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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
nbdocker
 
Resource Report
Resource Website
nbdocker (RRID:SCR_017159) software resource, software application Software tool as Jupyter Notebook extension for Docker. Each Docker container encapsulates its individual computing environment to allow different programming languages and computing environments to be included in one single notebook, provides user to document code as well as computing environment. Jupyter, notebook, extension, docker, container, code, computing, environment, data is related to: University of Washington; Seattle; USA NHLBI U54 HL127624;
NIGMS R01 GM126019;
Institute of Technology at University of Washington Tacoma
DOI:10.1101/309567 Free, Available for download, Freely available https://hub.docker.com/r/biodepot/nbdocker/ SCR_017159 2026-08-01 12:11:07 0
Nuclear Receptor Signaling Atlas
 
Resource Report
Resource Website
100+ mentions
Nuclear Receptor Signaling Atlas (RRID:SCR_003287) NURSA biomaterial supply resource, material resource THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 25, 2022.Software tool as knowledge environment resource that accrues, develops, and communicates information that advances understanding of structure, function, and role in disease of nuclear receptors (NRs) and coregulators. It specifically seeks to elucidate roles played by NRs and coregulators in metabolism and development of metabolic disorders. Includes large validated data sets, access to reagents, new findings, library of annotated prior publications in field, and journal covering reviews and techniques.As of March 20, 2020, NURSA is succeeded by the Signaling Pathways Project (SPP). nuclear receptor, coregulator, metabolism, metabolic disorder, type 2 diabetes, obesity, osteoporosis, lipid dysregulation, cardiovascular disease, oncology, regenerative medicine, environmental agent, genomics, proteomics, reagent, ligand, microarray, gene expression, data set, data analysis service, nuclear receptor signaling, signaling, high through put screening, receptor, ligand, journal, molecule, affinity purification, q-pcr, chip-chip, animal model, antibody, cell line, primer, transcriptomine, clinical trial, disease, drug, data set is used by: NIF Data Federation
is used by: NIDDK Information Network (dkNET)
is recommended by: National Library of Medicine
lists: NURSA Transcriptomine
lists: STRING
lists: Nuclear Receptor Cistrome
is listed by: NIH Data Sharing Repositories
is listed by: NIDDK Research Resources
is listed by: NIDDK Information Network (dkNET)
is related to: dkCOIN
is related to: Integrated Manually Extracted Annotation
has parent organization: Baylor College of Medicine; Houston; Texas
Metabolic disorder, Type 2 diabetes mellitus, Obesity, Osteoporosis, Lipid dysregulation, Cardiovascular disease, Diabetes, Cancer NHLBI ;
NIEHS ;
NICHD ;
NIDDK DK097748
DOI:10.1101/401729 Free, Freely available nif-0000-03208 https://dknet.org/about/NURSA_Archive http://www.nursa.org SCR_003287 NURSA - Nuclear Receptor Signaling Atlas, NURSA - The Nuclear Receptor Signaling Atlas 2026-08-01 12:10:45 135
LINCS Data Portal
 
Resource Report
Resource Website
10+ mentions
LINCS Data Portal (RRID:SCR_014939) data or information resource, portal Portal which provides a unified interface for searching LINCS dataset packages and reagents. Users can use the portal to access datasets, small molecules, cells, genes, proteins and peptides, and antibodies. portal, assay, lincs, kinome, dataset, small molecule, cell, gene, protein, peptide, and antibodies. is related to: LINCS Data Portal 2.0
has parent organization: University of Miami; Florida; USA
is parent organization of: CycIF.org
NIH Common Fund ;
NHLBI 1U01HL111561;
NHLBI 3U01HL111561-01S1;
NHLBI 3U01HL111561-02S1;
NHGRI U54HG006097;
NHGRI U54 HG006093
Freely available SCR_014939 2026-08-02 09:07:04 13
HMS LINCS Center
 
Resource Report
Resource Website
10+ mentions
HMS LINCS Center (RRID:SCR_016370) HMS LINCS organization portal, data or information resource, portal Center that is part of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) Program. Its goals are to collect and disseminate data and analytical tools needed to understand how human cells respond to perturbation by drugs, the environment, and mutation. LINCS, Program, library, network, cell, signature, analysis, drugs, human, research is related to: HMS LINCS Database
has parent organization: Harvard Medical School; Massachusetts; USA
NHLBI U54 HL127365 PMID:29199020 SCR_016370 LINCS Center, Harvard Medical School LINCS Center, Harvard Medical School LINCS, Harvard Medical School (HMS) LINCS Center 2026-08-02 09:07:19 15
LINCS Data Portal 2.0
 
Resource Report
Resource Website
1+ mentions
LINCS Data Portal 2.0 (RRID:SCR_022566) LDP v2 data or information resource, portal Primary access point for compendium of LINCS data with substantial changes in data architecture and APIs, completely redesigned user interface, and enhanced curated metadata annotations to support more advanced, intuitive and deeper querying, exploration and analysis capabilities. LINCS datasets are accessible at data point level enabling users to directly access and download any subset of signatures across entire library independent from originating source, project or assay. Newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures. LINCS Data Portal, Cell, molecules, drug is related to: LINCS Data Portal NHLBI U54HL127624;
BD2K-LINCS Data Coordination and Integration Center ;
NCATS U24TR002278;
NLM U01LM012630
PMID:31701147 Free, Freely available SCR_022566 Library of Integrated Network Based Cellular Signatures 2.0 2026-08-02 09:08:32 2
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 2026-08-02 09:07:35 0
Ribosomal Database Project
 
Resource Report
Resource Website
1000+ mentions
Ribosomal Database Project (RRID:SCR_006633) RDP resource, data or information resource, database A database which provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences. It specifically contains information on quality-controlled, aligned and annotated bacterial and archaean 16S rRNA sequences, fungal 28S rRNA sequences, and a suite of analysis tools for the scientific community. Most of the RDP tools are now available as open source packages for users to incorporate in their local workflow. microbiome, database, rrna gene sequence, rrna, ribosome, genome browser, high-throughput sequencing, bacteria, archaea, fungi, FASEB list is listed by: OMICtools
is listed by: Human Microbiome Project
has parent organization: Michigan State University; Michigan; USA
is parent organization of: RDPipeline
DOE DE-FG02-99ER62848;
DOE DE-SC0004601;
DOE DE-FC02-07ER64494;
NIEHS P42 ES004911;
NSF DBI-0328255;
USDA 2008-35107-04542;
NHLBI U01HL098961;
NIDDK UH3 DK083993
PMID:24288368
PMID:17586664
Open source r3d100012372, nif-0000-03404, OMICS_01513 https://doi.org/10.17616/R3C087 SCR_006633 Ribosomal Database Project 2026-08-03 09:33:11 1441
Human Reference Protein Interactome Project
 
Resource Report
Resource Website
10+ mentions
Human Reference Protein Interactome Project (RRID:SCR_015670) HuRI portal, database, web application, data or information resource, software resource, project portal Project portal for the Human Reference Protein Interactome Project, which aims generate a first reference map of the human protein-protein interactome network by identifying binary protein-protein interactions (PPIs). It achieves this by systematically interrogating all pairwise combinations of predicted human protein-coding genes using proteome-scale technologies. protein interactome, protein-protein interaction, ppi, pairwise combination, proteome, human reference NHGRI R01/U01HG001715;
NHGRI P50HG004233;
NHLBI U01HL098166;
NHLBI U01HL108630;
NCI U54CA112962;
NCI R33CA132073;
NIH RC4HG006066;
NICHD ARRA R01HD065288;
NICHD ARRA R21MH104766;
NICHD ARRA R01MH105524;
NIMH R01MH091350;
NSF CCF-1219007;
NSERC RGPIN-2014-03892
PMID:25416956 Freely Available, Free, Available for download SCR_015670 HuRI: The Human Reference Protein Interactome Mapping Project 2026-08-03 09:36:22 20
Polysolver
 
Resource Report
Resource Website
10+ mentions
Polysolver (RRID:SCR_022278) software resource, data processing software, software application, data analysis software Software tool for HLA typing based on whole exome sequencing data and infers alleles for three major MHC class I genes. Enables accurate inference of germline alleles of class I HLA-A, B and C genes and subsequent detection of mutations in these genes using inferred alleles as reference. HLA typing, whole exome sequencing data, accurate inference of germline alleles, high precision HLA-typing, alleles of class I HLA-A, B and C genes, detection of mutations, inferred alleles has parent organization: Broad Institute Blavatnik Family Foundation ;
NHLBI 1RO1HL103532;
NCI 1R01CA155010;
AACR
PMID:26372948 Free, Available for download, Freely available SCR_022278 POLYmorphic loci reSOLVER, POLYSOLVER 2026-08-03 09:37:50 30
SigCom LINCS
 
Resource Report
Resource Website
1+ mentions
SigCom LINCS (RRID:SCR_022275) web service, data access protocol, software resource Web server that serves over million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. Data and metadata search engine for gene expression signatures. FAIR data, data and metadata search engine, gene expression signatures, gene expression signature processed, analyzed, and visualized, LINCS, GTEx, GEO, gene expression signatures, NHLBI U54HL127624;
NIDDK R01DK131525;
NIH Office of the Director OT2OD030160
PMID:35524556 Free, Freely available https://github.com/MaayanLab/sigcom-lincs SCR_022275 SigCom Library of Integrated Network-based Cellular Signatures 2026-08-03 09:37:50 7
sei
 
Resource Report
Resource Website
1+ mentions
sei (RRID:SCR_022571) web service, data access protocol, software resource Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types. systematically predicting sequence regulatory activities, applying sequence information, human genetics data, sequence class predictions National Science Foundation Graduate Research Fellowship Program ;
NHGRI R01HG005998;
NHLBI U54HL117798;
NIGMS R01GM071966
PMID:35817977 Free, Available for download, Freely available https://hb.flatironinstitute.org/sei SCR_022571 2026-08-03 09:38:02 6
X2K Web
 
Resource Report
Resource Website
10+ mentions
X2K Web (RRID:SCR_023624) X2K web service, data access protocol, software resource Web service to predict involvement of upstream cell signaling pathways, given signature of differentially expressed genes. Used to linking expression signatures to upstream cell signaling networks. predicts involvement of upstream cell signaling pathways, differentially expressed genes, linking expression signatures, upstream cell signaling networks, has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA NHLBI U54 HL127624;
NCI U24 CA224260;
NIH Office of the Director OT3 OD025467
PMID:29800326 Free, Freely available https://github.com/MaayanLab/x2k_web SCR_023624 eXpression2Kinases (X2K) Web 2026-08-03 09:38:27 10
Poly Peak Parser
 
Resource Report
Resource Website
1+ mentions
Poly Peak Parser (RRID:SCR_023776) web service, data access protocol, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 25,2025. Web tool to parse Sanger sequencing chromatograms with double peaks into wildtype and alternative allele sequences. Used to separate chromatogram data containing ambiguous base calls into wildtype and mutant allele sequences.Used for identification of unknown indels using sanger sequencing of polymerase chain reaction products. unknown indels identification, parse Sanger sequencing chromatograms, chromatograms with double peaks, separate chromatogram data, ambiguous base calls, wildtype sequences, mutant allele sequences, alternative allele sequences, NHLBI U01HL0981;
NHLBI U01HL098188;
NHLBI 1F32HL115881
PMID:25160973 THIS RESOURCE IS NO LONGER IN SERVICE http://yosttools.genetics.utah.edu/PolyPeakParser/ SCR_023776 2026-08-03 09:38:30 5
mgatk
 
Resource Report
Resource Website
1+ mentions
mgatk (RRID:SCR_021159) software toolkit, software resource, software application, data processing software Software python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. This package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays. processing .bam files, mitochondrial reads, heteroplasmy estimation, sequencing data, mitochondrial genotypes, mtscATAC-seq NCI F31 CA232670;
NCI R01 CA208756;
NCI P01 CA206978;
NCI U10 CA180861;
NIDDK R01 DK103794;
NHLBI R33 HL120791
DOI:10.1038/s41587-020-0645-6 Free, Available for download, Freely available SCR_021159 mitochondrial genome analysis toolkit 2026-08-03 09:37:33 2
xHLA
 
Resource Report
Resource Website
1+ mentions
xHLA (RRID:SCR_022277) software resource, software application, data processing software Software tool for fast and accurate HLA typing from short read sequence data. Iteratively refines mapping results at amino acid level to achieve four digit typing accuracy for both class I and II HLA genes, taking only 3 min to process 30× whole genome BAM file on desktop computer. HLA typing, short read sequence data, refines mapping results, amino acid level, four digit typing accuracy NCI 5U24CA076518;
NHLBI 5U10HL069294;
Health Resources and Services Administration ;
Office of Naval Research Grants
PMID:28674023 Free, Available for download, Freely available SCR_022277 2026-08-03 09:37:36 2
Body Mass Index Calculator
 
Resource Report
Resource Website
Body Mass Index Calculator (RRID:SCR_000122) BMI Calculator data analysis service, service resource, analysis service resource, production service resource Body Mass Index (BMI) for adults can be calculated using only height and weight. Body mass index (BMI) is a measure of body fat based on height and weight that applies to adult men and women. adult human, body mass, male, female is listed by: NIDDK Information Network (dkNET)
is listed by: Genetic Analysis Software
has parent organization: National Heart Lung and Blood Institute
NHLBI Free, Public nlx_152731 SCR_000122 Calculate Your Body Mass Index 2026-08-03 09:30:58 0
NeuroPedia
 
Resource Report
Resource Website
10+ mentions
NeuroPedia (RRID:SCR_001551) NeuroPedia data or information resource, database A neuropeptide encyclopedia of peptide sequences (including genomic and taxonomic information) and spectral libraries of identified MS/MS spectra of homolog neuropeptides from multiple species. proteomics, peptide, neuropeptide, mass spectrometry assay, peptide sequence, spectrum, homolog has parent organization: Center for Computational Mass Spectrometry NCRR P41-RR024851;
NIDA 5K01DA23065;
NINDS R01 NS24553;
NIDA R01 DA04271;
NIMH R01 MH077305;
NHLBI P01 HL58120
PMID:21821666 Free, Freely available nlx_152894 SCR_001551 NeuroPedia: Neuropeptide database and spectra library 2026-08-03 09:31:26 12
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 2026-08-03 09:31:55 17565
MITOMAP - A human mitochondrial genome database
 
Resource Report
Resource Website
100+ mentions
MITOMAP - A human mitochondrial genome database (RRID:SCR_002996) MITOMAP data or information resource, database Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf. gene, genome, diabetes, disease, disease-association, high resolution screening, human, inversion, metabolism, mitochondrial dna, mutation, phenotype, polymorphism, polypeptide assignment, pseudogene, restriction site, rna, sequence, trna, unpublished, variation, mitochondria, dna, insertion, deletion, FASEB list is used by: HmtVar
is listed by: OMICtools
is related to: Hereditary Hearing Loss Homepage
has parent organization: Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA
has parent organization: Emory University School of Medicine; Atlanta; Georgia; USA
NIH ;
Muscular Dystrophy Foundation ;
Ellison Foundation ;
Diputacion General de Aragon Grupos consolidados B33 ;
NIGMS GM46915;
NINDS NS21328;
NHLBI HL30164;
NIA AG10130;
NIA AG13154;
NINDS NS213L8;
NHLBI HL64017;
NIH Biomedical Informatics Training Grant T15 LM007443;
NSF EIA-0321390;
Spanish Fondo de Investigacion Sanitaria PI050647;
Ciber Enfermedades raras CB06/07/0043
PMID:17178747
PMID:15608272
PMID:9399813
PMID:9016535
PMID:8594574
Except where otherwise noted, Creative Commons Attribution License, The community can contribute to this resource nif-0000-00511, OMICS_01641 SCR_002996 2026-08-03 09:32:10 368
LINCS Information Framework
 
Resource Report
Resource Website
1+ mentions
LINCS Information Framework (RRID:SCR_003937) data or information resource, database LIFE search engine contains data generated from LINCS Pilot Phase, to integrate LINCS content leveraging semantic knowledge model and common LINCS metadata standards. LIFE makes LINCS content discoverable and includes aggregate results linked to Harvard Medical School and Broad Institute and other LINCS centers, who provide more information including experimental conditions and raw data. Please visit LINCS Data Portal. bioassay, cell, small molecule, kinase protein, compound, cell, gene, metadata standard, cell line, primary cell, rnai reagent, rnai, reagent, protein reagent, protein, antibody reagent, antibody, perturbagen, growth factor, ligand, linked data, organ, disease, data set uses: HMS LINCS Database
uses: Bioassay Ontology
uses: Molecular Libraries Program
is related to: Broad Institute
is related to: Harvard Medical School; Massachusetts; USA
is related to: Columbia University; New York; USA
is related to: Yale University; Connecticut; USA
is related to: Arizona State University; Arizona; USA
has parent organization: University of Miami; Florida; USA
NHLBI U01 HL111561;
NHGRI
PMID:29140462 Free, Freely available nlx_158348 http://dev3.ccs.miami.edu:8080/datasets-beta/ http://lifekb.org/ SCR_003937 lifekb, LIFE LINCS Information Framework 2026-08-03 09:32:36 1

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