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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NIH Figshare Archive Resource Report Resource Website 1+ mentions |
NIH Figshare Archive (RRID:SCR_017580) | NIH Figshare | data or information resource, data repository, database, service resource, storage service resource | 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 | 2026-09-05 06:28:26 | 9 | |||||||
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AmoebaDB Resource Report Resource Website 1+ mentions |
AmoebaDB (RRID:SCR_017592) | analysis service resource, data or information resource, database, production service resource, 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 |
Department of Health and Human Services ; NIDA ; NIH |
PMID:20974635 | Free, Freely available | biotools:amoebadb, r3d100012457 | https://bio.tools/amoebadb, https://doi.org/10.17616/R3PX9Q | SCR_017592 | 2026-09-05 06:28:26 | 8 | ||||||
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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 | data repository, service resource, 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 | 2026-09-05 06:28:26 | 58 | ||||||
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National COVID Cohort Collaborative Resource Report Resource Website 100+ mentions |
National COVID Cohort Collaborative (RRID:SCR_018757) | N3C | data or information resource, data repository, disease-related portal, portal, service resource, storage service resource, topical portal | 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 | 2026-09-05 06:28:42 | 116 | |||||||
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ApiNATOMY Resource Report Resource Website 1+ mentions |
ApiNATOMY (RRID:SCR_018998) | data processing software, data visualization software, software application, software resource, software toolkit | 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 | 2026-09-05 06:28:45 | 1 | ||||||||
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NCI Imaging Data Commons Resource Report Resource Website 1+ mentions |
NCI Imaging Data Commons (RRID:SCR_019127) | NCI IDC | data or information resource, data repository, disease-related portal, portal, service resource, storage service resource, topical portal | 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 | 2026-09-05 06:28:46 | 9 | ||||
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Cancer Research Data Commons Resource Report Resource Website 10+ mentions |
Cancer Research Data Commons (RRID:SCR_019128) | CRDC | data or information resource, data repository, disease-related portal, portal, service resource, storage service resource, topical portal | 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 | 2026-09-05 06:28:46 | 13 | |||||||
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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, laboratory portal, organization portal, 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 |
NIH ; United States Veterans Association |
Free, Freely available | SCR_019235 | 2026-09-05 06:28:47 | 1 | ||||||||
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Agilent: Bravo NGS Resource Report Resource Website 1+ mentions |
Agilent: Bravo NGS (RRID:SCR_019473) | instrument resource | Workstation is built on Bravo automated liquid handling robot preconfigured for library prep and target enrichment using Next-Generation Sequencing protocols. Workstation modules add microplate handling. Intuitive Agilent VWorks software enables setup of preprogrammed protocols and allows users to create custom protocols., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Agilent, NGS, Instrument Equipment | NIH GM137200; NIH U24NS120055 |
THIS RESOURCE IS NO LONGER IN SERVICE | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_019473.pdf | SCR_019475, Model_Number_Agilent_Bravo_NGS | SCR_019473 | Agilent Bravo NGS Workstation | 2026-09-05 06:28:52 | 5 | |||||||
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METAGENOTE Resource Report Resource Website 1+ mentions |
METAGENOTE (RRID:SCR_018494) | data access protocol, software resource, web service | Quick and intuitive way to annotate data from genomics studies including microbiome. Project to aid researchers in applying standardized metadata describing what, where, how, and when of samples collected in genomics study. Collection of METAdata of GEnomics studies on web based NOTEbook. Metadata are stored in centralized repository and validated according to guidelines from Genomics Standard Consortium, which are also supported by repositories and large microbiome initiatives such as NCBI, European Bioinformatics Institute (EBI), and Earth Microbiome Project. Upon request from researchers, data will also be submitted for publication via NCBI Sequence Read Archive (SRA) repository. | Annotate data, genomics study, microbiome, metadata, genomics, data |
is related to: NCBI Sequence Read Archive (SRA) is related to: NCBI |
NIH | Free, Freely available | SCR_018494 | METAdata of GEnomics studies on a web based NOTEbook | 2026-09-05 06:30:10 | 1 | ||||||||
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DrugCentral Resource Report Resource Website 100+ mentions |
DrugCentral (RRID:SCR_015663) | data or information resource, database, software resource, web application | Database of drug information created and maintained by the Division of Translational Informatics at University of New Mexico. It provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic action. | drug, chemical, pharmaceutical, active ingredient, translational informatics, FASEB list | has parent organization: University of New Mexico; New Mexico; USA | NIH 1U54CA189205-01 | PMID:27789690 | Freely Available, Free, Available for download | SCR_015663 | Drug Central, DrugCentral: Online Drug Compendium | 2026-09-05 06:27:57 | 129 | |||||||
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Clearcut Resource Report Resource Website 10+ mentions |
Clearcut (RRID:SCR_016059) | data processing software, data visualization software, software application, software resource, standalone 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 |
INBRE Program of the National Center for Research Resources ; NIH P20 RR16448; NIH P20 RR16454; NSF EPS 00809035 |
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 | 2026-09-05 06:28:03 | 26 | ||||||
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Monocle2 Resource Report Resource Website 100+ mentions |
Monocle2 (RRID:SCR_016339) | data analysis software, data processing software, software application, 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 | Alfred P. Sloan Foundation Research Fellowship ; NIH DP2 HD088158 |
PMID:24658644 | Free, Available for download, Freely available | SCR_016339 | Monocle 2 | 2026-09-05 06:28:07 | 227 | ||||||||
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MAST Resource Report Resource Website 100+ mentions |
MAST (RRID:SCR_016340) | MAST | data analysis software, data processing software, software application, 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 | Bill and Melinda Gates Foundation OPP1032317; NIBIB R01 EB008400; NIH DP2 DE023321 |
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 | 2026-09-05 06:28:07 | 106 | ||||||
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MAxEntScan Resource Report Resource Website 50+ mentions |
MAxEntScan (RRID:SCR_016707) | MAxEntScan | service resource, simulation software, software application, software resource | Software tool as a framework for modeling the sequences of short sequence motifs based on the maximum entropy principle (MEP). Used for sequence motifs such as those involved in RNA splicing. | modeling, sequence, short, motif, maximum, entropy, principle, MEP, RNA, splicing |
is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
Lee Kuan Yew Scholarship for the goverment of Singapore ; NIH ; NSF Grant 0218506 |
PMID:15285897 | Free, Available for download, Freely available | SCR_016707 | Maximum Entropy Scan, MAxEntScan, MAximumEntropyScan | 2026-09-05 06:28:13 | 70 | ||||||
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COSMIIC HORNET Resource Report Resource Website |
COSMIIC HORNET (RRID:SCR_023679) | COSMIIC | software repository, software resource | Open source neurostimulation and recording hardware instrument platform. Part of the SPARC project. COSMIIC is based on the Networked Neuroprosthesis developed at Case Western Reserve University. | Networked Neuroprosthesis, neurostimulation and recording hardware, instrument platform, SPARC project, | is related to: Case Western Reserve University; Ohio; USA | NIH U41NS129436 | Free, Freely available | SCR_023679 | Cleveland Open Source Modular Implant Innovators Community | 2026-09-05 06:33:15 | 0 | |||||||
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GlimmerHMM Resource Report Resource Website 500+ mentions |
GlimmerHMM (RRID:SCR_002654) | GlimmerHMM | software resource, source code | A gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single). | gene, hidden markov model |
is related to: Glimmer has parent organization: Johns Hopkins University; Maryland; USA |
NIH ; NLM R01-LM06845; NLM R01-LM007938 |
PMID:15145805 | Free, Available for download, Freely available | nlx_156092 | SCR_002654 | GlimmerHMM - Eukaryotic Gene-Finding System | 2026-09-05 06:33:23 | 643 | |||||
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NIH Data Sharing Repositories Resource Report Resource Website 1+ mentions |
NIH Data Sharing Repositories (RRID:SCR_003551) | NIH Data Sharing Repositories | data or information resource, data set | A listing of NIH supported data sharing repositories that make data accessible for reuse. Most accept submissions of appropriate data from NIH-funded investigators (and others), but some restrict data submission to only those researchers involved in a specific research network. Also included are resources that aggregate information about biomedical data and information sharing systems. The table can be sorted according by name and by NIH Institute or Center and may be searched using keywords so that you can find repositories more relevant to your data. Links are provided to information about submitting data to and accessing data from the listed repositories. Additional information about the repositories and points-of-contact for further information or inquiries can be found on the websites of the individual repositories. | data repository |
lists: NIDDK Information Network (dkNET) lists: Nuclear Receptor Signaling Atlas lists: Biospecimens/Biorepositories: Rare Disease-HUB (RD-HUB) lists: Eukaryotic Pathogen Database Resources lists: Immune Epitope Database and Analysis Resource (IEDB) lists: LONI Image and Data Archive lists: BEI Resource Repository lists: Nanomaterial Registry lists: Metabolomics Workbench lists: National Database for Clinical Trials related to Mental Illness lists: RDoCdb lists: Database of Interacting Proteins (DIP) lists: NIH MRI Study of Normal Brain Development lists: PubChem lists: 1000 Functional Connectomes Project lists: Parkinson's Progression Markers Initiative lists: Mouse Genome Informatics (MGI) lists: Federal Interagency Traumatic Brain Injury Research Informatics System lists: NIH Human Connectome Project lists: Biological General Repository for Interaction Datasets (BioGRID) lists: Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) lists: Nanomaterial Registry is related to: NIH MRI Study of Normal Brain Development is related to: Eukaryotic Pathogen Database Resources is related to: Parkinson's Progression Markers Initiative is related to: Federal Interagency Traumatic Brain Injury Research Informatics System is related to: NIH Human Connectome Project is related to: National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) is related to: Cancer Imaging Archive (TCIA) is related to: Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) is related to: NIDDK Information Network (dkNET) is related to: UniProt is related to: GeneNetwork is related to: Zebrafish Information Network (ZFIN) is related to: WormBase is related to: Database of Interacting Proteins (DIP) is related to: iDASH is related to: PubChem is related to: CardioVascular Research Grid (CVRG) is related to: 1000 Functional Connectomes Project is related to: Mouse Genome Informatics (MGI) is related to: FlyBase is related to: PeptideAtlas is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: GRDR is related to: National Institute on Drug Abuse Center for Genetic Studies is related to: BEI Resource Repository has parent organization: National Library of Medicine |
NIH | nlx_157683 | SCR_003551 | 2026-09-05 06:33:24 | 5 | ||||||||
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neurospy Resource Report Resource Website |
neurospy (RRID:SCR_007016) | neurospy | software resource, source code | neurospy is a free software for functional imaging of fast neuronal activity. neurospy is a modular cross-platform application framework written in Java for the NetBeans Platform. At this time it runs on Windows XP-based LeCroy oscilloscopes and drives acousto-optic scanners via USB using the Analog Devices 9959 Direct Digital Synthesis chip. This combination makes one of the most powerful systems for scanning microscopy available today at any price. neurospy is very easy to port to other kinds of acquisition and scanning hardware. | imaging, neuron, microscopy, functional imaging, java, neuronal activity |
has parent organization: SourceForge has parent organization: Howard Hughes Medical Institute has parent organization: Salk Institute for Biological Studies has parent organization: University of California at San Diego; California; USA |
Howard Hughes Medical Institute ; NIH |
PMID:17684546 | Open unspecified license | nlx_149367 | SCR_007016 | 2026-09-05 06:33:27 | 0 | ||||||
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Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING Resource Report Resource Website 1+ mentions |
Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING (RRID:SCR_007412) | data or information resource, data set | Data sets, tools and computational techniques for modeling of protein interactions, including docking benchmarks, docking decoys and docking templates. Adequate computational techniques for modeling of protein interactions are important because of the growing number of known protein 3D structures, particularly in the context of structural genomics. The first release of the DOCKGROUND resource (Douguet et al., Bioinformatics 2006; 22:2612-2618) implemented a comprehensive database of cocrystallized (bound) protein-protein complexes in a relational database of annotated structures. Additional releases added features to the set of bound structures, such as regularly updated downloadable datasets: automatically generated nonredundant set, built according to most common criteria, and a manually curated set that includes only biological nonobligate complexes along with a number of additional useful characteristics. Also included are unbound (experimental and simulated) protein-protein complexes. Complexes from the bound dataset are used to identify crystallized unbound analogs. If such analogs do not exist, the unbound structures are simulated by rotamer library optimization. Thus, the database contains comprehensive sets of complexes suitable for large scale benchmarking of docking algorithms. Advanced methodologies for simulating unbound conformations are being explored for the next release. The Dockground project is developed by the Vakser lab at the Center for Bioinformatics at the University of Kansas. Parts of Dockground were co-developed by Dominique Douguet from the Center of Structural Biochemistry (INSERM U554 - CNRS UMR5048), Montpellier, France. | protein 3d structure, protein interaction, protein interface, protein model, structural genomics, co-crystallized, protein complex, protein recognition, protein modeling, structure prediction, protein-protein complex, benchmark |
is listed by: 3DVC is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of Kansas; Kansas; USA |
NIH ; NIGMS R01 GM074255; NIGMS R01 GM61889 |
PMID:17803215 PMID:16928732 |
nif-0000-02757 | SCR_007412 | Dockground, Dockground: Benchmarks Docoys Templates other knowledge resources for DOCKING, Dockground: Benchmarks Docoys Templates and other knowledge resources for DOCKING | 2026-09-05 06:33:28 | 8 |
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