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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.

i5k Workspace

About the i5k Workspace@NAL

The i5k Workspace (https://i5k.nal.usda.gov) is an inclusive genome portal for any arthropod genome project that would like to make use of our resources. We provide download services, BLAST, the JBrowse genome browser, and the Apollo manual curation service. Over 50 arthropod genomes are now part of the i5k Workspace, and users are encouraged to browse the genomes that we host, and contribute to the curation of each genome. For more information about the i5k Workspace, you can read our paper on the i5k Workspace, view our posters and talks, and find our software projects on github. The Ag Data Commons is now hosting a growing number of i5k Workspace datasets.

About the i5k initiative

The i5k initiative is a transformative project that aims to sequence and analyze the genomes of 5,000 arthropod species. The National Agricultural Library has partnered with the i5k initiative to create the i5k Workspace@NAL, which serves any ‘orphaned’ arthropod genome project's hosting needs. For more information about the i5k initiative, read the paper and visit the website.

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i5k Datasets

94 datasets

Data from: Tripal EUtils - A Tripal module to increase exchange and reuse of genome assembly metadata

    A core component of NCBI’s BioSample metadata are the BioSample “packages” ([https://www.ncbi.nlm.nih.gov/biosample/docs/packages/](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/)). Data submitters can choose a package, which contain a variety of attribute sets, such as plant- or insect-specific attributes, attribute values as recommended by the MIxS standard, etc. Here, we provide suggested ontology term mappings for attributes from the Invertebrate 1.0 and Plant 1.0 packages. This dataset corresponds to Table 4 in the corresponding publication in the journal Database.

    Genes of viral origin in the Fopius arisanus genome

      *Fopius arisanus* (Sonan) is a braconid wasp (subfamily Opiinae) and biological control agent of a broad range of tephritid fruit fly species, including the global pests Mediterranean fruit fly *Ceratitis capitata* and the Oriental fruit fly *Bactrocera dorsalis*. In an effort to create foundational genomic resources for this species, the complete genome and transcriptomes for several wasp life stages have been recently generated. Manual annotation of 55 viral genes and phylogenetic analysis revealed that *F. arisanus* has independently acquired a symbiotic virus related to alpha-nudiviruses.

      Genes of viral origin in the Microplitis demolitor genome

        *Microplitis demolitor* (Hymenoptera: Braconidae) is a parasitoid used as a biological control agent to control larval-stage Lepidoptera and serves as a model for studying the function and evolution of symbiotic viruses in the genus Bracovirus. Using RNA-Seq data for this species and manual annotation of genes of viral origin, we annotated a high-quality gene set including 171 virus-derived protein-coding genes.

        Microplitis demolitor Official Gene Set micdem_OGSv1.0

          This dataset presents the *Microplitis demolitor* Official Gene Set (OGS) v1.0. The OGS is an integration of automatic gene predictions from *Microplitis demolitor* genome annotations NCBI-RefSeq's gene set NCBI Microplitis demolitor Annotation Release 101, with manual annotations by the research community, performed via the Apollo manual curation software. Manual annotations were QC'd via the GFF3toolkit and NCBI's table2asn_GFF software, and merged with NCBI Microplitis demolitor Annotation Release 101 via the GFF3toolkit.

          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.