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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Blood Exposome Database
 
Resource Report
Resource Website
1+ mentions
Blood Exposome Database (RRID:SCR_017610) data or information resource, database Collection of chemical compounds and associated information that were automatically extracted by text mining content of PubMed and PubChem databases. Unifies chemical lists from metabolomics, systems biology, environmental epidemiology, occupational expossure, toxiology and nutrition fields. Chemical, compound, collection, extracted, text, mining, PubMed chemical compounds list, PubChem chemical compounds list, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: University of California at Davis; California; USA
NIAID U54 AI138370;
NIA U19 AG023122;
NIEHS U2C ES030158
PMID:31557052 Free, Available for download, Freely available biotools:blood-exposome-db https://github.com/barupal/exposome, https://bio.tools/blood-exposome-db SCR_017610 The Blood Exposome Database, exposome 2026-07-28 09:44:38 7
The 10000 Immunomes
 
Resource Report
Resource Website
1+ mentions
The 10000 Immunomes (RRID:SCR_016624) 10KIP data or information resource, database Collection of reference datasets for human immunology, derived from control subjects in the NIAID ImmPort database . Available data include flow cytometry, CyTOF, multiplex ELISA, gene expression, HAI titers, clinical lab tests, HLA type, and others. collection, reference, dataset, human, immunology, control, subject, NIAID, ImmPort, database is related to: The Immunology Database and Analysis Portal (ImmPort)
is related to: NIAID
NIAID HHSN272201200028C PMID:30304689 Public, Free, Available for download, Freely available SCR_016624 10K Immunomes Project, 000 Immunomes Project, 000 Immunomes, 10 2026-07-28 09:44:23 1
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
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
HIV-1 Human Protein Interaction Database
 
Resource Report
Resource Website
10+ mentions
HIV-1 Human Protein Interaction Database (RRID:SCR_006879) HIV-1 Human Protein Interaction Database data or information resource, database A database of interactions between HIV-1 and human proteins published in the peer-reviewed literature. The goal is to provide a concise, yet detailed, summary of all known interactions of HIV-1 proteins with host cell proteins, other HIV-1 proteins, or proteins from disease organisms associated with HIV/AIDS. For each HIV-1 human protein interaction the following information is provided: * NCBI Reference Sequence (RefSeq) protein accession numbers. * NCBI Entrez Gene ID numbers. * Amino acids from each protein that are known to be involved in the interaction. * Brief description of the protein-protein interaction. * Keywords to support searching for interactions. * PubMed identification numbers (PMIDs) for all journal articles describing the interaction. In addition, all protein-protein interactions documented in the database are integrated into Entrez Gene records and listed in the ''HIV-1 protein interactions'' section of Entrez Gene reports. The database is also tightly linked to other databases through Entrez Gene, enabling users to search for an abundance of information related to HIV pathogenesis and replication. protein-protein interaction, protein, interaction, cellular protein is related to: VirHostNet: Virus-Host Network
has parent organization: NCBI
Human immunodeficiency virus, Type 1 NIAID contract N01-AI-05415;
NIAID N01-AI-70042
PMID:18927109
PMID:19025396
PMID:19262354
Acknowledgement requested nif-0000-02964 SCR_006879 HIV-1: Human Protein Interaction Database, Human immunodeficiency virus type 1 human protein interaction database at NCBI 2026-07-28 09:41:40 13
CuticleDB
 
Resource Report
Resource Website
10+ mentions
CuticleDB (RRID:SCR_007045) cuticleDB data or information resource, database A relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the five sequenced genomes where manual annotation has been applied to cuticular proteins: Anopheles gambiae, Apis mellifera, Bombyx mori, Drosophila melanogaster, and Nasonia vitripennis. Some sequences were confirmed as authentic cuticular proteins because protein sequencing revealed that they were present in cuticle; others were identified by sequence homology and other criteria. Entries provides information about whether sequences are putative or authentic cuticular proteins. CuticleDB was primarily designed to contain correct and full annotation of cuticular protein data. The database will be of help to future genome annotators. Users will be able to test hypotheses for the existence of known and also of yet unknown motifs in cuticular proteins. An analysis of motifs may contribute to understanding how proteins contribute to the physical properties of cuticle as well as to the precise nature of their interaction with chitin. genome, cuticle, cuticle protein, cuticular protein, cdna, protein, insect, exoskeleton, annotation, chitin, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: University of Athens Biophysics and Bioinformatics Laboratory
University of Athens; Athens; Greece ;
NIAID AI055624
PMID:15453918 biotools:cuticledb, nif-0000-02708 https://bio.tools/cuticledb SCR_007045 CuticleDB - A relational database of Arthropod cuticular proteins 2026-07-28 09:41:43 12
AnoBase: An Anopheles database
 
Resource Report
Resource Website
1+ mentions
AnoBase: An Anopheles database (RRID:SCR_008166) data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 22, 2023. A database containing genomic/biological information on anopheline mosquitoes, with an emphasis on Anopheles gambiae, the world''''s most important malaria vector. AnoBase is an integrated, relational database of basic biological and genetic data on anopheline species, with a particular emphasis on Anopheles gambiae. It has been designed as an information source and research support tool for the broad vector biology community. Although AnoBase is not a primary genomic database that develops and provides tools to access the genome of the malaria mosquito, it nevertheless contains several sections that offer data of genomic interest such as in situ hybridization images, an integrated gene tool and direct online access to AnoXcel, the proteomic database of An. gambiae. Moreover, AnoBase also contains information on non-gambiae mosquito species and a novel section on studies related to insecticide resistance. gene, genetic, anopheles gambiae, anopheline, biological, biology, community, genomic, in-situ hybridization, insecticide, invertebrate databases, malaria, mosquito, proteomic, specie, vector, image is related to: VectorBase
has parent organization: Foundation for Research and Technology-Hellas; Heraklion; Greece
is parent organization of: Malaria Ontology
NIAID THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-21031 http://www.anobase.org/ SCR_008166 AnoBase 2026-07-28 09:42:01 2
VDJbase
 
Resource Report
Resource Website
1+ mentions
VDJbase (RRID:SCR_022599) data or information resource, database Open source adaptive immune receptor genotype and haplotype database. Core collection is inferred from immune receptor repertoire sequences and genomically derived material. Provides customisable reports, which allow users to study gene and allele usage in various ways. Adaptive immune receptor genes, genotypes and haplotypes, immune receptor repertoire sequences, customisable reports, gene and allele European Union ;
NIAID R01AI127877;
NIAID R01AI125567;
NIAID R01AI130398
DOI:10.1093/nar/gkz872 Free, Freely available SCR_022599 2026-07-28 09:45:38 6
ReBATE
 
Resource Report
Resource Website
ReBATE (RRID:SCR_017139) software toolkit, software resource Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity . compare, relief, feature, algorithm, data, mining, variable, heterogeneous, pattern, genetic has parent organization: University of Pennsylvania; Philadelphia; USA NIAID AI116794;
NIDDK DK112217;
NIEHS ES013508;
NEI EY022300;
NHLBI HL134015;
NLM LM009012;
NLM LM010098;
NLM LM011360;
NCATS TR001263;
Warren Center for Network and Data Science
PMID:30030120 Free, Available for download, Freely available https://epistasislab.github.io/ReBATE/ SCR_017139 Relief Based Algorithm Training Environment 2026-07-28 09:44:30 0
MaAsLin2
 
Resource Report
Resource Website
100+ mentions
MaAsLin2 (RRID:SCR_023241) software toolkit, software resource SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. Microbiome Multivariable Associations with Linear Models, NSF DEB-2028280;
NIAID U19AI110820;
NHGRI R01HG005220;
NIDDK R24DK110499;
NIDDK U54DK102557
DOI:10.1371/journal.pcbi.1009442 Free, Available for download, Freely available https://huttenhower.sph.harvard.edu/maaslin/ SCR_023241 2026-07-28 09:45:53 170
New York University School of Medicine IonLab Core Facility
 
Resource Report
Resource Website
1+ mentions
New York University School of Medicine IonLab Core Facility (RRID:SCR_021754) access service resource, service resource, core facility Electrophysiology core facility that is part of Ion Channels and Transporters in Immunity Research Program.Research area includes ion channel and transporter function and ionic signaling in immune cells.Users who are studying other cell types or organ systems are welcome.Provides assistance with experimental design, training, implementation, and data analysis. USEDit, ABRF, ion channel, transporter function, ionic signaling, immune cells is listed by: ABRF CoreMarketplace
has parent organization: New York University School of Medicine; New York; USA
NIAID AI097302 open ABRF_1221 https://coremarketplace.org/?FacilityID=1221 SCR_021754 IonLab 2026-07-28 09:45:17 8
ColabFold
 
Resource Report
Resource Website
100+ mentions
ColabFold (RRID:SCR_025453) source code, software resource Software application offers accelerated prediction of protein structures and complexes by combining homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. Used for protein folding. prediction of protein structures and complexes, protein folding, protein structure prediction, Max Planck Society ;
University of Göttingen ;
National Research Foundation of Korea ;
Seoul National University ;
NIH Office of the Director DP5OD026389;
NIAID R21AI156595;
NSF
PMID:35637307 Free, Available for download, Freely available https://github.com/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb SCR_025453 2026-07-28 09:46:21 391
ClipKIT
 
Resource Report
Resource Website
10+ mentions
ClipKIT (RRID:SCR_026411) software application, source code, software resource Software fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others. Multiple sequence alignment-trimming algorithm for accurate phylogenomic inference. multiple sequence, alignment trimming, accurate phylogenomic inference, Howard Hughes Medical Institute ;
National Science Foundation ;
Guggenheim Foundation ;
Burroughs Wellcome Fund ;
NIAID 1R56AI146096;
Zhejiang University ;
Fundamental Research Funds for the Central Universities
PMID:33264284 Free, Available for download, Freely available SCR_026411 2026-07-28 09:46:38 35
Pathogens Portal Node Toolbox
 
Resource Report
Resource Website
Pathogens Portal Node Toolbox (RRID:SCR_027086) source code, software toolkit, software resource Software package and code for Pathogen Portal node (i.e. a local Pathogens Portal, such as the Swedish and Dutch Pathogens Portals). Allows users to create their own node quickly and easily. Pathogen Portal node, Swedish Pathogens Portal, Dutch Pathogens Portal, SciLifeLab NIAID U24AI183840 Free, Available for download, Freely available SCR_027086 2026-07-28 09:46:59 0
InterProSurf
 
Resource Report
Resource Website
InterProSurf (RRID:SCR_027791) web service, web application, data access protocol, software resource Web server for predicting interacting sites on protein surfaces. Analyzes solvent-accessible residues likely to participate in PPIs.Predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of protein complex. Analyzes solvent-accessible residues, predicting interacting sites on protein surfaces, interacting amino acid residues in proteins, proteins that are most likely to interact with other proteins, NIAID R21 AI055746;
NIAID R01 AI064913
PMID:17933856 Free, Freely available, SCR_027791 2026-07-28 09:47:03 0
MS-GF+
 
Resource Report
Resource Website
100+ mentions
MS-GF+ (RRID:SCR_015646) software resource Software that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database. protein idenitification, peptide sequence, ms, ms spectrum, proteomic, bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
has parent organization: Pacific Northwest National Laboratory
NCRR RR018522;
NCRR 1-P41-RR024851;
NIAID ;
W.R. Wiley Environmental Molecular Science Laboratory
PMID:25358478 Free, Available for download, Acknowledgment requested biotools:ms-gf https://github.com/sangtaekim/msgfplus, https://bio.tools/ms-gf SCR_015646 MSGF+, MSGFPlus 2026-07-25 12:08:11 155
Cryptococcus Neoformans cDNA Sequencing
 
Resource Report
Resource Website
1+ mentions
Cryptococcus Neoformans cDNA Sequencing (RRID:SCR_008462) software resource Cryptococcus neoformans is an encapsulated yeast that infects the human host via the respiratory tract where it usually causes an inapparent infection. In the susceptible host, it may disseminate, typically producing a chronic and life-threatening meningitis. The Cryptococcus neoformans serotypes A and D are responsible for the overwhelming majority of pulmonary infections in AIDS patients. Cryptococcus neoformans strain H99 Latest Data Release - May 19, 2004 To date, we have isolated ca. 3750 cDNA clones from Cryptococcus neoformans strain H99 in collaboration with Drs. Juneann Murphy and Dave Dyer at the University of Oklahoma Health Sciences Center''s Department of Microbiology and Immunology in Oklahoma City and Kent Buchanan at the Tulane University Medical School, New Orleans, LA. The Cryptococcus neoformans strain H99 EST''s have been generated by Doris Kupfer, Heather Bell, Sunkyoung So, Yuong Tang, and Jennifer Lewis at the University of Oklahoma''s Advanced Center for Genome Technology, in the Department of Chemistry and Biochemistry. We now have end sequenced all available templates (ca. 7500 reactions) from both ends of the directionally cloned inserts after excision into pBlueScript SK-. . All of our data is available from our ftp site, and we now have added the ability to perform blast searches on this data. A keyword search of a blastx search of GenBank with this data also is available but we have not yet linked this to a unigene database as the number of EST''s sequenced doesn''t warrent this yet. has parent organization: University of Oklahoma; Oklahoma; USA NIAID AI147079 nif-0000-30397 SCR_008462 cDNA Sequencing 2026-07-25 12:06:48 1
IBEX Knowledge Base
 
Resource Report
Resource Website
1+ mentions
IBEX Knowledge Base (RRID:SCR_025296) knowledge base Open, global repository as central resource for reagents, protocols, panels, publications, software, and datasets. In addition to IBEX, we support standard, single cycle multiplexed imaging (Multiplexed 2D imaging), volume imaging of cleared tissues with clearing enhanced 3D (Ce3D), highly multiplexed 3D imaging (Ce3D-IBEX), and extension of the IBEX dye inactivation protocol to the Leica Cell DIVE (Cell DIVE-IBEX). Committed to sharing knowledge related to multiplexed imaging. Antibody validation community knowledgebase. Antibody, validation, multiplexed imaging, NCI ;
NIAID ;
Schroeder Allergy and Immunology Research Institute ;
McMaster University ;
CA ;
Chan Zuckerberg Initiative ;
Wellcome Trust
Free, Freely available https://zenodo.org/records/7693279 SCR_025296 Iterative Bleaching Extends Multiplexity (IBEX) Knowledge-Base 2026-07-25 12:14:56 3
Dynamic Regulatory Events Miner
 
Resource Report
Resource Website
1+ mentions
Dynamic Regulatory Events Miner (RRID:SCR_003080) DREM software application, software resource, data processing software The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze, and visualize transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression data and static transcription factor-gene interaction data (e.g. ChIP-chip data), and produces as output a dynamic regulatory map. The dynamic regulatory map highlights major bifurcation events in the time series expression data and transcription factors potentially responsible for them. DREM 2.0 was released and supports a number of new features including: * new static binding data for mouse, human, D. melanogaster, A. thaliana * a new and more flexible implementation of the IOHMM supports dynamic binding data for each time point or as a mix of static/dynamic TF input * expression levels of TFs can be used to improve the models learned by DREM * the motif finder DECOD can be used in conjuction with DREM and help find DNA motifs for unannotated splits * new features for the visualization of expressed TFs, dragging boxes in the model view, and switching between representations transcription, gene regulation, dynamics, time series, gene expression, static, dynamic, transcription factor-gene interaction, chip-chip, transcription factor, regulatory network, hidden markov model, systems biology, gene regulatory network, times series expression data, dynamic network, chip-seq has parent organization: Carnegie Mellon University; Pennsylvania; USA NIH ;
NIGMS 1RO1 GM085022;
NIAID DNO1 AI-5001;
NSF 0448453
PMID:22897824 Free, Available for download, Freely available nif-0000-30478 SCR_003080 Dynamic Regulatory Events Miner (DREM) 2026-07-26 09:03:21 5
Short Time-series Expression Miner (STEM)
 
Resource Report
Resource Website
50+ mentions
Short Time-series Expression Miner (STEM) (RRID:SCR_005016) STEM software application, software resource, data processing software The Short Time-series Expression Miner (STEM) is a Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments (~8 time points or fewer). STEM allows researchers to identify significant temporal expression profiles and the genes associated with these profiles and to compare the behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology (GO) database supporting GO category gene enrichment analyses for sets of genes having the same temporal expression pattern. STEM also supports the ability to easily determine and visualize the behavior of genes belonging to a given GO category or user defined gene set, identifying which temporal expression profiles were enriched for these genes. (Note: While STEM is designed primarily to analyze data from short time course experiments it can be used to analyze data from any small set of experiments which can naturally be ordered sequentially including dose response experiments.) Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible statistical analysis, term enrichment, visualization, cluster, compare, short time series, gene expression, microarray, expression profile, gene, gene ontology, gene enrichment analyses, FASEB list is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: Carnegie Mellon University; Pennsylvania; USA
NIAID NO1 AI-5001;
NSF 0448453
PMID:16597342
PMID:15961453
Open unspecified license - Free for academic use nlx_97053 SCR_005016 Short Time-series Expression Miner 2026-07-26 09:03:50 81

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