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http://www.jcvi.org/mpidb

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.

Proper citation: MPIDB (RRID:SCR_001898) Copy   

•   Source: SciCrunch Registry

http://ecogene.org/

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.

Proper citation: EcoGene (RRID:SCR_002437) Copy   

•   Source: SciCrunch Registry

http://dejavu.vbi.vt.edu/dejavu/

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.

Proper citation: Deja Vu: a Database of Highly Similar and Duplicate Citations (RRID:SCR_002292) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/proteinclusters

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

Proper citation: Protein Clusters (RRID:SCR_003459) Copy   

•   Source: SciCrunch Registry

http://senselab.med.yale.edu/brainpharm/

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.

Proper citation: Brain Pharmacological Database (RRID:SCR_003042) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/gene/about-generif

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.

Proper citation: Gene Reference into Function (RRID:SCR_003436) Copy   

•   Source: SciCrunch Registry

https://www.jax.org/research-and-faculty/resources/knockout-mouse-project/high-throughput-production

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.

Proper citation: Knockout Mouse Project (RRID:SCR_005571) Copy   

•   Source: SciCrunch Registry

http://www.nihclinicalcollection.com

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.

Proper citation: NIH Clinical Collection (RRID:SCR_007349) Copy   

•   Source: SciCrunch Registry

http://drugcentral.org/

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.

Proper citation: DrugCentral (RRID:SCR_015663) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.hungry.com/clearcut/

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.

Proper citation: Clearcut (RRID:SCR_016059) Copy   

•   Source: SciCrunch Registry

http://cole-trapnell-lab.github.io/monocle-release/docs/

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.

Proper citation: Monocle2 (RRID:SCR_016339) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/MAST.html

Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.

Proper citation: MAST (RRID:SCR_016340) Copy   

•   Source: SciCrunch Registry

http://www.metabolomicsworkbench.org

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.

Proper citation: Metabolomics Workbench (RRID:SCR_013794) Copy   

•   Source: SciCrunch Registry

http://chavi-id.org

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.

Proper citation: CHAVI-ID (RRID:SCR_014047) Copy   

•   Source: SciCrunch Registry

https://datajoint.org/

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.

Proper citation: DataJoint (RRID:SCR_014543) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/pubmedcommons/

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.

Proper citation: Pubmed Commons (RRID:SCR_014021) Copy   

•   Source: SciCrunch Registry

https://metagenote.niaid.nih.gov/

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.

Proper citation: METAGENOTE (RRID:SCR_018494) Copy   

•   Source: SciCrunch Registry

https://commonfund.nih.gov/hmp/

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.

Proper citation: Human Microbiome Project (RRID:SCR_012956) Copy   

•   Source: SciCrunch Registry

http://nhprtr.org/

Nonhuman Primate reference transcriptome resource consisting of deep sequencing complete transcriptomes (RNA-seq) from multiple NHP species.

Proper citation: Nonhuman Primate Reference Transcriptome Resource (RRID:SCR_017534) Copy   

•   Source: SciCrunch Registry

https://cic.ini.usc.edu/

Project to create complete mesoscale connectivity atlas of the C57Black/6 mouse brain and to subsequently generate its global neural networks.

Proper citation: Mouse Connectome Project (RRID:SCR_017313) Copy   

•   Source: SciCrunch Registry