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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Rice Kinase Database Resource Report Resource Website |
Rice Kinase Database (RRID:SCR_006990) | RKD | data or information resource, database | It was created to host functional genomic information gathered as part of a large NSF funded rice kinase proteomics project. The goal is to integrate disparate data sets into a logical, user friendly format. To accomplish this, they have developed a platform to display user selected functional genomic data on a phylogenetic tree. The RKD also includes an interactive chromosomal map showing the positions of all rice kinases and an interactive protein-protein interaction maps. | chromosomal map, genomic data, genomic information, phylogenetic tree, protein, proteomic, rice kinase | nif-0000-20910 | SCR_006990 | Rice Kinase Database | 2026-08-29 11:29:55 | 0 | |||||||||
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CuticleDB Resource Report Resource Website 10+ mentions |
CuticleDB (RRID:SCR_007045) | cuticleDB | data or information resource, database | A relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the five sequenced genomes where manual annotation has been applied to cuticular proteins: Anopheles gambiae, Apis mellifera, Bombyx mori, Drosophila melanogaster, and Nasonia vitripennis. Some sequences were confirmed as authentic cuticular proteins because protein sequencing revealed that they were present in cuticle; others were identified by sequence homology and other criteria. Entries provides information about whether sequences are putative or authentic cuticular proteins. CuticleDB was primarily designed to contain correct and full annotation of cuticular protein data. The database will be of help to future genome annotators. Users will be able to test hypotheses for the existence of known and also of yet unknown motifs in cuticular proteins. An analysis of motifs may contribute to understanding how proteins contribute to the physical properties of cuticle as well as to the precise nature of their interaction with chitin. | genome, cuticle, cuticle protein, cuticular protein, cdna, protein, insect, exoskeleton, annotation, chitin, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
University of Athens; Athens; Greece ; NIAID AI055624 |
PMID:15453918 | biotools:cuticledb, nif-0000-02708 | https://bio.tools/cuticledb | SCR_007045 | CuticleDB - A relational database of Arthropod cuticular proteins | 2026-08-29 11:29:49 | 14 | |||||
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UCSD-Nature Signaling Gateway Molecule Pages Resource Report Resource Website 10+ mentions |
UCSD-Nature Signaling Gateway Molecule Pages (RRID:SCR_006907) | SGMP | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Relational database of all significant published qualitative and quantitative information on cell signaling proteins. The Molecule Pages database was developed with the specific aim of allowing interactions, and indeed whole pathways, to be modeled. The goal is to filter the data to present only validated information. In addition, the Gateway is the home of Signaling Update, which provides a one-stop overview of the latest and hottest research in cell signaling for both the specialist and non-specialist alike. | database, data model, cell signaling pathway, molecule, protein, signal transduction |
is listed by: 3DVC has parent organization: University of California at San Diego; California; USA |
Genentech Inc ; National Institute of General Medical Sciences |
PMID:21505029 PMID:17965093 PMID:12478304 |
THIS RESOURCE IS NO LONGER IN SERVICE | r3d100011690, nif-0000-03604, SCR_013230, nif-0000-20810 | https://doi.org/10.17616/R3V343 | SCR_006907 | Molecule Pages: A comprehensive signaling database, UCSD - Signaling Gateway Molecule Pages, Alliance for Cellular Signaling Molecule Pages Database | 2026-08-29 11:29:53 | 13 | ||||
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Everything Added to Food in the United States Resource Report Resource Website 1+ mentions |
Everything Added to Food in the United States (RRID:SCR_006747) | data or information resource, database | PAFA contains administrative, chemical and toxicological information on over 2000 substances directly added to food. In addition, the database contains only administrative and chemical information on less than 1000 such substances. The more than 3000 total substances together comprise an inventory often referred to as Everything Added to Food in the United States (EAFUS). The EAFUS list of substances contains ingredients added directly to food that FDA has either approved as food additives or listed or affirmed as GRAS. Nevertheless, it contains only a partial list of all food ingredients that may in fact be lawfully added to food, because under federal law some ingredients may be added to food under a GRAS determination made independently from the FDA. The list contains many, but not all, of the substances subject to independent GRAS determinations. :Sponsors: This information is generated from a database maintained by the U.S. Food and Drug Administration (FDA) Center for Food Safety and Applied Nutrition (CFSAN) under an ongoing program known as the Priority-based Assessment of Food Additives (PAFA). | food, additive, chemical, color, ingredient, nutrition, public health databases, safety, secondary, status, substance, toxicological | nif-0000-21137 | http://www.cfsan.fda.gov/~dms/eafus.html | SCR_006747 | EAFUS | 2026-08-29 11:29:44 | 1 | |||||||||
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Pythonxy Resource Report Resource Website 10+ mentions |
Pythonxy (RRID:SCR_006903) | Python-xy, Python(x, y) | software application, software development tool, software resource, source code | Scientific and engineering development software for numerical computations, data analysis and data visualization based on Python programming language, Qt graphical user interfaces and Spyder interactive scientific development environment. Used to interpreted languages (such as MATLAB or IDL) or compiled languages (C/C++ or Fortran) to switch to Python. | program, language, python, computation, data analysis, data visualization, plugin | is related to: Spyder | Free, Available for download, Freely available | nlx_149232 | http://www.pythonxy.com, https://code.google.com/p/pythonxy/wiki/Welcome | SCR_006903 | pythonxy - Scientific-oriented Python Distribution based on Qt and Spyder, Python(x, y) - Scientific oriented Python Distribution based on Qt and Spyder | 2026-08-29 11:29:45 | 10 | ||||||
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SUB-cellular location database for Arabidopsis proteins II Resource Report Resource Website 1+ mentions |
SUB-cellular location database for Arabidopsis proteins II (RRID:SCR_006668) | data or information resource, database | SUBA provides a powerful tool to investigate subcellular localization in Arabidopsis. SUBA houses large scale proteomic and GFP localization sets from cellular compartments of Arabidopsis, and also contains pre-compiled bioinformatic predictions for protein subcellular localizations. The Database functions through the unification of disparate datasets and through the provision of a web accessible interface for the construction of user based queries resulting in a one-stop-shop for protein localization in this model plant. Subcellular localization information can contribute towards our understanding of protein function, protein redundancy and of biological inter-relationships. In an attempt to get a clearer picture of our experimental data and to more generally understand subcellular partitioning we have brought together various data sources to build SUBA. | arabidopsis, arabidopsis genome, gfp, protein subcellular localization, proteomics, subcellular, subcellular localization | has parent organization: University of Western Australia; Perth; Australia | nif-0000-03505 | SCR_006668 | SUBA II | 2026-08-29 11:29:51 | 4 | |||||||||
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Cooperative Human Tissue Network Western Division at Vanderbilt University Medical Center Resource Report Resource Website |
Cooperative Human Tissue Network Western Division at Vanderbilt University Medical Center (RRID:SCR_006661) | CHTN Western Division | biomaterial supply resource, material resource, tissue bank | The Cooperative Human Tissue Network- Western Division at Vanderbilt University Medical Center is one of six institutions throughout the country funded by the National Cancer Institutes to procure and distribute remnant human tissues to biomedical researchers throughout the United States and Canada. CHTN operates through a shared networking system which allows investigators greater access to available research specimens. CHTN offers a variety of preparation and preservation techniques to ensure investigators are receiving the quality specimens needed for research. Remnant tissues are obtained from surgical resections and autopsies and are procured to the specifications of the investigator. | tissue |
lists: Biospecimens/Biorepositories: Rare Disease-HUB (RD-HUB) is listed by: One Mind Biospecimen Bank Listing is related to: Vanderbilt University Medical Center; Tennessee; USA has parent organization: Vanderbilt University; Tennessee; USA |
All | NCI | Public | nlx_143710 | SCR_006661 | CHTN Western Division at VUMC, Cooperative Human Tissue Network - Western Division, VUMC Tissue Repository | 2026-08-29 11:29:43 | 0 | |||||
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re3data.org Resource Report Resource Website 50+ mentions |
re3data.org (RRID:SCR_006782) | re3data.org | data or information resource, database, registry | Global registry of research data repositories from all academic disciplines that allows the easy identification of appropriate research data repositories, both for data producers and users. Information icons display principal attributes of a repository that can be used for multi-faceted searches. Repository operators can suggest their infrastructures to be listed via a simple application form. A repository is indexed when the minimum requirements are met, i.e. mode of access to the data and repository, as well as the terms of use. | vocabulary, registry, metadata standard, data sharing, FASEB list |
lists: Academic Seismic Portal at UTIG lists: National Addiction and HIV Data Archive Program (NAHDAP) lists: Alaska Climate Research Center lists: MINT lists: Internet Archive lists: MatrixDB lists: Animal QTLdb lists: MPIDB lists: BeetleBase lists: Conserved Domain Database lists: NeuroMorpho.Org lists: Marine Geoscience Data System lists: Cell Centered Database lists: dbMHC lists: Human Mortality Database lists: UniProt lists: Ligand-Gated Ion Channel Database lists: EcoGene lists: NCBI Genome lists: ESTHER lists: Genomes Online Database lists: Gramene lists: American FactFinder lists: Human Proteinpedia lists: IMGT/HLA lists: Influenza Virus Resource lists: DOE Joint Genome Institute lists: MetaCrop lists: ISPS Data Archive lists: MorphBank lists: miRBase lists: Inter-university Consortium for Political and Social Research (ICPSR) lists: Mouse Phenome Database (MPD) lists: MorphoBank lists: dbVar lists: Open Science Framework lists: TalkBank lists: Nucleic Acid Database lists: NCBI Taxonomy lists: NCBI Protein Database lists: PHI-base lists: Alberta Geological Survey lists: Protein Clusters lists: Reactome lists: Cell Image Library (CIL) lists: eyeMoviePedia lists: ALLBUS - German General Social Survey lists: TPA lists: Agency for Healthcare Research and Quality lists: Alaska Satellite Facility lists: Current German Weather Stations lists: NCBI Structure lists: BOLD lists: PDBe - Protein Data Bank in Europe lists: FishBase lists: Nucleotide database lists: NCBI BioSystems Database lists: SGD lists: Data.gov lists: RHEA lists: European Bioinformatics Institute lists: NCBI Probe lists: NCBI Nucleotide lists: Database of Genomic Variants Archive (DGVa) lists: NCBI Popset lists: Whole Brain Atlas lists: EMAGE Gene Expression Database lists: Limited Access Datasets From NIMH Clinical Trials lists: Tree of Life Web Project lists: TreeBASE lists: UCSC Genome Browser lists: UniPROBE lists: Crystallography Open Database (COD) lists: National Archive of Computerized Data on Aging (NACDA) lists: EOL - Encyclopedia of Life lists: VectorBase lists: caArray lists: NCBI Epigenomics lists: GWAS Central lists: QTL Archive lists: Proteome Commons lists: XNAT Central lists: 4TU.Datacentrum lists: Amazon Web Services Public Data Sets lists: ChemSpider lists: DataStaR lists: Rat Genome Database (RGD) lists: Atlas of Living Australia lists: Electron Microscopy Data Bank at PDBe (MSD-EBI) lists: Phytozome lists: FlyBase lists: MaizeGDB lists: Tuberculosis Database lists: InterPro lists: UNAVCO lists: The Human Protein Atlas lists: InnateDB lists: UniSTS lists: Launchpad lists: Surveillance Epidemiology and End Results lists: FAOSTAT lists: Adult Blood Lead Epidemiology and Surveillance Interactive Database lists: HIstome: The Histone Infobase lists: HPRD - Human Protein Reference Database lists: Biological General Repository for Interaction Datasets (BioGRID) lists: INFEVERS lists: Reciprocal Net lists: Africa Centre for Health and Population Studies lists: BeeBase lists: Biodiversity Heritage Library lists: Databrary lists: ACADIS Gateway lists: ACEpepDB lists: AIMS Data Centre lists: ALADDIN lists: ASTER lists: Access to Archival Databases lists: AidData lists: Alaska Ocean Observing System lists: J. Craig Venter Institute lists: Wellcome Trust Sanger Institute; Hinxton; United Kingdom lists: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) lists: myExperiment lists: BioModels lists: Addgene lists: Antarctic and Southern Ocean Data Portal lists: OpenTopography lists: National Snow and Ice Data Center lists: Biological Magnetic Resonance Data Bank (BMRB) lists: dbSNP lists: Ensembl lists: DNA DataBank of Japan (DDBJ) lists: Entrez Gene lists: Zebrafish Information Network (ZFIN) lists: GitHub lists: DrugBank lists: NCBI database of Genotypes and Phenotypes (dbGap) lists: Gene Expression Nervous System Atlas lists: SumsDB lists: GenBank lists: GermOnline lists: HGNC lists: Greengenes lists: Neuroscience Information Framework lists: HomoloGene lists: ArrayExpress lists: JASPAR lists: WormBase lists: Database of Interacting Proteins (DIP) lists: EMDataResource.org lists: ResearchCompendia lists: Proteomics Identifications (PRIDE) lists: RefSeq lists: FAIRsharing lists: PubChem lists: FigShare lists: UniGene lists: NIMH Data Archive lists: TAIR lists: NCBI BioProject lists: SMD lists: OpenNeuro lists: SoyBase lists: Beta Cell Biology Consortium lists: Biomedical Informatics Research Network lists: Dryad Digital Repository lists: Atlantic Canada Conservation Data Centre lists: Agri-environmental Research Data Repository lists: Australian Antarctic Data Centre lists: Antibody Registry lists: Mouse Genome Informatics (MGI) lists: European Nucleotide Archive (ENA) lists: NIDDK Central Repository lists: GigaScience lists: PeptideAtlas lists: 1000 Genomes: A Deep Catalog of Human Genetic Variation lists: IntAct lists: fMRI Data Center lists: Gene Expression Omnibus lists: Data and Specimen Hub (NICHD DASH) lists: NIDA Data Share lists: The NINDS Human Cell and Data Repository (NHCDR) lists: Microphysiology Systems Database lists: Dataverse Network Project lists: Mendeley lists: Vivli lists: Metabolomics Workbench lists: Qualitative Data Repository lists: Protocols.io lists: ZENODO lists: STRENDA lists: Code Ocean lists: Brain Image Library lists: German Collection of Microorganisms and Cell Cultures lists: INPTDAT lists: DataONE lists: GBIF - Global Biodiversity Information Facility lists: Lamont-Doherty Core Repository lists: CaltechDATA lists: Synapse lists: Incorporated Research Institutions for Seismology lists: Cancer Imaging Archive (TCIA) lists: Mendeley Data lists: UK Data Archive lists: GigaDB lists: PhysioNet lists: Project Data Sphere lists: Influenza Research Database (IRD) lists: Simtk.org lists: ResearchGate lists: Virus Pathogen Resource (ViPR) lists: Cambridge Structural Data Base lists: 4TU.ResearchData lists: Aperta Turkey Open Archive lists: Polar Data Catalogue lists: Arch lists: Australian Data Archive lists: Australian Ocean Data Network lists: Barbara A. Mikulski Archive for Space Telescopes lists: Aston Data Explorer lists: Birkbeck Research Data lists: B2SHARE Eudat lists: BioHeritage National Science Challenge Data Repository lists: Bolin Centre Database lists: Brown Digital Repository is listed by: FORCE11 is related to: U.S. Census Bureau is related to: Rat Genome Database (RGD) is related to: ResearchCompendia has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Karlsruhe Institute of Technology; Karlsruhe; Germany |
DFG | The community can contribute to this resource | nlx_152589 | SCR_006782 | Registry of Research Data Repositories, re3data.org: Registry of Research Data Repositories, re3data | 2026-08-29 11:29:52 | 89 | ||||||
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PRODORIC Resource Report Resource Website 50+ mentions |
PRODORIC (RRID:SCR_007074) | PRODORIC | data or information resource, database | Database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites. A variety of bioinformatics tools for the prediction, analysis and visualization of regulons and gene reglulatory networks is included. The integrated approach provides information about molecular networks in prokaryotes with focus on pathogenic organisms. In detail this concerns: * transcriptional regulation (transcription factors and their DNA binding sites * signal transduction (two-component systems, phosphylation cascades) * protein interactions (complex formation, oligomerization) * biochemical pathways (chemical reactions) * other regulation events (e.g. codon usage, etc. ...) It aims to be a resource to model protein-host interactions and to be a suitable platform to analyze high-throughput data from proteomis and transcriptomics experiments (systems biology). Currently it mainly contains detailed information about operon and promoter structures including huge collections of transcription factor binding sites. If an appropriate number of regulatory binding sites is available, a position weight matrix (PWM) and a sequence logo is provided, which can be used to predict new binding sites. This data is collected manually by screening the original scientific literature. PRODORIC also handles protein-protein interactions and signal-transduction cascades that commonly occur in form of two-component systems in prokaryotes. Furthermore it contains metabolic network data imported from the KEGG database., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene regulation, transcription factor binding site, promoter structure, gene expression, genome, regulon, network, visualization, gene regulatory network, pathogen, transcriptional regulation, transcription factor, dna binding site, signal transduction, protein interaction, pathway, regulation, protein-protein interaction, signal-transduction cascade, operon, promoter, structure, position weight matrix, FASEB list |
is listed by: OMICtools is related to: KEGG has parent organization: Technical University of Braunschweig; Braunschweig; Germany |
BMBF | PMID:18974177 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03343, OMICS_01872 | http://www.prodoric.de | SCR_007074 | Prokaryotic Database of Gene Regulation | 2026-08-29 11:29:49 | 57 | ||||
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TAED - The Adaptive Evolution Database Resource Report Resource Website 1+ mentions |
TAED - The Adaptive Evolution Database (RRID:SCR_006930) | TAED | data or information resource, database | A database of sequence alignments and phylogenetic trees for chordates and embryophytes. The Adaptive Evolution Database (TAED) was first presented as a collection of branches from chordate and embryophyte gene families with fast evolutionary rates mapped onto the NCBI taxonomy (1,2). The original gene families were from the Master Catalog and are proprietary (3). A new version of TAED is now presented as a taxonomic shell together with a gene family database. In addition to multiple sequence alignments and phylogenetic trees for all families of chordate and embryophyte sequences, the ratio of non-synonymous to synonymous nucleotide substitution rates (Ka/Ks) is provided for each branch of every phylogenetic tree. This ratio, when significantly greater than 1, is an indicator of positive selection and potentially a change of function of the encoded protein. With a gene tree to species tree mapping, the branches significantly greater than 1 are collated together in a phylogenetic context. The framework is expandable to incorporate other genomic-scale information in a phylogenetic context. Ultimately, the database is designed both to provide high-quality gene families with multiple sequence alignments and phylogenetic trees for chordates and embryophytes, and to enable asking the question, What makes each species unique at the molecular genomic level? | evolution, phylogenetic tree, taxonomy | has parent organization: University of Wyoming; Wyoming; USA | nif-0000-03533, r3d100012568 | https://doi.org/10.17616/R3DF5W | SCR_006930 | The Adaptive Evolution Database | 2026-08-29 11:29:54 | 1 | |||||||
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Potential Drug Target Database Resource Report Resource Website 10+ mentions |
Potential Drug Target Database (RRID:SCR_007069) | PDTD | data or information resource, database | It is a dual function database that associates an informatics database to a structural database of known and potential drug targets. PDTD is a comprehensive, web-accessible database of drug targets, and focuses on those drug targets with known 3D-structures. PDTD contains 1207 entries covering 841 known and potential drug targets with structures from the Protein Data Bank (PDB). Drug targets of PDTD were categorized into 15 and 13 types according to two criteria: therapeutic areas and biochemical criteria. The database supports extensive searching function using PDB ID, target name and category, related disease. | drug, biochemical, informatics, protein, structural, therapeutic | nif-0000-20891 | SCR_007069 | Potential Drug Target Database | 2026-08-29 11:29:55 | 19 | |||||||||
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Rickettsia Genome Database Resource Report Resource Website 1+ mentions |
Rickettsia Genome Database (RRID:SCR_007102) | data or information resource, database, image | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. Rickettsia are obligate intracellular bacteria living in arthropods. They occasionally cause diseases in humans. To understand their pathogenicity, physiologies and evolutionary mechanisms, RicBase is sequencing different species of Rickettsia. Up to now we have determined the genome sequences of R. conorii, R. felis, R. bellii, R. africae, and R. massiliae. The RicBase aims to organize the genomic data to assist followup studies of Rickettsia. This website contains information on R. conorii and R. prowazekii. A R. conorii and R. prowazekii comparative genome map is also available. Images of genome maps, dendrogram, and sequence alignment allow users to gain a visualization of the diagrams. | evolutionary, africae, alignment, arthropod, bacteria, bellii, conorii, dendrogram, disease, genome, genomic, human, intracellular, massiliae, mechanism, pathogenicity, physiology, prowazekii, rickettsia, sequence, specie, journal article, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20993 | SCR_007102 | RicBase | 2026-08-29 11:29:48 | 1 | |||||||||
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Gait in Parkinson's Disease Resource Report Resource Website 1+ mentions |
Gait in Parkinson's Disease (RRID:SCR_006891) | data or information resource, database | Database that contains measures of gait from 93 patients with idiopathic PD (mean age: 66.3 years; 63% men), and 73 healthy controls (mean age: 66.3 years; 55% men). The database includes the vertical ground reaction force records of subjects as they walked at their usual, self-selected pace for approximately 2 minutes on level ground. Underneath each foot were 8 sensors (Ultraflex Computer Dyno Graphy, Infotronic Inc.) that measure force (in Newtons) as a function of time. The output of each of these 16 sensors has been digitized and recorded at 100 samples per second, and the records also include two signals that reflect the sum of the 8 sensor outputs for each foot. This database also includes demographic information, measures of disease severity (i.e., using the Hoehn & Yahr staging and/or the Unified Parkinson's Disease Rating Scale) and other related measures (available in HTML or xls spreadsheet format). A subset of the database includes measures recorded as subjects performed a second task (serial 7 subtractions) while walking, which shows excerpts of swing time series from a patient with PD and a control subject, under usual walking conditions and when performing serial 7 subtractions. Under usual walking conditions, variability is larger in the patient with PD (Coefficient of Variation = 2.7%), compared to the control subject (CV = 1.3%). Variability increases during dual tasking in the subject with PD (CV = 6.5%), but not in the control subject (CV = 1.2%). | gait, speed, treadmill, stride variability |
is used by: NIF Data Federation is used by: Aging Portal has parent organization: Physiobank |
Parkinson's disease | NIH ; National Parkinson's Foundation ; Parkinson's Disease Foundation |
PMID:16053531 | Acknowledgement requested | nif-0000-00248 | SCR_006891 | 2026-08-29 11:29:53 | 1 | ||||||
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Arabidopsis Gene Regulatory Information Server Resource Report Resource Website 50+ mentions |
Arabidopsis Gene Regulatory Information Server (RRID:SCR_006928) | AGRIS | data or information resource, database | An information resource of Arabidopsis promoter sequences, transcription factors and their target genes that contains three databases. *AtcisDB consists of approximately 33,000 upstream regions of annotated Arabidopsis genes (TAIR9 release) with a description of experimentally validated and predicted cis-regulatory elements. *AtTFDB contains information on approximately 1,770 transcription factors (TFs). These TFs are grouped into 50 families, based on the presence of conserved domains. *AtRegNet contains 11,355 direct interactions between TFs and target genes. They provide free download of Arabidopsis thaliana cis-regulatory database (AtcisDB) and transcription factor database (AtTFDB). | gene regulatory, gene, arabidopsis thaliana, promoter sequence, target gene, transcription factor, FASEB list |
is listed by: OMICtools has parent organization: Ohio State University; Ohio; USA |
NSF | PMID:21059685 PMID:16524982 PMID:12820902 |
Free, Acknowledgement requested | OMICS_00548, nif-0000-02540 | SCR_006928 | 2026-08-29 11:29:46 | 53 | ||||||
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EMBRYS Resource Report Resource Website 1+ mentions |
EMBRYS (RRID:SCR_006689) | EMBRYS | data or information resource, database | Data collection of gene expression patterns mapped in whole-mount mouse embryo (ICR strain) of mid-gestational stages (Embryonic Day 9.5, 10.5, 11.5), in which most striking dynamics in pattern formation and organogenesis is observed. Collection of gene expression patterns of transcription factors (TFs) and TF-related factors such as transcription cofactors. Genes were extracted from databases including RIKEN Transcription Factor Database and Panther Classification System. | Gene, expression, pattern, mapped, whole mount, mouse, embryo, ICR strain, mid gestational stage, transcription, factor, cofactor, data |
uses: RIKEN uses: MGC uses: PANTHER |
Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japanese Ministry of Health Labor and Welfare |
Free, Freely available | nlx_153839 | http://embrys.jp/embrys/html/MainMenu.html | SCR_006689 | Embryonic Gene Expression Database for Biomedical Research Source, Embryonic gene expression Database as a Biomedical Research Source | 2026-08-29 11:29:48 | 8 | |||||
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UniSTS Resource Report Resource Website 10+ mentions |
UniSTS (RRID:SCR_006843) | UniSTS | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences. Chromosome maps are labeled by name of the originating organism, the map title, total markers, total UniSTSs and links to view maps as well as research documents available through PubMed, another NCBI database. The search functions within UniSTS allow the user to search by gene marker, chromosome, gene symbol and gene description terms to locate markers on specified genes. A representation of the UniSTS datasets is available by ftp. NOTE: All data from this resource have been moved to the Probe database, http://www.ncbi.nlm.nih.gov/probe. You can retrieve all UniSTS records by searching the probe database using the search term unists(properties). (use brackets insead of parenthesis). Additionally, legacy data remain on the NCBI FTP Site in the UniSTS Repository (ftp://ftp.ncbi.nih.gov/pub/ProbeDB/legacy_unists). | marker, primer sequence, mapping, sequence tagged site, genomic position, gene, sequence, nucleotide, nucleotide sequence, chromosome, gold standard |
is listed by: re3data.org is related to: NCBI Probe has parent organization: NCBI |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03614 | SCR_006843 | UniSTS: Integrating Markers and Maps, NCBI UniSTS, Entrez UniSTS | 2026-08-29 11:29:53 | 41 | |||||||
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COG Resource Report Resource Website 1000+ mentions |
COG (RRID:SCR_007139) | COG, COG Cluster, COG Function, COG Pathway | data or information resource, database | A database for phylogenetic classification for proteins encoded in complete genomes. Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. Please be aware that COGs hasn't been updated in many years and will not be. | ortholog, protein, cog, conserved protein sequence, unicellular cluster, genome, order, class, phyla, eukaryotic cluster, gold standard |
is listed by: OMICtools is related to: MLTreeMap is related to: ProOpDB is related to: Conserved Domain Database has parent organization: NCBI is parent organization of: Clusters of Orthologous Groups Analysis Ontology |
PMID:12969510 PMID:9381173 |
OMICS_01688, nif-0000-02672 | SCR_007139 | COG Database, Clusters of Orthologous Groups of proteins, COGs, COGs - Clusters of Orthologous Groups of proteins, COGs - Phylogenetic classification of proteins encoded in complete genomes, COG Cluster, COG Pathway, COG Function | 2026-08-29 11:29:57 | 1278 | |||||||
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Subcellular Location Image Finder Resource Report Resource Website 1+ mentions |
Subcellular Location Image Finder (RRID:SCR_006723) | SLIF | data or information resource, database, image | SLIF finds fluorescence microscope images in on-line journal articles, and indexes them according to cell line, proteins visualized, and resolution. Images can be accessed via the SLIF Web database. SLIF takes on-line papers and scans them for figures that contain fluorescence microscope images (FMIs). Figures typically contain multiple FMIs, to SLIF must segment these images into individual FMIs. When the FMI images are extracted, annotations for the images (for instance, names of proteins and cell-lines) are also extracted from the accompanying caption text. Protein annotation are also used to link to external databases, such as the Gene Ontology DB. The more detailed process includes: segmentation of images into panels; panel classification, to find FMIs; segmentation of the caption, to find which portions of the caption apply to which panels; text-based entity extraction; matching of extracted entities to database entries; extraction of panel labels from text and figures; and alignment of the text segments to the panels. Extracted FMIs are processed to find subcellular location features (SLFs), and the resulting analyzed, annotated figures are stored in a database, which is accessible via SQL queries. | fluorescence, annotation, cell, journal, microscope, protein, subcellular, image, cell line, fluorescence microscope, information retrieval, data mining |
is listed by: Biositemaps has parent organization: Carnegie Mellon University; Pennsylvania; USA |
Commonwealth of Pennsylvania Tobacco Settlement Fund ; National Center for Integrative Biomedical Informatics ; NIGMS R01 GM078622; NIDA U54 DA021519 |
PMID:17990497 | nif-0000-10308 | SCR_006723 | SLIF - Subcellular Location Image Finder | 2026-08-29 11:29:44 | 1 | ||||||
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Musculoskeletal Transplant Foundation - MTF Resource Report Resource Website 1+ mentions |
Musculoskeletal Transplant Foundation - MTF (RRID:SCR_006684) | MTF | biomaterial supply resource, material resource, tissue bank | The Musculoskeletal Transplant Foundation is a non-profit service organization dedicated to providing quality allograft tissue through a commitment to excellence in education, research, recovery and care for recipients, donors and their families. We are a national consortium comprised of academic medical institutions, organ procurement organizations and tissue recovery organizations. MTF was created as a charitable organization with a mission that is dedicated to the needs of donors, donor families, patients and surgeons. We focus on respectful stewardship of the donated gift while advancing the science and practice of bone, ligament, cartilage and skin transplantation. Since our inception in 1987, MTF has recovered more than 60,000 donors and distributed more than 3 million grafts for transplantation. We also support research to expand the science of transplantation, and we encourage the efforts of our members and non-member clients to improve the understanding of donation and transplantation among the medical community and the public at large. Our policies are developed and implemented by MTF''''s Medical Board of Trustees, Donation Board of Trustees and Board of Directors, composed of physicians and recovery agency representatives who are dedicated to the mission of the Foundation. This fundamental commitment enables us to set and maintain the highest levels of safety assurance and quality control in all phases of our operations. |
is listed by: One Mind Biospecimen Bank Listing is parent organization of: International Institute for the Advancement of Medicine |
nlx_89982 | SCR_006684 | Musculoskeletal Transplant Foundation | 2026-08-29 11:29:51 | 1 | |||||||||
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MPact: Representation of Interaction Data at MIPS Resource Report Resource Website 1+ mentions |
MPact: Representation of Interaction Data at MIPS (RRID:SCR_006687) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. It provides a common access point to interaction resources at MIPS. It is designed to support the PSI-MI standard, for both downloading and uploading data. It provides the user with intuitive query forms to quickly retrieve the interactions of interest. Graphical representations allow an easy navigation through the protein interaction networks. |
is related to: Interaction Reference Index works with: IMEx - The International Molecular Exchange Consortium |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03164 | http://mips.gsf.de/genre/proj/mpact | SCR_006687 | Mpact | 2026-08-29 11:29:44 | 2 |
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