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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.

Chelonus insularis Official Gene Set OGSv1.0

    This Official Gene Set is an integration ([NCBI Cephus cinctus Annotation Release 101](https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Cephus_cinctus/101/)) from NCBI's eukaryotic annotation pipeline v8.0 with manual annotations by the research community (done via the Apollo manual annotation software). QC and Merge of the dataset was performed using the GFF3toolkit software ([https://github.com/NAL-i5K/GFF3toolkit](https://github.com/NAL-i5K/GFF3toolkit)).

    Oncopeltus fasciatus Official Gene set v1.2

      This dataset presents the Oncopeltus fasciatus Official Gene Set (OGS) v1.2. The OGS is an update of OGSv1.1. Manual annotations from the Apollo manual annotation tool were merged with OGSv1.1 using the NAL's [prototype Merge program](https://github.com/NAL-i5K/I5KNAL_OGS).

      Ephemera danica Official Gene Set ephdan_OGSv1.0

        This dataset presents the *Ephemera danica* Official Gene Set (OGS) v1.0. The OGS is an integration of automatic gene predictions from *Ephemera danica* genome annotations v0.5.3, with manual annotations by the research community. Manual and automated annotations were lifted over from genome assembly *Ephemera danica* genome assembly v1.0 to genome assembly Edan_2.0 using the coordinates_conversion and remap-gff3 programs.

        Neodiprion lecontei Official Gene Set v1.1

          This dataset presents the *Neodiprion* Official Gene Set (OGS) v1.1. It was generated using Maker v2.31.8, followed by CrossMap re-mapping of coordinates to genome assembly Nlec1.1 ([https://www.ncbi.nlm.nih.gov/assembly/GCA_001263575.2/](https://www.ncbi.nlm.nih.gov/assembly/GCA_001263575.2/)).

          Ephemera danica manual annotations on genome assembly Edan_1.0

            This dataset presents manual annotations of Ephemera danica genome annotations v0.5.3 and genome assembly v1.0. Manual annotations were performed by individual annotators in the Apollo software at the i5k Workspace@NAL, and QC'd via the GFF3toolkit software and manual inspection. Manual annotations are presented here on the original coordinate system of genome assembly v1.0.

            Frankliniella occidentalis Official Gene Set OGSv1.1

              The *Frankliniella occidentalis* genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The *Frankliniella occidentalis* research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.0. OGSv1.0 was generated by merging gene set FOCC-V0.5.3-Models generated by the Baylor College of Medicine, and community-curated models in the Apollo software, after QC of the Apollo output. After the merge, scaffolds that were likely bacterial contamination were identified by John H. Werren, and gene models overlapping with these contaminated regions were removed from the OGS.

              Halyomorpha halys Official Gene Set v1.2

                This dataset presents the Halyomorpha halys Official Gene Set (OGS) v1.2. OGSv1.2 and is an update of Halyomorpha halys OGSv1.1 (https://doi.org/10.15482/USDA.ADC/1504240) to the coordinates of genome assembly GCA_000696795.3 (https://www.ncbi.nlm.nih.gov/assembly/GCA_000696795.3) using https://github.com/NAL-i5K/coordinates_conversion/.