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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | Combinatorial miRNA targeting, ComiR: Combinatorial miRNA target prediction tool, ComiR - Combinatorial miRNA target prediction tool | 2026-09-12 01:02:09 | 26 | ||||
|
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 | CoMet - a web-server for fast comparative functional profiling of metagenomes | 2026-09-12 01:02:07 | 991 | |||||||||
|
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 | RetNet | 2026-09-12 01:02:08 | 34 | ||||||||||
|
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 | ARE Datebase | 2026-09-12 01:02:09 | 23 | |||||||||||
|
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 | European ribosomal RNA database, SILVA rRNA database, SILVA - high quality ribosomal RNA databases | 2026-09-12 01:02:08 | 654 | |||||||
|
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 | 2026-09-12 01:02:07 | 12 | |||||||
|
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 | SWISS-MODEL Repository | 2026-09-12 01:02:09 | 331 | |||||||||
|
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 | Replication Domain | 2026-09-12 01:02:08 | 20 | |||||||||||
|
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 | Pitt Health Sciences Library System, Pitt HSLS, Health Sciences Library System | 2026-09-12 01:02:07 | 10 | ||||||||
|
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 | 2026-09-12 01:02:07 | 10 | ||||||
|
NCL Resource - A gateway for Batten disease Resource Report Resource Website 10+ mentions |
NCL Resource - A gateway for Batten disease (RRID:SCR_012826) | data or information resource, database | It serves as a gateway for clinicians, families and researchers who have an interest in or are affected by Batten disease or who wish to find out more. Information can be accessed via four main routes - Clinicians, Families, Researchers, Professional Support. The Clinical route describes Batten disease and includes details on diagnosis and diagnostic services. The Family route also describes Batten disease and lists support groups. The Research route includes the NCL Mutation Database, established in 1998, and other useful information. The Professional Support route includes details of coordinated initiatives to support those affected by Batten disease. A fifth route, Research Consortia, serves to meet research needs and currently act as a focus for collaborative efforts to identify the remaining human and animal NCL genes and facilitate functional approaches. An additional route, Creativity, has been launched to display creative items from families with Batten disease, and to celebrate life, in both its fullness and fragility. | FASEB list | has parent organization: University College London; London; United Kingdom | nif-0000-03182 | SCR_012826 | NCL Resource | 2026-09-12 01:02:08 | 34 | |||||||||
|
NASCs International Affymetrix Service Resource Report Resource Website 10+ mentions |
NASCs International Affymetrix Service (RRID:SCR_012825) | data or information resource, database | The NASC International Affymetrix Service is a commercial website that provides transcripomics services for a fee. This data is available for any available species, any consortium chip, and any kind of experiment. The website also provides open source and free Xspecies software and techniques that can be (examples) used to perform GeneChip transcriptomics experiments on species for which no current Affymetrix chip exists. | FASEB list | nif-0000-03176 | SCR_012825 | NASCarrays | 2026-09-12 01:02:08 | 44 | ||||||||||
|
HealthNewsReview Blog Resource Report Resource Website |
HealthNewsReview Blog (RRID:SCR_012791) | blog, data or information resource, narrative resource | Health News Review Blog: Gary Schwitzer Blog on recent biomedical studies | nlx_78805 | SCR_012791 | Health News Review Blog | 2026-09-12 01:02:08 | 0 | |||||||||||
|
gsGator Resource Report Resource Website |
gsGator (RRID:SCR_012035) | gsGator | analysis service resource, data analysis service, production service resource, service resource | A web-based platform for functional interpretation of gene sets with features such as cross-species Gene Set Analysis (GSA), Flexible and Interactive GSA, simultaneous GSA for multiple gene set, and and a fully integrated network viewer for both visualizing GSA results and molecular networks. | linux, windows, gene, orthology, pathway, phenotype, mirna target, molecular network, genomic annotation, function |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Ewha Womans University; Seoul; South Korea |
PMID:24423189 | Free, Public | OMICS_02233 | SCR_012035 | 2026-09-12 01:02:08 | 0 | |||||||
|
Material Safety Data Sheets for Infectious Substances of Canada Resource Report Resource Website |
Material Safety Data Sheets for Infectious Substances of Canada (RRID:SCR_013003) | MSDS Canada | data or information resource, database | Material Safety Data Sheets for chemical products are available to laboratory workers for most chemicals and reagents. However because many laboratory workers, whether in research, public health, teaching, etc., are exposed to not only chemicals but infectious substances as well, there was a large gap in the readily available safety literature for employees. These MSDS are produced for personnel working in the life sciences as quick safety reference material relating to infectious micro-organisms. The MSDS are organized to contain health hazard information such as infectious dose, viability (including decontamination), medical information, laboratory hazard, recommended precautions, handling information and spill procedures. The intent of these documents is to provide a safety resource for laboratory personnel working with these infectious substances. Because these workers are usually working in a scientific setting and are potentially exposed to much higher concentrations of these human pathogens than the general public, the terminology in these MSDS is technical and detailed, containing information that is relevant specifically to the laboratory setting. It is hoped along with good laboratory practices, these MSDS will help provide a safer, healthier environment for everyone working with infectious substances. The MSDS is ran by the Public Health Agency of Canada. The Public Health Agency of Canada (PHAC) is the main Government of Canada agency responsible for public health in Canada. PHACs primary goal is to strengthen Canadas capacity to protect and improve the health of Canadians and to help reduce pressures on the health-care system. To do this, the Agency is working to build an effective public health system that enables Canadians to achieve better health and well-being in their daily lives by promoting good health, helping prevent and control chronic diseases and injury, and protecting Canadians from infectious diseases and other threats to their health. PHAC is also committed to reducing health disparities between the most advantaged and disadvantaged Canadians. Because public health is a shared responsibility, the Public Health Agency of Canada works in close collaboration with all levels of government (provincial, territorial and municipal) to build on each others skills and strengths. The Agency also works closely with non-government organizations, including civil society and business, and other countries and international organizations like the World Health Organization (WHO) to share knowledge, expertise and experiences. | chemical, chronic, decontamination, disease, dose, hazardous, health, health-care, human, infectious, injury, laboratory, life science, material, material safety data sheet, medical, micro-organism, msds, pathogen, research, safety, substance, toxicology databases, viability | nif-0000-21275 | SCR_013003 | 2026-09-12 01:02:09 | 0 | ||||||||||
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OrthoDB Resource Report Resource Website 1000+ mentions |
OrthoDB (RRID:SCR_011980) | data or information resource, database | Database of orthologous protein coding genes across vertebrates, arthropods, fungi, basal metazoans, and bacteria. | Hierarchical catalog, ortholog, protein coding genes, mapping genomics to functional data, FASEB list |
is listed by: OMICtools has parent organization: University of Geneva; Geneva; Switzerland |
Swiss National Foundation | PMID:23180791 | Free, Freely available | OMICS_01692 | http://cegg.unige.ch/orthodb7 | SCR_011980 | OrthoDB: Database of Orthologous Groups, OrthoDB v7, OrthoDB - The Hierarchical Catalog of Orthologs, OrthoDB v10 | 2026-09-12 01:02:07 | 1143 | |||||
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Household Products Database Resource Report Resource Website 1+ mentions |
Household Products Database (RRID:SCR_013006) | data or information resource, database | A database of ingredients in brand-name household products linked to health information from Material Safety Data Sheets (MSDS) provided by manufacturers. The database is designed to help answer the following typical questions: *What are the chemical ingredients and their percentage in specific brands? *Which products contain specific chemical ingredients? *Who manufactures a specific brand? How do I contact this manufacturer? *What are the acute and chronic effects of chemical ingredients in a specific brand? *What other information is available about chemicals in the toxicology-related databases of the National Library of Medicine? NLM and its Contractor (the Database Providers) do not test products nor investigate to determine if this information is complete or accurate. | drug, chemical, consumer, health, toxicology, toxicology databases | has parent organization: National Library of Medicine | National Center for Environmental Health of the Centers for Disease Control and Prevention | nif-0000-21198 | SCR_013006 | HPD | 2026-09-12 01:02:09 | 4 | ||||||||
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CoreGenomics Resource Report Resource Website |
CoreGenomics (RRID:SCR_011985) | CoreGenomics | blog, data or information resource, narrative resource | This blog focusses on next-generation sequencing and microarray technologies. | is listed by: OMICtools | OMICS_01713 | SCR_011985 | 2026-09-12 01:02:07 | 0 | ||||||||||
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BWH Specimen Bank Resource Report Resource Website |
BWH Specimen Bank (RRID:SCR_012316) | BWH Specimen Bank | biomaterial supply resource, material resource, tissue bank |
Core facility that provides the following services: Open repositories service, Sample processing service, Medical/pathology informatics support service, BWH tissue repository service. The Specimen Bank provides materials to investigators with IRB-approved protocols. Staff are available to assist with selection of samples appropriate for downstream applications, development of processing protocols or preparation of derivatives from clinical materials. IT Staff are also available to assist researchers with creation of queries for prospective sample collection or queries to select samples from specific cohorts. Their goal is to drive quality research in an efficient and cost-effective manner. Each year they provide tens of thousands of samples to area researchers. Getting started: Partners investigators and study staff may request a Crimson user account to help manage studies and collected materials. |
clinical sample processing, clinical sample, clinical study management tool, clinical testing service, diagnostics development, microbial isolates service, tissue procurement, clinical |
is listed by: One Mind Biospecimen Bank Listing is listed by: ScienceExchange is listed by: Eagle I is listed by: Brigham and Women's Hospital Labs and Facilities |
SciEx_11650 | http://harvard.eagle-i.net/i/0000012e-5957-2b52-55da-381e80000000 | http://crimson.bwh.harvard.edu/ | SCR_012316 | Brigham and Women''''s Hospital Specimen Bank, Specimen Bank (BWH) | 2026-09-12 01:02:08 | 0 | ||||||
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Bio-IT World Resource Report Resource Website 1+ mentions |
Bio-IT World (RRID:SCR_011986) | Bio-IT World | blog, data or information resource, narrative resource | A leading source of news on technology and innovation in life sciences IT, informatics, genomics, next-gen, drug discovery, development, and clinical trials. | informatics, computer science, biomedical research, drug discovery, information technology, next-generation technology, big data, personalized medicine | is listed by: OMICtools | OMICS_01727 | SCR_011986 | Bio-ITWorld.com, Bio-ITWorld | 2026-09-12 01:02:07 | 3 |
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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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