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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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aneurIST Resource Report Resource Website 1+ mentions |
aneurIST (RRID:SCR_007427) | aneurIST | data or information resource, portal, disease-related portal, topical portal | Project focused on cerebral aneurysms and provides integrated decision support system to assess risk of aneurysm rupture in patients and to optimize their treatments. IT infrastructure has been developeded for management and processing of vast amount of heterogeneous data acquired during diagnosis. | gene, genetic, adult, cerebral aneurysm, cerebral brain hemorrhage, cerebral hemorrhage, cerebral parenchymal hemorrhage, cerebral hemorrhage, clinical, genomic, human, intracerebral hemorrhage, intracranial aneurysm, subarachnoid hemorrhage, risk, aneurysm rupture, patient, treatment, infrastructure, platform, genomics, disease, personalized risk assessment, bioinformatics, clinical, data management, data integration, data processing, software tool, cerebrum | has parent organization: Pompeu Fabra University; Barcelona; Spain | Cerebral aneurysm, Subarachnoid hemorrhage, Aging | European Union ; Sixth FPPriority 2 of the Information Society Technologies IST |
nif-0000-00538 | http://www.cilab.upf.edu/aneurist1/ | SCR_007427 | aneurIST - Integrated Biomedical Informatics for the Management of Cerebral Aneurysms, (at)neurIST, (at)neurIST - Integrated Biomedical Informatics for the Management of Cerebral Aneurysms | 2026-02-12 09:44:27 | 3 | |||||
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INFEVERS Resource Report Resource Website 10+ mentions |
INFEVERS (RRID:SCR_007738) | Infevers | data repository, service resource, storage service resource, data or information 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 | 2026-02-12 09:44:44 | 37 | |||
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TRANSPATH Resource Report Resource Website 1+ mentions |
TRANSPATH (RRID:SCR_005640) | TRANSPATH | analysis service resource, service resource, production service resource, database, data analysis service, data or information resource | Database on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. It can either be used as an encyclopedia, for both specific and general information on signal transduction, or can serve as a network analyzer. Cross-references to important sequence and signature databases such as EMBL/GenBank UniProt/Swiss-Prot InterPro or Ensembl EntrezGene RefSeq are provided. The database is equipped with the tools for data visualization and analysis. It has three modules: the first one is the data, which have been manually extracted, mostly from the primary literature; the second is PathwayBuilder, which provides several different types of network visualization and hence facilitates understanding; the third is ArrayAnalyzer, which is particularly suited to gene expression array interpretation, and is able to identify key molecules within signalling networks (potential drug targets). These key molecules could be responsible for the coordinated regulation of downstream events. Manual data extraction focuses on direct reactions between signalling molecules and the experimental evidence for them, including species of genes/proteins used in individual experiments, experimental systems, materials and methods. This combination of materials and methods is used in TRANSPATH to assign a quality value to each experimentally proven reaction, which reflects the probability that this reaction would happen under physiological conditions. Another important feature in TRANSPATH is the inclusion of transcription factor-gene relations, which are transferred from TRANSFAC, a database focused on transcription regulation and transcription factors. Since interactions between molecules are mainly direct, this allows a complete and stepwise pathway reconstruction from ligands to regulated genes. | signal transduction, network analyzer, transcriptional regulator, transcription factor, metabolic pathway, signaling pathway, protein-protein interaction, gene-regulatory pathway, signal transduction pathway, complex, signaling molecule, reaction, molecule, gene, pathway, gene expression |
is related to: TRANSFAC is related to: GeneTrail has parent organization: BIOBASE Corporation |
BMBF 031U210B; BMBF 0313092; European Union FP6 contract LSHG-CT-2004-503568; European Union MRTN-CT-2004-512285 |
PMID:18629064 PMID:16381929 PMID:12519957 PMID:11724734 |
Free for academic use, Free for non-profit use, Account required | nif-0000-03580 | http://transpath.gbf.de, http://www.gene-regulation.com/pub/databases.html, http://www.biobase.de/pages/products/databases.html | SCR_005640 | 2026-02-12 09:44:07 | 2 | |||||
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InterProScan Resource Report Resource Website 5000+ mentions |
InterProScan (RRID:SCR_005829) | analysis service resource, software resource, data access protocol, service resource, web service, production service resource, software application, data analysis service, data analysis software, data processing software | Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service. | functional, analysis, sequence, protein, nucleotide, predict, presence, domain, site, proteome, genome, metagenome, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: RARTF is related to: InterPro is related to: LegumeIP is related to: UniProtKB has parent organization: European Bioinformatics Institute |
European Union ; Biotechnology and Biological Sciences Research Council ; EMBL |
PMID:15980438 PMID:17202162 PMID:24451626 |
Free, Available for download, Freely available | OMICS_01479, biotools:interproscan_4, nlx_149337 | https://www.ebi.ac.uk/interpro/download.html https://bio.tools/interproscan_4 |
SCR_005829 | InterProScan Sequence Search, InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5 | 2026-02-12 09:44:07 | 6936 | |||||
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GOTaxExplorer Resource Report Resource Website |
GOTaxExplorer (RRID:SCR_005720) | GOTaxExplorer | analysis service resource, software resource, service resource, production service resource, database, data analysis service, data or information resource | GOTaxExplorer presents a new approach to comparative genomics that integrates functional information and families with the taxonomic classification. It integrates UniProt, Gene Ontology, NCBI Taxonomy, Pfam and SMART in one database. GOTaxExplorer provides four different query types: selection of entity sets, comparison of sets of Pfam families, semantic comparison of sets of GO terms, functional comparison of sets of gene products. This permits to select custom sets of GO terms, families or taxonomic groups. For example, it is possible to compare arbitrarily selected organisms or groups of organisms from the taxonomic tree on the basis of the functionality of their genes. Furthermore, it enables to determine the distribution of specific molecular functions or protein families in the taxonomy. The comparison of sets of GO terms allows to assess the semantic similarity of two different GO terms. The functional comparison of gene products makes it possible to identify functionally equivalent and functionally related gene products from two organisms on the basis of GO annotations and a semantic similarity measure for GO. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, molecular function, protein family, taxonomy, visualization, functional similarity, semantic similarity, analysis, comparative genomics analysis, comparative genomics, search engine, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, function, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: UniProt is related to: NCBI Taxonomy is related to: Pfam is related to: SMART is related to: FSST - Functional Similarity Search Tool has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
German National Genome Research Network ; BMBF 016R0453; DFG KFO 129/1-1; European Union contract LSHG-CT-2003-503265 |
PMID:17346342 | Free for academic use | nlx_149179 | SCR_005720 | 2026-02-12 09:44:15 | 0 | ||||||
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ViBE-Z Resource Report Resource Website 1+ mentions |
ViBE-Z (RRID:SCR_005895) | ViBE-Z | software resource, database, atlas, software application, data processing software, data or information resource, image processing software | An imaging and image analysis framework for virtual colocalization studies in larval zebrafish brains, currently available for 72hpf, 48hpf and 96hpf old larvae. ViBE-Z contains a database with precisely aligned gene expression patterns (1����m^3 resolution), an anatomical atlas, and a software. This software creates high-quality data sets by fusing multiple confocal microscopic image stacks, and aligns these data sets to the standard larva. The ViBE-Z database and atlas are stored in HDF5 file format. They are freely available for download. ViBE-Z provides a software that automatically maps gene expression data with cellular resolution to a 3D standard larval zebrafish (Danio rerio) brain. ViBE-Z enhances the data quality through fusion and attenuation correction of multiple confocal microscope stacks per specimen and uses a fluorescent stain of cell nuclei for image registration. It automatically detects 14 predefined anatomical landmarks for aligning new data with the reference brain. ViBE-Z performs colocalization analysis in expression databases for anatomical domains or subdomains defined by any specific pattern. The ViBE-Z database, atlas and software are provided via a web interface. | brain, larval zebrafish, gene expression, confocal microscopy | has parent organization: University of Freiburg; Baden-Wurttemberg; Germany | Excellence Initiative of the German Federal and State Governments ; European Union |
PMID:22706672 | nlx_149465 | SCR_005895 | Virtual Brain Explorer for Zebrafish, Virtual Brain Explorer, ViBE-Z: The Virtual Brain Explorer for Zebrafish | 2026-02-12 09:44:16 | 4 | ||||||
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LHP LHDL Resource Report Resource Website |
LHP LHDL (RRID:SCR_005928) | LHP, LHDL | data or information resource, software application, software resource, simulation software | Distributed repository of anatomo-functional data and of simulation algorithms, fully integrated into a seamless simulation environment and directly accessible. This infrastructure will be used to create the physiome of the human musculo-skeletal system. | algorithm, anatomo-functional data, human, musculo-skeletal, physiome, repository, simulation, system, training tools | is listed by: 3DVC | European Union | nif-0000-10464 | SCR_005928 | The Living Human Digital Library, The Living Human Project | 2026-02-12 09:44:13 | 0 | |||||||
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VectorBase Resource Report Resource Website 500+ mentions |
VectorBase (RRID:SCR_005917) | VectorBase | data repository, service resource, storage service resource, database, data or information resource | Bioinformatics Resource Center for invertebrate vectors. Provides web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases. | blast, clustalw, hmmer, vector, genomics, genome, sequence, population, insecticide resistance, annotation, microarray, gene expression, anatomy, pathogen, human, transcript, transcriptome, protein, proteome, mitochondria sequence, bioinformatics resource center, pathogen, arthropoda, vector control, ontology, software, source code, mitochondrial sequence, data analysis service, image collection, FASEB list |
is recommended by: National Library of Medicine is listed by: re3data.org is related to: Clustal W2 is related to: AnoBase: An Anopheles database is related to: Hmmer has parent organization: European Bioinformatics Institute has parent organization: University of Notre Dame; Indiana; USA |
NIAID ; Evimalar network of excellence 242095; INFRAVEC 228421; European Union |
PMID:22135296 PMID:19028744 PMID:18262474 PMID:18237287 PMID:17145709 |
Restricted | nif-0000-03624, r3d100010880 | https://doi.org/10.17616/R3CK6B | SCR_005917 | VectorBase - Bioinformatics Resource for Invertebrate Vectors of Human Pathogens, VectorBase, vector base | 2026-02-12 09:44:08 | 835 | ||||
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European Mouse Mutant Archive Resource Report Resource Website 50+ mentions |
European Mouse Mutant Archive (RRID:SCR_006136) | EMMA | organism supplier, material resource, biomaterial supply resource | Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.With more than 8400 mutant mouse strains and asmall but increasing number of rat mutant strains available, EMMA is the primary mouse repository in Europe and the third largest non-profit repository worldwide. | RIN, Resource Information Network, mutant mouse repository, mouse, mutant strain, mutant mouse strain, , RRID Community Authority |
is used by: EUCOMMTOOLS is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network is related to: European Conditional Mouse Mutagenesis Program is related to: International Knockout Mouse Consortium is related to: Federation of International Mouse Resources is related to: MGI strains has parent organization: Helmholtz Center Munich Institute of Experimental Genetics works with: International Mouse Strain Resource |
partner institutions ; national research programmes ; European Union |
PMID:19783817 PMID:17709347 |
Public, Free to researchers | nlx_151625 | https://www.infrafrontier.eu | emmanet.org | SCR_006136 | European Mouse Mutant Archive - EMMA, European Mouse Mutant Archive (EMMA) | 2026-02-12 09:44:17 | 58 | |||
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Interaction Proteome Project Resource Report Resource Website 1+ mentions |
Interaction Proteome Project (RRID:SCR_008043) | IPP | software resource, simulation software, topical portal, software application, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 28, 2013. (URL is no longer valid) A platform for high-throughput proteomic analysis. Major objectives of IPP include the establishment of a broadly applicable platform of routine methods for the analysis of protein interaction networks in bio-medical research. A multidisciplinary approach will address; * their validation by cell biological, biochemical and biophysical methods. * their collection in a new type of public database. * their exploitation and use for in silico simulations of protein-interaction networks. The innovations generated in IPP will provide the basis for an efficient analysis and systems modeling of fundamental biological processes in health and disease. It will develop novel technology, including a high-end mass spectrometer with extremely large dynamic range, high-density peptide arrays, and improved visualization technology for light and electron microscopy. Additionally, the novel technologies will be validated with selected model systems of high relevance to medicine and biotechnology. Extensive bioinformatics support is a key element in the project to cope with the massive increase in experimental data on protein interactions obtained using the novel technologies. In particular, the efficient integration of disparate data sets represents a key challenge in proteomics and functional genomics. Therefore, the consortium includes the creator of the only European protein-interactions database, MINT. The multi-disciplinary efforts required in the scientific program of IPP are organized into four sub-projects (SP): * SP1: Tools for interaction analysis - SP1 is dedicated to the development of innovative proteomics technology to map protein-interaction networks and their cellular topology for the interaction analyses in SP2 and SP3. * SP2: Identification of interaction partners for protein domains - SP2 will generate (high throughput) data for important protein-protein interactions defined by bioinformatics and biomedical interest and by SP3, utilizing technology developed in SP1. * SP3: Functional analysis of interactions - SP3 focuses on the validation of technologies and tools developed in SP1. It will perform functional analyses of protein-interactions in medically and biochemically relevant prokaryotic and eukaryotic (mammalian) model systems. * SP4: Interactome database and modelling - SP4 provides the required bioinformatics infrastructure for the project, comprising the improvement of the public MINT database for the collection and dissemination of the interactome data; modelling and simulation of protein-interaction networks characterised in SP2 and SP3; and the dissemination of the technology developments to the scientific community. | electron, eukaryotic, biochemical, bioinformatics, biological, biomedical, biophysical, biotechnology, cell, development, disease, domain, genomics, health, interaction, light, mammalian, map, mass spectrometer, medicine, microscopy, model, modeling, network, peptide array, prokayotic, protein interaction, proteome, proteomics, silico, simulation, system, technology, tool, protein interaction | has parent organization: Max Planck Institute of Biochemistry; Martinsried; Germany | European Union | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10259 | SCR_008043 | Interaction Proteome | 2026-02-12 09:44:45 | 1 | ||||||
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CAST Resource Report Resource Website 10+ mentions |
CAST (RRID:SCR_000628) | CAST | sequence analysis software, software resource, software application, data analysis software, data processing software | A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity. | low-complexity region detection and selective masking, query sequence against twenty homopolymers, infinite gap penalties, masked query sequence, | has parent organization: University of Athens Biophysics and Bioinformatics Laboratory | European Molecular Biology Laboratory; Heidelberg; Germany ; European Union ; TMR Proramme ; IBM Research |
PMID:11120681 | nlx_151779 | http://www.ebi.ac.uk/research/cgg/services/cast/ | SCR_000628 | CAST - Compositional Bias Detection Algorithm | 2026-02-12 09:43:01 | 10 | |||||
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Proteome 2D-PAGE Database Resource Report Resource Website 1+ mentions |
Proteome 2D-PAGE Database (RRID:SCR_001678) | 2D-PAGE | software resource, data repository, service resource, storage service resource, database, data or information resource | The Proteome 2D-PAGE Database system for microbial research is a curated database for storing and investigating proteomics data. Software tools are available and for data submission, please contact the Database Curator. Established at the Max Plank Institution for Infection Biology, this system contains four interconnected databases: i.) 2D-PAGE Database: Two dimensional electrophoresis (2-DE) and mass spectrometry of diverse microorganisms and other organisms. This database currently contains 4971 identified spots and 1228 mass peaklists in 44 reference maps representing experiments from 24 different organisms and strains. The data were submitted by 84 Submitters from 24 Institutes and 12 nations. It also contains various software tools that are important in formatting and analyzing gels and mass peaks; software include: *TopSpot: Scanning the gel, editing the spots and saving the information *Fragmentation: Fragmentation of the gel image into sections *MS-Screener: Perl script to compare the similarity of MALDI-PMF peaklists *MS-Screener update: MS-Screener can be used to compare mass spectra (MALDI-MS(/MS) as well as ESI-MS/MS spectra) on the basis of their peak lists (.dta, .pkm, .pkt, or .txt files), to recalibrate mass spectra, to determine and eliminate exogenous contaminant peaks, and to create matrices for cluster analyses. *GelCali: Online calibration of the Mr- and pI-axis of 2-DE gels with mathematical regression methods ii.)Isotope Coded Affinity Tag (ICAT)-LC/MS database: Isotope Coded Affinity Tag (ICAT)-LC/MS data for Mycobacterium tuberculosis strain BCG versus H37Rv. iii.) FUNC_CLASS database: Functional classification of diverse microorganism. This database also integrates genomic, proteomic, and metabolic data. iv.) DIFF database: Presentation of differently regulated proteins obtained by comparative proteomic experiments using computerized gel image analysis. | microbial research, electrophoresis, mass spectrometry, mycobacterium tuberculosis, protein regulation | has parent organization: Max Planck Institute for Infection Biology; Berlin; Germany | BMBF 031U107A; European Union QLRT-1999-31536; European Union QLK2-CT-2001-02018 |
Free, Freely Available | nif-0000-02523 | SCR_001678 | 2026-02-12 09:43:12 | 5 | |||||||
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iMITS Resource Report Resource Website |
iMITS (RRID:SCR_016552) | iMITS | data or information resource, database, catalog | This resource has been replaced by GenTaR. Software tool for the planning of all IMPC mouse production. Allows IMPC production centers to record the progress of mouse production, cre-excision and to summarise the progress of phenotype data collection and transfer to the IMPC DCC. Stores all the mutation molecular structures made for the IKMC, catalogs of all IKMC products. | international, tracking, system, mouse, production, data, store, catalog, phenotype, collection, mutation, molecular, structure, IKMC, IMPC |
is affiliated with: International Mouse Phenotyping Consortium (IMPC) is related to: GenTaR |
NIH KOMP2; European Union 223592 |
Restricted | SCR_016552 | international Micro Injection Tracking System | 2026-02-12 09:46:22 | 0 | |||||||
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RNAmmer Resource Report Resource Website 100+ mentions |
RNAmmer (RRID:SCR_017075) | analysis service resource, standalone software, software resource, data access protocol, service resource, web service, production service resource, software application, data analysis service, data analysis software, data processing software | Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes. | predict, ribosomal, RNA, gene, full, genome, sequence, HMM, rRNA | has parent organization: Technical University of Denmark; Lyngby; Denmark | EMBIO at the University of Oslo ; Research Council of Norway ; Danish Center for Scientific Computing ; European Union |
PMID:17452365 | Restricted | SCR_017075 | 2026-02-12 09:47:00 | 103 | ||||||||
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Perseus Resource Report Resource Website 1000+ mentions |
Perseus (RRID:SCR_015753) | software resource, software application, data analysis software, data processing software | Software that supports biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization, pattern recognition, time-series analysis, cross-omics comparisons and multiplehypothesis testing. | shotgun proteomics data analysis, protein quantification, post-translational modification data, statistical analysis, omics data | European Union 686547; European Union GA ERC-2012-SyG_318987–ToPAG |
PMID:27348712 | Free, Available for download, Runs on Windows, Runs on Mac OS, Tutorial available, Account required | http://www.biochem.mpg.de/5111810/perseus | SCR_015753 | 2026-02-12 09:46:19 | 3632 | ||||||||
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DTU Center for Biological Sequence Analysis Resource Report Resource Website 1000+ mentions |
DTU Center for Biological Sequence Analysis (RRID:SCR_003590) | CBS, DTU CBS | analysis service resource, data access protocol, software resource, service resource, web service, production service resource | Center for Biological Sequence Analysis of the Technical University of Denmark conducts basic research in the field of bioinformatics and systems biology and directs its research primarily towards topics related to the elucidation of the functional aspects of complex biological mechanisms. A large number of computational methods have been produced, which are offered to others via WWW servers. Several data sets are also available. The center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. The on-line prediction services at CBS are available as interactive input forms. Most of the servers are also available as stand-alone software packages with the same functionality. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services. The center also educates engineering students in biotechnology and systems biology and offers a wide range of courses in bioinformatics, systems biology, human health, microbiology and nutrigenomics. | nucleotide, sequence, amino acid, dna, microarray, molecule, immunology, protein function, protein structure, protein, post-translational, whole genome, sequence analysis |
has parent organization: Technical University of Denmark; Lyngby; Denmark is parent organization of: NESbase is parent organization of: O-GLYCBASE is parent organization of: OligoWiz is parent organization of: SignalP |
Danish National Research Foundation ; Danish Research Councils ; Danish Center for Scientific Computing ; Villum Kann Rasmussen Foundation ; Novo Nordisk Foundation ; European Union ; NIH |
nlx_12329 | http://www.cbs.dtu.dk/index.shtml | SCR_003590 | 2026-02-12 09:43:39 | 1434 | |||||||
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Gene Ontology Resource Report Resource Website 10000+ mentions |
Gene Ontology (RRID:SCR_002811) | GO | project portal, knowledge environment resource, organization portal, consortium, data or information resource, portal | Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases. | gene, product, annotation, molecular, function, cellular, biological, role, database, query, obo, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: GreenPhylDB is used by: LIPID MAPS Proteome Database is used by: Aging Portal is used by: ChannelPedia is used by: Open PHACTS is used by: CoPub is used by: PhenoGO is used by: Database for Annotation Visualization and Integrated Discovery is used by: MitoMiner is used by: dcGO is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: barleyGO is used by: SynGO is used by: Functional Annotation is used by: SwissLipids is listed by: BioPortal is listed by: OBO is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: Mouse Genome Informatics: The Gene Ontology Project is related to: GenNav is related to: SynaptomeDB is related to: High-Throughput GoMiner is related to: Onto-Design is related to: OnEx - Ontology Evolution Explorer is related to: Avadis is related to: GONUTS is related to: PiNGO is related to: Automated Microarray Pipeline is related to: categoryCompare is related to: globaltest is related to: Semantic Measures Library is related to: WegoLoc is related to: AnimalTFDB is related to: MEME Suite - Motif-based sequence analysis tools is related to: Arabidopsis Hormone Database is related to: DAVID is related to: Arabidopsis thaliana Protein Interactome Database is related to: TM4 Microarray Software Suite - TIGR MultiExperiment Viewer is related to: pSTIING is related to: GoMiner is related to: FunSimMat is related to: GeneSpeed- A Database of Unigene Domain Organization is related to: Centre for Modeling Human Disease Gene Trap Resource is related to: Patterns of Gene Expression in Drosophila Embryogenesis is related to: Babelomics is related to: BioPerl is related to: GeneCruiser is related to: GOLEM An interactive, graphical gene-ontology visualization, navigation, and analysis tool is related to: GOToolBox Functional Investigation of Gene Datasets is related to: Cotton EST Database is related to: MouseNET is related to: PLANTTFDB is related to: T-profiler is related to: Physico-Chemical Process is related to: Integrated Molecular Interaction Database is related to: SEGS is related to: GOCat is related to: Quantitative Enrichment of Sequence Tags is related to: Neural-Immune Gene Ontology is related to: INMEX is related to: StRAnGER is related to: QuickGO is related to: Repository of molecular brain neoplasia data is related to: Cardiovascular Gene Ontology Annotation Initiative is related to: PANTHER is related to: Short Time-series Expression Miner (STEM) is related to: DATFAP is related to: GORetriever is related to: Gene Ontology Browsing Utility (GOBU) is related to: GeneTools is related to: GOSlimViewer is related to: go-moose is related to: Network Ontology Analysis is related to: Onto-Compare is related to: Onto-Express is related to: OntoVisT is related to: STRAP is related to: CGAP GO Browser is related to: COBrA is related to: Gene Class Expression is related to: GeneInfoViz is related to: GOfetcher is related to: GoFish is related to: GOProfiler is related to: GOanna is related to: Manatee is related to: Pandora - Protein ANnotation Diagram ORiented Analysis is related to: TAIR Keyword Browser is related to: Wandora is related to: GOTaxExplorer is related to: Onto-Miner is related to: Onto-Translate is related to: ToppGene Suite is related to: DBD - Slim Gene Ontology is related to: ONTO-PERL is related to: Blip: Biomedical Logic Programming is related to: OWL API is related to: CLENCH is related to: BiNGO: A Biological Networks Gene Ontology tool is related to: CateGOrizer is related to: FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products is related to: ProteInOn is related to: GeneMerge is related to: GraphWeb is related to: ClueGO is related to: CLASSIFI - Cluster Assignment for Biological Inference is related to: GOHyperGAll is related to: FuncAssociate: The Gene Set Functionator is related to: GOdist is related to: FuncExpression is related to: FunCluster is related to: FIVA - Functional Information Viewer and Analyzer is related to: GARBAN is related to: GOEx - Gene Ontology Explorer is related to: SGD Gene Ontology Slim Mapper is related to: GOArray is related to: SNPsandGO is related to: GoSurfer is related to: GOtcha is related to: MAPPFinder is related to: GoAnnotator is related to: MetaGeneProfiler is related to: OntoGate is related to: ProfCom - Profiling of complex functionality is related to: SerbGO is related to: SOURCE is related to: Ontologizer is related to: THEA - Tools for High-throughput Experiments Analysis is related to: Generic GO Term Mapper is related to: GREAT: Genomic Regions Enrichment of Annotations Tool is related to: GoBean - a Java application for Gene Ontology enrichment analysis is related to: TXTGate is related to: GO-Module is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures is related to: G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools is related to: MalaCards is related to: FSST - Functional Similarity Search Tool is related to: Expression Profiler is related to: GOChase is related to: GoPubMed is related to: Whatizit is related to: REViGO is related to: WEGO - Web Gene Ontology Annotation Plot is related to: Blast2GO is related to: InterProScan is related to: PubSearch is related to: TrED is related to: CharProtDB: Characterized Protein Database is related to: VirHostNet: Virus-Host Network is related to: Pathbase is related to: GO Online SQL Environment (GOOSE) is related to: Neurobehavior Ontology is related to: InterSpecies Analysing Application using Containers is related to: KOBAS is related to: ConceptWiki is related to: GeneTerm Linker is related to: Bioconductor is related to: ErmineJ is related to: Gene Ontology For Functional Analysis (GOFFA) is related to: MGI GO Browser is related to: Comparative Toxicogenomics Database (CTD) is related to: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit is related to: Ontology Lookup Service is related to: LexGrid is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: g:Profiler is related to: OwlSim is related to: GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool is related to: YeTFaSCo is related to: FastSemSim is related to: RamiGO is related to: AutismKB is related to: GeneCodis is related to: FunSpec is related to: FunNet - Transcriptional Networks Analysis is related to: PhenoM - Phenomics of yeast Mutants is related to: agriGO is related to: GOblet is related to: DynGO is related to: SeqExpress is related to: ProbeExplorer is related to: ECgene: Gene Modeling with Alternative Splicing is related to: Organelle DB is related to: Gemma is related to: Candidate Genes to Inherited Diseases is related to: Proteome Analyst PA-GOSUB is related to: Network Analysis, Visualization and Graphing TORonto is related to: GOstat is related to: Onto-Express To Go (OE2GO) is related to: Tk-GO is related to: EGAN: Exploratory Gene Association Networks is related to: Spotfire is related to: GOMO - Gene Ontology for Motifs is related to: GFINDer: Genome Function INtegrated Discoverer is related to: Generic GO Term Finder is related to: Agile Protein Interactomes DataServer is related to: AgingDB is related to: UBERON is related to: Algal Functional Annotation Tool is related to: gsGator is related to: Flash Gviewer is related to: Cerebellar Development Transcriptome Database is related to: PlantNATsDB - Plant Natural Antisense Transcripts DataBase is related to: EASE: the Expression Analysis Systematic Explorer is related to: PiGenome is related to: L2L Microarray Analysis Tool is related to: MeGO is related to: CELDA Ontology is related to: Diabetes Disease Portal is related to: MatrixDB is related to: Kidney and Urinary Pathway Knowledge Base is related to: MouseCyc is related to: Candida Genome Database is related to: Honey Bee Brain EST Project is related to: ECO is related to: FlyMine is related to: Gramene is related to: 3D-Interologs is related to: Biomine is related to: UniProtKB is related to: NCBI BioSystems Database is related to: EBIMed is related to: Coremine Medical is related to: EMAGE Gene Expression Database is related to: GeneMANIA is related to: Yeast Search for Transcriptional Regulators And Consensus Tracking is related to: GeneTrail is related to: Magic is related to: Mouse Genome Informatics (MGI) is related to: FlyBase is related to: InterPro is related to: InnateDB is related to: canSAR is related to: HPRD - Human Protein Reference Database is related to: CRCView is related to: Integrated Manually Extracted Annotation is related to: LegumeIP is related to: Renal Disease Portal is related to: PhenoGO is related to: DOAF is related to: OBO is related to: biomaRt is related to: OncoboxPD is parent organization of: AmiGO is parent organization of: GOlr is parent organization of: RefGenome is parent organization of: OBO-Edit is parent organization of: OWLTools is parent organization of: Gene Ontology Tools is parent organization of: Gene Ontology Extension is parent organization of: SO is parent organization of: go-db-perl is parent organization of: go-perl works with: topGO works with: DIANA-mirPath works with: GOnet |
European Union QLRI-CT-2001-0098; European Union QLRI-CT-2001-00015; NHGRI P41 HG002273 |
PMID:23161678 PMID:10802651 |
Free, Freely available, Available for download | biotools:go, OMICS_02278, nif-0000-02915 | http://bioportal.bioontology.org/ontologies/GO https://bio.tools/go |
SCR_002811 | the Gene Ontology, GO, Gene Ontology Resource, Gene Ontology | 2026-02-12 09:43:27 | 10623 | ||||
|
IMEx - The International Molecular Exchange Consortium Resource Report Resource Website 100+ mentions |
IMEx - The International Molecular Exchange Consortium (RRID:SCR_002805) | IMEx | organization portal, data repository, service resource, storage service resource, database, consortium, community building portal, data or information resource, portal | Interaction database from international collaboration between major public interaction data providers who share curation effort and develop set of curation rules when capturing data from both directly deposited interaction data or from publications in peer reviewed journals. Performs complete curation of all protein-protein interactions experimentally demonstrated within publication and makes them available in single search interface on common website. Provides data in standards compliant download formats. IMEx partners produce their own separate resources, which range from all encompassing molecular interaction databases, such as are maintained by IntAct, MINT and DIP, organism-centric resources such as BioGrid or MPIDB or biological domain centric, such as MatrixDB. They have committed to making records available, via PSICQUIC webservice, which have been curated to IMEx rules and are available to users as single, non-redundant set of curated publications which can be searched at the IMEx website. Data is made available in standards-compliant tab-deliminated and XML formats, enabling to visualize data using wide range of tools. Consortium is open to participation of additional partners and encourages deposition of data, prior to publication, and will supply unique accession numbers which may be referenced within final article. Submitters may send their data directly to any of member databases using variety of formats, but should conform to guidelines as to minimum information required to describe data. | protein-protein interaction, nonredundant, protein interaction, interaction, proteomics, metadata standard, short course, molecular interaction, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: MINT is related to: MatrixDB is related to: MPIDB is related to: Database of Interacting Proteins (DIP) is related to: Database of Interacting Proteins (DIP) is related to: InnateDB is related to: IntAct is related to: Interaction Reference Index is related to: MPIDB is related to: UniProt is related to: InnateDB is related to: MatrixDB is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: I2D is related to: Molecular Connections NetPro is related to: SIB Swiss Institute of Bioinformatics is related to: IntAct is related to: PSI-MI is related to: PSICQUIC Registry is related to: mentha is related to: Bioconductor has parent organization: European Bioinformatics Institute works with: CellPhoneDB works with: Cytoscape works with: IntAct works with: MINT works with: MPact: Representation of Interaction Data at MIPS works with: Molecular Connections NetPro works with: Biological General Repository for Interaction Datasets (BioGRID) works with: InnateDB works with: BIND |
European Union | PMID:22453911 PMID:17893861 |
Free, Freely available, Available for download | nif-0000-00447, OMICS_01545, r3d100010669, biotools:imex | http://imex.sourceforge.net/ https://bio.tools/imex https://doi.org/10.17616/R3090W |
SCR_002805 | The International Molecular Exchange Consortium, International Molecular Exchange Consortium | 2026-02-12 09:43:27 | 144 | ||||
|
FunSimMat Resource Report Resource Website 1+ mentions |
FunSimMat (RRID:SCR_002729) | FunSimMat | analysis service resource, data access protocol, software resource, service resource, web service, production service resource, database, data analysis service, data or information resource | FunSimMat is a comprehensive resource of semantic and functional similarity values. It allows ranking disease candidate proteins for OMIM diseases and searching for functional similarity values for proteins (extracted from UniProt), and protein families (Pfam, SMART). FunSimMat provides several different semantic and functional similarity measures for each protein pair using the Gene Ontology annotation from UniProtKB and the Gene Ontology Annotation project at EBI (GOA). There are several search options available: Disease candidate prioritization: * Rank candidate proteins using any OMIM disease entry * Compare a list of proteins to any OMIM disease entry * Compare all human proteins to any OMIM disease entry Functional similarity: * Compare one protein / protein family to a list of proteins / protein families * Compare a list of GO terms to a list of proteins / protein families Semantic similarity: * For a list of GO terms, FunSimMat performs an all-against-all comparison and displays the semantic similarity values. FunSimMat provides an XML-RPC interface for performing automatic queries and processing of the results as well as a RestLike Interface. Platform: Online tool | functional similarity value, protein family, protein similarity, semantic similarity value, similarity value, functional similarity, disease gene candidate prioritization, disease, protein, protein family, disease candidate prioritization, semantic similarity, gene ontology, visualization, annotation, database or data warehouse |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
German National Genome Research Network 01GR0453; Klinische Forschergruppe KFO 129/1-1; Klinische Forschergruppe KFO 129/1-2; European Union LSHG-CT-2003-503265 |
PMID:19923227 PMID:17932054 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02860 | SCR_002729 | FunSimMat - Functional Similarity Matrix | 2026-02-12 09:43:26 | 1 | |||||
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GUDMAP Ontology Resource Report Resource Website 1+ mentions |
GUDMAP Ontology (RRID:SCR_002637) | GUDMAP Ontology | data or information resource, resource, ontology, controlled vocabulary | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A high-resolution ontology has been developed by members of the GUDMAP consortium to describe the subcompartments of the developing murine genitourinary tract. This ontology incorporates what can be defined histologically and begins to encompass other structures and cell types already identified at the molecular level. The GUDMAP ontology encompasses Theiler stage (TS) 17-27 of development as well as the sexually mature adult. It has been written as a partonomic, text-based, hierarchical ontology that, for the embryological stages, has been developed as a high-resolution expansion of the existing Edinburgh Mouse Atlas Project (EMAP) ontology. It also includes group terms for well-characterized structural and/or functional units comprising several sub-structures, such as the nephron and juxtaglomerular complex. Each term has been assigned a unique identification number. Synonyms have been used to improve the success of query searching and maintain wherever possible existing EMAP terms relating to this organ system. | murine, genitourinary tract, development, in situ hybridization, theiler stage, adult mouse, newborn mouse, adolescent mouse, embryonic mouse |
is used by: GATACA GUDMAP Gene Explorer is used by: Kidney Development Database lists: GOA lists: EuReGene lists: Embryo Images Normal and Abnormal Mammalian Development lists: Stem Cell Genome Anatomy Projects lists: Eurexpress lists: Gene Expression Database lists: ToppGene Suite is related to: eMouseAtlas is related to: GenePaint Interactive Anatomy Atlas is related to: EMAGE Gene Expression Database is related to: Gene Expression Omnibus has parent organization: GenitoUrinary Development Molecular Anatomy Project |
NIDDK DK070136-02; NIDDK DK070181; NIDDK DK07020001; European Union FP6 005085 |
PMID:17452023 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156063 | SCR_002637 | 2026-02-12 09:43:25 | 2 |
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