{
  "@type": "dcat:Dataset",
  "accessLevel": "public",
  "bureauCode": [
    "005:18"
  ],
  "contactPoint": {
    "fn": "Poelchau, Monica, F.",
    "hasEmail": "mailto:Monica.poelchau@usda.gov"
  },
  "description": "<p dir=\"ltr\">Manual annotation at the i5k Workspace@NAL (<a href=\"https://i5k.nal.usda.gov/\" target=\"_blank\">https://i5k.nal.usda.gov</a>) is the review and improvement of gene models derived from computational gene prediction. Community curators compare an existing gene model to evidence such as RNA-Seq or protein alignments from the same or closely related species and modify the structure or function of the gene accordingly, typically following the i5k Workspace@NAL manual annotation guidelines (<a href=\"https://i5k.nal.usda.gov/content/rules-web-apollo-annotation-i5k-pilot-project\" target=\"_blank\">https://i5k.nal.usda.gov/content/rules-web-apollo-annotation-i5k-pilot-project</a>). If a gene model is missing, the annotator can also use this evidence to create a new gene model. Because manual annotation, by definition, improves or creates gene models where computational methods have failed, it can be a powerful tool to improve computational gene sets, which often serve as foundational datasets to facilitate research on a species.</p><p dir=\"ltr\">Here, community curators used manual annotation at the i5k Workspace@NAL to improve computational gene predictions from the dataset <i>Agrilus planipennis</i> genome annotations v0.5.3. The i5k Workspace@NAL set up the Apollo v1 manual annotation software and multiple evidence tracks to facilitate manual annotation. From 2014-10-20 to 2018-07-12, five community curators updated 263 genes, including developmental genes; cytochrome P450s; cathepsin peptidases; cuticle proteins; glycoside hydrolases; and polysaccharide lyases. For this dataset, we used the program LiftOff v1.6.3 to map the manual annotations to the genome assembly GCF_000699045.2. We computed overlaps with annotations from the RefSeq database using gff3_merge from the GFF3toolkit software v2.1.0. FASTA sequences were generated using gff3_to_fasta from the same toolkit. These improvements should facilitate continued research on <i>Agrilus planipennis</i>, or emerald ash borer (EAB), which is an invasive insect pest.</p><p dir=\"ltr\">While these manual annotations will not be integrated with other computational gene sets, they are available to view at the i5k Workspace@NAL (https://i5k.nal.usda.gov) to enhance future research on <i>Agrilus planipennis.</i></p>",
  "distribution": [
    {
      "@type": "dcat:Distribution",
      "downloadURL": "https://ndownloader.figshare.com/files/44244485",
      "format": "gz",
      "mediaType": "application/x-gzip",
      "title": "Apla_2.0-manual-annotations-v2024.tar.gz"
    }
  ],
  "identifier": "10.15482/USDA.ADC/25076114.v1",
  "keyword": [
    "Agrilus planipennis",
    "Coleoptera",
    "Emerald ash borer",
    "Genome annotation",
    "Manual annotation"
  ],
  "license": "https://creativecommons.org/licenses/by/4.0/",
  "modified": "2024-11-19",
  "programCode": [
    "005:040"
  ],
  "publisher": {
    "@type": "org:Organization",
    "name": "Agricultural Research Service"
  },
  "temporal": "2014-10-20/2024-01-26",
  "title": "Agrilus planipennis community manual annotations"
}