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The Ag Data Commons is migrating

The Ag Data Commons is migrating to a new institutional portal on Figshare. The current system is available for search and download only. The new platform is open for submission with assistance from Ag Data Commons curators. Please contact NAL-ADC-Curator@usda.gov, if you need to publish or update your datasets.

Data from: Use of long-read sequencing simulators to assess real-world applications for food safety

    The goal of this project was to use NanoSim-H software to simulate Oxford Nanopore sequencing reads to assess the feasibility of sequencing-based foodborne pathogen detection and guide experimental design. Sequencing reads were simulated for STEC, *L. monocytogenes*, and a 1:1 combination of STEC and *Bos taurus* genomes using NanoSim-H. This dataset includes all of the simulated reads generated by the project in fasta format.

    Data from: Evaluating plant biodiversity measurements and exotic species detection in National Resources Inventory Sampling protocols using examples from the Northern Great Plains of the USA

      The use of the standardized Whitaker plot method allows the authors to combine plant biodiversity and soil data from the northern Great Plains with other databases worldwide for larger-scale meta-analyses. The multiscale technique also enables comparison of vegetation dynamics at multiple scales.

      Comparison of methods to detect low levels of Salmonella enterica in surface waters to support antimicrobial resistance surveillance efforts performed in multiple laboratories

        Identifying and developing effective and sensitive detection methods for antimicrobial resistant Salmonella enterica from surface water is a goal of the U.S. National Antimicrobial Resistance Monitoring System (NARMS). No specific microbiological methods used in surveillance efforts for Salmonella enterica or antimicrobial resistant S. enterica in water have been standardized or reported in the U.S. Here we describe a multi-laboratory evaluation of four methods, bulk water enrichment (BW), vertical Modified Moore Swab (VMMS), modified Standard Method 9260.B3 (SM), and dead-end ultrafiltration (DEUF), to recover S. enterica from surface water.

        Data from: High genetic diversity in the landscape suggests frequent seedling recruitment by Euphorbia virgata Waldst. & Kit. (leafy spurge) in the northern U.S.A.

          Site information and field-collected data from a 1-year 100-site survey of leafy spurge (Euphorbia virgata/esula) populations in the northern U.S. Data include: 1) estimates of leafy spurge density and relative prevalence of ramets versus genets; 2) the abundance and composition of Aphthona species complex biological control agents; 3) presence/absence of two additional biological control agents (Oberea erythrocephala and Hyles euphorbiae).

          SNAPMe: A Benchmark Dataset of Food Photos with Food Records for Evaluation of Computer Vision Algorithms in the Context of Dietary Assessment

            We conducted the Surveying Nutrient Assessment with Photographs of Meals (SNAPMe) Study (ClinicalTrials ID: NCT05008653) to develop a benchmark dataset of food photographs paired with traditional food records. The SNAPMe DB includes 1,475 “before” photos of non-packaged foods, 1,436 “after” photos of non-packaged foods, 203 “front” photos of packaged foods, and 196 “ingredient” labels of packaged foods. Each line item of each ASA24 food record is linked to the relevant photo. These data will be transformative for the improvement of artificial intelligence algorithms for the adoption of photo-based dietary assessment in nutrition research.