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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Hierarchical Data Modeling Framework Resource Report Resource Website 1+ mentions |
Hierarchical Data Modeling Framework (RRID:SCR_021303) | HDMF | software toolkit, software resource, software application, data processing software | Open source software Python package for working with hierarchical data. Provides APIs for specifying data models, reading and writing data to different storage backends, and representing data with Python object.Used for working with standardizing, reading, and writing hierarchical object data. | Hierarchical data, data models, reading data, writing data, unified data format, different storage backends, Python object, data, data standards |
is used by: PyNWB is related to: Neurodata Without Borders is related to: Neurodata Extensions Catalog is related to: HDMF Documentation Utilities is related to: HDMF Common Schema |
DOI:10.1109/BigData47090.2019.9005648 | Free, Available for download, Freely available | SCR_021303 | 2026-08-03 09:37:35 | 1 | ||||||||
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viral_seq Resource Report Resource Website 1+ mentions |
viral_seq (RRID:SCR_018515) | software resource, software application, data processing software | Ruby Gem with bioinformatics tools for processing viral NGS data. Specifically for Primer-ID sequencing and HIV drug resistance analysis. | Processing viral data, next generation sequencing data, viral data, sequencing, HIV drug resistance analysis, Primer ID sequencing, data | Free, Available for download, Freely available | https://github.com/ViralSeq/viral_seq | SCR_018515 | 2026-08-03 09:36:59 | 2 | ||||||||||
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DecodingDynamic Resource Report Resource Website 1+ mentions |
DecodingDynamic (RRID:SCR_021099) | data or information resource, software resource, source code | Data, code, and notebooks for replicating analyses reported in Rogers et al., Evidence for deep, distributed and dynamic semantic code in human ventral anterior temporal cortex. | ECoG, neural networks, semantics, replicating analyses, data, code, notebooks, human ventral anterior temporal cortex, semantic code | Medical Research Council Programme ; European Research Council |
DOI:10.1101/695049 | Free, Freely available | SCR_021099 | 2026-08-03 09:37:32 | 1 | |||||||||
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CustomCDF Resource Report Resource Website 1+ mentions |
CustomCDF (RRID:SCR_018527) | software resource, software application, data processing software | Brainarray custom CDFs for processing raw Affymetrix data. Used to map probe to probesets. Oligonucleotide probes on GeneChips are reorganized based on latest genome and transcriptome information. | Brainarray, custom CDF, processing raw Affymetrix data, data processing, map probe, probset, oligonucleotide probe, GeneChips, genome, transcriptome, data | PMID:16284200 | Free, Freely available | https://gist.github.com/rmflight/3108891, https://rdrr.io/github/jakejh/metapredict/man/installCustomCdfPackages.html | SCR_018527 | 2026-08-03 09:37:17 | 8 | |||||||||
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MS Bioworks Resource Report Resource Website |
MS Bioworks (RRID:SCR_001043) | data analysis service, service resource, analysis service resource, production service resource | A protein mass spectrometry service provider that delivers data to industrial and government organizations as well as academic institutions. Protein services include protein identification, mapping, profiling, and mass measurement. Post-translational modification services include PTM profiling, phospho-screening, and glyco-screening. Quantitative proteomics services include workflows for label free, TMT, SILAC, and PRM. MS Bioworks also provides immunoprecipitated protein analysis and custom analysis. | mass spectrometry, protein, data, biomarkers, glycoproteins, proteomics service, analysis service resource, post translational modification, quantitative proteomics | is listed by: ScienceExchange | Services available for purchase | SciEx_4856 | http://www.scienceexchange.com/facilities/ms-bioworks | SCR_001043 | MS Bioworks - Protein Mass Spectrometry Services | 2026-08-03 09:31:13 | 0 | |||||||
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PhenoBank Resource Report Resource Website 1+ mentions |
PhenoBank (RRID:SCR_000930) | video resource, data or information resource, database | A database that provides primary data from two high-content screens that profile the set of ~900 essential C. elegans genes (~5% of the genome) required for embryo production and/or events during the first two embryonic divisions. Phenobank houses the movies, scored defects, and phenotypic classification data for the embryo-filming and gonad morphology screens. | phenotype, data, c elegans, genome, embryo, gonad, morphology, classification | has parent organization: Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_73232 | SCR_000930 | 2026-08-03 09:31:12 | 1 | |||||||||
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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 | 2026-08-03 09:31:55 | 17565 | |||||
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QIIME 2 View Resource Report Resource Website 50+ mentions |
QIIME 2 View (RRID:SCR_018074) | data acquisition software, software application, data processing software, service resource, software resource, data visualization software | Web based serverless viewer of QIIME 2 artifacts and visualizations. Client side interface for viewing QIIME 2 artifacts and visualizations. Not needed working QIIME 2 installation to inspect QIIME 2 results. Supports viewing externally hosted files by automatically downloading and displaying them when links to files are provided. | QIIME 2, visualization, data, interface, file viewing, file download and displaying | Free, Freely available | https://github.com/qiime2/q2view | SCR_018074 | q2view | 2026-08-03 09:37:11 | 71 | |||||||||
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PremierBiosoft Proteo IQ Software Resource Report Resource Website 10+ mentions |
PremierBiosoft Proteo IQ Software (RRID:SCR_018072) | software application, data processing software, data analysis software, data analytics software, software resource | Software package as comprehensive qualitative and quantitative suite for proteomics. Used to validate and quantify proteins by combining results from popular mass spectrometry platforms and database search engines. Provides customizable interface to support any form of biological annotation. Used to compare protein quantitative results in relation to biological pathways, protein localization, protein function, or to transcript abundance. Every protein identification can be linked to any external or internal knowledge database. Custom links are provided to GenBank, UniProt, IPI, and SwissProt databases or in-house LIMS. | Proteomic, qualitative, quantitative, protein identification, data, PREMIER Biosoft, mass spectrometry data, database search engine |
works with: GenBank works with: UniProtKB works with: IPI |
Restricted | SCR_018072 | ProteoIQ | 2026-08-03 09:36:51 | 34 | |||||||||
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CircaDB Resource Report Resource Website 10+ mentions |
CircaDB (RRID:SCR_018078) | CircaDB | web service, database, data access protocol, data or information resource, software resource | Database of mammalian circadian gene expression profiles. Works with link outs to Wikipedia, HomoloGene, Refseq, etc.. Open source database of circadian transcriptional profiles from time course expression experiments from mice and humans. | Mammalian circadian gene, gene expression, expression profile, mice, human, gene annotation, data, time course expression data | PMID:23180795 | Free, Freely available | http://github.com/itmat/circadb | SCR_018078 | Circadian gene expression profiles DataBase | 2026-08-03 09:36:58 | 19 | |||||||
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QuB Resource Report Resource Website 1+ mentions |
QuB (RRID:SCR_018076) | QuB | software toolkit, software application, data processing software, data analysis software, software resource | Integrated software platform for ion channel biophysics and neurophysiology.Used to explore dynamics of hidden states in memoryless system. Open source software suite for solving kinetic models, for report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. Can be applied to any data modeled with Markov kinetics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Ion channel biophysics, neurophysiology data, hiddent state, memoryless system, solving kinetic model, data, Markov kinetics, analysis | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_018076 | Quantify unknown Biophysics | 2026-08-03 09:36:51 | 2 | |||||||||
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Vivli Resource Report Resource Website 1000+ mentions |
Vivli (RRID:SCR_018080) | data or information resource, service resource, nonprofit organization | Independent, non-profit organization that has developed global data-sharing and analytics platform to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through creation and implementation of sustainable global data-sharing enterprise. Our focus is on sharing individual participant-level data from completed clinical trials. Users can search listed studies, request data sets from data contributors, aggregate data, or share data of their own. Vivli (Center for Clinical Research Data) is launching a portal to share participant-level data from COVID trials. | Global data sharing, clinical research data, data, sharing, analytical platform, clinical trial, COVID-19-related trials |
is used by: NIH Heal Project is recommended by: NIDDK Information Network (dkNET) is listed by: Data and Computational Resources to Address COVID-19 is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing |
COVID-19 | Doris Duke Charitable Foundation ; Leona M. and Harry B. Helmsley Charitable Trust ; Lyda Hill Philanthropies ; Phrma |
Restricted | DOI:10.17616/R3SB9S, DOI:10.25504/FAIRsharing.uovQrT, DOI:10.25934, r3d100012823 | https://vivli.org/vivli-covid-19-portal-2/, https://doi.org/10.17616/R3SB9S, https://doi.org/10.17616/r3sb9s, https://doi.org/10.25934/, https://dx.doi.org/10.25934/, https://fairsharing.org/10.25504/FAIRsharing.uovQrT, https://doi.org/10.17616/R3SB9S | SCR_018080 | 2026-08-03 09:37:11 | 1532 | ||||||
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MOON Resource Report Resource Website 1+ mentions |
MOON (RRID:SCR_018005) | software toolkit, software application, data processing software, data analysis software, software resource | Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid. | Diagnosis, rare disease, next generation sequencing, NGS, data, artificial intelligence, analysis, Diploid | Restricted | SCR_018005 | 2026-08-03 09:36:58 | 6 | |||||||||||
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ChiCMaxima Resource Report Resource Website 1+ mentions |
ChiCMaxima (RRID:SCR_018178) | production service resource, web service, analysis service resource, data access protocol, service resource, software resource | Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling. | Chromatin loop, CHi-C promoter, data, Hi-C visualization, interaction calling, data, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:31118054 | Free, Freely available | biotools:ChiCMaxima | https://bio.tools/ChiCMaxima | SCR_018178 | 2026-08-03 09:37:13 | 2 | |||||||
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MaxTRAQ Resource Report Resource Website 1+ mentions |
MaxTRAQ (RRID:SCR_018188) | software resource, data processing software, software application, data analysis software | Software package for motion capture analysis by Innovision Systems Inc. | Motion capture, analysis, data, data tracking, Innovision Systems Inc. | Restricted | SCR_018188 | Innovision Systems MaxTRAQ software | 2026-08-03 09:36:59 | 1 | ||||||||||
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MS Amanda Resource Report Resource Website 1+ mentions |
MS Amanda (RRID:SCR_018396) | software application, data processing software, algorithm resource, data analysis software, software resource | Software scoring system to identify peptides out of tandem mass spectrometry data using database of known proteins. Universal identification algorithm optimized for high resolution and high accuracy tandem mass spectra. Software tool as peptide and protein identification algorithm developed by Bioinformatics Research Group University of Applied Sciences Upper Austria in close cooperation with group of Karl Mechtler at IMP Vienna, Austria. | Tandem mass spectrometry, protein database, scoring system, peptide identification, data, search algorithm, protein identification algorithm, peptide identification, proteomic | is related to: PeptideShaker | Austrian Science Fund ; European Community Seventh Framework Programme ; MeioSys |
PMID:24909410 | Free, Available for download, Freely available | https://ms.imp.ac.at/?goto=msamanda | SCR_018396 | MS Amanda 2.0, Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra | 2026-08-03 09:37:02 | 2 | ||||||
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Interactive Dotplot Resource Report Resource Website 1+ mentions |
Interactive Dotplot (RRID:SCR_018329) | production service resource, web service, analysis service resource, data access protocol, service resource, software resource | Web-based tool to create customized interactive graphics, including univariate scatterplots, box plots, and violin plots, for comparing values of continuous variable across different study groups, visualization of subgroups or clusters of non-independent data. Web visualization tool for creating dot plots, box plots and violin plots for small sample size data sets. | Customized interactive graphic, univariate scatterplot, box plot, violin plot, continuous variable comparing, across different study group, subgroup visualization, subgroup cluster, non independent data visualization, data, data set | NCATS UL1 TR000135 | PMID:28974579 | Free, Freely available | SCR_018329 | 2026-08-03 09:36:56 | 1 | |||||||||
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Database of Immune Cell Epigenomes Resource Report Resource Website 50+ mentions |
Database of Immune Cell Epigenomes (RRID:SCR_018259) | DICE | web service, database, data access protocol, data or information resource, software resource | 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 | 2026-08-03 09:37:00 | 59 | ||||||
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gProfiler2 Resource Report Resource Website 50+ mentions |
gProfiler2 (RRID:SCR_018190) | software resource, data processing software, software application, data analysis software | Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool. | Gene list, functional enrichment analysis, namespace conversion, data, analysis |
is listed by: ELIXIR Tools and Data Services Registry is related to: R Project for Statistical Computing works with: g:Profiler |
Estonian Research Council grants ; European Regional Development Fund for CoE of Estonian ICT research EXCITE projects |
PMID:31066453 | Free, Available for download, Freely available | SCR_018190 | gprofiler2 | 2026-08-03 09:36:53 | 53 | |||||||
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SEDFIT Resource Report Resource Website 10+ mentions |
SEDFIT (RRID:SCR_018365) | software resource, data processing software, software application, data analysis software | Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly. | Analytical ultracentrifugation, biophysical analysis, macromolecular assembly, data, analysis, National Institute of Biomedical Imaging and Bioengineering | is listed by: SoftCite | NIH | Free, Available for download, Freely available | SCR_018365 | SEDFIT version 14.7g | 2026-08-03 09:36:57 | 25 |
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