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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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JCVI CMR Resource Report Resource Website 10+ mentions |
JCVI CMR (RRID:SCR_005398) | JCVI_CMR, JCVI CMR, TIGR_CMR, TIGR CMR | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | Database of all of the publicly available, complete prokaryotic genomes. In addition to having all of the organisms on a single website, common data types across all genomes in the CMR make searches more meaningful, and cross genome analysis highlight differences and similarities between the genomes. CMR offers a wide variety of tools and resources, all of which are available off of our menu bar at the top of each page. Below is an explanation and link for each of these menu options. * Genome Tools: Find organism lists as well as summary information and analyses for selected genomes. * Searches: Search CMR for genes, genomes, sequence regions, and evidence. * Comparative Tools: Compare multiple genomes based on a variety of criteria, including sequence homology and gene attributes. SNP data is also found under this menu. * Lists: Select and download gene, evidence, and genomic element lists. * Downloads: Download gene sequences or attributes for CMR organisms, or go to our FTP site. * Carts: Select genome preferences from our Genome Cart or download your Gene Cart genes. The Omniome is the relational database underlying the CMR and it holds all of the annotation for each of the CMR genomes, including DNA sequences, proteins, RNA genes and many other types of features. Associated with each of these DNA features in the Omniome are the feature coordinates, nucleotide and protein sequences (where appropriate), and the DNA molecule and organism with which the feature is associated. Also available are evidence types associated with annotation such as HMMs, BLAST, InterPro, COG, and Prosite, as well as individual gene attributes. In addition, the database stores identifiers from other centers such as GenBank and SwissProt, as well as manually curated information on each genome or each DNA molecule including website links. Also stored in the Omniome are precomputed homology data, called All vs All searches, used throughout the CMR for comparative analysis. | microbial, prokaryotic, genome, annotation, dna sequence, protein, rna gene, blast, FASEB list |
is used by: NIF Data Federation is related to: AmiGO has parent organization: J. Craig Venter Institute is parent organization of: JCVI GenProp |
NSF ; NIAID ; DOE |
Free | nif-0000-03555 | SCR_005398 | JCVI Comprehensive Microbial Resource, J. Craig Venter Institute Comprehensive Microbial Resource, CMR, Comprehensive Microbial Resource | 2026-07-28 09:41:22 | 37 | ||||||
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EVidenceModeler Resource Report Resource Website 1000+ mentions |
EVidenceModeler (RRID:SCR_014659) | EVM | software application, data analysis software, sequence analysis software, software resource, data processing software | Software tool for automated eukaryotic gene structure annotation that reports eukaryotic gene structures as weighted consensus of all available evidence. Used to combine ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. Inputs include genome sequence, gene predictions, and alignment data (in GFF3 format). | sequence analysis software, framework, ab intio gene, gene prediction, protein alignment, transcript alignment, consensus gene structure | NIAID N01 AI30071; NLM R01 LM006845 |
PMID:18190707 | Free, Available for download, Freely available | SCR_017649 | SCR_014659 | 2026-07-28 09:43:30 | 1135 | |||||||
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NIAID Overview of Coronaviruses Resource Report Resource Website 1+ mentions |
NIAID Overview of Coronaviruses (RRID:SCR_018290) | funding resource, data or information resource, topical portal, portal | Information about coronaviruses, including COVID-19. NIAID provides research funding and resources for scientific community to facilitate development of vaccines, therapeutics, and diagnostics for infectious diseases, including those caused by coronaviruses. | Coronavirus, COVID-19, data, infectious disease, NIAID |
is listed by: Data and Computational Resources to Address COVID-19 is related to: NIAID |
COVID-19 | NIAID | Free, Freely available | SCR_018290 | 2026-07-28 09:44:39 | 3 | ||||||||
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CytoMAP Resource Report Resource Website 10+ mentions |
CytoMAP (RRID:SCR_021227) | software application, data analysis software, software resource, data processing software, data analytics software, software toolkit | Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information. | Histo cytometric multidimensional, analysis pipeline, whole tissue sections, spatial analysis, single cell data with position information, phenotype local neighborhoods, global tissue architecture | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | NIAID R01 AI134713; NIAID R21 AI142667; NIAID R01 AI134246; NIAID R01 AI076327; NIAID U19 AI135976; NIAID T32 AI10667; NIGMS T32 GM007270; NICHD T32 HD007233; NSF DGE 1762114 |
PMID:32320656 | Free, Available for download, Freely available | SCR_021227 | Histo-Cytometric Multidimensional Analysis Pipeline | 2026-07-28 09:45:08 | 22 | |||||||
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SpiecEasi Resource Report Resource Website 10+ mentions |
SpiecEasi (RRID:SCR_022712) | SpiecEasi | software application, software resource, data analysis software, data processing software | Software R package for microbiome network analysis. Used for inference of microbial ecological networks from amplicon sequencing datasets. Combines data transformations developed for compositional data analysis with graphical model inference framework that assumes underlying ecological association network is sparse. | microbiome network analysis, amplicon sequencing datasets, microbial ecological networks inference | NIAID AI007180; NIDDK DK103358; NIGMS GM63270; Simons Foundation |
PMID:25950956 | Free, Available for download, Freely available | SCR_022712 | SParse InversE Covariance Estimation for Ecological Association Inference | 2026-07-28 09:45:45 | 15 | |||||||
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Clinical Trials in Organ Transplantation (CTOT) Resource Report Resource Website 1+ mentions |
Clinical Trials in Organ Transplantation (CTOT) (RRID:SCR_015859) | CTOT | project portal, data or information resource, organization portal, consortium, portal | Project portal for a cooperative research program to improve short and long-term graft and patient survival. CTOT is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for transplant recipients. | graft, graft patient, patient survival, clinical study, transplant, transplant recipient, mechanistic study |
is listed by: NIDDK Information Network (dkNET) is listed by: Diabetes Research Centers is related to: Clinical Trials in Organ Transplantation in Children (CTOT-C) |
NIAID UM2 AI117870 | Public, Available to the scientific community | SCR_015859 | Clinical Trials in Organ Transplantation | 2026-07-28 09:44:09 | 1 | |||||||
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Clinical Trials in Organ Transplantation in Children (CTOT-C) Resource Report Resource Website 1+ mentions |
Clinical Trials in Organ Transplantation in Children (CTOT-C) (RRID:SCR_015860) | CTOT-C | project portal, data or information resource, organization portal, consortium, portal | Project portal for a cooperative research program sponsored by the National Institute of Allergy and Infectious Diseases (NIAID). CTOT-C is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for pediatric heart, lung, or kidney transplant recipients. | heart, kidney, lung, pediatric, cooperative research program, niaid, clinical study, mechanistic study, transplant |
is listed by: NIDDK Information Network (dkNET) is related to: Clinical Trials in Organ Transplantation (CTOT) |
NIAID UM2 AI117870 | Public, Available to the scientific community | SCR_015860 | NIAID Clinical Trials in Organ Transplantation in Children, Clinical Trials in Organ Transplantation in Children, NIAID CTOT-C | 2026-07-28 09:43:59 | 1 | |||||||
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Center for Expanded Data Annotation and Retrieval Resource Report Resource Website 1+ mentions |
Center for Expanded Data Annotation and Retrieval (RRID:SCR_016269) | CEDAR | data or information resource, organization portal, ontology, controlled vocabulary, portal | Develops information technologies that make authoring complete metadata more manageable. Its products aim to facilitate using the metadata in further research.Center to improve metadata and its use throughout biomedical sciences. Develops information technologies that make authoring complete metadata more manageable through better interfaces, terminology, metadata practices, and analytics. Optimizes metadata pathway from provider to end user. Provides way for funders to specify what metadata they want to collect as part of research life cycle. | Metadata, interface, metadata practice, analytics, metadata pathway, funded research, data repository, data collection, |
is related to: Stanford University; Stanford; California is related to: Yale University; Connecticut; USA is related to: University of Oxford; Oxford; United Kingdom has parent organization: Stanford Center for Biomedical Informatics Research is parent organization of: CEDAR Workbench |
NIAID U54 AI117925 | SCR_018150 | https://more.metadatacenter.org/ | SCR_016269 | 2026-07-28 09:44:09 | 4 | |||||||
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UniProt Resource Report Resource Website 10000+ mentions |
UniProt (RRID:SCR_002380) | UniProt | data or information resource, database | Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB. | collection, protein, sequence, annotation, data, functional, information |
is used by: LIPID MAPS Proteome Database is used by: ChannelPedia is used by: Open PHACTS is used by: DisGeNET is used by: Smart Dictionary Lookup is used by: MitoMiner is used by: Cytokine Registry is used by: MobiDB is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: Phospho.ELM is used by: GEROprotectors is used by: SwissLipids is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: LabWorm is related to: Clustal W2 is related to: UniProt DAS is related to: UniParc at the EBI is related to: ProDom is related to: LegumeIP is related to: Pathway Commons is related to: NIH Data Sharing Repositories is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: 3D-Interologs is related to: Biomine is related to: EBIMed is related to: STOP is related to: Coremine Medical is related to: BioExtract is related to: STRAP is related to: GOTaxExplorer is related to: GoAnnotator is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures is related to: Whatizit is related to: MOPED - Model Organism Protein Expression Database is related to: Polbase is related to: PredictSNP is related to: PSICQUIC Registry is related to: IntAct is related to: p300db is related to: UniProt Proteomes is related to: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation has parent organization: European Bioinformatics Institute has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: Protein Information Resource is parent organization of: UniProtKB is parent organization of: NEWT is parent organization of: UniParc is parent organization of: UniProt Chordata protein annotation program is parent organization of: UniRef works with: Genotate works with: CellPhoneDB works with: MOLEonline works with: MiMeDB |
NHGRI U41 HG006104; NHGRI P41 HG02273; NIGMS 5R01GM080646; NIGMS R01 GM080646; NLM G08 LM010720; NCRR P20 RR016472; NSF DBI-0850319; British Heart Foundation ; NEI ; NHLBI ; NIA ; NIAID ; NIDDK ; NIMH ; NCI ; EMBL ; PDUK ; ARUK ; NHGRI U24 HG007722 |
PMID:19843607 PMID:18836194 PMID:18045787 PMID:17142230 PMID:16381842 PMID:15608167 PMID:14681372 |
nif-0000-00377, SCR_018750, r3d100010357 | http://www.ebi.uniprot.org, http://www.uniprot.org/uniprot/, http://www.pir.uniprot.org, ftp://ftp.uniprot.org, https://doi.org/10.17616/R3BW2M | SCR_002380 | , The Universal Protein Resource, Universal Protein Resource, UNIPROT Universal Protein Resource | 2026-07-28 09:40:24 | 17565 | |||||
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PolymiRTS Resource Report Resource Website 100+ mentions |
PolymiRTS (RRID:SCR_003389) | PolymiRTS | data or information resource, database | Database of naturally occurring DNA variations in microRNA (miRNA) seed regions and miRNA target sites. MicroRNAs pair to the transcripts of protein-coding genes and cause translational repression or mRNA destabilization. SNPs and INDELs in miRNAs and their target sites may affect miRNA-mRNA interaction, and hence affect miRNA-mediated gene repression. The PolymiRTS database was created by scanning 3'UTRs of mRNAs in human and mouse for SNPs and INDELs in miRNA target sites. Then, the potential downstream effects of these polymorphisms on gene expression and higher-order phenotypes are identified. Specifically, genes containing PolymiRTSs, cis-acting expression QTLs, and physiological QTLs in mouse and the results of genome-wide association studies (GWAS) of human traits and diseases are linked in the database. The PolymiRTS database also includes polymorphisms in target sites that have been supported by a variety of experimental methods and polymorphisms in miRNA seed regions. | polymorphism, microrna, human, disease, trait, snp, indel, pathway, genetic variant, gene expression, phenotype, chromosome, chromosome location, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
PhRMA Foundation ; UT Center for Integrative and Translational Genomics ; NICHD HD052472; NIAAA AA014425; NIDA DA021131; NINR NR009270; NIAID AI081050; NIAID AI019782; American Heart Association 0830134N; United States Department of Defense W81XHW-05-01-0227 |
PMID:24163105 PMID:22080514 |
Free, Available for download, Freely available | nif-0000-03324, biotools:polymirts, OMICS_00391 | https://bio.tools/polymirts | http://compbio.utmem.edu/miRSNP/ | SCR_003389 | Polymorphism in microRNA Target Site, PolymiRTS Database, Polymorphism in microRNAs and their TargetSites | 2026-07-28 09:40:47 | 149 | |||
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ERIC Resource Report Resource Website 500+ mentions |
ERIC (RRID:SCR_007644) | ERIC | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | ERIC is a resource of annotated enterobacterial genomes. Information is available and accessed through a open web portal uniting biological data and analysis tools. ERIC contains information on Escherichia, Shigella, Salmonella, Yersinia, and other microorgansims. ERIC has recently been moved over to PATRIC: The PATRIC BRC is now responsible for all bacterial species in the NIAID Category A-C Priority Pathogen lists for biodefense research, and pathogens causing emerging/reemerging infectious diseases. For ERIC users, we understand that the resource was valuable to your work. As such, we will be doing our very best to create a useful PATRIC resource to continue supporting your work. We realize that the transition will cause disruptions. However, it is a priority for us to work with established BRC users and communities to identify and prioritize our transition efforts. We have concentrated on the transfer of genomic data for this initial release. We anticipate adding new data, tools, and website features over the next several months. We look forward to working with you during the next 5 years., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | enterobacteria, enterobacteria pathogen, biodefense, disease bioinformatics, human disease, pathogen, pathogenic bacteria, cronobacter, enterobacter, erwinia, klebsiella, pectobacterium, photorhabdus, proteus, serratia, escherichia, shigella, salmonella, yersinia, citrobacter, FASEB list | has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA | NIAID | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02813 | http://www.ericbrc.org | SCR_007644 | Enteropathogen Resource Integration Center (ERIC), Enteropathogen Resource Integration Center | 2026-07-28 09:42:08 | 950 | |||||
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Induced Mutant Resource Resource Report Resource Website 1+ mentions |
Induced Mutant Resource (RRID:SCR_008366) | IMR | organism supplier, biomaterial supply resource, material resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 08, 2012. The function of the IMR is to select, import, cryopreserve, maintain, and distribute these important strains of mice to the research community. To improve their value for research, the IMR also undertakes genetic development of stocks, such as transferring mutant genes or transgenes to defined genetic backgrounds and combining transgenes and/or targeted mutations to create new mouse models for research. The function of the IMR is to: * select biomedically important stocks of transgenic, chemically induced, and targeted mutant mice * import these stocks into the Jackson Laboratory by rederivation procedures that rid them of any pathogens they might carry * cryopreserve embryos from these stocks to protect them against accidental loss and genetic contamination * backcross the mutation onto an inbred strain, if necessary * distribute them to the scientific community More than 1000 mutant stocks have been accepted by the IMR from 1992 through December 2006. Current holdings include models for research on cancer; breast cancer; immunological and inflammatory diseases; neurological diseases; behavioral, cardiovascular and heart diseases; developmental, metabolic and other diseases; reporter (e.g., GFP) and recombinase (e.g., cre/loxP) strains. About eight strains a month are being added to the IMR holdings. Research is being conducted on improved methods for assisted reproduction and speed congenic production. Most of the targeted mutants arrive on a mixed 129xC57BL/6 genetic background, and as many of these as possible are backcrossed onto an inbred strain (usually C57BL/6J). In addition, new mouse models are being created by intercrossing carriers of specific transgenes and/or targeted mutations. Simple sequence length polymorphism DNA markers are being used to characterize and evaluate differences between inbred strains, substrains, and embryonic stem cell lines. | embryo, genetic, behavioral, biomedical, breast cancer, cancer, cardiovascular, chemical, cre, cryopreserved, developmental, disease, distribution, dna, gfp, heart, immunological, inflammatory, loxp, marker, metabolic, model, mouse, mutation, neurological, pathogen, polymorphism, recombinase, research, stock, targeting, transgene | has parent organization: Jackson Laboratory | March of Dimes Birth Defects Foundation ; American Cancer Society ; American Heart Association ; Cystic Fibrosis Foundation ; National Multiple Sclerosis Society ; Amyotrophic Lateral Sclerosis Association ; NIAID ; NIAMS ; Howard Hughes Medical Institute ; Department of the Army Breast Cancer Research Initiative. ; NCRR P40 RR009781 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25566 | SCR_008366 | 2026-07-28 09:42:08 | 3 | |||||||
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Sequencing of Candida Albicans Resource Report Resource Website 10+ mentions |
Sequencing of Candida Albicans (RRID:SCR_013437) | data or information resource, topical portal, portal | The Stanford Genome Technology Center began a whole genome shotgun sequencing of strain SC5314 of Candida albicans. After reaching its original goal of 1.5X mean coverage of the haploid genome (16Mb) in summer, 1998, Stanford was awarded a supplemental grant to continue sequencing up to a coverage of 10X, performing as much assembly of the sequence as possible, using recognizable genes as nucleation points. Candida albicans is one of the most commonly encountered human pathogens, causing a wide variety of infections ranging from mucosal infections in generally healthy persons to life-threatening systemic infections in individuals with impaired immunity. Oral and esophogeal Candida infections are frequently seen in AIDS patients. Few classes of drugs are effective against these fungal infections, and all of them have limitations with regard to efficacy and side-effects. | stanford, genome, technology, shotgun, sequencing, strain, haploid, gene, nucleation, health, life, aids, drug, patient | has parent organization: Stanford University; Stanford; California | Burroughs Wellcome Fund ; NIDCR DE12302-02S2; NIAID RO1AI16567; NIAID RO1AI46351; NIAID NO1AI05406; NIDCR R01DE12940; NIDCR P01DE07946 |
nif-0000-30294 | SCR_013437 | Candida Albicans | 2026-07-28 09:43:29 | 21 | ||||||||
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PlasmoDB Resource Report Resource Website 1000+ mentions |
PlasmoDB (RRID:SCR_013331) | service resource, data or information resource, data repository, data analysis service, storage service resource, database, data access protocol, software resource, production service resource, web service, analysis service resource | Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene. | Functional, genomic, database, malaria, parasite, data, analysis, visualization, gene, genome, annotation, transcription, proteomics, protein, evolution, FASEB list |
uses: SynView is related to: GeneDB Pfalciparum has parent organization: Eukaryotic Pathogen Database Resources has parent organization: Pennsylvania State University has parent organization: University of Georgia; Georgia; USA |
malaria | NIAID | PMID:18957442 | nif-0000-03314, SCR_017665, r3d100011569 | SCR_013331 | PlasmoDB, Plasmodium Genomics Resource, PlasmoDB 5.5, Plasmodium genome-resource | 2026-07-28 09:43:12 | 1239 | ||||||
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Collaboratory of AIDS Researchers for Eradciation (CARE) Resource Report Resource Website |
Collaboratory of AIDS Researchers for Eradciation (CARE) (RRID:SCR_013681) | CARE | data or information resource, organization portal, consortium, portal | The Collaboratory of AIDS Researchers for Eradication (CARE) is a consortium of scientific experts in the field of HIV latency from several U.S. and European academic research institutions as well as Merck Research Laboratories working together to find a cure for HIV. | AIDS, HIV, drug development, data-sharing enabler, |
is related to: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA is related to: Gladstone Institute of Neurological Disease is related to: UCSF School of Medicine; California; USA is related to: Case Western Reserve University; Ohio; USA is related to: Merck is related to: UC Davis School of Medicine; California; USA is related to: University of California at San Diego; California; USA is related to: University of Utah School of Medicine; Utah; USA is related to: University of Minnesota Twin Cities; Minnesota; USA |
NIAID ; NIMH |
SCR_013681 | 2026-07-28 09:43:17 | 0 | |||||||||
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Immune Tolerance Network TrialShare Resource Report Resource Website 10+ mentions |
Immune Tolerance Network TrialShare (RRID:SCR_013699) | ITN TrialShare, TrialShare | service resource, data or information resource, data repository, clinical trial, storage service resource | Immune tolerance data management and visualization portal for studies sponsored by Immune Tolerance Network (ITN) and collaborating investigators. Data from published studies are accessible to any user; data from current in-progress studies are accessible to study investigators and collaborators. Includes links to published Figures, tools for visualization and analysis of data, and ability to query study data by subject, group, or any other study parameter. | clinical trial, clinical data, biological specimens, |
is recommended by: National Library of Medicine is related to: Immune Tolerance Network (ITN) |
Type 1 diabetes, Diabetes, Allergy, Asthma, Autoimmune disease, Transplantation, Immunological disorder | NIAID | Restricted | https://www.itntrialshare.org/login/home/login.view?returnUrl=%2Fproject%2Fhome%2Fstart.view%3F | SCR_013699 | , ITN, TrialShare, Trial Share, Immune Tolerance Network | 2026-07-28 09:43:37 | 27 | |||||
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VDJ Server Resource Report Resource Website 10+ mentions |
VDJ Server (RRID:SCR_014356) | software application, web application, data analysis software, software resource, data processing software, collaboration tool | A web application immune repertoire management, analysis, and archiving. Users can collaborate and share data either privately or publicly. Users can perform a variety of tasks, such as create and share projects with other users, conduct pre-processing tasks on single end reads, run IgBlast, and obtain basic repertoire characterization results for B cell receptor and T cell receptor repertoires. | omics data, web application, scalable resource, immune repertoire |
has parent organization: University of Texas Southwestern Medical Center; Texas; USA has parent organization: J. Craig Venter Institute has parent organization: Yale University; Connecticut; USA |
NIAID 1R01A1097403 | Free, Open source analysis software is available for local use | http://wiki.vdjserver.org/vdjserver/index.php/VDJServer_Wiki | SCR_014356 | VDJServer | 2026-07-28 09:43:25 | 16 | |||||||
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Pathosystems Resource Integration Center Resource Report Resource Website 1000+ mentions |
Pathosystems Resource Integration Center (RRID:SCR_004154) | PATRIC | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource, bioinformatics resource center | A Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available. | genomics, genome, transcriptomics, protein-protein interaction, sequence typing, proteobacteria, brucella, rickettsia, coxiella, coronavirus, calicivirus, lyssavirus, virus, hepatitis a, hepatitis e, pathway, proteome, metabolic pathway, drug, vaccine, diagnostics, FASEB list |
is listed by: OMICtools has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA |
NIAID | PMID:24225323 PMID:17142235 |
Free, Public, Acknowledgement requested | r3d100010142, OMICS_01658, nlx_17476 | http://patricbrc.vbi.vt.edu/portal/portal/patric/Home, https://doi.org/10.17616/R3WS3X | http://patric.vbi.vt.edu/ | SCR_004154 | PathoSystems Resource Integration Center, PATRIC, Pathosystems Resource Integration Center | 2026-07-28 09:40:53 | 1083 | |||
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HCV Databases Resource Report Resource Website 50+ mentions |
HCV Databases (RRID:SCR_002863) | HCV Databases | disease-related portal, data or information resource, topical portal, portal | The Hepatitis C Virus (HCV) Database Project strives to present HCV-associated genetic and immunologic data in a user-friendly way, by providing access to the central database via web-accessible search interfaces and supplying a number of analysis tools. | hcv, hepatitis c virus, hepatitis c, database, data analysis service, sequence, immunology, annotation, FASEB list |
has parent organization: HIV Databases is parent organization of: HCV Sequence Database is parent organization of: HCV Immunology Database |
Hepatitis C | NIAID | Free, Freely available | nif-0000-02944 | SCR_002863 | Hepatitis C Virus Database, Hepatitis C Virus Database Project, HCV Database, Hepatitis C Virus Databases, Hepatitis C Virus (HCV) Database Project | 2026-07-28 09:40:41 | 66 | |||||
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Database of Immune Cell Epigenomes Resource Report Resource Website 50+ mentions |
Database of Immune Cell Epigenomes (RRID:SCR_018259) | DICE | data or information resource, database, data access protocol, software resource, web service | Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis. | Data set, immune cell expression, expression quantitative trait loci, epigenomics, data, cis-eQLC, gene, protein coding gene, human cell type, genetic polymorphism disease, immune cell, pathogenesis | has parent organization: La Jolla Institute for Immunology | William K. Bowes Jr Foundation ; NIAID R24 AI108564; NCRR S10 RR027366; NIH Office of the Director S10 OD016262 |
PMID:30449622 | Free, Freely available | SCR_018259 | Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics | 2026-07-28 09:44:39 | 59 |
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