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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Minimum Information about Biosynthetic Gene cluster Resource Report Resource Website 50+ mentions |
Minimum Information about Biosynthetic Gene cluster (RRID:SCR_023660) | MIBiG | data or information resource, project portal, portal, database | MIBiG is genomic standards consortium project and biosynthetic gene cluster database used as reference dataset. Provides community standard for annotations and metadata on biosynthetic gene clusters and their molecular products. Standardised data format that describes minimally required information to uniquely characterise biosynthetic gene clusters. MIBiG 2.0 is expended repository for biosynthetic gene clusters of known function. MIBiG 3.0 is database update comprising large scale validation and re-annotation of existing entries and new entries. Community driven effort to annotate experimentally validated biosynthetic gene clusters. | Genomic standards consortium project, community standard, annotations and metadata standards, biosynthetic gene clusters, sequence framework, biosynthetic gene cluster data, | Netherlands Organization for Scientific Research VENI grant ; NSF CAREER Award ; UK Biotechnology and Biological Sciences Research Council ; Novo Nordisk Foundation ; NIH U41 AT008718; Danish National Research Foundation ; NCCIH U24 AT010811; NCCIH F32 AT011475; Natural Sciences and Engineering Council of Canada Discovery grant ; European Union Horizon 2020 projects CARTNET ; Horizon 2020 Marie Skłodowska-Curie ; U.S. Department of Energy ; Portuguese Science and Technology Foundation ; U.S. National Science Foundation ; National Research Foundation of Korea ; NIGMS GM134688; NIAID R01AI155694; Netherlands eScience Center Accelerating Scientific Discoveries Grant ; Funds of the Chemical Industry Germany ; UK government Department for Environment ; Food and Rural Affairs ; German Chemical Industry ; Natural Sciences and Engineering Council of Canada |
PMID:36399496 DOI:10.1093/nar/gkz882 |
Free, Freely available | SCR_023660 | MIBiG 3.0, MIBiG 2.0 | 2026-02-17 10:04:36 | 55 | |||||||
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CoSMoS_Analysis Resource Report Resource Website 10+ mentions |
CoSMoS_Analysis (RRID:SCR_016896) | CoSMoS Analysis | software application, data processing software, data analysis software, software resource, image analysis software | Software tools for analyzing co-localization single-molecule spectroscopy image data. | co-localization, single, molecule, spectroscopy, image, data, analysis | NIGMS ; NIH |
Free, Available for download, Freely available | SCR_016896 | co-localization single-molecule spectroscopy, Co-localization Single-Molecule Spectroscopy Analysis, co-localization single molecule spectroscopy, CoSMoS | 2026-02-17 10:03:29 | 17 | ||||||||
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ValIdated Systematic IntegratiON of epigenomic data Resource Report Resource Website 1+ mentions |
ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) | VISION | data or information resource, catalog, project portal, database, portal | International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human. | analyze, mouse, human, hematopoietic, cell, blood, component, collection, epigenomic, data, catalog, gene, regulation | is listed by: NIDDK Information Network (dkNET) | National Institute for Diabetes and Digestive Diseases ; NIH ; NIDDK |
SCR_016921 | ValIdated Systematic IntegratiON of epigenomic data, ValIdated Systematic IntegratiON | 2026-02-17 10:02:46 | 9 | ||||||||
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PanoramaWeb Resource Report Resource Website |
PanoramaWeb (RRID:SCR_017136) | data access protocol, storage service resource, data or information resource, service resource, software resource, web service, data repository | Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents. | repository, software, targeted, mass, spectrometry, data, proteomic, quantitative, viewing, sharing, disseminating, result, , bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA works with: Skyline |
NIGMS R01 GM103551; NIGMS R01 GM121696; NHGRI U54 HG008097; NIH R01 AR071762; University of Washington Proteomics Resource |
DOI:10.1074/mcp.RA117.000543 | Free, Freely available | biotools:panorama | https://bio.tools/panorama | SCR_017136 | 2026-02-17 10:03:09 | 0 | ||||||
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NIH Figshare Archive Resource Report Resource Website 1+ mentions |
NIH Figshare Archive (RRID:SCR_017580) | NIH Figshare | storage service resource, data or information resource, database, service resource, data repository | Repository to make datasets resulting from NIH funded research more accessible, citable, shareable, and discoverable. Data submitted will be reviewed to ensure there is no personally identifiable information in data and metadata prior to being published and in line with FAIR -Findable, Accessible, Interoperable, and Reusable principles. Data published on Figshare is assigned persistent, citable DOI (Digital Object Identifier) and is discoverable in Google, Google Scholar, Google Dataset Search, and more.Complited on July,2020. Researches can continue to share NIH funded data and other research product on figshare.com. | Respository, data, NIH funded, data set, FAIR |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is related to: FigShare is related to: FigsharePlus |
NIH | Restricted | SCR_017580 | NIH, Figshare, Fig Share, NIH Figshare, NIH Fig share, National Institute of Health | 2026-02-17 10:02:53 | 9 | |||||||
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AmoebaDB Resource Report Resource Website 1+ mentions |
AmoebaDB (RRID:SCR_017592) | data or information resource, production service resource, analysis service resource, database, service resource | Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers. | Genomic, functional, database, Entamoeba, Acanthamoeba, parasite, microarray, expression, data, experimental, isolate, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Eukaryotic Pathogen Database Resources |
NIDA ; Department of Health and Human Services ; NIH |
PMID:20974635 | Free, Freely available | biotools:amoebadb, r3d100012457 | https://bio.tools/amoebadb https://doi.org/10.17616/R3PX9Q |
SCR_017592 | 2026-02-17 10:03:16 | 7 | ||||||
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Distributed Archives for Neurophysiology Data Integration Resource Report Resource Website 50+ mentions |
Distributed Archives for Neurophysiology Data Integration (RRID:SCR_017571) | DANDI | service resource, data repository, storage service resource | Free, cloud-based platform for publishing, sharing, and processing standardized neurophysiology data, primarily using the Neurodata Without Borders (NWB) format. Supported by the BRAIN Initiative, it enables researchers to collaborate, reuse datasets, and adhere to FAIR data principles. | publishing data, sharing data, processing data, neurophysiology data, BRAIN Initiative, |
is used by: BICCN is recommended by: BRAIN Initiative is listed by: DataCite is listed by: FAIRsharing is related to: BRAIN Initiative is related to: Allen Institute for Brain Science is related to: NeuroSift is related to: Ecosystem for Multi-modal Brain-behavior Experimentation and Research |
NIH R24 MH117295 | Free, Freely available | DOI:10.25504/FAIRsharing.f2c119, DOI:10.48324, r3d100013638 | https://doi.org/10.48324/ https://dx.doi.org/10.48324/ https://fairsharing.org/10.25504/FAIRsharing.f2c119 https://doi.org/10.17616/R31NJN0M |
SCR_017571 | 2026-02-17 10:03:36 | 52 | ||||||
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LIGER Resource Report Resource Website 10+ mentions |
LIGER (RRID:SCR_018100) | data analysis software, software application, data processing software, software resource | Software R package for integrating and analyzing multiple single-cell datasets. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors. Used for analysis of multiple scRNA-seq data sets. | Single cell genomic, data integration, dataset, cell identity, integrative analysis, gene regulation, disease state, scRNA seq analysis, shared factor among data set, | has parent organization: Broad Institute | NIH | PMID:31178122 | Free, Available for download, Freely available | https://github.com/MacoskoLab/liger | SCR_018100 | Linked Inference of Genomic Experimental Relationships | 2026-02-17 10:03:44 | 12 | ||||||
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Multi-omics Visualization Platform Resource Report Resource Website 1+ mentions |
Multi-omics Visualization Platform (RRID:SCR_018077) | MVP | software application, data processing software, data analysis software, software resource, data visualization software | Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach. | Proteogenomics, data, multi-omics, mass spectrometry, proteomics, genomics, transcriptomics, Galaxy Project, data visualization, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIH U24 CA199347 | Free, Available for download, Freely available | biotools:mvp_a | http://galaxyp.org https://bio.tools/mvp_a |
SCR_018077 | Multi-omics Visualization Platform, Galaxy MVP | 2026-02-17 10:03:23 | 1 | |||||
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NIH COVID-19 Portfolio Resource Report Resource Website 10+ mentions |
NIH COVID-19 Portfolio (RRID:SCR_018295) | data access protocol, data or information resource, service resource, software resource, web service | NIH comprehensive, curated source for publications related to COVID-19. Includes articles from PubMed and pre-prints from arXiv, medRxiv, bioRxiv, and ChemRxiv. Updated daily. NIH Office of Portfolio Analysis has developed this resource to explore and analyze set of advances in COVID‑19 research as they accumulate in real time, and complements efforts by NLM to aggregate full text documents broadly related to COVID-19 and other outbreaks, and articles on COVID‑19 specific to PubMed database. | COVID-19 publication, COVID-19 article, COVID-19 data, COVID-19 full text document, COVID-19 pre-print | COVID-19 | NIH | Free, Freely available | SCR_018295 | iSearch COVID-19 portfolio, COVID-19 Portfolio Tool From the Office of Portfolio Analysis, iSearch COVID-19 Portfolio, COVID-19 Portfolio | 2026-02-17 10:03:03 | 17 | ||||||||
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Data and Computational Resources to Address COVID-19 Resource Report Resource Website |
Data and Computational Resources to Address COVID-19 (RRID:SCR_018274) | data or information resource, topical portal, portal, disease-related portal | COVID-19 open access data and computational resources provided by federal agencies, including NIH, public consortia, and private entities. Continuously updated as more information becomes available. These resources are being shared for scientific and public health interests, and content is responsibility of resource organizers. | COVID-19, COVID-19 data, federal agency data, computational resource, public health information, SARS-CoV-2, NIH |
lists: Nextstrain lists: outbreak.info lists: Research Data Alliance Working Group lists: UC Health clinical data warehouse lists: Vivli lists: Cloud resources for COVID-19 research lists: COVID-19 High Performance Computing Consortium lists: Data-Against-COVID Team lists: NASEM Standing Committee on Emerging Infectious Diseases and 21st Century Health Threats lists: NIAID Overview of Coronaviruses lists: Schema.org lists: Virus Pathogen Resource (ViPR) lists: Modeling Infectious Disease Agents Study online portal for COVID-19 lists: LitCovid lists: Broad Terra cloud commons for pathogen surveillance lists: COVID-19 research data on Figshare lists: Dimensions COVID-19 publications, datasets and clinical trials lists: COVID-19 Open Research Dataset lists: Global Initiative on Sharing All Influenza Data |
COVID-19 | NIH | Free, Freely available | SCR_018817 | SCR_018274 | Open Access Data and Computational Resources to Address COVID-19, NIH Open-Access Data and Computational Resources to Address COVID-19 | 2026-02-17 10:03:44 | 0 | ||||||
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GLYCAM-Web Resource Report Resource Website 50+ mentions |
GLYCAM-Web (RRID:SCR_018260) | data access protocol, data or information resource, topical portal, software resource, web service, portal | Web provides tools for modeling 3D structures of molecules and complexes containing carbohydrates including oligosaccharide conformation modeling and glycoprotein 3D structure modeling. Used to simplify prediction of three dimensional structures of carbohydrates and macromolecular structures involving carbohydrates. | Glycosylated SARS-Cov-2 Spike protein, SARS-Cov-2, SARS-Cov-2 Spike protein, spike protein, 3D structure, carbohydrate, oligosaccharide conformation, modeling, structure modeling, data | has parent organization: University of Georgia; Georgia; USA | COVID-19, COVID19 | NIH | Free, Freely available | SCR_018260 | GLYCAM | 2026-02-17 10:03:26 | 96 | |||||||
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National COVID Cohort Collaborative Resource Report Resource Website 100+ mentions |
National COVID Cohort Collaborative (RRID:SCR_018757) | N3C | storage service resource, data or information resource, topical portal, disease-related portal, service resource, portal, data repository | Portal for centralized national data to study COVID-19 and identify potential treatments.Centralized, secure analytics platform where patient privacy is protected. Enables collection and analysis of clinical, laboratory and diagnostic data from hospitals and health care plans. Data are provided after executing data transfer agreement with National Center for Advancing Translational Sciences. N3C is partnership among NCATS supported Clinical and Translational Science Awards Program hubs and National Center for Data to Health with overall stewardship by NCATS. | COVID-19, national data resource, study COVID-19, COVID-19 data, COVID-19 treatment identification, NCATS, clinical data, laboratory data, diagnostic data, health care, analytics platform, patient privacy | COVID-19 | NIH | r3d100013422 | https://doi.org/10.17616/R31NJMUM | SCR_018757 | 2026-02-17 10:03:32 | 115 | |||||||
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NCI Imaging Data Commons Resource Report Resource Website 1+ mentions |
NCI Imaging Data Commons (RRID:SCR_019127) | NCI IDC | storage service resource, data or information resource, topical portal, disease-related portal, service resource, portal, data repository | Portal for finding and analyzing cancer imaging data. Part of Cancer Research Data Commons to support cancer imaging research. Provides cloud based access to medical imaging data and library of analytical tools and workflows to share, analyze, and visualize multi modal imaging data from both clinical and basic cancer research studies. | Imaging Data Commons Data, cloud based data analysis, FAIR data, cancer imaging data, metadata |
uses: DICOM standard is related to: FAIRsharing is related to: Cancer Imaging Archive (TCIA) is related to: Cancer Research Data Commons |
Cancer | NIH | Free, Freely available | r3d100014074 | https://doi.org/10.17616/R31NJNCQ | SCR_019127 | National Cancer Institute Imaging Data Commons | 2026-02-17 10:03:37 | 6 | ||||
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Cancer Research Data Commons Resource Report Resource Website 1+ mentions |
Cancer Research Data Commons (RRID:SCR_019128) | CRDC | storage service resource, data or information resource, topical portal, disease-related portal, service resource, portal, data repository | Cloud based data science infrastructure that provides secure access to cancer research data from NCI programs and key external cancer programs. Serves as coordinated resource for public data sharing of NCI funded programs. Users can explore and use analytical and visualization tools for data analysis. Enables to search and aggregate data across repositories including Cancer Data Service, Clinical Trial Data Commons, Genomic Data Commons, Imaging Data Commons, Integrated Canine Data Commons, Proteomic Data Commons. |
is related to: NCI Imaging Data Commons is related to: FAIRsharing is related to: The Cancer Genome Atlas is related to: Cancer Cell Line Encyclopedia is related to: Genomic Data Commons Data Portal (GDC Data Portal) is related to: Proteomic Data Commons |
Cancer | NIH | Restricted | SCR_019128 | NCI Cancer Research Data Commons, NCI CRDC | 2026-02-17 10:03:55 | 9 | |||||||
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ApiNATOMY Resource Report Resource Website 1+ mentions |
ApiNATOMY (RRID:SCR_018998) | software application, data processing software, software resource, software toolkit, data visualization software | Software toolkit for visualizing multiscale anatomy schematics with phenotype related information. Used for visualisation of multiscale physiology circuitboards and to support clinical and scientific graphical user interfaces and dashboards for biomedical resource management and data analytics. Creates FAIR models of vascular and neural connectivity information for molecular, subcellular, cellular and tissue conduits across multiple scales. Provides interface between physiology knowledge and data relevant to physiology through intuitive graphical interface for managing semantic metadata and ontologies relevant to physiology. Brings together expertise in computer science, image processing, bioengineering and medicine to manage knowledge in physiology and pathology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Ontology visualization, physiology circuitboards visualization, biomedical resource management, data analytics, vascular connectivity, neural connectivity, physiology data, metadata, physiology ontology, |
is used by: SPARC Portal has parent organization: University College London; London; United Kingdom has parent organization: University of Auckland; Auckland; New Zealand is organization facet of: SPARC Portal |
NIH OD030541 | PMID:22616108 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_018998 | 2026-02-17 10:03:35 | 1 | ||||||||
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FAIR Data Informatics Laboratory Resource Report Resource Website 1+ mentions |
FAIR Data Informatics Laboratory (RRID:SCR_019235) | FAIR Data Informatics Laboratory, FAIR Data Informatics Lab, FDI Laboratory, FDI Lab, FDIL | data or information resource, portal, laboratory portal, organization portal | UCSD based bioinformatics lab composed of several projects in different biomedical disciplines. Established in 2008 as Neuroscience Information Framework and has since expanded to include broader field of biomedical research. Leader in developing and providing novel informatics infrastructure and tools for making data FAIR: Findable, Accessible, Interoperable and Reusable. FAIR Data informatics laboratory develops SciCrunch.org platform. | FAIR Data, Data Integration, Data Federation, RRID, Ontology, Terminology, Semantic knowledge, Knowledge Graph, Data Curation, Neuroscience Information Framework |
is related to: NIDDK Information Network (dkNET) is related to: SciCrunch Registry is related to: Neuroscience Information Framework has parent organization: University of California at San Diego; California; USA is parent organization of: Open Data Commons for Traumatic Brain Injury |
United States Veterans Association ; NIH |
Free, Freely available | SCR_019235 | 2026-02-17 10:03:39 | 1 | ||||||||
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Clearcut Resource Report Resource Website 10+ mentions |
Clearcut (RRID:SCR_016059) | software application, standalone software, data processing software, software resource, data visualization software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023.Software as a stand-alone reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm. Used in distance-based phylogenetic tree reconstruction method to process large sequence datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | rnj, phylogenetic, tree, construction, neighbor, joining, distance, method, reference, standalone, implemetation, relaxed, algorithm, phylogenetic, tree, reconstruction, sequence |
is listed by: Debian is listed by: OMICtools is related to: University of Idaho; Idaho; USA |
NIH P20 RR16448; INBRE Program of the National Center for Research Resources ; NSF EPS 00809035; NIH P20 RR16454 |
PMID:16752216 DOI:10.1007/s00239-005-0176-2 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_15083 | https://github.com/ibest/clearcut https://sources.debian.org/src/clearcut/ |
SCR_016059 | 2026-02-17 10:02:38 | 26 | ||||||
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Monocle2 Resource Report Resource Website 100+ mentions |
Monocle2 (RRID:SCR_016339) | software application, data processing software, data analysis software, software resource, software toolkit | Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations. | analysis, heterogenous, population, single, cell, gene, expression, data, large, single-cell RNA-Seq, transcriptional, regulation, heterogen | NIH DP2 HD088158; Alfred P. Sloan Foundation Research Fellowship |
PMID:24658644 | Free, Available for download, Freely available | SCR_016339 | Monocle 2 | 2026-02-17 10:03:23 | 203 | ||||||||
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MAST Resource Report Resource Website 50+ mentions |
MAST (RRID:SCR_016340) | MAST | software application, data processing software, data analysis software, software resource, software toolkit | Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. | model, based, analysis, single, cell, transcriptomics, RNA, sequencing, data | NIH DP2 DE023321; NIBIB R01 EB008400; Bill and Melinda Gates Foundation OPP1032317 |
DOI:10.5281/zenodo.18539 | Free, Available for download, Freely available | https://github.com/RGLab/MAST/ | SCR_016340 | Model based Analysis of Single Cell Transcriptomics | 2026-02-17 10:03:00 | 86 |
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