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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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DGIL Porcine Immunology and Nutrition Datebase Resource Report Resource Website 1+ mentions |
DGIL Porcine Immunology and Nutrition Datebase (RRID:SCR_012743) | data or information resource, database | Performs studies demonstrating the nutritional and biochemical effects of trace elements with special emphasis on chromium. Performs studies to elucidate the role of natural products in the improvement of the function of insulin with emphasis on polyphenols from tea and cinnamon. Performs studies on the role of dietary polyphenols on neuropathological changes including those associated with Alzheimers disease. The ultimate goal of the research is to prevent or alleviate early signs and symptoms of the metabolic syndrome which is important in the prevention of type 2 diabetes, cardiovascular, Alzheimers and related diseases. Our database is focused on immunologically-related genes classified under the following categories: Apoptosis CD markers Chemokines Chemokine receptors Cytokines Cytokine receptors Dendritic cell associated genes Type 1 IFN induced proteins Inflammation NFKB signaling pathway Toll receptor signaling pathway T cell activation TH1 cell development TH2 cell development Partners. Partnering with the Diet, Genomics, and Immunology Laboratory | has parent organization: U.S. Department of Agriculture | Type 2 diabetes, Diabetes, Cardiovasculat disease, Alzheimer's disease | nif-0000-30452 | SCR_012743 | SciCrunch Registry | PIN | 2026-10-17 01:33:33 | 8 | |||||||||
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FINDbase Worldwide Resource Report Resource Website 10+ mentions |
FINDbase Worldwide (RRID:SCR_012744) | data or information resource, database | 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. | genetic disorder, human mutation, inherited disorder, mutation pathogenesis, bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:findbase, nif-0000-02838 | https://bio.tools/findbase | SCR_012744 | SciCrunch Registry | FINDbase | 2026-10-17 01:34:13 | 13 | ||||||||
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VIOLIN: Vaccine Investigation and Online Information Network Resource Report Resource Website 10+ mentions |
VIOLIN: Vaccine Investigation and Online Information Network (RRID:SCR_012749) | VIOLIN | data or information resource, database | A web-based central resource that integrates vaccine literature data mining, vaccine research data curation and storage, and curated vaccine data analysis for vaccines and vaccine candidates developed against various pathogens of high priority in public health and biological safety. The vaccine data includes research data from vaccine studies using humans, natural and laboratory animals.VIOLIN extracts and stores vaccine-related, peer-reviewed papers from PubMed. Several powerful literature searching and data mining programs have been developed. These include an advanced keywords search program, a natural languagae processing (NLP) based literature retrieval program, a MeSH-based literature browser, and a literature alert program. Registered users can subscribe to our email alert service and will be notified of any newly published vaccine papers in the areas of interest. These literature mining programs are designed to help the user and VIOLIN database curators to find efficiently needed vaccine articles and sentences within full-text articles that contain searched keywords or categories.A web-based literature mining and curation system (Limix) is available for registered users/curators to search, curate, and submit structured vaccine data into the VIOLIN database. The curated vaccine-related information contains many categories such as general pathogenesis, protective immunity, vaccine preparation and characteristics, host responses including vaccination protocol and efficacy against virulent pathogen infections. All data within the database is edited manually and is derived primarily from peer-reviewed publications. The curated data is stored in a relational database and can be queried using various VIOLIN search programs. Vaccine-related pathogen and host genes are annotated and available for searchs based on a customized BLAST program. All VIOLIN data are available for download into an XML-based data exchange format.VIOLIN is designed to be a vital source of vaccine information and will provide researchers in basic and clinical sciences with curated data and bioinformatics tools to facilitate understanding and development of vaccines to fight infectious diseases. Category: Other Molecular Biology Databases Subcategory: Drugs and drug design | immunology, infectious diseases, molecular biology, pathogen, public health, vaccine | has parent organization: University of Michigan; Ann Arbor; USA | NIAID U24 AI125008 | nif-0000-03629 | SCR_012749 | SciCrunch Registry | Violin 2.0, Vaccine Investigation and Online Information Network | 2026-10-17 01:33:32 | 27 | |||||||
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RegTransBase Resource Report Resource Website 1+ mentions |
RegTransBase (RRID:SCR_013047) | data or information resource, database | It consists of two modules - a database of regulatory interactions based on literature and an expertly curated database of transcription factor binding sites. The literature based information in RegTransBase is a manually curated database of regulatory interactions in prokaryotes, captures the knowledge in published scientific literature using a controlled vocabulary. RegTransBase describes a large number of regulatory interactions reported in many organisms and contains various types of experimental data, in particular: * the activation or repression of transcription by an identified direct regulator * determining the transcriptional regulatory function of a protein (or RNA) directly binding to DNA or RNA * mapping or prediction of binding sites for a regulatory protein * characterization of regulatory mutations The analysis section of RegtransBase is based on a set of manually curated alignments of transcription factor binding sites and allows you to search for new binding sites and verify conservation of bindings sites across multiple species through the use of web based analysis tools. | nif-0000-03398 | SCR_013047 | SciCrunch Registry | RegTransBase | 2026-10-17 01:33:32 | 6 | |||||||||||
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GABI-KAT Resource Report Resource Website 50+ mentions |
GABI-KAT (RRID:SCR_012751) | data or information resource, database | GABI-Kat is a database of flanking sequence tags (FSTs) from T-DNA mutagenised A. thaliana plants. Over time, an increasing number of lines will become available from NASC. The "show sequence" page of SimpleSearch will display if a GABI-Kat line for a given FST has already been donated to NASC. Lines that have so far not been regrown and confirmed are only available from GABI-Kat directly. We have used four vectors: pAC106 (GenBank:AJ537513), pAC161 (GenBank:AJ537514), pGABI1 (GenBank:AY529716) and pADIS1 (GenBank:AY529717). Sequence and overview map data of all vectors are available from the download page. Features of interest which are not included in the map should be deduced from the sequence. For a specified line, the vector is displayed in the "Show Sequence" page of SimpleSearch. | a. thaliana, a. thaliana genome, mutagen, plant genome, FASEB list | has parent organization: Bielefeld University; North Rhine-Westphalia; Germany | nif-0000-02865 | SCR_012751 | SciCrunch Registry | GABI-KAT | 2026-10-17 01:35:05 | 56 | |||||||||
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Comparative Fungal Genomics Platform Resource Report Resource Website 10+ mentions |
Comparative Fungal Genomics Platform (RRID:SCR_012910) | data or information resource, database |
The CFGP (Comparative Fungal Genomics Platform) was designed for comparative genomics projects with diverse fungal genomes. The CFGP provides important bioinformatic tools, such as BLAST search, ClustalW analysis, InterPro Scan, SignalP, and PSORT2, which are very common tools for the researchers in the field of genomics. Many of them have been executed in the unix environment, so some specific computing knowledge is required. In the CFGP, users can use these tools simply by clicking their mouse button. In addition, all of the results of the analysis will be stored in the CFGP, so you can easily share those results with other members. |
fungal genome, comparative genomics, genomics | has parent organization: Seoul National University; Seoul; South Korea | nif-0000-02653 | http://cfgp.snu.ac.kr | SCR_012910 | SciCrunch Registry | CFGP | 2026-10-17 01:35:07 | 23 | ||||||||
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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 | SciCrunch Registry | 2026-10-17 01:33:32 | 135 | |||||||||
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CancerResource Resource Report Resource Website 1+ mentions |
CancerResource (RRID:SCR_011945) | data or information resource, database | 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. | compound, drug, target gene, cancer relevant proteins, compound interactions, drug-target relationships, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Cancer | DFG ; European Union ; Federal Ministry of Education and Research BMBF ; International Research Training Group IRTG |
PMID:20952398 | Free, Freely available | biotools:cancerresource, OMICS_01576 | https://bio.tools/cancerresource | http://bioinf-data.charite.de/cancerresource/index.php?site=home | SCR_011945 | SciCrunch Registry | 2026-10-17 01:33:31 | 5 | ||||
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Blue Collar Bioinformatics Resource Report Resource Website 1+ mentions |
Blue Collar Bioinformatics (RRID:SCR_012913) | Blue Collar Bioinformatics | blog, data or information resource, narrative resource | This blog will appeal to those dealing with the practical day to day work of biological data analysis and presentation. | is listed by: OMICtools | OMICS_01712 | SCR_012913 | SciCrunch Registry | 2026-10-17 01:34:13 | 1 | ||||||||||
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NHLBI Exome Sequencing Project (ESP) Resource Report Resource Website 1000+ mentions |
NHLBI Exome Sequencing Project (ESP) (RRID:SCR_012761) | EVS | data or information resource, database | 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 | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
NHLBI | biotools:esp, nlx_156901, biotools:exome_variant_server | https://bio.tools/esp, https://bio.tools/exome_variant_server | SCR_012761 | SciCrunch Registry | Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP) | 2026-10-17 01:33:32 | 2231 | ||||||
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PhenomicDB Resource Report Resource Website 10+ mentions |
PhenomicDB (RRID:SCR_013051) | PhenomicDB | data or information resource, database | PhenomicDB is a multi-organism phenotype-genotype database including human, mouse, fruit fly, C.elegans, and other model organisms. The inclusion of gene indices (NCBI Gene) and orthologs (same gene in different organisms) from HomoloGene allows to compare phenotypes of a given gene over many organisms simultaneously. PhenomicDB contains data from publicly available primary databases: FlyBase, Flyrnai.org, WormBase, Phenobank, CYGD, MatDB, OMIM, MGI, ZFIN, SGD, DictyBase, NCBI Gene, and HomoloGene. We brought this wealth of data into a single integrated resource by coarse-grained semantic mapping of the phenotypic data fields, by including common gene indexes (NCBI Gene), and by the use of associated orthology relationships (HomoloGene). PhenomicDB is thought as a first step towards comparative phenomics and will improve the understanding of the gene functions by combining the knowledge about phenotypes from several organisms. It is not intended to compete with the much more dedicated primary source databases but tries to compensate its partial loss of depth by linking back to the primary sources. The basic functional concept of PhenomicDB is an integrated meta-search-engine for phenotypes. Users should be aware that comparison of genotypes or even phenotypes between organisms as different as yeast and man can have serious scientific hurdles. Nevertheless finding that the phenotype of a given mouse gene is described as ��similar to psoriasis�� and at the same time that the human ortholog has been described as a gene causing skin defects can lead to novelty and interesting hypotheses. Similarly, a gene involved in cancer in mammalian organisms could show a proliferation phenotype in a lower organism such as yeast and thus, give further insights to a researcher. | phenotype, human, mouse, drosophila, caenorhabditis elegans, dictyostelium discoideum, yeast, zebrafish | PMID:20562418 | nif-0000-03274 | SCR_013051 | SciCrunch Registry | 2026-10-17 01:35:08 | 10 | |||||||||
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ComiR Resource Report Resource Website 10+ mentions |
ComiR (RRID:SCR_013023) | ComiR | analysis service resource, data analysis service, production service resource, service resource | Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data. | mirna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Pittsburgh; Pennsylvania; USA |
NLM ; Fondazione RiMED |
PMID:23703208 PMID:23284279 |
Acknowledgement requested | OMICS_00395, biotools:comir | https://bio.tools/comir | SCR_013023 | SciCrunch Registry | Combinatorial miRNA targeting, ComiR: Combinatorial miRNA target prediction tool, ComiR - Combinatorial miRNA target prediction tool | 2026-10-17 01:35:08 | 26 | ||||
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CoMet Resource Report Resource Website 500+ mentions |
CoMet (RRID:SCR_011925) | CoMet | analysis service resource, data analysis service, production service resource, service resource | A web-server for fast comparative functional profiling of metagenomes. | is listed by: OMICtools | OMICS_01477 | SCR_011925 | SciCrunch Registry | CoMet - a web-server for fast comparative functional profiling of metagenomes | 2026-10-17 01:35:02 | 991 | |||||||||
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Retinal Information Network Resource Report Resource Website 10+ mentions |
Retinal Information Network (RRID:SCR_012733) | data or information resource, database | RetNet provides tables of genes and loci causing inherited retinal diseases, such as retinitis pigmentosa, macular degeneration and Usher syndrome, and related information. This information is provided to the research community and other interested individuals for research purposes only. The information should not be used for medical or commercial purposes. Although we strive for accuracy and completeness, we cannot guarantee that all information is correct and complete. We welcome comments and suggestions! | has parent organization: University of Texas System; Texas; USA | nif-0000-31454 | SCR_012733 | SciCrunch Registry | RetNet | 2026-10-17 01:33:32 | 34 | ||||||||||
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AU-RICH ELEMENT-CONTAINING mRNA DATABASE Resource Report Resource Website 10+ mentions |
AU-RICH ELEMENT-CONTAINING mRNA DATABASE (RRID:SCR_012978) | data or information resource, database | The ARE-mRNA database (ARED) reveals that ARE-mRNAs encode a wide repertoire of functionally diverse proteins belonging to different biological processes and important in several disease states. Cluster analysis was performed using the ARE sequences to demonstrate potential relationships between the type and number of ARE motifs, and the functional characteristics of the proteins. Sponsors: This database is supported by The King Faisal Specialist Hospital and Research Center. Keywords: mRNA, Database, Au-rich, Element, Biological, Disease, State, Cluster, Analysis, Motif, Functional, Characterstic, Protein, | nif-0000-30039 | SCR_012978 | SciCrunch Registry | ARE Datebase | 2026-10-17 01:34:14 | 23 | |||||||||||
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European ribosomal RNA database Resource Report Resource Website 500+ mentions |
European ribosomal RNA database (RRID:SCR_012735) | data or information resource, database | Database compiles all complete or nearly complete SSU (small subunit) and LSU (large subunit) ribosomal RNA sequences. Sequences are provided in aligned format. Alignment takes into account secondary structure information derived by comparative sequence analysis of thousands of sequences. Additional information such as literature references, taxonomy, secondary structure modles and nucleotide variability maps, is also available. | ribosomal RNA sequences, small subunit, large subunit, aligned format sequences, literature references, taxonomy, secondary structure modles, nucleotide variability maps, |
is related to: SILVA has parent organization: Ghent University; Ghent; Belgium |
Free, Freely available | nif-0000-02820 | http://www.psb.ugent.be/rRNA/ | SCR_012735 | SciCrunch Registry | European ribosomal RNA database, SILVA rRNA database, SILVA - high quality ribosomal RNA databases | 2026-10-17 01:34:13 | 654 | |||||||
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PhyloPythiaS Resource Report Resource Website 10+ mentions |
PhyloPythiaS (RRID:SCR_011923) | PPS | analysis service resource, data analysis service, production service resource, service resource | Web Server for Taxonomic Assignment of Metagenome Sequences that is a fast and accurate sequence composition-based classifier that utilizes the hierarchical relationships between clades. Taxonomic assignments with the web server can be made with a generic model, or with sample-specific models that users can specify and create. Several interactive visualization modes and multiple download formats allow quick and convenient analysis and downstream processing of taxonomic assignments. | metagenome, sequence, taxonomy, classification | is listed by: OMICtools | PMID:22745671 PMID:21358620 |
OMICS_01460 | http://phylopythias.cs.uni-duesseldorf.de/index.php?phase=wait | SCR_011923 | SciCrunch Registry | 2026-10-17 01:33:31 | 12 | |||||||
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SWISS-MODEL Repository Resource Report Resource Website 100+ mentions |
SWISS-MODEL Repository (RRID:SCR_013032) | data or information resource, database | Database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL. | protein structure, structural homology, model |
is listed by: 3DVC has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: University of Basel; Basel; Switzerland is provided by: SWISS-MODEL |
nif-0000-03522, r3d100010605 | SCR_013032 | SciCrunch Registry | SWISS-MODEL Repository | 2026-10-17 01:33:33 | 331 | |||||||||
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Replication Domain Resource Report Resource Website 10+ mentions |
Replication Domain (RRID:SCR_012941) | data or information resource, database | ReplicationDomain is an online database resource for storing, sharing and visualizing DNA replication timing and transcription data, as well as other numerical epigenetic data types. Data is typically obtained from DNA microarrays or DNA sequencing. Our site has a user registration system that allows registered users to upload their own data sets. While non-registered users may freely view and download public data sets, registered users may upload their own data sets and view them privately, share them with other registered users, or make published data sets publicly available. In addition we have implemented additional mechanisms that allow users to restrict sharing of data sets to a user designated group of registered users. Further details on the database usage are in the User Guide Page, while data set details are in the Documentation Page. Replication timing data were obtained by hybridizing early and late replication intermediates to Nimblegen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early and late stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. After unbiased amplification of recovered DNA, the samples are differentially labeled with Cy3 and Cy5 and hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 5.8 kb across the mouse genome (Nimblegen, 2006-07-26_MM8_WG_CGH). Raw data from two independent biological replicates in which the early and late replicating DNA were labeled reciprocally with Cy3 and Cy 5 (dye switch) are loess-normalized and scaled to have the same median-absolute deviation using the limma package (R/Bioconductor) and then averaged. Finally, the data are smoothed with a weighted moving average (loess: local polynomial smoothing). | nif-0000-31444 | SCR_012941 | SciCrunch Registry | Replication Domain | 2026-10-17 01:33:32 | 20 | |||||||||||
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University of Pittsburgh, Health Sciences Library System Resource Report Resource Website 10+ mentions |
University of Pittsburgh, Health Sciences Library System (RRID:SCR_011975) | HSLS | data or information resource, database | Database access to information services, educational opportunities, and resources in print and electronic format to faculty, students, and researchers in the schools of the health sciences. | journal, book, video |
is listed by: OMICtools has parent organization: University of Pittsburgh; Pennsylvania; USA |
PMID:17108360 | SCR_011975 | SciCrunch Registry | Pitt Health Sciences Library System, Pitt HSLS, Health Sciences Library System | 2026-10-17 01:34:13 | 10 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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