Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Artificial Selected Proteins/Peptides Database Resource Report Resource Website 1+ mentions |
Artificial Selected Proteins/Peptides Database (RRID:SCR_007557) | ASPD | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 04, 2014. Curated database on selected from randomized pools proteins and peptides designed for accumulation of experimental data on protein functionality obtained by in vitro directed evolution methods (phage display, ribosome display, SIP etc.) ASPD is integrated by means of hyperlinks with different databases (SWISS-PROT, PDB, PROSITE, etc). The database also contains modules for pairwise correlation analysis and BLAST search. | amino acid, ligand, nucleotide sequence database, peptide, phage, protein, ribosome, transcriptional regulator site, transcription factor, blast, pairwise correlation analysis |
is listed by: 3DVC has parent organization: Siberian Branch of the Russian Academy of Sciences; Novosibirsk; Russia |
Russian Foundation for Basic Research and INTAS 00-04-49229; Russian Foundation for Basic Research and INTAS YSF 00-177 |
PMID:11752292 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02576 | http://www.sgi.sscc.ru/mgs/gnw/aspd/ | SCR_007557 | Artificial Selected Proteins Peptides Database | 2026-09-05 06:31:40 | 3 | ||||
|
Biomolecular Object Network Databank Resource Report Resource Website 10+ mentions |
Biomolecular Object Network Databank (RRID:SCR_007433) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 19,2019.BOND, which requires registration of a free account, is a resource used to perform cross-database searches of available sequence, interaction, complex and pathway information. BOND integrates a range of component databases including GenBank and BIND, the Biomolecular Interaction Network Database. BOND contains 70+ million biological sequences, 33,000 structures, 38,000 GO terms, and over 200,000 human curated interactions contained in BIND, and is open access. BOND serves the interests of the developing global interactome effort encompassing the genomic, proteomic and metabolomic research communities. BOND is the first open access search resource to integrate sequence and interaction information. BOND integrates BLAST functionality, and contains a well-documented API. BOND also stores annotation links for sequences, including links to Genome Ontology descriptions, MedLine abstracts, taxon identifiers, associated structures, redundant sequences, sequence neighbors, conserved domains, data base cross-references, Online Mendalian Inheritance in Man identifiers, LocusLink identifiers and complete genomes. BIND on BOND The Biomolecular Interaction Network Database (BIND), a component database of BOND, is a collection of records documenting molecular interactions. The contents of BIND include high-throughput data submissions and hand-curated information gathered from the scientific literature. BIND is an interaction database with three classifications for molecular associations: molecules that associate with each other to form interactions, molecular complexes that are formed from one or more interaction(s) and pathways that are defined by a specific sequence of two or more interactions.Interactions A BIND record represents an interaction between two or more objects that is believed to occur in a living organism. A biological object can be a protein, DNA, RNA, ligand, molecular complex, gene, photon or an unclassified biological entity. BIND records are created for interactions which have been shown experimentally and published in at least one peer-reviewed journal. A record also references any papers with experimental evidence that support or dispute the associated interaction. Interactions are the basic units of BIND and can be linked together to form molecular complexes or pathways. The BIND interaction viewer is a tool to visualize and analyze molecular interactions, complexes and pathways. The BIND interaction viewer uses Ontoglyphs to display information about a protein via attributes such as molecular function, biological process and sub-cellular localization. Ontoglyphs allow to graphically and interactively explore interaction networks, by visualizing interactions in the context of 34 functional, 25 binding specificity and 24 sub-cellular localization Ontoglyphs categories. We will continue to provide an open access version of BOND, providing its subscribers with free, unlimited access to a core content set. But we are confident you will soon want to upgrade to BONDplus. | gene, genes, genome, annotation, binding specificity, biological process, complex, dna, genomes, genomic, human, interaction, interactome, ligand, metabolomic, molecular, molecular complex, molecular function, molecular interaction, mouse, ontoglyphs, ontology terms, pathway, photon, protein, protein-protein interactions, proteomic, rna, sequence, structure, sub-cellular localization, taxonomy, unclassified biological entity | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00571 | SCR_007433 | BOND | 2026-09-05 06:31:39 | 17 | |||||||||
|
Alternative Splicing Database Resource Report Resource Website |
Alternative Splicing Database (RRID:SCR_007555) | data or information resource, database |
It has been established with the intention of assembling in a central, publicly accessible site information about alternatively spliced genes, their products and expression patterns. Version 2.1 of ASDB consists of two divisions, ASDB(proteins) , which contains amino acid sequences, and ASDB(nucleotides) with genomic sequences. SWISS-PROT uses two formats for description of alternative splicing Thus the protein sequences were selected from SWISS-PROT using full text search for both the words alternative splicing (usually in the CC lines) and varsplic (in the FT lines). In order to group proteins that could arise by alternative splicing of the same gene, we developed the clustering procedure. Two proteins were linked if they had a common fragment of at least 20 amino acids, and clusters were initially defined as maximum connected groups of linked proteins. It turned out that some clusters were chimeric, in the sense that they contained members of multi-gene families, but not alternatively spliced variants of one gene. Therefore the multiple alignments were subject to additional analysis aimed at detection of chimeric clusters. Each cluster is represented by multiple alignment of its members constructed using CLUSTALW. The distribution of cluster size, representation of species and other relevant statistics of ASDB(proteins) can be accessed through the links below. This processing covers the cases when alternatively spliced variants are described in separate SWISS-PROT entries. The other kinds of ASDB records, originating from the SWISS-PROT entries with the varsplic field in the feature table, usually describe the proteins that are not part of any cluster. In these cases, the information on the variable fragments of the several proteins which result from the alternative splicing of a single gene is contained in the entry itself. ASDB(proteins) entries are marked with different symbols to allow for easy differentiation among the three types: those proteins which are part of the ASDB clusters and the corresponding multialignments, those which have the information on different variants in the associated SWISS-PROT entries, and those for which the information on the variants is not available at the present time. ASDB contains internal links between entries and/or clusters, as well as external links to Medline, GenBank and SWISS-PROT entries. The ASDB(nucleotides) division was generated by collecting all GenBank entries containing the words alternative splicing and further selection of those entries that contain complete gene sequences (all CDS fields are complete, i.e. they do not have continuation signs). Sponsors: This work was supported by the Director, Office of Energy Research, Office of Biological and Environmental Research, of the US Department of Energy under Contract No. DE-ACO3-76SF00098. Additional support came from grants from the Russian Fund of Basic Research (99-04-48347), the Russian State Scientific Program Human Genome (65/99), and the Merck Genome Research Institute (244). |
exon, exon splice site, gene expression, gene structure, alternative splicing, amino acid, amino acid sequence, genomic sequence, human genome, human orf, intron, intron splice site, nucleotide, nucleotide sequence, protein, protein sequence, vertebrate genome | has parent organization: Lawrence Berkeley National Laboratory | nif-0000-02574 | http://hazelton.lbl.gov/~teplitski/alt/ | SCR_007555 | ASDB | 2026-09-05 06:31:40 | 0 | ||||||||
|
Colibri Resource Report Resource Website 100+ mentions |
Colibri (RRID:SCR_007606) | Colibri | data or information resource, database | Database dedicated to the analysis of the genome of Escherichia coli. Its purpose is to collate and integrate various aspects of the genomic information from E. coli, the paradigm of Gram-negative bacteria. Colibri provides a complete dataset of DNA and protein sequences derived from the paradigm strain E. coli K-12, linked to the relevant annotations and functional assignments. It allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.). The data contained in Colibri originates from two major sources of information, the reference genomic DNA sequence from the E. coli Genome Project and the feature annotations from the EcoGene data collection., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | dna, genome, protein, escherichia coli, escherichia coli genome, escherichia coli protein |
is related to: EcoGene has parent organization: Pasteur Institute |
CNRS ; French Ministry of Higher Education and Research |
PMID:8246843 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02676 | SCR_007606 | 2026-09-05 06:31:41 | 229 | ||||||
|
DB-PABP: a database of polyanion binding proteins Resource Report Resource Website |
DB-PABP: a database of polyanion binding proteins (RRID:SCR_007603) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. DB-PABP is an attempt to document the publicly available experimentally determined polyanion binding proteins (PABPs). The purpose of the database is to provide life scientists who are interested in PA/PABP interactions with a comprehensive data repository, as well as computer scientists with a publicly available dataset to perform knowledge discovery and datamining studies. The database is manually curated. It uses protein annotations from NCBI protein database and literature information is retrieved from PubMed. Whenever applicable, links to NCBI protein database and PubMed are provided so users may access additional information available in these public databases. | pabp, polyanion, polyanion binding protein, polyanion binding protein interaction, polyanion interactions, protein | has parent organization: University of Kansas; Kansas; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02724 | SCR_007603 | DB-PABP | 2026-09-05 06:31:41 | 0 | ||||||||
|
MIPS Ustilago maydis Database Resource Report Resource Website 1+ mentions |
MIPS Ustilago maydis Database (RRID:SCR_007563) | data or information resource, database | The MIPS Ustilago maydis Genome Database aims to present information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Ustilago maydis. The underlying sequence is the initial release of the high quality draft sequence of the Broad Institute. The goal of the MIPS database is to provide a comprehensive genome database in the Genome Research Environment in parallel with other fungal genomes to enable in depth fungal comparative analysis. The specific aims are to: 1. Generate and assemble Whole Genome Shotgun sequence reads yielding 10X coverage of the U. maydis genome 2. Integrate the genomic sequence assembly with physical maps generated by Bayer CropScience 3. Perform automated annotation of the sequence assembly 4. Align the strain 521 assembly with the FB1 assembly provided by Exelixis 5. Release the sequence assembly and results of our annotation and analysis to public Ustilago maydis is a basidiomycete fungal pathogen of maize and teosinte. The genome size is approximately 20 Mb. The fungus induces tumors on host plants and forms masses of diploid teliospores. These spores germinate and form haploid meiotic products that can be propagated in culture as yeast-like cells. Haploid strains of opposite mating type fuse and form a filamentous, dikaryotic cell type that invades plant tissue to reinitiate infection. Ustilago maydis is an important model system for studying pathogen-host interactions and has been studied for more than 100 years by plant pathologists. Molecular genetic research with U. maydis focuses on recombination, the role of mating in pathogenesis, and signaling pathways that influence virulence. Recently, the fungus has emerged as an excellent experimental model for the molecular genetic analysis of phytopathogenesis, particularly in the characterization of infection-specific morphogenesis in response to signals from host plants. Ustilago maydis also serves as an important model for other basidiomycete plant pathogens that are more difficult to work with in the laboratory, such as the rust and bunt fungi. Genomic sequence of U. maydis will also be valuable for comparative analysis of other fungal genomes, especially with respect to understanding the host range of fungal phytopathogens. The analysis of U. maydis would provide a framework for studying the hundreds of other Ustilago species that attack important crops, such as barley, wheat, sorghum, and sugarcane. Comparisons would also be possible with other basidiomycete fungi, such as the important human pathogen C. neoformans. Commercially, U. maydis is an excellent model for the discovery of antifungal drugs. In addition, maize tumors caused by U. maydis are prized in Hispanic cuisine and there is interest in improving commercial production. The complete putative gene set of the Broad Institute''s second release is loaded into the database and in addition all deviating putative genes from a putative gene set produced by MIPS with different gene prediction parameters are also loaded. The complete dataset will then be analysed, gene predictions will be manually corrected due to combined information derived from different gene prediction algorithms and, more important, protein and EST comparisons. Gene prediction will be restricted to ORFs larger than 50 codons; smaller ORFs will be included only if similarities to other proteins or EST matches confirm their existence or if a coding region was postulated by all prediction programs used. The resulting proteins will be annotated. They will be classified according to the MIPS classification catalogue receiving appropriate descriptions. All proteins with a known, characterized homolog will be automatically assigned to functional categories using the MIPS functional catalog. All extracted proteins are in addition automatically analysed and annotated by the PEDANT suite. | drug, environment, filamentous, functional, fungal, fungal genome databases, fungus, gene, genetic, basidiomycete, cell, codon, culture, dikaryotic, diploid, genome, genomic, germinate, haploid, host, human, infection, maize, mating, meiotic, model, molecular, morphogenesis, network, orf, pathogen, pathologist, phytopathogen, phytopathogenesis, plant, protein, recombination, sequence, signal, spore, strain, structure, teliospore, teosinte, tissue, tumor, ustilago maydis, virulence, yeast | nif-0000-21276 | SCR_007563 | MUMDB | 2026-09-05 06:31:40 | 9 | ||||||||||
|
Combinatorial Extension (CE) Resource Report Resource Website 1+ mentions |
Combinatorial Extension (CE) (RRID:SCR_007585) | CE | data or information resource, database | CE is a databases of alignments for all polypeptide chains. A representative set of proteins is available and kept current with the PDB, a method for calculating pairwise structure alignments. CE aligns two polypeptide chains using characteristics of their local geometry as defined by vectors between C alpha positions. Matches are termed aligned fragment pairs (AFPs). Heuristics are used in defining a set of optimal paths joining AFPs with gaps as needed. The path with the best RMSD is subject to dynamic programming to achieve an optimal alignment. For specific families of proteins additional characteristics are used to weight the alignment. Complete details are described in the paper (PDF format). Databases of alignments for all polypeptide chains and a representative set of proteins is available and kept current with the PDB | polypeptide, polypeptide chain, protein, protein alignment, protein structure |
is listed by: 3DVC is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of California at San Diego; California; USA |
nif-0000-02648 | http://cl.sdsc.edu/ce.html | SCR_007585 | Combinatorial extension | 2026-09-05 06:31:40 | 5 | |||||||
|
WU-BLAST Resource Report Resource Website 100+ mentions |
WU-BLAST (RRID:SCR_011824) | WU-BLAST | analysis service resource, data analysis service, production service resource, service resource | Tool to find regions of sequence similarity within selected protein databases quickly, with minimum loss of sensitivity. | protein, dna, rna |
is listed by: OMICtools is listed by: SoftCite has parent organization: European Bioinformatics Institute |
OMICS_01001 | SCR_011824 | 2026-09-05 06:32:01 | 135 | |||||||||
|
OMA Browser Resource Report Resource Website 10+ mentions |
OMA Browser (RRID:SCR_011978) | OMA | data or information resource, database | A database that identifies orthologs among publicly available, complete genomes. It offers a comprehensive search and numerous display options for 4.7 million proteins from 1000 species. The main features are the orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. | protein |
is listed by: OMICtools is related to: GermOnline has parent organization: ETH Zurich; Zurich; Switzerland |
PMID:21113020 PMID:17545180 |
Creative Commons Attribution-ShareAlike License, 2.5 | OMICS_01690 | SCR_011978 | Orthologous MAtrix | 2026-09-05 06:32:01 | 10 | ||||||
|
DBAli. A Database of Structure Alignments. Resource Report Resource Website |
DBAli. A Database of Structure Alignments. (RRID:SCR_013418) | data or information resource, database | DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. It is not currently being updated; however, updates should resume in the near future. All pairwise structural comparisons in DBAli have been obtained using the MAMMOTH program developed in the group of Prof. Angel R. Ortiz. All multiple structure alignments in DBAli have been obtained using the SALIGN command in MODELLER developed in the group of Prof. Andrej Sali. | protein, protein structure comparison | nif-0000-02725 | SCR_013418 | DBAli | 2026-09-05 06:32:06 | 0 | ||||||||||
|
ExTopoDB Resource Report Resource Website 1+ mentions |
ExTopoDB (RRID:SCR_013143) | ExTopoDB | data or information resource, database | A publicly accessible database of experimentally derived topological models of transmembrane proteins. It contains experimental information about the topology of 2143 transmembrane proteins. This information was collected from studies in the literature that reported the use of biochemical methods for the determination of the topology of transmembrane proteins. Each record contains unique information about the given protein, such as its sequence, cross-references to many publicly available databases worldwide, the protein''s name and organism source. The web interface of the database offers the user the ability to submit advanced queries for text search within ExTopoDB''s protein entries and there is also an interface for running BLAST against the database. Furthermore, the results of topology prediction using the HMM-TM algorithm are included for each protein in the database (unconstrained prediction) and we also incorporated the experimental information about the topology of the proteins in the HMM-TM prediction procedure, producing more reliable topology models (constrained prediction). | transmembrane protein, protein structure, topological model, blast, transmembrane, protein, model |
is listed by: 3DVC has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
PMID:20601677 | Public | nlx_151724 | SCR_013143 | 2026-09-05 06:32:04 | 2 | |||||||
|
TCMGeneDIT Resource Report Resource Website 10+ mentions |
TCMGeneDIT (RRID:SCR_013396) | data or information resource, database | TCMGeneDIT is a database system providing association information about traditional Chinese medicines (TCMs), genes, diseases, TCM effects and TCM ingredients automatically mined from vast amount of biomedical literature. Integrated protein-protein interaction and biological pathways information collected from public databases are also available. In addition, the transitive relationships among genes, TCMs and diseases could be inferred through the shared intermediates. Furthermore, TCMGeneDIT is useful in deducing possible synergistic or antagonistic contributions of the prescription components to the overall therapeutic effects. TCMGeneDIT is a unique database of various association information about TCMs. The database integrating TCMs with life sciences and biomedical studies would facilitate the modern clinical research and the understanding of therapeutic mechanisms of TCMs and gene regulations. | drug, gene, antagonistic, biomedical, clinical, disease, ingredient, interaction, life science, literature, medicine, pathway, prescription, protein, regulation, research, synergistic, therapeutic | has parent organization: National Taiwan University; Taipei; Taiwan | National Science Council Taiwan ; NTU Frontier and Innovative Research Projects NTUPFIR-96R0107 |
PMID:18854039 | nif-0000-32868 | SCR_013396 | 2026-09-05 06:32:06 | 14 | ||||||||
|
Cerebellar Development Transcriptome Database Resource Report Resource Website 1+ mentions |
Cerebellar Development Transcriptome Database (RRID:SCR_013096) | CDT-DB | atlas, data or information resource, database | Transcriptomic information (spatiotemporal gene expression profile data) on the postnatal cerebellar development of mice (C57B/6J & ICR). It is a tool for mining cerebellar genes and gene expression, and provides a portal to relevant bioinformatics links. The mouse cerebellar circuit develops through a series of cellular and morphological events, including neuronal proliferation and migration, axonogenesis, dendritogenesis, and synaptogenesis, all within three weeks after birth, and each event is controlled by a specific gene group whose expression profile must be encoded in the genome. To elucidate the genetic basis of cerebellar circuit development, CDT-DB analyzes spatiotemporal gene expression by using in situ hybridization (ISH) for cellular resolution and by using fluorescence differential display and microarrays (GeneChip) for developmental time series resolution. The CDT-DB not only provides a cross-search function for large amounts of experimental data (ISH brain images, GeneChip graph, RT-PCR gel images), but also includes a portal function by which all registered genes have been provided with hyperlinks to websites of many relevant bioinformatics regarding gene ontology, genome, proteins, pathways, cell functions, and publications. Thus, the CDT-DB is a useful tool for mining potentially important genes based on characteristic expression profiles in particular cell types or during a particular time window in developing mouse brains. | gene expression, fluorescence, function, gene, gene chip, genome, bioinformatics, brain, cell, cerebellum, development, in situ hybridization, fluroescence differential display, cerebellar development, microarray, mining, mouse, mrna, ontology, pathway, protein, rt-pcr, molecular neuroanatomy resource, transcriptiome, spatiotemporal, cdna microarray, genechip, postnatal, histochemistry, image, postnatal development |
is related to: Gene Ontology is related to: RIKEN integrated database of mammals has parent organization: RIKEN Brain Science Institute |
Brain development, Brain disorder | INCF Japan Node ; Japan Society for the Promotion of Science ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japan Science and Technology Agency |
PMID:18603407 | To be used for research and educational purposes only. Any reproduction or use for commercial purposes is prohibited without the prior express written permission of the RIKEN. | nif-0000-00008 | SCR_013096 | 2026-09-05 06:32:04 | 1 | |||||
|
Biological Interaction database for Protein-nucleic Acid Resource Report Resource Website |
Biological Interaction database for Protein-nucleic Acid (RRID:SCR_013371) | BIPA | data or information resource, database |
A database for protein-nucleic acid interaction that provides various features of protein-nucleic acid interfaces. There are 2333 protein-nucleic acid PDB complexes, 9547 SCOP domains, and 9633 domain-nucleic acid interfaces in BIPA. BIPA also provides a multiple structural alignment of representative structures at the SCOP family level using the program SALIGN, and the structural alignments were further annotated using the program JOY to detect local environments of amino acids. |
amino acid, interaction, nucleic acid, protein | has parent organization: University of Cambridge; Cambridge; United Kingdom | nif-0000-20819 | http://www-cryst.bioc.cam.ac.uk/bipa | SCR_013371 | Biological Interaction database for Protein-nucleic Acid | 2026-09-05 06:32:06 | 0 | |||||||
|
doRiNA Resource Report Resource Website 10+ mentions |
doRiNA (RRID:SCR_013222) | doRiNA | data or information resource, database | In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions. | binding site, rna binding protein, microrna, post-transcription, rna, gene, genome, mammal, population variation, gene expression, transcript, regulator, protein, binding |
is related to: UCSC Genome Browser has parent organization: Max Delbruck Center for Molecular Medicine; Berlin; Germany |
MDC Systems Biology Network ; BMBF ; Senate of Berlin; Berlin; Germany ; DFG |
PMID:22086949 | nlx_151321, r3d100011087 | SCR_013222 | 2026-09-05 06:32:05 | 15 | |||||||
|
FlyTrap- GFP Protein Trap Database Resource Report Resource Website 10+ mentions |
FlyTrap- GFP Protein Trap Database (RRID:SCR_013354) | data or information resource, database | The FlyTrap database presents the current results of large scale protein trapping screens that provide both information on which cells express each tagged gene, and subcellular localization of GFP-tagged proteins. Expression is under the control of endogenous promoter and enhancer elements, allowing for visualization of normal expression patterns. Drosophila proteins tagged with Green Fluorescent Protein (GFP) were created by insertion into genes of an artificial exon encoding GFP flanked by splice acceptor (SA) and splice donor (SD) sequences so that expression of GFP relies on splicing into mature mRNAs and in-frame fusion. | gfp-tagged protein, protein, protein trapping screen | has parent organization: Yale University; Connecticut; USA | nif-0000-02849 | SCR_013354 | FlyTrap | 2026-09-05 06:32:06 | 26 | |||||||||
|
Drosophila melanogaster Exon Database Resource Report Resource Website 1+ mentions |
Drosophila melanogaster Exon Database (RRID:SCR_013441) | DEDB | data or information resource, database | Database on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers. | exon, gene, alternative splicing, annotation, classification, cluster, domain, genome, graph, homology, protein, splicing, structure, transcript, visualize, blast |
is listed by: OMICtools is related to: FlyBase has parent organization: National University of Singapore; Singapore; Singapore |
Agency for Science Technology and Research | PMID:15581431 | nif-0000-21118, OMICS_01894 | SCR_013441 | DEDB - Drosophila melanogaster Exon Database, DEDB : Drosophila melanogaster Exon Database | 2026-09-05 06:32:07 | 2 | ||||||
|
RARTF Resource Report Resource Website 1+ mentions |
RARTF (RRID:SCR_013457) | RARTF | data or information resource, database | Database of complete sets of Arabidopsis transcription factors with a variety of information on Arabidopsis thaliana transcription factor families including: full-length cDNA sequences, Ds-tagged mutants, multiple sequences alignments of family members, phylogenic trees, functional motifs, and so on. In addition, expression profiles of all transcription factor genes are available. | transcription factor, protein, gene, microarray, expression profile |
is listed by: OMICtools is related to: InterProScan |
PMID:16769687 | Free | OMICS_00562 | SCR_013457 | RARTF: RIKEN Arabidopsis Transcription Factor database, RIKEN Arabidopsis Transcription Factor database | 2026-09-05 06:32:07 | 2 | ||||||
|
Embassy-domsearch Resource Report Resource Website |
Embassy-domsearch (RRID:SCR_016086) | software resource, software toolkit, source code | Source code for EMBOSS commands to search for protein domains. Its functions include removing redundant and fragment sequences from DHF files, generating PSI-BLAST hits (DHF file) from a DAF file, removing ambiguous classified sequences from DHF files, and generating DHF files from keyword search of UniProt. | dhf, daf, redundancy, protein, domain, psi-blast, uniprot, molecular, biology |
is used by: RAVEN is listed by: Debian |
Free, Available for download, Freely available | https://sources.debian.org/src/embassy-domsearch/ | SCR_016086 | 2026-09-05 06:32:12 | 0 | |||||||||
|
Mass Spectral Library Resource Report Resource Website 10+ mentions |
Mass Spectral Library (RRID:SCR_014668) | data or information resource, database | A library containing spectra upwards of 200,000 chemical compounds. Spectra include metabolites, peptides, contaminants, and lipids. All spectra and chemical structures are examined by professionals. | library, database, spectra, mass spectrometry, metabolomics, metabolites, protein, lipid, contaminant | is listed by: Metabolomics Workbench | Available with the NIST MS Search Program for Windows | SCR_014668 | 2026-09-05 06:32:10 | 21 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
