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Ag Data Commons Maintenance - Friday 03/31/23

The Ag Data Commons website and application may experience brief, intermittent outages due to network issues. Avoid adding or editing datasets during this period to prevent losing information.. We apologize for the inconvenience. This notice will be removed once the issue is resolved.

Data from: Taxonomic, geographic, and diversity trends for exotic plant pests in recent biosurveillance articles

    PestLens is a Plant Protection and Quarantine (PPQ) biosurveillance system wherein analysts search online, open-source material for information on exotic plant pests that have relevance to plant health in the United States (https://pestlens.info/). The objectives are to provide early-warning information about those pests, and to facilitate timely and appropriate safeguarding responses.

    Data from: United States wildlife and wildlife product imports from 2000–2014

      Data are presented on 15 years of the importation of wildlife and their derived products into the United States (2000–2014), originally collected by the United States Fish and Wildlife Service. These data include >2 million wildlife or wildlife product shipments, representing >60 biological classes and >3.2 billion live organisms. The data were curated and cleaned, and taxonomic information added to improve usability.

      CottonGen Sequence Retrieval

        Sequence Retrieval allows users to download nucleotide and protein sequences including chromosomes, scaffolds, genes, mRNAs, transcript coding sequences, protein, reftrans contigs and unigene contigs. For the sequences aligned to larger sequences, such as genes, mRNAs and transcript coding sequences, a numeric value specifying the number of upstream bases and downstream bases can be entered.

        CottonGen Map Viewer

          MapViewer is a graphical tool for viewing and comparing *Gossypium* spp. genetic maps. It includes dynamically scrollable maps, correspondence matrices, dot plots, links to details about map features, and exporting functionality. It was developed by the MainLab at Washington State University and is available for download for use in other Tripal databases.

          CottonGen JBrowse

            CottonGen has an instance of the JBrowse genome browser for viewing genome data. A list of the Whole Genomes and Chloroplast Genomes is available together with a JBrowse tutorial for more details about how to navigate and use JBrowse.

            CottonGen BLAST

              CottonGen offers BLAST with genome, transcriptome, peptide and marker sequence databases from *Gossypium* species. This can be done using nucleotide sequences or peptide sequences. BLAST functionality is similar to that on NCBI.

              CottonGen CottonCyc Pathways Database

                The CottonGen CottonCyc Pathways Database supports searching and browsing the CottonCyc databases: * Cyc pathways for JGI v2.0 *G. raimondii* D5 genome assembly * Cyc pathways for CGP-BGI v1.0 *G. hirsutum* AD1 genome assembly