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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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AgedBrainSYSBIO Resource Report Resource Website 1+ mentions |
AgedBrainSYSBIO (RRID:SCR_003825) | AgedBrainSYSBIO | data or information resource, organization portal, consortium, portal | Consortium focused on identifying the foundational pathways responsible for the aging of the brain, with a focus on Late Onset Alzheimer's disease. They aim to identify the interactions through which the aging phenotype develops in normal and in disease conditions; modeling novel pathways and their evolutionary properties to design experiments that identify druggable targets. As early steps of neurodegenerative disorders are expected to impact synapse function the project will focus in particular on pre- or postsynaptic protein networks. The concept is to identify subsets of pathways with two unique druggable hallmarks, the validation of interactions occurring locally in subregions of neurons and a human and/or primate accelerated evolutionary signature. The consortium will do this through six approaches: * identification of interacting protein networks from recent Late-Onset Alzheimer Disease-Genome Wide Association Studies (LOAD-GWAS) data, * experimental validation of interconnected networks working in subregion of a neuron (such as dendrites and dendritic spines), * inclusion of these experimentally validated networks in larger networks obtained from available databases to extend possible protein interactions, * identification of human and/or primate positive selection either in coding or in regulatory gene sequences, * manipulation of these human and/or primate accelerated evolutionary interacting proteins in human neurons derived from induced Pluripotent Stem Cells (iPSCs) * modeling predictions in drosophila and novel mouse transgenic models * validation of new druggable targets and markers as a proof-of-concept towards the prevention and cure of aging cognitive defects. The scientists will share results and know-how on Late-Onset Alzheimer Disease-Genome Wide Association Studies (LOAD-GWAS) gene discovery, comparative functional genomics in mouse and drosophila models, in mouse transgenic approaches, research on human induced pluripotent stem cells (hiPSC) and their differentiation in vitro and modeling pathways with emphasis on comparative and evolutionary aspects. The four European small to medium size enterprises (SMEs) involved will bring their complementary expertise and will ensure translation of project results to clinical application. | consortium, drug, drug development, brain, phenotype, presynaptic, protein network, postsynaptic, systems biology, synapse, neuron, protein interaction, network, induced pluripotent stem cell, pathway, genome wide association study, cognitive defect, gene, protein |
is listed by: Consortia-pedia is related to: Pasteur Institute of Lille; Lille; France is related to: Mouse Clinical Institute; Alsace; France is related to: Hybrigenics is related to: Inserm Transfert is related to: VIB; Flanders; Belgium is related to: Quretec is related to: Gene Bridges is related to: European Bioinformatics Institute is related to: Tel Aviv University; Ramat Aviv; Israel is related to: SIB Swiss Institute of Bioinformatics is related to: Babraham Institute has parent organization: National Institute of Health and Medical Research; Rennes; France has parent organization: Inserm Transfert |
European Union FP7 305299 | nlx_158132 | SCR_003825 | 2026-02-16 09:46:12 | 3 | ||||||||
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SeWeR - SEquence analysis using WEb Resources Resource Report Resource Website |
SeWeR - SEquence analysis using WEb Resources (RRID:SCR_004167) | software resource, topical portal, portal, service resource, data or information resource | Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser. It doesn''t require any server to host itself. The goal of SeWeR is to turn your web-browser into a powerful sequence-analysis tool. It is written entirely in JavaScript1.2. SeWeR can be downloaded and mirrored freely. The whole package is just around 300K. You can even run it from a floppy. SeWeR is not compatible with Netscape 6. SeWeR now generates graphics. Savvy is a plasmid drawing software that generates plasmid map in the revolutionary Scalable Vector Graphics format from W3C. | nucleic acid, protein, pcr, alignment, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Centre for Cellular and Molecular Biology; Hyderabad; India |
PMID:11395442 | biotools:sewer, nlx_18981 | https://bio.tools/sewer | SCR_004167 | SEquence analysis using WEb Resources, SeWeR | 2026-02-16 09:46:12 | 0 | |||||||
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NEWMEDS Resource Report Resource Website 1+ mentions |
NEWMEDS (RRID:SCR_003872) | NEWMEDS | data or information resource, organization portal, consortium, portal | Consortium that will develop new models and methods to enable novel treatments for schizophrenia and depression including three important missing tools that will facilitate the translation of scientific findings into benefits for patients. The project will focus on developing new animal models which use brain recording and behavioral tests to identify innovative and effective drugs for schizophrenia. The project will develop standardized paradigms, acquisition and analysis techniques to apply brain imaging, especially fMRI and PET imaging to drug development. It will examine how new genetic findings (duplication and deletion or changes in genes) influence the response to various drugs and whether this information can be used to choose the right drug for the right patient. And finally, it will try and develop new approaches for shorter and more efficient trials of new medication - trials that may require fewer patients and give faster results. | drug, biomarker, neuroimaging, drug development, tool development, animal model, fmri, pet, gene, medicine, clinical trial, genetic variation, molecule, model, dna, protein |
is listed by: Consortia-pedia is related to: Abbott Diagnostics is related to: Janssen Research and Development is related to: Orion is related to: Pfizer Animal Genetics is related to: Roche is related to: King's College London; London; United Kingdom is related to: Karolinska Institute; Stockholm; Sweden is related to: University of Cambridge; Cambridge; United Kingdom is related to: Central Institute of Mental Health; Mannheim; Germany is related to: Spanish National Research Council; Madrid; Spain is related to: University of Manchester; Manchester; United Kingdom is related to: Bar-Ilan University; Ramat Gan; Isreal is related to: Psynova Neurotech is related to: deCODE genetics is related to: GABO:mi is related to: AbbVie has parent organization: King's College London; London; United Kingdom is parent organization of: DepressionTools.org Clinical Significance Calculator is parent organization of: Pharmacological Imaging and Pattern Recognition toolbox is parent organization of: DUPCheck |
Innovative Medicines Initiative 115008; EFPIA |
nlx_158196 | SCR_003872 | Novel Methods leading to New Medications in Depression and Schizophrenia, NEWMEDS - Novel Methods leading to New Medications in Depression and Schizophrenia | 2026-02-16 09:46:09 | 6 | |||||||
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GMD Resource Report Resource Website 100+ mentions |
GMD (RRID:SCR_006625) | GMD | web service, data access protocol, database, software resource, service resource, data or information resource | It facilitates the search for and dissemination of mass spectra from biologically active metabolites quantified using Gas chromatography (GC) coupled to mass spectrometry (MS). Use the Search Page to search for a compound of your interest, using the name, mass, formula, InChI etc. as query input. Additionally, a Library Search service enables the search of user submitted mass spectra within the GMD. In parallel to the library search, a prediction of chemical sub-groups is performed. This approach has reached beta level and a publication is currently under review. Using several sub-group specific Decision Trees (DTs), mass spectra are classified with respect to the presence of the chemical moieties within the linked (unknown) compound. Prediction of functional groups (ms analysis) facilitates the search of metabolites within the GMD by means of user submitted GC-MS spectra consisting of retention index (n-alkanes, if vailable) and mass intensities ratios. In addition, a functional group prediction will help to characterize those metabolites without available reference mass spectra included in the GMD so far. Instead, the unknown metabolite is characterized by predicted presence or absence of functional groups. For power users this functionality presented here is exposed as soap based web services. Functional group prediction of compounds by means of GC-EI-MS spectra using Microsoft analysis service decision trees All currently available trained decision trees and sub-structure predictions provided by the GMD interface. Table describes the functional group, optional use of an RI system, record date of the trained decision tree, number of MSTs with proportion of MSTs linked to metabolites with the functional group present for each tree. Average and standard deviation of the 50-fold CV error, namely the ratio false over correctly sorted MSTs in the trained DT, are listed. The GMD website offers a range of mass spectral reference libraries to academic users which can be downloaded free of charge in various electronic formats. The libraries are constituted by base peak normalized consensus spectra of single analytes and contain masses in the range 70 to 600 amu, while the ubiquitous mass fragments typically generated from compounds carrying a trimethylsilyl-moiety, namely the fragments at m/z 73, 74, 75, 147, 148, and 149, were excluded. | drug, expression, functional, gas chromatography, gene, general chemistry databases, bioinformatic, biological extract, biology, biotechnology, compound, genomic, herbicide, mass spectra, mass spectrometry, metabolism, metabolite, metabolomics, organism, profiling, protein, spectral, system, FASEB list | has parent organization: Max Planck Institute of Molecular Plant Physiology; Golm; Germany | PMID:15613389 PMID:15733837 PMID:18501684 PMID:20526350 |
r3d100011046, nif-0000-21180 | http://csbdb.mpimp-golm.mpg.de/csbdb/gmd/gmd.html https://doi.org/10.17616/R3MC9K |
SCR_006625 | Golm Metabolome Data Base, The Golm Metabolome Database, Golm Metabolome Database | 2026-02-16 09:46:46 | 157 | ||||||
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ESPript 2.2 Resource Report Resource Website 100+ mentions |
ESPript 2.2 (RRID:SCR_006587) | ESPript | software application, data processing software, data analysis service, analysis service resource, software resource, production service resource, service resource | A utility, whose output is a PostScript file of aligned sequences with graphical enhancements. Its main input is an ascii file of pre-aligned sequences. Optional files allow further rendering. The program calculates a similarity score for each residue of the aligned sequences. The output shows: * Secondary Structures * Aligned sequences * Similarities * Accessibility * Hydropathy * User-supplied markers * Intermolecular contacts In addition, similarity score can be written in the bfactor column of a pdb file, to enable direct display of highly conserved areas. You can run ESPript from this server with the HTML interface. It is configured for a maximum of 1,000 sequences. Links to webESPript * ENDscript: you can upload a PDB file or enter a PDB code such as 1M85. The programs DSSP and CNS are executed via the interface, so as to obtain an ESPript figure with a lot of structural information (secondary structure elements, intermolecular contacts). You can also find homologous sequences with a BLAST search, perform multiple sequence alignments with MULTALIN or CLUSTALW and create an image with BOBSCRIPT or MOLSCRIPT to show similarities on your 3D structure. * ProDom: you can enter a sequence identifier to find homologous domains, perform multiple sequence alignments with MULTALIN and click on the link to ESPript. * Predict Protein: you can receive a mail in text (do not use the HTML option when you submit your request in Predict Protein) with aligned sequences and numerous information including secondary structure prediction. Click on a special html link to upload your mail in ESPript. * NPS(at): you can execute the programs BLAST and CLUSTALW to obtain multiple alignments. You can predict secondary structure elements and click on the link to ESPript. This program started in the laboratory of Dr Richard Wade at the Institut de Biologie Structurale, Grenoble. It moved later to the Laboratory of Molecular Biophysics in Oxford, then to the Institut de Pharmacologie et de Biologie Structurale in Toulouse. It is now developed in the Laboratoire de BioCristallographie of Dr Richard Haser, Institut de Biologie et de Chimie des Prot��������ines, Lyon and in the Laboratoire de Biologie Mol��������culaire et de Relations Plantes-Organismes, group of Dr Daniel Kahn, Institut National de la Recherche Agronomique de Toulouse. | postscript, aligned sequence, sequencing, blast, protein | has parent organization: Institute of Biology and Chemistry of Proteins; Lyon; France | PMID:10320398 PMID:12824317 |
Free for academic use, Fee for commercial users, Licenses for accompanying programs used in ENDscript must be requested separately. | nif-0000-30499 | http://genopole.toulouse.inra.fr/ESPript | SCR_006587 | Easy Sequencing in Postscript | 2026-02-16 09:46:45 | 361 | |||||
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Global Proteome Machine Database (GPM DB) Resource Report Resource Website 100+ mentions |
Global Proteome Machine Database (GPM DB) (RRID:SCR_006617) | The GPM | software application, data processing software, data analysis software, data repository, software resource, storage service resource, database, service resource, data or information resource | The Global Proteome Machine Organization was set up so that scientists involved in proteomics using tandem mass spectrometry could use that data to analyze proteomes. The projects supported by the GPMO have been selected to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results. The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. This database has been integrated into GPM server pages, allowing users to quickly compare their experimental results with the best results that have been previously observed by other scientists. | mass spectrometry, pattern, peptide, protein, proteome, scientist, spectra, tandem, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
r3d100010883, nif-0000-10455 | https://www.thegpm.org/GPMDB/index.html https://researchdata.ands.org.au/gpm-global-proteome-machine-database/11342 https://doi.org/10.17616/R30C90 |
SCR_006617 | GPM, The Global Proteome Machine Organization: Proteomics Database and Open Source Software, Global Proteome Machine Database, GPM DB, The Global Proteome Machine Database, The Global Proteome Machine, Global Proteome Machine Database (GPM DB), The Global Proteome Machine Organization | 2026-02-16 09:46:47 | 258 | |||||||
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Common Fund Protein Capture Reagents Resource Report Resource Website 1+ mentions |
Common Fund Protein Capture Reagents (RRID:SCR_006570) | Protein Capture Reagents | funding resource, data or information resource, topical portal, portal | Program that is developing new resources and tools to understand the critical role the multitude of cellular proteins play in normal development and health as well as in disease. These resources will support a wide-range of research and clinical applications that will enable the isolation and tracking of proteins of interest and permit their use as diagnostic biomarkers of disease onset and progression. The program is being implemented in phases, with three Funding Opportunity Announcements (FOAs): * FOA 1: Antigen Production (RFA-RM-10-007) To produce human transcription factor antigens for making monoclonal antibodies or other affinity capture reagents; this effort is already underway. * FOA 2: Anti-Transcription Factor Antibodies Production (RFA-RM-10-017) To optimize and scale anti-transcription factor capture reagent production to develop a community antibody resource. * FOA 3: New Reagent Technology Development and Piloting (RFA-RM-10-018) To develop improvements in the reagent production pipeline with regard to quality, utility, cost, and production scalability. To understand what makes a cell function normally and what may go awry in disease, we need better tools and resources, such as renewable protein capture reagents and probes, to study how proteins work in isolation and how they interact with other proteins, carbohydrates, or DNA regions within a cell. Ideally, this resource would allow us to identify and isolate all proteins within cells, in their various forms the so called proteome to ensure broad application in research and clinical studies aimed at understanding, preventing, detecting and treating disease. Existing protein capture reagents, such monoclonal antibodies, have been developed for a number of protein targets, although these represent only a subset of all proteins comprising the human proteome. In addition, many monoclonal antibodies lack the desired level of specificity and do not reliably target only the protein of interest. This is particularly problematic given the multiple forms of any one protein and the broad range of protein types in the body. The Protein Capture Reagents Program is organized as a pilot program using transcription factors as a test case to examine the feasibility and value of generating a community resource of low cost, renewable affinity reagents for all human proteins. The reagents must be specifically designed for high quality and broad experimental utility in order to meet the growing demands of biomedical researchers. Based on what is learned from these funding initiatives, the program may expand to a larger production effort to provide a broad community resource of human protein capture reagents. | protein, reagent, proteome, antigen, anti-transcription factor, antibody, protein capture, transcription factor | has parent organization: NIH Common Fund | nlx_151642 | https://proteincapture.org https://proteincapture.org/reagent_portal/ |
SCR_006570 | Protein Capture Reagents Program, NIH Common Fund Protein Capture Reagents Program, Common Fund Protein Capture Reagents Program | 2026-02-16 09:46:45 | 2 | |||||||
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Plant Organelles Database Resource Report Resource Website 1+ mentions |
Plant Organelles Database (RRID:SCR_006520) | PODB, PODB2 | video resource, narrative resource, experimental protocol, image collection, data repository, database, storage service resource, service resource, data or information resource | Database of images, movies, and protocols to promote a comprehensive understanding of plant organelle dynamics, including organelle function, biogenesis, differentiation, movement, and interactions with other organelles. It consists of 5 individual parts, ''Perceptive Organelles Database'', ''The Organelles Movie Database'', ''The Organellome Database'', ''The Functional Analysis Database'', and ''External Links to other databases and Web pages''. All the data and protocols in ''The Organelle Movie Database'', ''The Organellome Database'' and ''The Functional Analysis Database'' are populated by direct submission of experimentally determined data from plant researchers. Your active contributions by submission of data and protocols to our database would also be appreciated. * Perceptive Organelles Database: This database contains images and movies of organelles in various tissues during different developmental stages in response to environmental stimuli. * Organelles Movie Database: This database contains time-lapse images, Z slices and projection images of organelles in various tissues during different developmental stages, visualized using fluorescent and non-fluorescent probes. * Organellome Database: This database contains images for cellular structures that are composed of organelle images in various tissues during different developmental stages, visualized with fluorescent and non-fluorescent probes. * Functional Analysis Database: This database is a collection of protocols for plant organelle research. * External Links: Access to biological databases. | organelle, developmental stage, environmental stimuli, development, environment, stimulus, biochemical assay, nucleic acid, protein, gene expression, genome mapping, histology, tissue isolation, organelle isolation, plant growth, maintenance, visualization, observation, plant organelle, movement, division, subcellular positioning, behavior, external stimuli, green fluorescent protein, biogenesis, differentiation, interaction |
is related to: Plant Organelles World has parent organization: National Institute for Basic Biology; Okazaki; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT 16085101; Japan Society for the Promotion of Science 228052 |
PMID:21115470 PMID:19755394 PMID:17932059 |
Free for scientific and educational use provided the contributor and the Organellome Database and the Organelles Movie Database are properly credited. If you wish to use commercially, Please contact the contributors of the corresponding images and movies for permission. | nlx_151998, r3d100011300 | https://doi.org/10.17616/R3933R | SCR_006520 | Plant Organelles Database 2 | 2026-02-16 09:46:46 | 7 | ||||
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Electron Microscopy Data Bank at PDBe (MSD-EBI) Resource Report Resource Website 100+ mentions |
Electron Microscopy Data Bank at PDBe (MSD-EBI) (RRID:SCR_006506) | EMDB at PDBe | data analysis service, analysis service resource, data repository, database, storage service resource, production service resource, service resource, data or information resource | Repository for electron microscopy density maps of macromolecular complexes and subcellular structures at Protein Data Bank in Europe. Covers techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. | electron microscopy, density map, macromolecule, complex, subcellular structure, single-particle analysis, electron tomography, electron crystallography, macromolecular complex, structure, protein, protein binding, electron, electron configuration, tomography, microscopy, gold standard |
is used by: DARC - Database for Aligned Ribosomal Complexes is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is related to: EMDataResource.org is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: PDBe - Protein Data Bank in Europe |
NIH | Public | r3d100010562, nlx_149453 | https://doi.org/10.17616/R3HP57 | SCR_006506 | MSD-EBI, Electron Microscopy Data Bank at Protein Data Bank in Europe, Electron Microscopy DataBank, Electron Microscopy Data Bank at PDBe (MSD-EBI), Electron Microscopy Data Bank at PDBe | 2026-02-16 09:46:44 | 144 | |||||
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Gene Expression Database Resource Report Resource Website 50+ mentions |
Gene Expression Database (RRID:SCR_006539) | GXD | data repository, database, storage service resource, service resource, data or information resource | Community database that collects and integrates the gene expression information in MGI with a primary emphasis on endogenous gene expression during mouse development. The data in GXD are obtained from the literature, from individual laboratories, and from large-scale data providers. All data are annotated and reviewed by GXD curators. GXD stores and integrates different types of expression data (RNA in situ hybridization; Immunohistochemistry; in situ reporter (knock in); RT-PCR; Northern and Western blots; and RNase and Nuclease s1 protection assays) and makes these data freely available in formats appropriate for comprehensive analysis. There is particular emphasis on endogenous gene expression during mouse development. GXD also maintains an index of the literature examining gene expression in the embryonic mouse. It is comprehensive and up-to-date, containing all pertinent journal articles from 1993 to the present and articles from major developmental journals from 1990 to the present. GXD stores primary data from different types of expression assays and by integrating these data, as data accumulate, GXD provides increasingly complete information about the expression profiles of transcripts and proteins in different mouse strains and mutants. GXD describes expression patterns using an extensive, hierarchically-structured dictionary of anatomical terms. In this way, expression results from assays with differing spatial resolution are recorded in a standardized and integrated manner and expression patterns can be queried at different levels of detail. The records are complemented with digitized images of the original expression data. The Anatomical Dictionary for Mouse Development has been developed by our Edinburgh colleagues, as part of the joint Mouse Gene Expression Information Resource project. GXD places the gene expression data in the larger biological context by establishing and maintaining interconnections with many other resources. Integration with MGD enables a combined analysis of genotype, sequence, expression, and phenotype data. Links to PubMed, Online Mendelian Inheritance in Man (OMIM), sequence databases, and databases from other species further enhance the utility of GXD. GXD accepts both published and unpublished data. | endogenous, expression assay, expression data, expression image, gene expression, genes, image, immunohistochemistry, in situ reporter, knock in, mouse, mouse mutant, northern blot, nuclease protection assay, rna in situ hybridization, rnase protection assay, rt-pcr, western blot, endogenous gene expression, mouse development, gene, transcript, protein, annotation, development, embryonic mouse, bio.tools, FASEB list |
is listed by: GUDMAP Ontology is listed by: NIDDK Information Network (dkNET) is listed by: Debian is listed by: bio.tools is related to: VisiGene Image Browser is related to: Mouse Genome Informatics (MGI) is related to: Mouse Genome Informatics: The Mouse Gene Expression Information Resource Project is related to: EMAGE Gene Expression Database is related to: aGEM has parent organization: Jackson Laboratory is parent organization of: Adult Mouse Anatomy Ontology is parent organization of: Mouse Anatomical Dictionary Browser |
NICHD HD033745 | PMID:21062809 | Free | nif-0000-01253, biotools:gxd, SCR_017529 | https://bio.tools/gxd | SCR_006539 | Jackson Lab Gene Expression Database | 2026-02-16 09:46:44 | 56 | ||||
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Descriptions of Plant Viruses Resource Report Resource Website 10+ mentions |
Descriptions of Plant Viruses (RRID:SCR_006656) | database, data or information resource, topical portal, portal | DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. For comparative purposes, it also contains a single representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA genome. The start and end positions of each feature (gene, non-translated region and the like) have been recorded and checked for accuracy. As far as possible, nomenclature for genes and proteins are standardized within genera and families. Sequences of features (either as DNA or amino acid sequences) can be directly downloaded from the website in FASTA format. The sequence information can also be accessed via client software for PC computers (freely downloadable from the website) that enable users to make an easy selection of sequences and features of a chosen virus for further analyses. The public sequence databases contain vast amounts of data on virus genomes but accessing and comparing the data, except for relatively small sets of related viruses can be very time consuming. The procedure is made difficult because some of the sequences on these databases are incorrectly named, poorly annotated or redundant. The NCBI Reference Sequence project (1) provides a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA) and protein products, for major research organisms. This now includes curated information for a single sequence of each fully sequenced virus species. While this is a welcome development, it can only deal with complete sequences. An important feature of DPV is the opportunity to access genes (and other features) of multiple sequences quickly and accurately. Thus, for example, it is easy to obtain the nucleotide or amino acid sequences of all the available accessions of the coat protein gene of a given virus species or for a group of viruses. To increase its usefulness further, DPVweb also contains a single representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA (ssDNA) genome. Sponsors: This site is supported by the Association of Applied Biologists and the Zhejiang Academy of Agricultural Sciences, Hangzhou, People''s Republic of China. | family, fungi, gene, amino acid, comparative, development, dna, genome, genomic, genus, nomenclature, non-translated, nucleotide, organism, plant, product, protein, protozoa, region, rna, satellite, sequence, single, specie, taxonomic, transcript, viral databases, viroid, virus, bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-21127, biotools:dpvweb | https://bio.tools/dpvweb | SCR_006656 | DPV | 2026-02-16 09:46:47 | 11 | ||||||||
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InParanoid: Eukaryotic Ortholog Groups Resource Report Resource Website 100+ mentions |
InParanoid: Eukaryotic Ortholog Groups (RRID:SCR_006801) | InParanoid | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | Collection of pairwise comparisons between 100 whole genomes generated by a fully automatic method for finding orthologs and in-paralogs between TWO species. Ortholog clusters in the InParanoid are seeded with a two-way best pairwise match, after which an algorithm for adding in-paralogs is applied. The method bypasses multiple alignments and phylogenetic trees, which can be slow and error-prone steps in classical ortholog detection. Still, it robustly detects complex orthologous relationships and assigns confidence values for in-paralogs. The original data sets can be downloaded. | protein, ortholog, genome, drosophila pseudoobscura, duplication, entamoeba histolytica, escherichia colik12, eukaryotic, gasterosteus aculeatus, gene, aedes aegypti, apis mellifera, bos taurus, caenorhabditis remanei, candida glabrata, canis familiaris, ciona intestinalis, cryptococcus neoformans, debaromyces hansenii, dictyostelium discoideum, genomic, homolog, inparalog, kluyveromyces lactis, macaca mulatta, monodelphis domestica, orthology, oryza sativa, outparalog, proteome, tetraodon nigroviridis, xenopus tropicalis, blast, proteome, ortholog cluster, cluster, in-paralog, paralog, automatic clustering, genome comparison, FASEB list | has parent organization: Stockholm University; Stockholm; Sweden | Swedish Research Council ; Karolinska Institutet; Stockholm; Sweden ; Pfizer Corporation |
PMID:19892828 PMID:18055500 PMID:15608241 PMID:11743721 |
Acknowledgement requested | nif-0000-03024 | http://www.cgb.ki.se/inparanoid/ | SCR_006801 | Inparanoid eukaryotic ortholog database | 2026-02-16 09:46:48 | 186 | ||||
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HAMSTeRS - The Haemophilia A Mutation Structure Test and Resource Site Resource Report Resource Website 1+ mentions |
HAMSTeRS - The Haemophilia A Mutation Structure Test and Resource Site (RRID:SCR_006883) | HAMSTeRS, HADB, HADB/HAMSTeRS, HADB / HAMSTeRS | data repository, database, storage service resource, service resource, data or information resource |
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 27, 2019. Database for those interested in the consequences of Factor VIII genetic variation at the DNA and protein level, it provides access to data on the molecular pathology of haemophilia A. The database presents a review of the structure and function of factor VIII and the molecular genetics of haemophilia A, a real time update of the biostatistics of each parameter in the database, a molecular model of the A1, A2 and A3 domains of the factor VIII protein (based on the crystal structure of caeruloplasmin) and a bulletin board for discussion of issues in the molecular biology of factor VIII. The database is completely updated with easy submission of point mutations, deletions and insertions via e-mail of custom-designed forms. A methods section devoted to mutation detection is available, highlighting issues such as choice of technique and PCR primer sequences. The FVIII structure section now includes a download of a FVIII A domain homology model in Protein Data Bank format and a multiple alignment of the FVIII amino-acid sequences from four species (human, murine, porcine and canine) in addition to the virtual reality simulations, secondary structural data and FVIII animation already available. Finally, to aid navigation across this site, a clickable roadmap of the main features provides easy access to the page desired. Their intention is that continued development and updating of the site shall provide workers in the fields of molecular and structural biology with a one-stop resource site to facilitate FVIII research and education. To submit your mutants to the Haemophilia A Mutation Database email the details. (Refer to Submission Guidelines) |
function, gene, genetic, analysis, bioinformatic, biological, biostatistic, caeruloplasmiin, crystal, haemophilia a, human, murine, porcine, canine, level, molecular, molecule, mutation, nucleic acid, or disease- specific databases, pathology, structural, structure, system-, vitromutagenesis, fviii genetic variation, dna, protein, factor viii, blood-clotting protein, point mutation, deletion, insertion | has parent organization: Imperial College London; London; United Kingdom | Pfizer UK ; MRC |
PMID:9399839 PMID:9016520 PMID:8594555 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21184 | http://europium.csc.mrc.ac.uk/WebPages/Main/main.htm, http://hadb.org.uk/ | SCR_006883 | HAMSTeRS - The Haemophilia A Mutation Structure Test Resource Site, Haemophilia A Mutation Database, Haemophilia A Mutation Structure Test and Resource Site, Haemophilia A Mutation Structure Test Resource Site | 2026-02-16 09:46:49 | 9 | ||||
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FastSemSim Resource Report Resource Website 1+ mentions |
FastSemSim (RRID:SCR_006919) | FastSemSim | software resource, software toolkit, software library | A package that implements several semantic similarity measures. It is both a library and an end-user application, featuring an intuitive graphical user interface (GUI). It has been implemented with the aim of being fast, expandable, and easy to use. It allows the user to work with the most updated version of GO database and customizable annotation corpora. It provides a set of logically-organized classes that can be easily exploited to both integrate semantic similarity into different analysis pipelines and extend the library with new measures. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, functional similarity, semantic similarity, graphical user interface, gene ontology, annotation, parse, gene, protein |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Padua; Padua; Italy has parent organization: SourceForge |
Open unspecified license - Free for academic use. GNU GPL license. However, This software is currently unpublished work. You must contact us before using it or its results or any work/app. based on top of it in any published work. | nlx_149309 | SCR_006919 | 2026-02-16 09:46:50 | 6 | ||||||||
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PeptideAtlas Resource Report Resource Website 100+ mentions |
PeptideAtlas (RRID:SCR_006783) | PeptideAtlas | data repository, database, storage service resource, service resource, data or information resource | Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. All results of sequence and spectral library searching are subsequently processed through the Trans Proteomic Pipeline to derive a probability of correct identification for all results in a uniform manner to insure a high quality database, along with false discovery rates at the whole atlas level. The raw data, search results, and full builds can be downloaded for other uses. All results of sequence searching are processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner ensuring a high quality database. All peptides are mapped to Ensembl and can be viewed as custom tracks on the Ensembl genome browser. The long term goal of the project is full annotation of eukaryotic genomes through a thorough validation of expressed proteins. The PeptideAtlas provides a method and a framework to accommodate proteome information coming from high-throughput proteomics technologies. The online database administers experimental data in the public domain. You are encouraged to contribute to the database. | proteomics, peptide, mass spectrometry, annotation, eukaryotic, genome, peptide sequence, high-throughput mass spectrometry, ensembl, peptideprophet, protein sequence, blood plasma, protein, eukaryotic cell, dna, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: ProteomeXchange is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Biositemaps is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: ProteomeXchange is related to: NIH Data Sharing Repositories is related to: Integrated Manually Extracted Annotation has parent organization: Institute for Systems Biology; Washington; USA |
NCI ; NHGRI ; NIGMS |
PMID:20013378 PMID:23215161 PMID:16381952 PMID:15642101 |
Public, The community can contribute to this resource, Acknowledgement requested | nif-0000-03266, r3d100010889, biotools:peptideatlas | https://bio.tools/peptideatlas https://doi.org/10.17616/R3BK61 |
SCR_006783 | Peptide Atlas, PeptideAtlas | 2026-02-16 09:46:48 | 479 | ||||
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canSAR Resource Report Resource Website 50+ mentions |
canSAR (RRID:SCR_006794) | canSAR | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | canSAR is an integrated database that brings together biological, chemical, pharmacological (and eventually clinical) data. Its goal is to integrate this data and make it accessible to cancer research scientists from multiple disciplines, in order to help with hypothesis generation in cancer research and support translational research. This cancer research and drug discovery resource was developed to utilize the growing publicly available biological annotation, chemical screening, RNA interference screening, expression, amplification and 3D structural data. Scientists can, in a single place, rapidly identify biological annotation of a target, its structural characterization, expression levels and protein interaction data, as well as suitable cell lines for experiments, potential tool compounds and similarity to known drug targets. canSAR has, from the outset, been completely use-case driven which has dramatically influenced the design of the back-end and the functionality provided through the interfaces. The Web interface provides flexible, multipoint entry into canSAR. This allows easy access to the multidisciplinary data within, including target and compound synopses, bioactivity views and expert tools for chemogenomic, expression and protein interaction network data. | molecular target, expression, cell line, compound, molecule, protein, structure, ligand, drug, 3d, genomics, 3d complex, bioactivity, protein affinity, cell line sensitivity, pathway, annotation, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: BindingDB is related to: Gene Ontology has parent organization: Cancer Research UK |
Cancer | Cancer Research UK C309/A8274 | PMID:22013161 | CanSAR is freely available to all cancer researchers. By using canSAR you are agreeing to the Terms of Use, Https://cansar.icr.ac.uk/cansar/terms-of-use/ | biotools:cansar, nlx_149410 | https://bio.tools/cansar | SCR_006794 | 2026-02-16 09:46:48 | 54 | ||||
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Psort Resource Report Resource Website 100+ mentions |
Psort (RRID:SCR_007038) | PSORT | software application, data processing software, data analysis software, data set, data analysis service, analysis service resource, software resource, topical portal, portal, production service resource, service resource, data or information resource | Portal to the PSORT family of computer programs for the prediction of protein localization sites in cells, as well as other datasets and resources relevant to localization prediction. The standalone versions are available for download for larger analyses. | subcellular, localization, prediction, gram, gram-positive, gram-negative, sequence, fasta, protein, protein localization, cell, motif, profile, amino acid, subcellular localization |
is listed by: OMICtools is related to: PSORT II has parent organization: Simon Fraser University; British Columbia; Canada |
OMICS_01634, nif-0000-31883 | http://psort.hgc.jp/ | SCR_007038 | Psort.org, PSORT: Prediction of Protein Sorting Signals and Localization Sites in Amino Acid Sequences | 2026-02-16 09:46:52 | 209 | |||||||
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ProDom Resource Report Resource Website 100+ mentions |
ProDom (RRID:SCR_006969) | ProDom | data analysis service, analysis service resource, database, production service resource, service resource, 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 | 2026-02-16 09:46:51 | 352 | |||||
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Antibiotic Resistance Genes Database Resource Report Resource Website 100+ mentions |
Antibiotic Resistance Genes Database (RRID:SCR_007040) | data or information resource, database, data computation service | The goals of Antibiotic Resistance Genes Database (ARGB) are to provide a centralized compendium of information on antibiotic resistance, to facilitate the consistent annotation of resistance information in newly sequenced organisms, and also to facilitate the identification and characterization of new genes. ARGB contains six types of database groups: - Resistance Type: This database contains information, such as resistance profile, mechanism, requirement, epidemiology for each type. - Resistance Gene: This database contains information, such as resistance profile, resistance type, requirement, protein and DNA sequence for each gene.This database only includes NON-REDUNDANT, NON-VECTOR, COMPLETE genes. - Antibiotic: This database contains information, such as producer, action mechanism, resistance type, for each gene. - Resistance Gene(NonRD): This database contains the same information as Resistance Gene. It does NOT include NON-REDUNDANT, NON-VECTOR genes, but includes INCOMPLETE genes. - Resistance Gene(ALL): This database contains the same information as Resistance Gene. It includes all REDUNDANT, VECTOR AND INCOMPLETE genes. - Resistance Species: This database contains resistance profile and corresponding resistance genes for each species. Furthermore, ARDB also contians three types BLAST database: - Resistance Genes Complete: Contains only NON-REDUNDANT, NON-VECTOR, COMPLETE genes sequences. - Resistance Genes Non-redundant: Contains NON-REDUNDANT, NON-VECTOR, COMPLETE, INCOMPLETE genes sequences. - Resistance Genes All: Contains all REDUNDANT, VECTOR, COMPLETE, INCOMPLETE genes sequences. Lastly, ARDB provides four types of Analytical tools: - Normal BLAST: This function allows an user to input a DNA or protein sequence, and find similar DNA (Nucleotide BLAST) or protein (Protein BLAST) sequences using blastn, blastp, blastx, tblastn, tblastx - RPS BLAST: A web RPSBLAST (RPS BLAST) interface is provided to align a query sequence against the Position Specific Scoring Matrix (PSSM) for each type. Normally, this will give the same annotation information as using regular BLAST mentioned above. - Multiple Sequences BLAST (Genome Annotation): This function allows an user to annotate multiple (less than 5000) query sequences in FASTA format. - Mutation Resistance Identification: This function allows an user to identify mutations that will cause potential antibiotic resistance, for 12 genes (16S rRNA, 23S rRNA, gyrA, gyrB, parC, parE, rpoB, katG, pncA, embB, folP, dfr). ������ :Sponsors: ARDB is funded by Uniformed Services University of the Health Sciences, administered by the Henry Jackson Foundation. : | genome, antibiotic, antibiotic resistance gene, dna, metagenome, mutation resistance, prokaryotic genomic database, protein, FASEB list | has parent organization: University of Maryland; Maryland; USA | nif-0000-02565 | SCR_007040 | ARDB | 2026-02-16 09:46:52 | 109 | |||||||||
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DART - Drug Adverse Reaction Targets Resource Report Resource Website 1+ mentions |
DART - Drug Adverse Reaction Targets (RRID:SCR_007041) | DART | data repository, database, storage service resource, service resource, data or information resource | Database that provides comprehensive information about adverse effect targets of drugs described in the literature, including information about known drug adverse reaction targets, functions and properties. Moreover, proteins involved in adverse effect targets of chemicals not yet confirmed as adverse drug reaction (ADR) targets are also included as potential targets. Associated references are also included. This database gives physiological function of each target, binding drugs / agonists / antagonists / activators / inhibitors, IC(50) values of the inhibitors, corresponding adverse effects, and type of ADR induced by drug binding to a target. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3-dimensional structure, function, and nomenclature of each target along with drug/ligand binding properties, and related literature. Each entry can be retrieved through multiple search methods including target name, target physiological function, adverse effect, ligand name, and biological pathways. A special page is provided for contribution of new or additional information. Function for ADR-target prediction by SVMDART: Submit protein primary sequence for ADR-related protein prediction. | drug, drug target, evaluation, adverse drug reaction, adverse reaction, agonist, antagonist, binding, ic value, inhibitor, ligand binding property, ligand, physiological function, protein prediction, protein, protein target, target, type, toxicity, data analysis service, toxic | has parent organization: National University of Singapore; Singapore; Singapore | PMID:12862503 | Non-commercial use, The community can contribute to this resource | nif-0000-02720 | SCR_007041 | 2026-02-16 09:46:52 | 2 |
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