NIAID R01AI127877; NIAID R01AI125567; NIAID R01AI130398 |
DOI:10.1093/nar/gkz872 | Free, Freely available | SCR_022599 | 2026-02-11 11:00:25 | 6 | |||||||||
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CancerResource Resource Report Resource Website 1+ mentions |
CancerResource (RRID:SCR_011945) | data or information resource, database | Comprehensive database of cancer relevant proteins and compound interactions supported by experimental knowledge.Knowledgebase for drug-target relationships related to cancer as well as for supporting information or experimental data. | compound, drug, target gene, cancer relevant proteins, compound interactions, drug-target relationships, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Cancer | International Research Training Group IRTG ; DFG ; Federal Ministry of Education and Research BMBF ; European Union |
PMID:20952398 | Free, Freely available | biotools:cancerresource, OMICS_01576 | https://bio.tools/cancerresource | http://bioinf-data.charite.de/cancerresource/index.php?site=home | SCR_011945 | 2026-02-11 10:58:33 | 5 | ||||
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Dictyostelium discoideum genome database Resource Report Resource Website 100+ mentions |
Dictyostelium discoideum genome database (RRID:SCR_006643) | dictyBase, dictyBase gene name, dictyBase REF, DictyBase | organism supplier, material resource, biomaterial supply resource | Model organism database for the social amoeba Dictyostelium discoideum that provides the biomedical research community with integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a ''''reference genome'''' in the Amoebozoa clade. They highlight several new features in the present update: (i) new annotations; (ii) improved interface with web 2.0 functionality; (iii) the initial steps towards a genome portal for the Amoebozoa; (iv) ortholog display; and (v) the complete integration of the Dicty Stock Center with dictyBase. The Dicty Stock Center currently holds over 1500 strains targeting over 930 different genes. There are over 100 different distinct amoebozoan species. In addition, the collection contains nearly 600 plasmids and other materials such as antibodies and cDNA libraries. The strain collection includes: * strain catalog * natural isolates * MNNG chemical mutants * tester strains for parasexual genetics * auxotroph strains * null mutants * GFP-labeled strains for cell biology * plasmid catalog The Dicty Stock Center can accept Dictyostelium strains, plasmids, and other materials relevant for research using Dictyostelium such as antibodies and cDNA or genomic libraries. | genome, sequence, est, literature, gene model, functional annotation, reference genome, gene, antibody, cdna, bacteria, dictyostelium discoideum, dictyostelium purpureum, dictyostelium fasciculatum, polysphondylium pallidium, bio.tools |
is used by: NIF Data Federation is listed by: One Mind Biospecimen Bank Listing is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: Textpresso has parent organization: Northwestern University; Illinois; USA has parent organization: Baylor University; Texas; USA has parent organization: University of Cologne; Cologne; Germany is parent organization of: Dictyostelium Discoideum Anatomy Ontology is parent organization of: Dictyostelium Anatomy Ontology is parent organization of: dictyBase - Teaching Tools Using Dictyostelium discoideum |
NIGMS GM64426; NIGMS GM087371; NHGRI HG0022; European Union |
PMID:23172289 PMID:21087999 PMID:18974179 PMID:14681427 PMID:16381903 |
nif-0000-20974, biotools:dictybase, SCR_008149, nif-0000-02751, OMICS_03158 | https://bio.tools/dictybase | http://genome.imb-jena.de/dictyostelium/ | SCR_006643 | dictyBase gene name, dictyBase REF, Dicty, dictyBase, Dictyostelium discoideum | 2026-02-12 09:44:17 | 306 | ||||
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Ensembl Genomes Resource Report Resource Website 100+ mentions |
Ensembl Genomes (RRID:SCR_006773) | data access protocol, software resource, web service, database, data or information resource | Database portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualization platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community - essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimized data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualized in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site. | genome, gold standard, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: Ensembl is related to: g:Profiler has parent organization: European Bioinformatics Institute |
European Molecular Biology Laboratory ; European Union FELICS 021902 (RII3); BBSRC BB/F019793/1 |
PMID:24163254 PMID:19884133 |
r3d100011197, OMICS_01648, nlx_65207, biotools:ensembl_genomes | https://bio.tools/ensembl_genomes https://doi.org/10.17616/R3MW6M |
SCR_006773 | Ensembl Genomes: Extending Ensembl across the taxonomic space, EnsemblGenomes, Ensembl Genome | 2026-02-12 09:44:18 | 276 | ||||||
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ProDom Resource Report Resource Website 100+ mentions |
ProDom (RRID:SCR_006969) | ProDom | analysis service resource, service resource, production service resource, database, data analysis service, data or information resource | Comprehensive set of protein domain families automatically generated from UniProt Knowledge Database. Automated clustering of homologous domains generated from global comparison of all available protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | set, protein, domain, family, automatically, generated, UniProt, database, homologous, sequence, compare, FASEB list |
is listed by: OMICtools is related to: UniProt is related to: InterPro has parent organization: PRABI |
‘Programme de Bio-Informatique InterOrganismes ; Re´seau des Ge´nopoles ; European Union |
PMID:15608179 PMID:12230033 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01698, nif-0000-03342 | http://prodom.prabi.fr/prodom/current/html/home.php | SCR_006969 | 2026-02-12 09:44:36 | 352 | |||||
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LifeDB Resource Report Resource Website 1+ mentions |
LifeDB (RRID:SCR_006899) | LifeDB | data or information resource, database, image collection | Database that integrates large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. LifeDB integrates data regarding full length cDNA clones and data on expression of encoded protein and their subcellular localization on mammalian cell line. LifeDB enables the scientific community to systematically search and select genes, proteins as well as cDNA of interest by specific database identifiers as well as gene name. It enables to visualize cDNA clone and subcellular location of proteins. It also links the results to external biological databases in order to provide a broader functional information. LifeDB also provides an annotation pipeline which facilitates an improved mapping of clones to known human reference transcripts from the RefSeq database and the Ensembl database. An advanced web interface enables the researchers to view the data in a more user friendly manner. Users can search using any one of the following search options available both in Search gene and cDNA clones and Search Sub-cellular locations of human proteins: By Keyword, By gene/transcript identifier, By plate name, By clone name, By cellular location. * The Search genes and cDNA clones results include: Gene Name, Ensemble ID, Genomic Region, Clone name, Plate name, Plate position, Classification class, Synonymous SNP''s, Non- synonymous SNP''s, Number of ambiguous positions, and Alignment with reference genes. * The Search sub-cellular locations of human proteins results include: Subcellular location, Gene Name, Ensemble ID, Clone name, True localization, Images, Start tag and End tag. Every result page has an option to download result data (excluding the microscopy images). On click of ''Download results as CSV-file'' link in the result page the user will be given a choice to open or save result data in form of a CSV (Comma Separated Values) file. Later the CSV file can be easily opened using Excel or OpenOffice. | human, protein, gene, cdna clone, subcellular, open reading frame, functional genomics | has parent organization: German Cancer Research Center | BMBF 01GR0101; BMBF 01GR0420; European Union grant 503438 |
PMID:16381901 PMID:14681468 |
nif-0000-03081 | SCR_006899 | 2026-02-12 09:44:28 | 1 | |||||||
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Lyngby Resource Report Resource Website 1+ mentions |
Lyngby (RRID:SCR_007143) | Lyngby | software resource, software application, data analysis software, data processing software | Matlab toolbox for the analysis of functional neuroimages (PET, fMRI). The toolbox contains a number of models: FIR-filter, Lange-Zeger, K-means clustering among others, visualizations and reading of neuroimaging files. | functional, statistical, fmri, pet, matlab, neuroimaging |
is listed by: Biositemaps has parent organization: THOR Center for Neuroinformatics |
Human Brain Project ; Danish Research Council ; European Union ; BIOMED2 ; MAPAWAMO ; NASA ; NSF ; DOE ; NIDA R01 DA09246; NIMH P20 MH57180 |
Free, Non-commercial | nif-0000-00324 | SCR_007143 | Lyngby Toolbox, Lyngby - A Toolbox for Functional Neuroimaging | 2026-02-12 09:44:38 | 2 | ||||||
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Genes to Cognition: Neuroscience Research Programme Resource Report Resource Website 10+ mentions |
Genes to Cognition: Neuroscience Research Programme (RRID:SCR_007121) | data or information resource, portal, topical portal | A neuroscience research program that studies genes, the brain and behavior in an integrated manner, established to elucidate the molecular mechanisms of learning and memory, and shed light on the pathogenesis of disorders of cognition. Central to G2C investigations is the NMDA receptor complex (NRC/MASC), that is found at the synapses in the central nervous system which constitute the functional connections between neurons. Changes in the receptor and associated components are thought to be in a large part responsible for the phenomenon of synaptic plasticity, that may underlie learning and memory. G2C is addressing the function of synapse proteins using large scale approaches combining genomics, proteomics and genetic methods with electrophysiological and behavioral studies. This is incorporated with computational models of the organization of molecular networks at the synapse. These combined approaches provide a powerful and unique opportunity to understand the mechanisms of disease genes in behavior and brain pathology as well as provide fundamental insights into the complexity of the human brain. Additionally, Genes to Cognition makes available its biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline. The resources are freely-available to interested researchers. | cognition, gene, neuroscience |
is listed by: 3DVC has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust ; MRC ; BBSRC ; Gatsby Charitable Foundation ; Human Frontiers Science Programme ; European Union ; Framework Programme ; EPSRC ; NSF |
nif-0000-10235 | SCR_007121 | G2C Neuroscience Research Program, G2C Research Programme, Genes to Cognition: Neuroscience Research Program, Genes to Cognition, G2C, Genes to Cognition - Neuroscience Research Programme, Genes to Cognition-Neuroscience Research Programme, G2C Research Program | 2026-02-12 09:44:22 | 19 |
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