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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
FaceBase Biorepository Resource Report Resource Website 1+ mentions |
FaceBase Biorepository (RRID:SCR_006001) | FaceBase Biorepository | biomaterial supply resource, tissue bank, material resource | THIS RESOURCE IS NO LONGER IN SERVICE,documented on January,18, 2022. FaceBase Biorepository is now collecting biological samples from people with cleft lip/palate and their family members. Information for Prospective Cases: Clefts of the lip and/or palate can be caused by a wide range of genetic, environmental and other factors. The FaceBase Biorepository will serve as a common source of both biological samples and information that can be made available to investigators trying to determine the underlying cause of these common birth defects. Genetic studies, in particular, will benefit from both family history information and having samples from affected individuals as well as their family members. DNA is the information containing molecules found in all the cells of our body and can be easily obtained from material such as blood or saliva samples. As part of the FaceBase Biorepository, we are requesting families to submit biological samples from specific family members as well as information from other family members that might be affected with either the same condition or a similar condition. The medical and family history information that is collected includes other relevant information such as exposure to possible environmental causes during pregnancy. The biorepository is managed by Nichole Nidey, a research study coordinator, and Jeff Murray, a pediatric clinical geneticist and researcher. They are available to speak with family members regarding questions they may have, including providing information about the biorepository and making arrangements for the collection of samples for those who wish to participate. All participation is voluntary. Your name or other personally identifiable information (name, address, etc) will be removed before information is placed in the biorepository. Summary data to show how the database itself has been used overall as well as updates on whether specific findings might have been made using this database will be available on the FaceBase website at www.facebase.org. A newsletter containing this information will also be given to families and referring clinicians so that they may discuss the specifics with the families if there appears to be information that might be relevant in a particular case. Families will also need to sign a consent form that has been approved by the Institutional Review Board at the University of Iowa. Also, any submitted samples or data can also be removed from the database at any time should the family no longer wish to participate. Investigators interested in requesting DNA samples or for more information, please contact cleftresearch (at) uiowa.edu, Nichole Nidey, nichole-nidey (at) uiowa.edu or (319) 353-4365, or Jeff Murray, jeff-murray (at) uiowa.edu. | birth defect, genetic, environment, gene |
is listed by: One Mind Biospecimen Bank Listing has parent organization: FaceBase |
Cleft lip, Cleft palate, Family member, Campomelic Dysplasia, Chromosome Abnormality, Congenital Heart Disease, Facial clefting-Tessier Type 4, Gordon Syndrome, Hemifacial Microsomia, Idiopathic Short Stature, Marshall/Stickler, Microtia, Multiple Congenital Anomaly, Neurofibromatosis, Pierre Robin, Popliteal Pterygium Syndrome, Robinow, Downs syndrome, Townes-Brock Syndrome, Van der Woude Syndrome, Popliteal Pterygium Syndrome, Wildervanck Syndrome | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151379 | SCR_006001 | 2026-08-15 11:28:43 | 1 | |||||||
|
GoPubMed Resource Report Resource Website 10+ mentions |
GoPubMed (RRID:SCR_005823) | GoPubMed | data or information resource, service resource, database | A web server which allows users to explore PubMed search results with the Gene Ontology, a hierarchically structured vocabulary for molecular biology. GoPubMed submits a user''''s keywords to PubMed, retrieves the abstracts, detects Gene Ontology terms in the abstracts, displays the subset of Gene Ontology relevant to the original query, and allows the user to browse through the ontology displaying associated papers and their GO annotation. Platform: Online tool | other analysis, literature curation and exploration, gene ontology, pubmed, literature, bio.tools |
is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: PubMed has parent organization: Biotechnology Center of the TU Dresden |
European Union IST-2004-506779 | PMID:15980585 | Free for academic use | biotools:gopubmed, nlx_149328, OMICS_01183 | https://bio.tools/gopubmed | SCR_005823 | 2026-08-15 11:28:42 | 29 | |||||
|
GOSlimViewer Resource Report Resource Website 10+ mentions |
GOSlimViewer (RRID:SCR_005665) | GOSlimViewer | analysis service resource, service resource, data analysis service, production service resource | Service to summarize the GO function associated with a data set using prepared GO Slim sets. The input is a tab separated list of gene product IDs and GO IDs. | agriculture, browser, slimmer-type tool, gene ontology, gene, ontology, ontology or annotation browser |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: AgBase |
USDA ; Mississippi State University; Mississippi; USA ; MSU Office of Research ; MSU Bagley College of Engineering ; MSU College of College of Veterinary Medicine ; MSU Life Science and Biotechnology Institute |
PMID:17135208 PMID:16961921 |
Free for academic use | nlx_149103, OMICS_02270 | SCR_005665 | GO Slim Viewer, GOSlim Viewer | 2026-08-15 11:28:46 | 40 | |||||
|
PIPE-CLIP Resource Report Resource Website 10+ mentions |
PIPE-CLIP (RRID:SCR_005820) | PIPE-CLIP | analysis service resource, service resource, data analysis service, production service resource | A Galaxy framework-based online pipeline for reliable analysis of data generated by three types of CLIP-seq protocols: HITS-CLIP, PAR-CLIP and iCLIP. It provides both data processing and statistical analysis to determine candidate cross-linking regions, which are comparable to those regions identified from the original studies or using existing computational tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | clip-seq, python, bioinformatics, r, high-thoughput sequencing, rna-binding protein, rna |
is listed by: OMICtools is related to: Galaxy has parent organization: University of Texas Southwestern Medical Center; Texas; USA has parent organization: Google Code |
PMID:24451213 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02254 | https://github.com/QBRC/PIPE-CLIP | SCR_005820 | PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis | 2026-08-15 11:28:42 | 10 | |||||
|
Expression Profiler Resource Report Resource Website 1+ mentions |
Expression Profiler (RRID:SCR_005821) | Expression Profiler | analysis service resource, service resource, data analysis service, production service resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice. | other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, gene, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: European Bioinformatics Institute |
European Union ; Wellcome Trust ; Estonian Science Foundation 5724; Estonian Science Foundation 5722 |
PMID:15215431 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:expression_profiler, nlx_149323 | https://bio.tools/expression_profiler | SCR_005821 | Expression Profiler at the EBI | 2026-08-15 11:28:47 | 6 | ||||
|
GOChase Resource Report Resource Website 1+ mentions |
GOChase (RRID:SCR_005822) | GOChase | analysis service resource, service resource, data analysis service, production service resource | GOChase is a set of web-based utilities to detect and correct the errors in GO-based annotations. # GOChase-History resolves the whole modification history of GO IDs. # GOChase-Correct highlights merged GO IDs and redirects to the correct primary term into which the secondary ID was merged. For obsolete GO terms, the nearest non-discarded parent term is recommended by GOChase. This function may be used by GO browsers such as AmiGO and QuickGO to fix broken hyperlinks. # A whole database (such as LocusLink) as a flat file can be loaded into GOChase, reporting the annotation errors and GOChase corrections. # When one inputs a GO ID, GOChase will resolve all gene products annotated with the GO ID across all the major databases. Platform: Online tool | other analysis, historical views of go, gene ontology, annotation |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Seoul National University College of Medicine; Seoul; South Korea |
Ministry of Health and Welfare - Republic of Korea 0405-BC0206040004 | PMID:15513987 | Free for academic use | nlx_149324 | SCR_005822 | GOChase: correcting errors from gene ontology-based annotations for gene products | 2026-08-15 11:28:45 | 1 | |||||
|
NRG-CING Resource Report Resource Website 1+ mentions |
NRG-CING (RRID:SCR_006079) | NRG-CING | data or information resource, database | NRG-CING presents a complete validation report for all 9,000+ wwPDB NMR entries including remediated experimental data such as chemical shifts from BMRB and restraints from NRG . These CING reports are compiled from internal analyses and those by CCPN, DSSP, PROCHECK-NMR/Aqua, ShiftX, Talos+, Vasco, Wattos, and WHAT_CHECK. The NRG-CING website is a collection of CING reports that has been pre-calculated for all PDB files solved by NMR. (See website for more information on CING.) In case the underlying experimental data is available, these have been cleaned up and made syntactically and semantically correct and homogeneous. For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists used in the structure calculation are accessible, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. Assessment of the quality of the structural result is paramount to their usage and a combined, integrated repository of both input data and structural results greatly facilitates such an analysis. In addition, the accuracy and precision of the coordinates in these macromolecular NMR ensembles can be improved by recalculations using the available experimental data and present-day software with improved protocols and force fields. Such efforts, however, generally fail on over half of all deposited structures due to the syntactic and semantic heterogeneity of the data and the wide variety of formats used for their deposition. We have combined the cleaned-up restraints information from the NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank in the weekly updated NRG-CING database. Eleven programs, in addition to CING itself, have been included in the NRG-CING production pipeline to arrive at validation reports that list for each entry the potential inconsistencies between the coordinates and the available restraint and chemical shift data. The longitudinal validation of this data yielded a set of indicators that can be used to judge the quality of every macromolecular structure solved with NMR. The cleaned up NMR experimental datasets and the validation reports are freely available. | macromolecular structure, nmr, macromolecule, restraint, chemical shift, validation report, validation, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Worldwide Protein Data Bank (wwPDB) is related to: NMR Restraints Grid is related to: Biological Magnetic Resonance Data Bank (BMRB) has parent organization: Radboud University; Nijmegen; The Netherlands |
Netherlands Organization for Scientific Research (NWO) 700.55.443; Netherlands Bioinformatics Centre (NBIC) ; EU FP6 LSHG-CT-2005-018988; EU FP6 LHSG-CT-2004-512092; EU FP7 261572; Brussels Institute for Research and Innovation BB2B 2010-1-12; NLM LM05799 |
PMID:22139937 | Free | nlx_151486, biotools:nrg-cing | https://bio.tools/nrg-cing | SCR_006079 | 2026-08-15 11:28:46 | 1 | |||||
|
SGD Gene Ontology Slim Mapper Resource Report Resource Website 10+ mentions |
SGD Gene Ontology Slim Mapper (RRID:SCR_005784) | GO Slim Mapper | analysis service resource, service resource, data analysis service, production service resource | The GO Slim Mapper (aka GO Term Mapper) maps the specific, granular GO terms used to annotate a list of budding yeast gene products to corresponding more general parent GO slim terms. Uses the SGD GO Slim sets. Three GO Slim sets are available at SGD: * Macromolecular complex terms: protein complex terms from the Cellular Component ontology * Yeast GO-Slim: GO terms that represent the major Biological Processes, Molecular Functions, and Cellular Components in S. cerevisiae * Generic GO-Slim: broad, high level GO terms from the Biological Process and Cellular Component ontologies selected and maintained by the Gene Ontology Consortium (GOC) Platform: Online tool | gene, annotation, gene ontology, protein complex, biological process, molecular function, cellular component, gene ontology, orf, yeast, statistical analysis, slimmer-type tool, function |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: SGD |
Free for academic use | nlx_149258 | SCR_005784 | GO Term Mapper, Gene Ontology Slim Mapper | 2026-08-15 11:28:42 | 31 | |||||||
|
YanHuang Project Resource Report Resource Website 50+ mentions |
YanHuang Project (RRID:SCR_006077) | data or information resource, database | This database presents the entire DNA sequence of the first diploid genome sequence of a Han Chinese, a representative of Asian population. The genome, named as YH, represents the start of YanHuang Project, which aims to sequence 100 Chinese individuals in 3 years. It was assembled based on 3.3 billion reads (117.7Gbp raw data) generated by Illumina Genome Analyzer. In total of 102.9Gbp nucleotides were mapped onto the NCBI human reference genome (Build 36) by self-developed software SOAP (Short Oligonucleotide Alignment Program), and 3.07 million SNPs were identified. The personal genome data is illustrated in a MapView, which is powered by GBrowse. A new module was developed to browse large-scale short reads alignment. This module enabled users track detailed divergences between consensus and sequencing reads. In total of 53,643 HGMD recorders were used to screen YH SNPs to retrieve phenotype related information, to superficially explain the donor's genome. Blast service to align query sequences against YH genome consensus was also provided. | genome, genetic, adult, chromosome, clinical, control, genomic, human, normal, FASEB list | has parent organization: BGI; Shenzhen; China | nif-0000-03654 | SCR_006077 | YH1 | 2026-08-15 11:28:43 | 53 | |||||||||
|
UniParc Resource Report Resource Website 50+ mentions |
UniParc (RRID:SCR_005818) | data or information resource, database | Database that contains publicly available protein sequences with stable and unique identifiers (UPI) which are never removed, changed or reassigned. UniParc tracks sequence changes in the source databases and archives the history of all changes. Information other than protein sequence must be retrieved from the UniParc source databases using the database cross-references. | protein sequence, database, public protein sequence, gold standard, upi, unique protein identifier, identifier, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: UniProt DAS is related to: WormBase is related to: FlyBase is related to: Ensembl is related to: RefSeq has parent organization: UniProt |
Public, Entries are available for download | SCR_004769, nif-0000-03610, r3d100011519, biotools:uniparc, nlx_76940 | https://bio.tools/uniparc, https://doi.org/10.17616/R3X33B | SCR_005818 | UniProt Archive | 2026-08-15 11:28:45 | 98 | |||||||
|
TRbase: A Database Of Tandem Repeats In The Human Genome Resource Report Resource Website 1+ mentions |
TRbase: A Database Of Tandem Repeats In The Human Genome (RRID:SCR_005658) | data or information resource, database | This TRbase is a relational tandem repeat database that relates tandem repeats to gene locations and disease genes of the human genome. The TRbase stores both perfect and imperfect repeats of 1 to 2000 bp unit lengths that were identified using the Tandem Repeat Finder program. Disease information for all 24 chromosomes was retrieved from the Online Mendelian Inheritance in Man (OMIM) database. There are five main search forms by which the user may query the database: 1. The Advanced tandem repeat search: This allows a complete search for tandem repeats using a combination of criteria, such as total tandem repeat length, repeat unit length, copy number of the repeats, percentage matches and the consensus repeat pattern. On submission, the number of repeats and the detailed tandem repeat characteristics of each repeat that match the user query are tabulated. 2. The Main search: This relates tandem repeat data to genes and diseases. The user may specify a gene of interest to view details of all repeats associated with it or search for tandem repeats present in a particular disease by entering the name/keyword for the disease or the MIM number of the disease gene. 3. The Composite search: This more advanced search allows the user to query specifically for repeats present in exons, introns or intergenic regions of a gene or disease gene. 4. The Gene Search: Further information on genes can be available by a simple gene name search on this page. 5. The Disease search: This allows extensive information on disease genes on all chromosomes of the human genome. Searching for a MIM number, or keyword searches specifying the features of the disease, will retrieve the information on the disease and the chromosome in which the disease gene occurs. Each entry retrieved is linked to the OMIM database for detailed literature and gene map information on the disease. | has parent organization: University of Exeter; Exeter; United Kingdom | nif-0000-03583 | SCR_005658 | TRbase | 2026-08-15 11:28:46 | 1 | ||||||||||
|
PoSSuM Resource Report Resource Website 10+ mentions |
PoSSuM (RRID:SCR_006109) | PoSSuM | data or information resource, database | Relational database of all the discovered similar pairs in a huge number of protein-ligand binding sites with annotations of various types (e.g., CATH, SCOP, EC number, Gene ontology). They used a tremendously fast algorithm called SketchSort that enables the enumeration of similar pairs in a huge number of protein-ligand binding sites. They conducted all-pair similarity searches for 3.4 million known and potential binding sites using the proposed method and discovered over 24 million similar pairs of binding sites. PoSSuM enables rapid exploration of similar binding sites among structures with different global folds as well as similar ones. Moreover, PoSSuM is useful for predicting the binding ligand for unbound structures. Basically, the users can search similar binding pockets using two search modes: # Search K is useful for finding similar binding sites for a known ligand-binding site. Post a known ligand-binding site (a pair of PDB ID and HET code) in the PDB, and PoSSuM will search similar sites for the query site. # Search P is useful for predicting ligands that potentially bind to a structure of interest. Post a known protein structure (PDB ID) in the PDB, and PoSSuM will search similar known-ligand binding sites for the query structure. | binding site, ligand-binding site, protein function, protein, prediction, small molecule, drug discovery |
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of Tokyo; Tokyo; Japan has parent organization: National Institute of Advanced Industrial Science and Technology |
Japan Society for the Promotion of Science KAKENHI 21680025; Japan Society for the Promotion of Science KAKENHI 23500374 |
PMID:22135290 PMID:22113700 |
Freely available, Acknowledgement required | nlx_151581 | SCR_006109 | PoSSuM - POcket Similarity Search Using Multiple-Sketches, Pocket Similarity Search using Multiple-Sketches (PoSSuM), PoSSuM Database, POcket Similarity Search Using Multiple-Sketches | 2026-08-15 11:28:44 | 30 | |||||
|
Tandem Repeats Database Resource Report Resource Website 10+ mentions |
Tandem Repeats Database (RRID:SCR_005659) | TRDB | data or information resource, database | A public repository of information on tandem repeats in genomic DNA and contains a variety of tools for their analysis. These currently include the Tandem Repeats Finder algorithm, query and filtering capabilities for finding particular repeats of interest, repeat clustering algorithms based on sequence similarity, polymorphism prediction based on common patterns of mutation, PCR primer selection, and data download in a variety of formats. In addition, TRDB serves as a centralized research workbench, provides storage space for results of analysis, and permits collaborators to privately share their data and analysis. | has parent organization: Boston University; Massachusetts; USA | nif-0000-03584 | SCR_005659 | Tandem Repeats Database | 2026-08-15 11:28:44 | 14 | |||||||||
|
GO-Module Resource Report Resource Website 1+ mentions |
GO-Module (RRID:SCR_005813) | GO-Module | analysis service resource, service resource, data analysis service, production service resource | GO-Module provides an interface to reduce the dimensionality of GO enrichment results and produce interpretable biomodules of significant GO terms organized by hierarchical knowledge that contain only true positive results. Users can download a text file of GO terms annotated with their significance and identified biomodules, a network visualization of resultant GO IDs or terms in PDF format, and view results in an online table. Platform: Online tool | functional similarity, visualization, other analysis, reduce the dimensionality of go enrichment results, produce interpretable biomodules of significant go terms, gene ontology, ontology or annotation visualization, annotation |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: AmiGO has parent organization: University of Illinois at Chicago; Illinois; USA |
NIH ; Cancer Research Foundation ; NLM K22 LM008308; NCI 1U54CA121852; NCRR UL1 RR024999 |
PMID:21421553 | Free for academic use | nlx_149322 | SCR_005813 | Hierarchical optimization of enriched GO terms | 2026-08-15 11:28:42 | 3 | |||||
|
JISC Open Citations Resource Report Resource Website 10+ mentions |
JISC Open Citations (RRID:SCR_005936) | Open Citations | data or information resource, database | Database of biomedical literature citations, harvested from the reference lists of all open access articles in PubMed Central that reference ~20% of all PubMed Central papers (approx. 3.4 million papers), including all the highly cited papers in every biomedical field. All the data are freely available for download and reuse. The web site allows these bibliographic records and citations to be browsed, individual articles to be selected, and its citation network to be visualized in a variety of displays. Details of each selected reference, and the data and diagrams for its citation network, may be downloaded in a variety of formats, while the entire Open Citations Corpus can be downloaded from our source data page in several formats including RDF and BibJSON. Their aim for the future is to work with publishers to make available the reference lists from many more current and recent journal articles, starting with the biomedical literature, and to make the citations contained within them available as Open Linked Data in the manner demonstrated by the existing exemplar data available here. | biomedical, literature, citation, open access, bibliographic, rdf triplestore, biomedical literature, open linked data, reference |
is listed by: FORCE11 is related to: PubMed Central is related to: CiTO - the Citation Typing Ontology has parent organization: University of Oxford; Oxford; United Kingdom |
JISC ; jiscEXPO strand |
Creative Commons Zero License, 1.0 | nlx_151283 | SCR_005936 | 2026-08-15 11:28:47 | 13 | |||||||
|
WorfDB Resource Report Resource Website 1+ mentions |
WorfDB (RRID:SCR_006028) | data or information resource, database | Database that integrates and disseminates the data from the cloning of complete set of predicted protein-encoding ORFs of Caenorhabditis elegans. It also allows the community to search for availability and quality of cloned ORFs. So far, ORF sequence tags (OSTs) obtained for all individual clones have allowed exon structure corrections for ORFs originally predicted by the C. elegans sequencing consortium. The database contains this OST information along with data pertinent to the cloning process. | open reading frame, c elegans, orf sequence tag |
has parent organization: Dana-Farber Cancer Institute has parent organization: Harvard Medical School; Massachusetts; USA |
NIGMS ; MGRI ; NHGRI 5R01HG01715-02; NCI 7 R33 CA81658-02 |
PMID:12519990 | nif-0000-03644 | SCR_006028 | WorfDB - Worm ORF Database, Worm ORFeome DataBase, Worm ORFeome | 2026-08-15 11:28:46 | 9 | |||||||
|
Atlas of the Brain Resource Report Resource Website 1+ mentions |
Atlas of the Brain (RRID:SCR_005967) | Atlas of the Brain | data or information resource, atlas | On line labeled atlas of the human brain developed by Dr. Rand Swenson of Dartmouth Medical School. It includes gross anatomical and MRI-generated slices (Axial T1-weighted MRI and Coronal T2 MRI weighted, along with Magnetic resonance arteriogram (MRA) and Magnetic resonance venogram (MRV)images. Labels may be turned on and off. A companion on-line textbook is also available. The site says it is still under construction, although the copyright is 2009. * Atlas of Gross Brain Topography * Atlas of the Brain Stem in Cross Section * Atlas of the Brain in Axial Slices * Atlas of the Brain in Coronal Slices * Atlas of the Head in Axial Slices * Axial T1-weighted MRI * Axial T2-weighted MRI * Coronal T1 MRI * Coronal T2 MRI * Magnetic resonance arteriogram (MRA) * Magnetic resonance venogram (MRV) | brain, magnetic resonance imaging, magnetic resonance venogram, magnetic resonance arteriogram, brainstem, radiographic anatomy, axial, coronal |
is related to: Review of Clinical and Functional Neuroscience is related to: Review of Clinical and Functional Neuroscience has parent organization: Dartmouth Medical School; New Hampshire; USA |
nlx_151327 | SCR_005967 | Atlas of the Brain - Structure with functional correlates | 2026-08-15 11:28:46 | 1 | ||||||||
|
Transcription Regulatory Regions Database Resource Report Resource Website 1+ mentions |
Transcription Regulatory Regions Database (RRID:SCR_005723) | data or information resource, database | TRRD is a unique information resource, accumulating information on structural and functional organization of transcription regulatory regions of eukaryotic genes. Only experimentally confirmed information is included into TRRD. Transcription Regulatory Regions Database (TRRD) is developed for accumulation of experimental information on the structure-function features of regulatory regions of eukaryotic genes. Each entry of TRRD corresponds to a particular gene. The annotated part of an entry includes the structure-function description of gene regulatory regions composed by regulatory units (promoters, silencers, enhancers, etc.), individual transcription factor binding sites that constitute these regulatory units, and transcription factors that bind to these sites. In addition, the entry contains the gene expression patterns and references to original publications. | has parent organization: Siberian Branch of the Russian Academy of Sciences; Novosibirsk; Russia | PMID:11752324 | nif-0000-03594 | SCR_005723 | TRRD | 2026-08-15 11:28:44 | 9 | |||||||||
|
Dr.VIS - Human Disease-Related Viral Integration Sites Resource Report Resource Website 1+ mentions |
Dr.VIS - Human Disease-Related Viral Integration Sites (RRID:SCR_005965) | Dr.VIS, Dr. VIS | data or information resource, database | Dr.VIS collects and locates human disease-related viral integration sites. So far, about 600 sites covering 5 virus organisms and 11 human diseases are available. Integration sites in Dr.VIS are located against chromosome, cytoband, gene and refseq position as specific as possible. Viral-cellular junction sequences are extracted from papers and nucleotide databases, and linked to corresponding integration sites Graphic views summarizing distribution of viral integration sites are generated according to chromosome maps. Dr.VIS is built with a hope to facilitate research of human diseases and viruses. Dr.VIS provides curated knowledge of integration sites from chromosome region narrow to genomic position, as well as junction sequences if available. Dr.VIS is an open resource for free. | disease, virus, viral integration, viral integration site, integration site, malignant disease, chromosome region, genomic position, viral-host junction sequence, junction sequence, oncogene, chromosome, catalog, graphic interface, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Tongji University; Shanghai; China |
State Key Basic Research Program 973 2011CB910204; National Natural Science Foundation of China ; Major State Basic Research Development Program ; 863 Hi-Tech Program of China ; National Key Technology R&D Program in the 11th Five Year Plan of China ; Major State Basic Research Development Program of China |
PMID:22135288 | Open - Free to browse and download data in Dr.VIS. | nlx_151323, biotools:dr.vis | http://www.scbit.org/dbmi/drvis, https://bio.tools/dr.vis | SCR_005965 | Dr. VIS - Database of Human Disease-related Viral Integration Sites, Database of Human Disease-related Viral Integration Sites | 2026-08-15 11:28:48 | 1 | ||||
|
GOanna Resource Report Resource Website 10+ mentions |
GOanna (RRID:SCR_005684) | GOanna | analysis service resource, service resource, data analysis service, production service resource | GOanna is used to find annotations for proteins using a similarity search. The input can be a list of IDs or it can be a list of sequences in FASTA format. GOanna will retrieve the sequences if necessary and conduct the specified BLAST search against a user-specified database of GO annotated proteins. The resulting file contains GO annotations of the top BLAST hits. The sequence alignments are also provided so the user can use these to access the quality of the match. Platform: Online tool | agriculture, annotation, protein, ontology or annotation search engine, ontology or annotation editor |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: AgBase |
USDA ; Mississippi State University; Mississippi; USA ; MSU Office of Research ; MSU Bagley College of Engineering ; MSU College of College of Veterinary Medicine ; MSU Life Science and Biotechnology Institute |
PMID:17135208 PMID:16961921 |
Free for academic use | nlx_149139 | SCR_005684 | AgBase GOanna | 2026-08-15 11:28:46 | 17 |
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 RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID 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 RRID then you can log in from here to get additional features in RRID 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 RRID 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.
