Biological General Repository for Interaction Datasets (BioGRID)

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,BioGRID is an online interaction repository with data on raw protein and genetic interactions from major model organism species. All interaction data are freely provided through our search index and available via download in a wide variety of standardized formats.,

MaizeGDB

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,MaizeGDB is a community-oriented, long-term, federally funded informatics service to researchers focused on the crop plant and model organism Zea mays. Genomic, genetic, sequence, germplasm, gene product, metabolic pathways, functional characterization, literature reference, diversity, and expression are among the datatypes stored at MaizeGDB. At the project's website are custom interfaces enabling researchers to browse data and to seek out specific information matching explicit search criteria. First released in 1991 with the name MaizeDB, the Maize Genetics and Genomics Database, now MaizeGDB (since 2003), is funded, developed, and hosted by the USDA-ARS located at Ames, Iowa.,,

Genome Workbench

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An integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix these data with your own data.

Genome

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This resource organizes NCBI information, resources, data, and tools and utilities on genomes including sequences, maps, chromosomes, assemblies, and annotations. Sequence and map data from the whole genomes of organisms. The genomes represent both completely sequenced organisms and those for which sequencing is in progress.

Gene Expression Omnibus (GEO)

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,Gene Expression Omnibus is a public functional genomics data repository supporting MIAME-compliant submissions of array- and sequence-based data. Tools are provided to help users query and download experiments and curated gene expression profiles.,

Genome Assembly Data

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A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. Genomes FTP site FAQ at https://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/

Genome In A Bottle - v2.0 Genome Stratifications (Deprecated)

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These stratification BED files from the Global Alliance for Genomics and Health (GA4GH) Benchmarking Team and the Genome in a Bottle Consortium are intended as a standard resource of BED files for use in stratifying true positive, false positive, and false negative variant calls. These v2.0 stratification BED files from the Global Alliance for Genomics and Health (GA4GH) Benchmarking Team and the Genome in a Bottle Consortium are intended as a standard resource of BED files for use in stratifying true positive, false positive, and false negative variant calls. v2.0 stratifications have been deprecated and replaced by v3.0 genome-stratifications.

Watford Novel application NPMI Biomedlit genesets usecase breast cancer

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We present a novel use of normalized pointwise mutual information (NPMI) to mine biomedical literature for gene associations with biological concepts as represented by Medical Subject Headings (MeSH terms) in PubMed. This dataset is associated with the following publication: Watford, S., R. Grashow, V. De La Rosa, R. Rudel, K. Paul-Friedman, and M. Martin. Novel application of normalized pointwise mutual information (NPMI) to mine biomedical literature for gene sets associated with disease: Use case in breast carcinogenesis. Computational Toxicology. Elsevier B.V., Amsterdam, NETHERLANDS, 7: 46-57, (2018).

Genome In A Bottle - v3.0 Genome Stratifications

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These v3.0 stratification BED files from the Global Alliance for Genomic Health (GA4GH) Benchmarking Team, the Genome in a Bottle Consortium and the Telomere-to-Telomere Consortium are intended as a standard resource of BED files for use in stratifying true positive, false positive, and false negative variant calls in challenging and targeted regions of the the genome. v3.0 stratifications contain new and revised stratification files and replace v2.0 stratifications.