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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MPIDB Resource Report Resource Website 1+ mentions |
MPIDB (RRID:SCR_001898) | MPIDB | data or information resource, database | Database that collects and provides all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, co-purification, and 3D domain contacts (iPfam, 3did). (spoke/matrix) binary interactions inferred from pull-down experiments are not included. | 3d domain, conservation, co-purification, interaction, microbial, protein, microbial interaction, protein interaction, interaction conservation, interaction co-purification, 3d domain contact, protein-protein interaction, microbial protein, microbiology |
is listed by: re3data.org is related to: IMEx - The International Molecular Exchange Consortium is related to: IntAct is related to: Database of Interacting Proteins (DIP) is related to: BIND is related to: MINT is related to: Interaction Reference Index is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry has parent organization: J. Craig Venter Institute |
J. Craig Venter Institute ; Indgen Life Technologies ; NIH ; NIMH R01GM79710 |
PMID:18556668 | THIS RESOURCE IS NO LONGER IN SERVICE | r3d100010673, nif-0000-10467 | http://jcvi.org/mpidb/ | SCR_001898 | The Microbial Protein Interaction Database, Microbial Protein Interaction Database | 2026-07-28 09:40:27 | 5 | ||||
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EcoGene Resource Report Resource Website 50+ mentions |
EcoGene (RRID:SCR_002437) | ECK, ECOGENE, ECOGENE G | data or information resource, database | Database that contains updated information about the Escherichia coli K-12 genome and proteome sequences, including extensive gene bibliographies. Users are able to download customized tables, perform Boolean query comparisons, generate sets of paired DNA sequences, and download any E. coli K-12 genomic DNA sub-sequence. BLAST functions, microarray data, an alphabetical index of genes, and gene overlap queries are also available. The Database Table Downloads Page provides a full list of EG numbers cross-referenced to the new cross-database ECK numbers and other common accession numbers, as well as gene names and synonyms. Monthly release archival downloads are available, but the live, daily updated version of EcoGene is the default mysql database for download queries. | life sciences, genomics, proteomics, gene, gene expression, genetics, protein, protein binding, protein-protein interaction, membrane, rna, dna, structure, function, functional annotation, annotation, blast, FASEB list |
is listed by: re3data.org is related to: RefSeq is related to: Colibri has parent organization: University of Miami Miller School of Medicine; Florida; USA |
NIH ; Lucille P. Markey Foundation ; NIGMS 5-R01-GM58560-05 |
PMID:23197660 PMID:10592181 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02784, r3d100010546 | https://doi.org/10.17616/R3KP5V | http://bmb.med.miami.edu/ http://bmb.med.miami.edu/EcoGene/EcoWeb/ http://www.ecogene.org/old/ | SCR_002437 | EcoGene Database of Escherichia coli Sequence and Function | 2026-07-28 09:40:25 | 56 | |||
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Deja Vu: a Database of Highly Similar and Duplicate Citations Resource Report Resource Website |
Deja Vu: a Database of Highly Similar and Duplicate Citations (RRID:SCR_002292) | data or information resource, database | Deja vu is a database of extremely similar Medline citations. Many, but not all, of which contain instances of duplicate publication and potential plagiarism. Deja vu is a dynamic resource for the community, with manual curation ongoing continuously, and we welcome input and comments. In the scientific research community plagiarism and multiple publications of the same data are considered unacceptable practices and can result in tremendous misunderstanding and waste of time and energy. Our peers and the public have high expectations for the performance and behavior of scientists during the execution and reporting of research. With little chance for discovery and decreasing budgets, yet sustained pressure to publish, or without a clear understanding of acceptable publication practices, the unethical practices of duplicate publication and plagiarism can be enticing to some. Until now, discovery has been through serendipity alone, so these practices have largely gone unchecked. | duplicate publication, plagiarism, publication | Hudson Foundation ; NIH |
nif-0000-02718 | SCR_002292 | Deja Vu, Deja Vu: a Database of Highly Similar Citations | 2026-07-28 09:40:35 | 0 | |||||||||
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Protein Clusters Resource Report Resource Website 1+ mentions |
Protein Clusters (RRID:SCR_003459) | ProtClustDB | data or information resource, database | Database of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTP | bacteriophage, mitochondrial organelle, chloroplast organelle, plasmid, phylogeny, nucleotide sequence, chloroplast, dna, virus, genome, organelle, gold standard |
is listed by: re3data.org has parent organization: NCBI |
NIH ; Intramural Research Program ; NLM |
PMID:18940865 | Free, Available for download, Freely available | nif-0000-03354, r3d100010861 | https://doi.org/10.17616/R3TS52 | SCR_003459 | Protein Clusters Database, NCBI Protein Clusters, Entrez Protein Clusters | 2026-07-28 09:40:43 | 4 | ||||
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Brain Pharmacological Database Resource Report Resource Website |
Brain Pharmacological Database (RRID:SCR_003042) | data or information resource, database | A database to support research on drugs for the treatment of different neurological disorders. It contains agents that act on neuronal receptors and signal transduction pathways in the normal brain and in nervous disorders. It enables searches for drug actions at the level of key molecular constituents, cell compartments and individual cells, with links to models of these actions. | database, brain mapping, neurological disorder, neural receptor, signal transduction pathway, development, ion channel, motor cortex, neuroinformatics, simulation, neurons, pathological mechanism, pathological element, pharmacological agent, alzheimer's disease | has parent organization: Yale University; Connecticut; USA | Alzheimer's disease | NIH ; NIDCD RO1 DC 009977 |
Free, Freely available | nif-0000-00168 | https://dknet.org/data/record/nlx_144509-1/SCR_003042/resolver | SCR_003042 | BrainPharm, Brain Pharmacology Database | 2026-07-28 09:40:43 | 0 | |||||
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Gene Reference into Function Resource Report Resource Website 10+ mentions |
Gene Reference into Function (RRID:SCR_003436) | GeneRIF | data or information resource, database | A database and annotation tool that provides a simple mechanism to allow scientists to add to the functional annotation of genes described in Gene. To be processed, a valid Gene ID must exist for the specific gene, or the Gene staff must have assigned an overall Gene ID to the species. The latter case is implemented via records in Gene with the symbol NEWENTRY. | functional annotation, gene, function |
is related to: Entrez Gene has parent organization: NCBI |
NIH | PMID:17094227 PMID:23725347 |
Free, Freely available | nlx_157765 | SCR_003436 | GeneRIF: Gene Reference into Function | 2026-07-28 09:40:42 | 14 | |||||
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Knockout Mouse Project Resource Report Resource Website 10+ mentions |
Knockout Mouse Project (RRID:SCR_005571) | KOMP, NIH KOMP | project portal, data or information resource, portal | Project is providing critical tools for understanding gene function and genetic causes of human diseases. Project KOMP is focused on generating targeted knockout mutations in mouse ES cells. Second phase, KOMP2, relies upon successful generation of strains of knockout mice from these ES cells. Information from JAX about their contributions to KOMP project. | Generating, knockout, mutation, mouse, ES cell, embryonic, stem, c57bl/6 |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources is related to: KOMP2 is related to: KOMP2 is related to: StatPackets has parent organization: International Knockout Mouse Consortium has parent organization: National Institutes of Health is parent organization of: Knockout Mouse Project Repository is parent organization of: Knockout Mouse Project Repository at JAX |
NIH ; NIH Blueprint for Neuroscience Research |
Free, Freely available | nlx_145296, SCR_017527 | https://grants.nih.gov/grants/guide/rfa-files/rfa-rr-06-005.html | http://www.nih.gov/science/models/mouse/knockout/index.html | SCR_005571 | NIH Knockout Mouse Project, Knock-Out Mouse Project | 2026-07-28 09:41:25 | 10 | ||||
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NIH Clinical Collection Resource Report Resource Website 10+ mentions |
NIH Clinical Collection (RRID:SCR_007349) | NCC | reagent supplier, material resource | A plated array of approximately 450 small molecules that have a history of use in human clinical trials. The collection was assembled by the National Institutes of Health (NIH) through the Molecular Libraries Roadmap Initiative as part of its mission to enable the use of compound screens in biomedical research. Similar collections of FDA approved drugs have proven to be rich sources of undiscovered bioactivity and therapeutic potential. The clinically tested compounds in the NCC are highly drug-like with known safety profiles. These compounds can provide excellent starting points for medicinal chemistry optimization and, for high-affinity targets, may even be appropriate for direct human use in new disease areas. | clinical, collection, drug, compound, chemistry, medicinal chemistry, target, affinity, human, disease, disorder, small molecule | is related to: Molecular Libraries Program | NIH | nif-0000-00254 | SCR_007349 | 2026-07-28 09:41:58 | 14 | ||||||||
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DrugCentral Resource Report Resource Website 100+ mentions |
DrugCentral (RRID:SCR_015663) | database, data or information resource, web application, software resource | 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 | 2026-07-28 09:43:55 | 116 | |||||||
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Clearcut Resource Report Resource Website 10+ mentions |
Clearcut (RRID:SCR_016059) | software application, software resource, data processing software, data visualization software, 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 |
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 | 2026-07-28 09:44:12 | 26 | ||||||
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Monocle2 Resource Report Resource Website 100+ mentions |
Monocle2 (RRID:SCR_016339) | software application, data analysis software, software resource, data processing software, 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 | 2026-07-28 09:44:17 | 203 | ||||||||
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MAST Resource Report Resource Website 50+ mentions |
MAST (RRID:SCR_016340) | MAST | software application, data analysis software, software resource, data processing software, 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 | 2026-07-28 09:44:11 | 86 | ||||||
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Metabolomics Workbench Resource Report Resource Website 500+ mentions |
Metabolomics Workbench (RRID:SCR_013794) | MetWB | service resource, data or information resource, storage service resource, data repository | Repository for metabolomics data and metadata which provides analysis tools and access to various resources. NIH grantees may upload data and general users can search metabolomics database. Provides protocols for sample preparation and analysis, information about NIH Metabolomics Program, data sharing guidelines, funding opportunities, services offered by its Regional Comprehensive Metabolomics Resource Cores (RCMRC)s, and training workshops. | repository, metabolomics, database, funding, training, protocol, bio.tools, FASEB list, DRKB |
is used by: NIH Heal Project is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases lists: NIH Metabolomics program lists: MetaCore lists: JMP lists: STATISTICA lists: Spotfire lists: Coordination of Standards in Metabolomics lists: MetaboLights lists: MetabolomeXchange lists: Metabolomics Society lists: Birmingham Metabolite Library lists: Glycan Mass Spectral Database (GMDB) lists: Mass Spectral Library lists: mzCloud lists: MetabolomeExpress lists: Spectral Database System (SDBS) lists: CTSgetR lists: Hierarchical Clustering lists: imDEV lists: Linear Discriminant Analysis lists: Principal Components Analysis lists: mwtabR lists: 3Omics lists: ACD/ NMR Processor lists: NIST Mass Spectrometry Data Center lists: Chemical Translation Service lists: Chenomx NMR Suite lists: DeviumWeb lists: MBRole lists: MetaMapR lists: MetaP lists: Metscape lists: SIMCA lists: TeachingDemos is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is listed by: re3data.org is listed by: DataCite has parent organization: University of California; California; USA is parent organization of: Metabolomics Workbench Metabolite Database |
NIH ; NIDDK DK141185 |
Free, Freely available | biotools:Metabolomics_Workbench, r3d100012314 | https://bio.tools/Metabolomics_Workbench, https://api.datacite.org/dois?prefix=10.21228 | SCR_013794 | Metabolomics Workbench, MetWB, UCSD Metabolomics Workbench, Metabolomics Workbench (MetWB) | 2026-07-28 09:43:38 | 534 | |||||
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CHAVI-ID Resource Report Resource Website |
CHAVI-ID (RRID:SCR_014047) | data or information resource, organization portal, consortium, portal | A consortium whose goal is to further HIV research and accelerate the development of a preventative HIV vaccine. Its main research target is to define immunogens and immunization regimens that induce sustained HIV cross-protective B cell and CD4+ T cell responses. | HIV, AIDS, HIV/AIDS, immunogen, immunization, vaccine, B cell, CD4+ T cell | is related to: bNAber | HIV/AIDS | NIH | SCR_014047 | Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps CHAVI-ID | 2026-07-28 09:43:41 | 0 | ||||||||
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DataJoint Resource Report Resource Website 10+ mentions |
DataJoint (RRID:SCR_014543) | software application, software resource, data management software | MATLAB and Python 3 high-level programming interface for MySQL databases to support data processing chains in science labs. Specifically designed to provide robust and intuitive data model for scientific data processing chains.Used for scientific data pipelines and workflow management. | programming interface, mysql, data processing chain, data model, MATLAB, Python, workflow management | is used by: DataJoint Elements | NIH U24 NS116470 | DOI:10.1101/031658 | Free, Freely available | SCR_014543 | DataJoint: Data management for science labs | 2026-07-28 09:43:53 | 35 | |||||||
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Pubmed Commons Resource Report Resource Website 1+ mentions |
Pubmed Commons (RRID:SCR_014021) | data or information resource, narrative resource, forum, discussion | A forum where authors who have published in PubMed may comment on any publication in PubMed. Members of PubMed Commons are not anonymous and must agree to certain terms and guidelines concerning appropriate and inapproriate comments. | forum, PubMed, commuication |
is listed by: Connected Researchers is related to: PubMed is related to: Connected Researchers |
NIH ; NLM |
Free, Membership required, The community can contribute to this resource | SCR_014021 | 2026-07-28 09:43:41 | 3 | |||||||||
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METAGENOTE Resource Report Resource Website 1+ mentions |
METAGENOTE (RRID:SCR_018494) | software resource, data access protocol, 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 | 2026-07-28 09:44:41 | 1 | ||||||||
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Human Microbiome Project Resource Report Resource Website 100+ mentions |
Human Microbiome Project (RRID:SCR_012956) | HMP, NIH HMP, HMP1 | project portal, data or information resource, portal | NIH Project to generate resources to characterize the human microbiota and to analyze its role in human health and disease at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract using metagenomic and traditional approach to genomic DNA sequencing studies.HMP was supported by the Common Fund from 2007 to 2016. | generate, resource, human, body, microbiota, analyze, health, disease, metagenomic, DNA, sequesncing, data |
lists: Pathogen Portal lists: DNACLUST lists: QIIME lists: mothur lists: Greengenes lists: Ribosomal Database Project lists: DeconSeq lists: FragGeneScan lists: MetAMOS lists: MetaPhlAn lists: MetaPhyler lists: METAREP lists: PRINSEQ lists: TagCleaner lists: BioCyc lists: MG-RAST lists: Core Gene Evaluation Script lists: IMG System lists: RAST Server lists: GINGKO lists: inVUE lists: LEfSe lists: Metastats lists: MicrobiomeUtilities lists: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP lists: HMPTrees lists: Simrank lists: speciateIT lists: Unifrac lists: Fast-Unifrac lists: SitePainter lists: BMTagger lists: HUMAnN lists: Metapath lists: IMG System is related to: biobakery is related to: Integrative Human Microbiome Project is related to: MicrobiomeDB is related to: Broad Institute Genomics Platform has parent organization: National Institutes of Health is parent organization of: HMP Data Analysis and Coordination Center |
NIH | nif-0000-25316 | https://www.hmpdacc.org/ihmp/, https://www.hmpdacc.org/hmp | http://nihroadmap.nih.gov/hmp/ | SCR_012956 | Human Microbiome Project, NIH HMP, HMP1, HMP, NIH Human Microbiome Project | 2026-07-28 09:43:20 | 385 | |||||
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Nonhuman Primate Reference Transcriptome Resource Resource Report Resource Website 10+ mentions |
Nonhuman Primate Reference Transcriptome Resource (RRID:SCR_017534) | NHPRTR | project portal, data or information resource, portal | Nonhuman Primate reference transcriptome resource consisting of deep sequencing complete transcriptomes (RNA-seq) from multiple NHP species. | Nonhuman, primate, reference, transcriptome, deep, sequencing, RNAseq, data, species | NIH | Free, Freely available | SCR_017534 | Nonhuman Primate Reference Transcriptome Resource | 2026-07-28 09:44:37 | 10 | ||||||||
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Mouse Connectome Project Resource Report Resource Website |
Mouse Connectome Project (RRID:SCR_017313) | MCP | project portal, data or information resource, portal | Project to create complete mesoscale connectivity atlas of the C57Black/6 mouse brain and to subsequently generate its global neural networks. | mesoscale, connectivity, atlas, C57Black/6, mouse, brain, neural, network |
is used by: BICCN has parent organization: University of Southern California; Los Angeles; USA |
NIH | Free, Freely available | SCR_017313 | The Mouse Connectome Project, Mouse Connectome Project | 2026-07-28 09:44:33 | 0 |
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