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http://diseases.jensenlab.org/
Database that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. It also assigns confidence scores that facilitate comparison of the different types and sources of evidence.
Proper citation: DISEASES (RRID:SCR_015664) Copy
Collection of transcription factor microRNA regulations. TransmiR v2.0 manually curated TF-miRNA regulations from publications during 2013-2017 and included ChIP-seq-derived TF-miRNA regulation data.
Proper citation: TransmiR (RRID:SCR_017499) Copy
Collection of chemical compounds and associated information that were automatically extracted by text mining content of PubMed and PubChem databases. Unifies chemical lists from metabolomics, systems biology, environmental epidemiology, occupational expossure, toxiology and nutrition fields.
Proper citation: Blood Exposome Database (RRID:SCR_017610) Copy
FINDbase Worldwide is an online repository of information about the frequency of different mutations leading to inherited disorders in various populations around the globe. Frequency data about 32 disorders, 25 genes within 98 populations covering 1226 mutations is now available. 28 curators worldwide contributed to this database containing data from 37 submissions.
Proper citation: FINDbase Worldwide (RRID:SCR_012744) Copy
http://data-analysis.charite.de/care/
Comprehensive database of cancer relevant proteins and compound interactions supported by experimental knowledge.Knowledgebase for drug-target relationships related to cancer as well as for supporting information or experimental data.
Proper citation: CancerResource (RRID:SCR_011945) Copy
http://evs.gs.washington.edu/EVS/
The goal of the project is to discover novel genes and mechanisms contributing to heart, lung and blood disorders by pioneering the application of next-generation sequencing of the protein coding regions of the human genome across diverse, richly-phenotyped populations and to share these datasets and findings with the scientific community to extend and enrich the diagnosis, management and treatment of heart, lung and blood disorders. The groups participating and collaborating in the NHLBI GO ESP include: Seattle GO - University of Washington, Seattle, WA Broad GO - Broad Institute of MIT and Harvard, Cambridge, MA WHISP GO - Ohio State University Medical Center, Columbus, OH Lung GO - University of Washington, Seattle, WA WashU GO - Washington University, St. Louis, MO Heart GO - University of Virginia Health System, Charlottesville, VA ChargeS GO - University of Texas Health Sciences Center at Houston
Proper citation: NHLBI Exome Sequencing Project (ESP) (RRID:SCR_012761) Copy
http://www.ebi.ac.uk/thornton-srv/databases/MACiE/
MACiE, which stands for Mechanism, Annotation and Classification in Enzymes, is a collaborative project on enzyme reaction mechanisms. MACiE currently contains 223 fully annotated enzyme reaction mechanisms, which comprise 218 EC numbers (161 EC sub-subclasses) and 310 distinct CATH codes. It is a joint effortbetween the Mitchell Group at the Unilever Centre for Molecular Informatics part of the University of Cambridge and the Thornton Group at the European Bioinformatics Institute.
Proper citation: MACiE (RRID:SCR_013296) Copy
H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, and molecular evolutionary features , protein-protein interactions (PPIs) and gene families/groups. This database is produced by the Genome Information Integration Project (2005-) based upon the annotation technology established in the H-Invitational Project for annotation of human full-length cDNAs.
Proper citation: H-InvDB (RRID:SCR_013265) Copy
THIS RESOURCE IS NO LONGER IN SERVICE,documented on August 16, 2019. Fugu genome is among the smallest vertebrate genomes and has proved to be a valuable reference genome for identifying genes and other functional elements such as regulatory elements in the human and other vertebrate genomes, and for understanding the structure and evolution of vertebrate genomes. This site presents version 4 of the Fugu genome, released in October 2004 by the International Fugu Genome Consortium. Fugu rubripes has a very compact genome, with less than 15 consisting of dispersed repetitive sequence, which makes it ideal for gene discovery. A draft sequence of the fugu genome was determined by the International Fugu Genome Consortium in 2002 using the ''whole-genome shotgun'' sequencing strategy. Fugu is the second vertebrate genome to be sequenced, the first being the human genome. This webpage presents the annotation made on the fourth assembly by the IMCB team using the Ensembl annotation pipeline. We are continuing with the gap filling work and linking of the scaffolds to obtain super-contigs.
Proper citation: Fugu Genome Project (RRID:SCR_013014) Copy
A manually curated database of protein-protein interactions for Death Domain Superfamily. The Death Domain Database provides a detailed summary of PPI data, which fits into 3 categories: interaction, characterization, and functional role. Users can find in-depth information specified in the literature on relevant analytical methods, structural information. The DD superfamily currently comprises four subfamilies: * Death domain (DD) subfamily * Death effector domain (DED) subfamily * Caspase recruitment domain (CARD) subfamily * Pyrin domain (PYD) subfamily
Proper citation: Death Domain database (RRID:SCR_013231) Copy
http://unicarb-db.biomedicine.gu.se
An experimental glycomic MS database initially created to meet the in-house need to store structural and MS-glycomic data. Users can search by taxonomy and tissue, mass and composition, and MS/MS.
Proper citation: UniCarb-DB (RRID:SCR_014407) Copy
A genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. Organisms * Toxoplasma gondii (ME49, RH, GT1, Veg strains) * Neospora caninum * environmental isolate sequences from numerous species Tools * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Toxoplasma, Neospora Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * Ancillary Genome Browse: Access Additional info like Probeset data and Toxoplasma Array info
Proper citation: ApiDB ToxoDB (RRID:SCR_013453) Copy
The HUGE protein database has been created to publicize the Human cDNA project at the Kazusa DNA Research Institute. This project will sequence and analyze long (>4 kb) human cDNAs and establish methods by using the sequence data how to predict the primary structure of proteins of various biological activities. Currently, it focuses on the analysis of cDNA clones encoding particularly large proteins (>50 kDa). The HUGE protein database contains various types of information derived from the predicted primary structure data of newly identified human proteins. The HUGE protein database are expected to cover various sets of large human proteins of hitherto unidentified functions. They are likely to be involved in cellular structure/motility (such as cytoskeleton, membrane skeleton, and motor proteins), gene expression and nucleic acid metabolism, cell signaling/communication (such as cellular adhesion, signal transduction, channels, and receptors), and so on.
Proper citation: HUGE - Human Unidentified Gene-Encoded large proteins (RRID:SCR_013482) Copy
http://db.systemsbiology.net/kaviar/
A database containing a compilation of SNVs, indels, and complex variants observed in humans, designed to facilitate testing for the novelty and frequency of observed variants.
Proper citation: KAVIAR (RRID:SCR_013737) Copy
A database of protein disorder and mobility annotations. The database features three levels of annotation: manually curated data (which are extracted from the DisProt database), indirect data, and predicted data. Additional annotations are included from external sources, including UniProt, Pfam, PDB, and STRING.
Proper citation: MobiDB (RRID:SCR_014542) Copy
https://rtips.cancer.gov/rtips/index.do
Database of cancer control interventions and program materials. It is designed to provide program planners and public health practitioners easy and immediate access to research-tested materials.
Proper citation: Research-tested Intervention Programs (RTIPs) (RRID:SCR_016042) Copy
http://floresta.eead.csic.es/3dfootprint
Database of DNA-binding protein structures that is updated with Protein Data Bank complexes. It provides structure-based binding specificities and sequence logos, classification and clusters of protein-DNA interfaces, and downloads/stats.
Proper citation: 3D-footprint (RRID:SCR_015713) Copy
Database for the identification of the human proteome and its use across the scientific community. Users can browse proteins and chromosomes and contribute to the data repository.
Proper citation: ProteomicsDB (RRID:SCR_015562) Copy
http://amp.pharm.mssm.edu/datasets2tools/
Database for the discovery and evaluation of biomedical digital objects. It includes a wide variety of enrichment analyses, gene interaction networks, interactive data visualizations, datasets, and computational tools.
Proper citation: Datasets2Tools (RRID:SCR_016174) Copy
http://mips.gsf.de/genre/proj/mfungd
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2019.Database for annotated mouse proteins and their occurrence in protein networks. It contains cDNA and protein sequences, annotation, gene models and mapping, FunCat, UCSC Genome Viewer, SIMAP, pseudogenes (Genome Viewer Track), InterPro, and splice variants. Protein function annotation is performed using the Functional Catalogue (FunCat) annotation scheme, which is a hierarchically structured classification system. To provide up-to-date similarity search results and InterPro domain analyses, the protein entries are interconnected with the SIMAP database. The gene models are based on the RefSeq mouse cDNAs. The work of our group is focussed on the annotation of biological systems. Therefore, results from the Mammalian Protein-Protein Interaction Database and the Comprehensive Resource of Mammalian Protein Complexes are linked to the MfunGD dataset. Links to external resources are also provided. MfunGD is implemented in GenRE, a J2EE based component oriented multi-tier architecture.
Proper citation: MfunGD - MIPS Mouse Functional Genome Database (RRID:SCR_007783) Copy
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