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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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dkCOIN Resource Report Resource Website 1+ mentions |
dkCOIN (RRID:SCR_004438) | dkCOIN | data or information resource, database, resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented October 13, 2014. The resource has moved to the NIDDKInformation Network (dkNET) project. Contact them at info_at_dknet.org with any questions. Database of large pools of data relevant to the mission of NIDDKwith the goal of developing a community-based network for integration across disciplines to include the larger DKuniverse of diseases, investigators, and potential users. The focus is on greater use of this data with the objective of adding value by breaking down barriers between sites to facilitate linking of different datasets. To date (2013/06/10), a total of 1,195 resources have been associated with one or more genes. Of 11,580 total genes associated with resources, the ten most represented are associated with 359 distinct resources. The main method by which they currently interconnect resources between the providers is via EntrezGene identifiers. A total of 780 unique genes provide the connectivity between 3,159 resource pairs across consortia. To further increase interconnectivity, the groups have been further annotating their data with additional gene identifiers, publications, and ontology terms from selected Open Biological and Biomedical Ontologies (OBO). | gene, adenovirus construct, antibody, co-immunoprecipitation, embryonic stem cell line, functional genomics, histology, mouse strain, pcr primer, protocol, real time pcr, metadata, diabetes, stem cell, metabolism, tissue development, web service, cloud, embryonic stem cell |
is used by: NIF Data Federation is related to: Beta Cell Biology Consortium is related to: NIDDK Information Network (dkNET) is related to: National Mouse Metabolic Phenotyping Centers is related to: Nuclear Receptor Signaling Atlas is related to: Diabetic Complications Consortium is related to: T1DBase is related to: OBO has parent organization: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
NIDDK 3U01DK072473-05S3; NIDDK 5U24DK076169; NIDDK U19DK062434 |
PMID:22734043 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_44256 | SCR_004438 | NIDDKConsortium Interconnectivity Network | 2026-02-14 02:00:41 | 1 | |||||
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WiCell Research Institute Resource Report Resource Website 100+ mentions |
WiCell Research Institute (RRID:SCR_004364) | WiCell | institution | A nonprofit organization offering research and clinical grade pluripotent stem cell lines, cytogenetic testing, quality control testing and cell banking services to researchers worldwide. The organization is focused on enhancing and expanding the study of human pluripotent stem cells by supporting basic research; establishing research protocols; creating and distributing cell lines; providing training to scientists worldwide; and supporting efforts to unlock the therapeutic potential of stem cell technologies. As home to the Wisconsin International Stem Cell (WISC) Bank, and previously the first US National Stem Cell Bank, WiCell serves the worldwide scientific stem cell community through banking, characterization, and distribution of stem cell lines as well as providing technical support. WiCell also offers cytogenetic services, quality control testing services and clinical grade cell lines to researchers across the globe. | stem cell, cell line, iinduced pluripotent stem cell |
is parent organization of: Wisconsin International Stem Cell Bank is parent organization of: National Stem Cell Bank |
ISNI: 0000 0004 0387 4731, Wikidata: Q7997962, grid.439113.d, nlx_38454 | https://ror.org/032ycrz75 | SCR_004364 | 2026-02-14 02:00:40 | 284 | ||||||||
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Stem Cell Commons Resource Report Resource Website 1+ mentions |
Stem Cell Commons (RRID:SCR_004415) | Stem Cell Commons | data repository, storage service resource, analysis service resource, data set, data or information resource, production service resource, source code, service resource, software resource, database | Open source environment for sharing, processing and analyzing stem cell data bringing together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons. Key features of the Stem Cell Commons * Contains stem cell related experiments * Includes microarray and Next-Generation Sequencing (NGS) data from human, mouse, rat and zebrafish * Data from multiple cell types and disease models * Carefully curated experimental metadata using controlled vocabularies * Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide * A community oriented resource with public data sets and freely available code in public code repositories such as GitHub Currently in development * Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine * ChIP-seq analysis pipeline (additional pipelines in development) * Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources Stem Cell Commons is based on open source software and is available for download and development. | therapeutic target, blood, stem cell, self-renewal, embryonic stem cell, hematopoietic stem cell, leukemia stem cell, gene, protein, phenotype, therapeutic, annotate, share, analyze, data sharing, statistics, visualize, analyze, microarray, next-generation sequencing, statistics, transcription profiling, genome, genome browser, disease model |
is related to: Galaxy is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Harvard Stem Cell Institute |
Normal, Acute Myelogenous Leukemia, Glioblastoma, Primitive Neuroectodermal Tumor, Etc. | PMID:24303302 | Open unspecified license | nlx_42085 | http://bloodprogram.hsci.harvard.edu/ | SCR_004415 | HSCI Blood Genomics, Harvard Stem Cell Institute Blood Genomics, Harvard Stem Cell Institute Blood Program, HSCI Blood Program | 2026-02-14 02:00:43 | 2 | ||||
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Mouse Brain Architecture Project Resource Report Resource Website 1+ mentions |
Mouse Brain Architecture Project (RRID:SCR_004683) | data or information resource, atlas, reference atlas, d spatial image | An atlas project whose goal is to enerate brainwide maps of inter-regional neural connectivity that specify the inputs and outputs of every brain region, at a "mesoscopic" level of analysis. A 3D injection viewer is used to view the mouse brain. To determine the outputs of a brain region, anterograde tracers are used which are taken up by neurons locally ("the input"), then transported actively down the axons to the "output regions." The whole brain is then sliced thinly, and each slice is digitally imaged. These 2-D images are reconstructed in 3D. The majority of the resulting 3-D brain image is unlabeled. Only the injected region and its output regions have tracer in them, allowing for identification of this small fraction of the connectivity map. This procedure is repeated identically, to account for individual variability. To determine the inputs to the same brain region as above, a retrograde tracer is injected in the same stereotaxic location ("the input"), and the process is repeated. In order to accumulate data from different mice (each of whom has a slightly different brain shape and size), 3-D spatial normalization is performed using registration algorithms. These gigapixel images of whole-brain sections can be zoomed to show individual neurons and their processes, providing a "virtual microscope." Each sampled brain is represented in about 500 images, each image showing an optical section through a 20 micron-thick slice of brain tissue. A multi-resolution viewer permits users to journey through each brain, following the pathways taken through three-dimensional brain space by tracer-labeled neuronal pathways. A key point is that at the mid-range "mesoscopic" scale, the team expects to assemble a picture of connections that are stereotypical and probably genetically determined in a species-specific manner. By dividing the volume of a hemisphere of the mouse brain into 250 equidistant, predefined grid-points, and administering four different kinds of tracer injections at each grid point -- in different animals of the same sex and age a complete wiring diagram that will be stitched together in "shotgun" fashion from the full dataset. | atlas, brain, brain architecture, connectivity, mouse brain architecture, neuroanatomy |
is related to: Brain Architecture Project has parent organization: Brain Architecture Project |
NIH Office of the Director ; NIMH RC1MH088659; NIMH R01MH087988 |
Fully accessible to the neuroscience community as well as interested members of the general public, Acknowledgement requested | nlx_146201 | http://www.brainarchitecture.org | http://www.brainarchitecture.org/mouse/about | SCR_004683 | MBA Project, Mouse Brain Architecture | 2026-02-14 02:01:00 | 5 | |||||
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Jackson Laboratory Resource Report Resource Website 10000+ mentions |
Jackson Laboratory (RRID:SCR_004633) | JAX | institution | An independent, nonprofit organization focused on mammalian genetics research to advance human health. Their mission is to discover the genetic basis for preventing, treating, and curing human disease, and to enable research for the global biomedical community. Jackson Laboratory breeds and manages colonies of mice as resources for other research institutions and laboratories, along with providing software and techniques. Jackson Lab also conducts genetic research and provides educational material for various educational levels. | genomic, disease, mouse model, human disease, biomaterial manufacture |
is listed by: One Mind Biospecimen Bank Listing is affiliated with: Integrative Human Microbiome Project is related to: ScienceExchange is related to: Federation of International Mouse Resources is related to: MGI strains is related to: One Mind Biospecimen Bank Listing is related to: Beta Cell Biology Consortium is related to: Mouse Mutagenesis Center for Developmental Defects is related to: GenomeMUSter is parent organization of: Mouse Models For Alzheimer's Disease Research is parent organization of: Type 1 Diabetes Resource is parent organization of: MouseCyc is parent organization of: Special Mouse Strains Resource is parent organization of: Gene Weaver is parent organization of: Mouse Phenome Database (MPD) is parent organization of: Jackson Laboratory Cytogenetic Models Resource is parent organization of: Parkinson's Disease Mouse Model Resource is parent organization of: Eye mutant resource - The Jackson Laboratory is parent organization of: Brainbow mouse resource at Jackson Labs is parent organization of: Short Course on the Genetics of Addiction is parent organization of: JAX Cre Repository is parent organization of: Donate a strain to The Jackson Laboratory Repository is parent organization of: Jackson Laboratory Neurobiology is parent organization of: QTL Archive is parent organization of: Mouse Genome Informatics: The Gene Ontology Project is parent organization of: Mouse Genome Informatics (MGI) is parent organization of: Mouse Tumor Biology Database is parent organization of: Gene Expression Database is parent organization of: The Jackson Laboratory Hearing Research Program is parent organization of: JAX Mice: Neural Tube Defects is parent organization of: JAX Neuroscience Mutagenesis Facility is parent organization of: Induced Mutant Resource is parent organization of: Mouse Mutant Resource is parent organization of: Mouse Genome Database is parent organization of: Mutant Mouse Resource and Research Center is parent organization of: eMouseAtlas is parent organization of: GBRS is parent organization of: Jackson Laboratory Scientific Instrument Services Core Facility provides: Knockout Mouse Project Repository |
Types 1 diabetes, Type 2 diabetes, Diabetes, Cardiovascular diseases, Metabolic disease, Cancer, Rare disease, Alzheimer's disease, Demantia | Available to the research community, Available to the educational community | nlx_63162, ISNI: 0000 0004 0374 0039, grid.249880.f, Crossref funder ID: 100005946 | https://ror.org/021sy4w91 | SCR_004633 | JAX Lab, Jackson Lab | 2026-02-14 02:01:00 | 14831 | |||||
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VARIANT Resource Report Resource Website 1000+ mentions |
VARIANT (RRID:SCR_005194) | VARIANT | data processing software, data analysis service, analysis service resource, data analysis software, production service resource, service resource, software application, software resource | Analysis tool that can report the functional properties of any variant in all the human, mouse or rat genes (and soon new model organisms will be added) and the corresponding neighborhoods. Also other non-coding extra-genic regions, such as miRNAs are included in the analysis. It not only reports the obvious functional effects in the coding regions but also analyzes noncoding SNVs situated both within the gene and in the neighborhood that could affect different regulatory motifs, splicing signals, and other structural elements. These include: Jaspar regulatory motifs, miRNA targets, splice sites, exonic splicing silencers, calculations of selective pressures on the particular polymorphic positions, etc. Software analysis pipelines used in the analysis of NGS data are highly modular, heterogeneous, and rapidly evolving. VARIANT can easily be incorporated into a NGS resequencing pipeline either as a CLI or invoked a webservice. It inputs data directly from the most widely used programs for SNV detection., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional property, variant, gene, non-coding region, mirna, function, single nucleotide variant, next generation sequencing, command line |
is listed by: OMICtools has parent organization: Principe Felipe Research Centre; Valencia; Spain |
Spanish Ministry of Science and Innovation BIO2011-27069 | PMID:22693211 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00193 | SCR_005194 | Variant effect, VARIant ANalysis Tool | 2026-02-14 02:00:50 | 1366 | |||||
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SeqAnt Resource Report Resource Website 1+ mentions |
SeqAnt (RRID:SCR_005186) | SeqAnt | data analysis service, analysis service resource, production service resource, service resource, software resource | A free web service and open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform. Variant sites are characterized with respect to their functional type (Silent, Replacement, 5' UTR, 3' UTR, Intronic, Intergenic), whether they have been previously submitted to dbSNP, and their evolutionary conservation. Annotated variants can be viewed directly on the web browser, downloaded in a tab delimited text file, or directly uploaded in a Browser Extended Data (BED) format to the UCSC genome browser. SeqAnt further identifies all loci harboring two or more coding sequence variants that help investigators identify potential compound heterozygous loci within exome sequencing experiments. In total, SeqAnt resolves a significant bottleneck by allowing an investigator to rapidly prioritize the functional analysis of those variants of interest. | annotation, dna sequence variant, single base mutation, insertion, deletion, sequencing, mutation, variant, sequence variant, perl, sequence, genome |
is listed by: OMICtools has parent organization: Emory University; Georgia; USA has parent organization: SourceForge |
PMID:20854673 | GNU General Public License, v2 | OMICS_00182 | SCR_005186 | SeqAnt - Sequence Annotator | 2026-02-14 02:00:52 | 2 | ||||||
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Picky Resource Report Resource Website 10+ mentions |
Picky (RRID:SCR_010963) | Picky | software resource | A software tool for selecting optimal oligonucleotides (oligos) that allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize. |
is listed by: OMICtools has parent organization: Iowa State University; Iowa; USA |
NSF DBI0850195 | PMID:15180932 PMID:19849862 PMID:20406469 |
Free, Public, Acknowledgement requested | OMICS_00833 | SCR_010963 | Picky: Optimal Oligonucleotide Design and Analysis | 2026-02-14 02:02:07 | 37 | ||||||
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oPOSSUM Resource Report Resource Website 100+ mentions |
oPOSSUM (RRID:SCR_010884) | oPOSSUM | data analysis service, analysis service resource, production service resource, service resource, software resource | A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences. | transcription factor binding site | is listed by: OMICtools | PMID:22973536 PMID:17576675 PMID:15933209 |
Acknowledgement requested | OMICS_00488 | SCR_010884 | oPOSSUM-3 | 2026-02-14 02:02:06 | 101 | ||||||
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Mouse Clinical Institute; Alsace; France Resource Report Resource Website 10+ mentions |
Mouse Clinical Institute; Alsace; France (RRID:SCR_011021) | MCI, ICS | institution | Research infrastructure for generation of new mouse models,being therefore the most important transgenic mouse production unit in France. | is related to: AgedBrainSYSBIO | nlx_158126, ISNI: 0000 0004 0404 8159, grid.452426.3 | https://ror.org/03cjqqq10 | SCR_011021 | Mouse Clinical Institute, Institut Clinique de la Souris, Institut Clinique de la Souris; Alsace; France | 2026-02-14 02:02:09 | 10 | ||||||||
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Annmap Resource Report Resource Website 1+ mentions |
Annmap (RRID:SCR_011783) | Annmap | data or information resource, software resource, database | A genome browser that includes mappings between genomic features and Affymetrix microarrays. Associated with annmap is: * a Bioconductor package, annmap that provides programmatic access to the underlying MySQL database tables (which are freely available for download on this site) * xmapbridge, a Bioconductor package that outputs numeric data in a form suitable for presentation in the browser. This is supported by XMapBridge, a Java client that sits on the local desktop and performs the graph rendering for the browser. | is listed by: OMICtools | Cancer Research UK ; Cancer Research UK Manchester Institute |
OMICS_00900 | SCR_011783 | 2026-02-14 02:02:27 | 6 | |||||||||
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IITC Life Sciences Plantar Test Apparatus Resource Report Resource Website 1+ mentions |
IITC Life Sciences Plantar Test Apparatus (RRID:SCR_012152) | Plantar Test Apparatus | instrument resource | The IITC Plantar Analgesia Meter for thermal paw can be used on 12 mice, 6 rats and other animals (cats, rabbits) unrestrained when testing for narcotic drugs. Experiments are easy to perform, simply slide the test head under test subject, align the heat source via our exclusive guide light (idle state) by the attached, adjustable, angled mirror on test head to test subject and perform tests. | testing apparatus, hargreaves, paw radiant heat assay, toe toaster, hargreaves method, hardware, instrument, equipment | rid_000075 | https://www.iitcinc.com/pdf/Plantar%20Test%20Hargreaves.pdf | SCR_012152 | Plantar Test Apparatus for Mice and Rats, Plantar Test Apparatus (Hargreaves Method) for Mice and Rats | 2026-02-14 02:02:37 | 2 | ||||||||
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Abgent Resource Report Resource Website 50+ mentions |
Abgent (RRID:SCR_008393) | commercial organization | Antibody supplier. | antibody, peptide, synthesis, protein, primary antibody, reagent, peptide synthesis, cell signaling, post-translational modification, stem cell, neuronal development, neurodegenerative disease, gene regulation, development, autophagy, apoptosis, stem cell, phosphorylation, cell function, gene, regulation, research, library, human, kinome, cdna clone, rnai, tissue, cell | is listed by: ScienceExchange | nif-0000-30051, SciEx_4353 | https://www.abcepta.com/ | SCR_008393 | Abgent Antibodies and Peptides, Abcepta | 2026-02-14 02:01:33 | 67 | ||||||||
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Textpresso Resource Report Resource Website 10+ mentions |
Textpresso (RRID:SCR_008737) | Textpresso | text-mining software, data or information resource, software application, software resource, database | An information extracting and processing package for biological literature that can be used online or installed locally via a downloadable software package, http://www.textpresso.org/downloads.html Textpresso's two major elements are (1) access to full text, so that entire articles can be searched, and (2) introduction of categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., methods, etc). A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature. The Textpresso project serves the biological and biomedical research community by providing: * Full text literature searches of model organism research and subject-specific articles at individual sites. Major elements of these search engines are (1) access to full text, so that the entire content of articles can be searched, and (2) search capabilities using categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or identify one (e.g., cell, gene, allele, etc). The search engines are flexible, enabling users to query the entire literature using keywords, one or more categories or a combination of keywords and categories. * Text classification and mining of biomedical literature for database curation. They help database curators to identify and extract biological entities and facts from the full text of research articles. Examples of entity identification and extraction include new allele and gene names and human disease gene orthologs; examples of fact identification and extraction include sentence retrieval for curating gene-gene regulation, Gene Ontology (GO) cellular components and GO molecular function annotations. In addition they classify papers according to curation needs. They employ a variety of methods such as hidden Markov models, support vector machines, conditional random fields and pattern matches. Our collaborators include WormBase, FlyBase, SGD, TAIR, dictyBase and the Neuroscience Information Framework. They are looking forward to collaborating with more model organism databases and projects. * Linking biological entities in PDF and online journal articles to online databases. They have established a journal article mark-up pipeline that links select content of Genetics journal articles to model organism databases such as WormBase and SGD. The entity markup pipeline links over nine classes of objects including genes, proteins, alleles, phenotypes, and anatomical terms to the appropriate page at each database. The first article published with online and PDF-embedded hyperlinks to WormBase appeared in the September 2009 issue of Genetics. As of January 2011, we have processed around 70 articles, to be continued indefinitely. Extension of this pipeline to other journals and model organism databases is planned. Textpresso is useful as a search engine for researchers as well as a curation tool. It was developed as a part of WormBase and is used extensively by C. elegans curators. Textpresso has currently been implemented for 24 different literatures, among them Neuroscience, and can readily be extended to other corpora of text. | literature, extract, process, bibliographic resource, database application, linux, macos, pdf, perl, posix/unix-like, sh, bash, unix shell, web service, search engine, curation tool, dicty, neuroscience, regulon db, ecoliwiki, ecocyc, curation, text-mining |
is listed by: OMICtools is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: WormBase is related to: Dictyostelium discoideum genome database |
NHGRI HG004090 | PMID:18949581 PMID:15383839 |
Textpresso License | nlx_143812, OMICS_01199 | http://www.nitrc.org/projects/textpresso-2-0/ | SCR_008737 | Text presso, Textpresso - literature search engine | 2026-02-14 02:01:45 | 10 | ||||
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TopFIND Resource Report Resource Website 10+ mentions |
TopFIND (RRID:SCR_008918) | TopFIND | data repository, storage service resource, data or information resource, service resource, database | An integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing state of proteins and functional implications thereof derived from research literature, contributions by the scientific community and biological databases. It lists more than 120,000 N- and C-termini and almost 10,000 cleavages. TopFIND is a resource for comprehensive coverage of protein N- and C-termini discovered by all available in silico, in vitro as well as in vivo methodologies. It makes use of existing knowledge by seamless integration of data from UniProt and MEROPS and provides access to new data from community submission and manual literature curating. It renders modifications of protein termini, such as acetylation and citrulination, easily accessible and searchable and provides the means to identify and analyse extend and distribution of terminal modifications across a protein. The data is presented to the user with a strong emphasis on the relation to curated background information and underlying evidence that led to the observation of a terminus, its modification or proteolytic cleavage. In brief the protein information, its domain structure, protein termini, terminus modifications and proteolytic processing of and by other proteins is listed. All information is accompanied by metadata like its original source, method of identification, confidence measurement or related publication. A positional cross correlation evaluation matches termini and cleavage sites with protein features (such as amino acid variants) and domains to highlight potential effects and dependencies in a unique way. Also, a network view of all proteins showing their functional dependency as protease, substrate or protease inhibitor tied in with protein interactions is provided for the easy evaluation of network wide effects. A powerful yet user friendly filtering mechanism allows the presented data to be filtered based on parameters like methodology used, in vivo relevance, confidence or data source (e.g. limited to a single laboratory or publication). This provides means to assess physiological relevant data and to deduce functional information and hypotheses relevant to the bench scientist. TopFIND PROVIDES: * Integration of protein termini with proteolytic processing and protein features * Displays proteases and substrates within their protease web including detailed evidence information * Fully supports the Human Proteome Project through search by chromosome location CONTRIBUTE * Submit your N- or C-termini datasets * Contribute information on protein cleavages * Provide detailed experimental description, sample information and raw data | protein, n-termini, c-termini, protease, protein cleavage, proteomics, cleavage site, terminus, modification, proteolytic processing, protein function, domain structure, protein termini, terminus modification, protease, substrate, protease inhibitor, protein interaction, protein-protein interaction, interaction, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: UniProtKB is related to: PSICQUIC Registry is related to: MEROPS has parent organization: University of British Columbia; British Columbia; Canada |
Canadian Institutes of Health Research ; Cancer Research Society ; British Columbia Proteomics Network ; Metalloproteinase Proteomics and Systems Biology ; Michael Smith Foundation for Health Research ; Breast Cancer Society of Canada ; Alexander von Humboldt-Stiftung ; BMBF ; German Academic Exchange Service |
PMID:22102574 PMID:21822272 |
Public, Acknowledgement requested | biotools:topfind, r3d100012721, nlx_151607 | https://bio.tools/topfind https://doi.org/10.17616/R3KB8J https://doi.org/10.17616/R3KB8J |
SCR_008918 | Termini oriented protein Function Inferred Database | 2026-02-14 02:01:48 | 29 | ||||
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National Mouse Metabolic Phenotyping Centers Resource Report Resource Website 500+ mentions |
National Mouse Metabolic Phenotyping Centers (RRID:SCR_008997) | MMPC, NIDDKMMPC | data or information resource, service resource, database | Center mission is to advance medical and biological research by providing the scientific community with standardized, high quality metabolic and physiologic phenotyping services for mouse models of diabetes, diabetic complications, obesity and related disorders. | phenotype, phenotyping, metabolism, cardiovascular, gastrointestinal, endocrine, energy, analytic, blood composition, in vivo, hormone, energy balance, eating, exercise, organ function, morphology, physiology, histology, experimental protocol, assay, strain, measurement, animal husbandry, FASEB list |
is used by: NIF Data Federation is used by: NIDDK Information Network (dkNET) is used by: Hypothesis Center is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources is related to: dkCOIN has parent organization: Augusta University; Georgia; USA has parent organization: Case Western Reserve University; Ohio; USA has parent organization: University of Cincinnati; Ohio; USA has parent organization: Vanderbilt University School of Medicine; Tennessee; USA has parent organization: University of California at Davis; California; USA has parent organization: University of Massachusetts Medical School; Massachusetts; USA has parent organization: Yale School of Medicine; Connecticut; USA is parent organization of: MMPC-Vanderbilt University School of Medicine Animal Health and Welfare Core is parent organization of: MMPC-Vanderbilt University School of Medicine Analytical Resources Core is parent organization of: MMPC-University of Michigan Medical School Microbiome Core is parent organization of: MMPC-Vanderbilt University School of Medicine Metabolic Regulation Core is parent organization of: MMPC-University of Michigan Medical School Microvascular Complications Core is parent organization of: MMPC-University of Massachusetts Medical School Cardiovascular Core is parent organization of: MMPC-Vanderbilt University School of Medicine is parent organization of: MMPC-University of Michigan Medical School is parent organization of: MMPC-University of Massachusetts Medical School Humanized Mouse Cell Transplantation and Assessment Core is parent organization of: MMPC-University of Cincinnati Medical Center Energy Metabolism Food Intake and Body Weight Regulation Core is parent organization of: MMPC-University of Massachusetts Medical School Islet Core is parent organization of: MMPC-University of Massachusetts Medical School Metabolism Core is parent organization of: MMPC-University of Massachusetts Medical School Animal Care Core is parent organization of: MMPC-University of Cincinnati Medical Center is parent organization of: University of Massachusetts Medical School Metabolic Disease Research Center Core Facility is parent organization of: MMPC-University of Massachusetts Medical School Analytical Core is parent organization of: MMPC-University of California Davis Energy Balance Exercise and Behavior Core is parent organization of: MMPC-University of Cincinnati Medical Center Lipid Lipoprotein and Glucose Metabolism Core is parent organization of: MMPC-University of California Davis Administrative Core is parent organization of: MMPC-University of California Davis Microbiome and Host Response Core is parent organization of: MMPC-University of Cincinnati Medical Center Cardiovascular and Renal Function Core is parent organization of: MMPC-University of California Davis Endocrinology and Metabolism Core is parent organization of: MMPC-University of California Davis is parent organization of: MMPC-University of California Davis Animal Care Surgery and Pathology Core is parent organization of: MMPC-University of Michigan Medical School Metabolism Bariatric Surgery and Behavior Core is parent organization of: MMPC-Vanderbilt University School of Medicine Cardiovascular Pathophysiology Core is parent organization of: MMPC-University of Michigan Medical School Animal Care and Germ-Free Mouse Core has organization facet: MMPC-University of California Davis has organization facet: MMPC-University of Cincinnati Medical Center has organization facet: University of Massachusetts Medical School Metabolic Disease Research Center Core Facility has organization facet: MMPC-University of Michigan Medical School has organization facet: MMPC-Vanderbilt University School of Medicine |
Diabetes, Obesity, Diabetic complication, Metabolic disease, Cardiovascular disease, Nephropathy, Neuropathy, Retinopathy | NIDDK U24 DK076174; NIDDK U24 DK092993; NIDDK U24 DK059630; NIDDK U24 DK093000; NIDDK U24 DK059637; NIDDK U24 DK059635 |
Freely available, | SCR_015358, nlx_152633 | SCR_008997 | Mouse Metabolic Phenotyping Centers | 2026-02-14 02:01:40 | 714 | |||||
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Renal Disease Portal Resource Report Resource Website |
Renal Disease Portal (RRID:SCR_009030) | Renal Disease Portal | portal, data set, data or information resource, disease-related portal, topical portal | An integrated resource for information on genes, QTLs and strains associated with a variety of kidney and renal system conditions such as Renal Hypertension, Polycystic Kidney Disease and Renal Insufficiency, as well as Kidney Neoplasms. | gene, quantitative trait locus, strain, renal hypertension, kidney neoplasm, phenotype, pathway, biological process, disease, kidney, genome, gviewer, chromosome, molecular function, cellular component, visualization, synteny |
is related to: NIDDK Information Network (dkNET) is related to: Gene Ontology has parent organization: Rat Genome Database (RGD) |
Renal disease, Renal hypertension, Polycystic kidney disease, Renal insufficiency, Kidney neoplasm, Diabetes Insipidus, Hyperoxaluria, Renal hypertension, Nephritis, Nephrocalcinosis, Nephrolithiasis, Nephrosis, Renal Fibrosis, Inborn Error of Renal Tubular Transport, Uremia | nlx_153941 | SCR_009030 | RGD Renal Disease Portal | 2026-02-14 02:01:49 | 0 | |||||||
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Digital Ageing Atlas Resource Report Resource Website 10+ mentions |
Digital Ageing Atlas (RRID:SCR_009020) | DAA | data repository, storage service resource, data or information resource, service resource, database | Database of age-related changes covering different biological levels, including molecular, physiological, psychological and pathological age-related data, to create an interactive portal that serves as a centralized collection of human aging changes and pathologies. To facilitate integrative, system-level studies of aging, the DAA provides a centralized source for aging-related data as well as basic tools to query and visualize the data, including anatomical models. Data in the DAA is manually curated from the literature and retrieved from public databases. For more detailed analyses users are able to download the entire database. More information on how to use the DAA is available on the help page. The DAA primarily focuses on human aging, but also includes supplementary mouse data, in particular gene expression data, to enhance and expand the information on human aging. If you would like to contribute to the database yourself, for instance if you have new data on aging, please use the contribute page to submit your data. | late adult human, anatomy, gene, molecular, pathological, physiological, psychological, tissue, reference, cellualar, gene expression | has parent organization: University of Liverpool; Liverpool; United Kingdom | Aging | The community can contribute to this resource, Creative Commons Attribution License, v3 Unported | nlx_153874 | SCR_009020 | Digital Aging Atlas | 2026-02-14 02:01:50 | 12 | ||||||
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PRISM (Stanford database) Resource Report Resource Website 10000+ mentions |
PRISM (Stanford database) (RRID:SCR_005375) | PRISM | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5,2022.Tool that predicts interactions between transcription factors and their regulated genes from binding motifs. Understanding vertebrate development requires unraveling the cis-regulatory architecture of gene regulation. PRISM provides accurate genome-wide computational predictions of transcription factor binding sites for the human and mouse genomes, and integrates the predictions with GREAT to provide functional biological context. Together, accurate computational binding site prediction and GREAT produce for each transcription factor: 1. putative binding sites, 2. putative target genes, 3. putative biological roles of the transcription factor, and 4. putative cis-regulatory elements through which the factor regulates each target in each functional role., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genomic, transcription factor, function, transcription factor binding site, transcription factor regulator, biological role, target gene, target genomic region, genome, FASEB list |
is listed by: OMICtools is listed by: SoftCite is related to: GREAT: Genomic Regions Enrichment of Annotations Tool has parent organization: Stanford University School of Medicine; California; USA |
PMID:23382538 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00489 | SCR_005375 | Predicting Regulatory Information from Single Motifs | 2026-02-14 02:01:06 | 40813 | ||||||
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CoPub Resource Report Resource Website 1+ mentions |
CoPub (RRID:SCR_005327) | CoPub | data access protocol, software resource, web service, service resource | Text mining tool that detects co-occuring biomedical concepts in abstracts from the MedLine literature database. It allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs. | microarray, gene, literature, enrich, annotate, network, database, differential expression, bio.tools |
uses: MEDLINE uses: Gene Ontology is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Netherlands Bioinformatics Centre |
Netherlands Bioinformatics Centre | PMID:18442992 | Free, Public, Acknowledgement requested | OMICS_01178, biotools:copub | https://bio.tools/copub | http://services.nbic.nl/cgi-bin/copub/CoPub.pl | SCR_005327 | 2026-02-14 02:00:52 | 5 |
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