| accessLevel |
public
|
| bureauCode |
{005:18}
|
| catalog_@context |
https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
|
| catalog_conformsTo |
https://project-open-data.cio.gov/v1.1/schema
|
| catalog_describedBy |
https://project-open-data.cio.gov/v1.1/schema/catalog.json
|
| identifier |
10.15482/USDA.ADC/1518751
|
| license |
https://creativecommons.org/licenses/by-sa/4.0/
|
| modified |
2024-01-29
|
| old-spatial |
{"type": "Polygon", "coordinates": [[[-172.96875, -85.973919490277], [-172.96875, 85.513398309887], [194.0625, 85.513398309887], [194.0625, -85.973919490277], [-172.96875, -85.973919490277]]]}
|
| programCode |
{005:040}
|
| publisher |
Agricultural Research Service
|
| resource-type |
Dataset
|
| source_datajson_identifier |
true
|
| source_hash |
e422f8388f75eb2bdeb37c171a26825659f19bb76f5b1e1304284e93bb058c29
|
| source_schema_version |
1.1
|
| spatial |
{"type": "Polygon", "coordinates": [[[-172.96875, -85.973919490277], [-172.96875, 85.513398309887], [194.0625, 85.513398309887], [194.0625, -85.973919490277], [-172.96875, -85.973919490277]]]}
|
| temporal |
2019-01-01/2019-01-01
|
| Groups |
- AmeriGEOSS
- National Provider
- North America
|
| Tags |
- AmeriGEO
- AmeriGEOSS
- CKAN
- GEO
- GEOSS
- National
- North America
- United States
- ars
- data-gov
- genome-annotation
- genome-assembly
- halyomorpha-halys
- sequence-analysis
|
| isopen |
True
|
| license_id |
cc-by-sa
|
| license_title |
Creative Commons Attribution Share-Alike
|
| license_url |
http://www.opendefinition.org/licenses/cc-by-sa
|
| maintainer |
Sparks, Michael
|
| maintainer_email |
Michael.Sparks2@USDA.GOV
|
| metadata_created |
2025-09-25T01:04:33.398864
|
| metadata_modified |
2025-09-25T01:04:33.398874
|
| notes |
<p>This dataset presents the <em>Halyomorpha halys</em> Official Gene Set (OGS) v1.2. OGSv1.2 is an update of <em>Halyomorpha halys</em> OGSv1.1 (<a href="https://doi.org/10.15482/USDA.ADC/1504240">https://doi.org/10.15482/USDA.ADC/1504240</a>) to the coordinates of genome assembly GCA_000696795.3 (<a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_000696795.3">https://www.ncbi.nlm.nih.gov/assembly/GCA_000696795.3</a>) using <a href="https://github.com/NAL-i5K/coordinates_conversion/">https://github.com/NAL-i5K/coordinates_conversion/</a>. </p>
<p>The original OGSv1.0 is an integration of automatic gene predictions from NCBI's eukaryotic annotation pipeline, NCBI Halyomorpha halys Annotation Release 100 (<a href="https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Halyomorpha_halys/100/">https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Halyomorpha_halys/100/</a>; ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/696/795/GCF_000696795.1_Hhal_1.0), with manual annotations by the research community (performed via the Apollo manual curation software, <a href="http://genomearchitect.org/">http://genomearchitect.org/</a>). Manual annotations performed by the community were downloaded from Apollo, QC'd, and merged with NCBI Halyomorpha halys Annotation Release 100 using the GFF3toolkit software (<a href="https://github.com/NAL-i5K/GFF3toolkit/releases/tag/v1.4.4">https://github.com/NAL-i5K/GFF3toolkit/releases/tag/v1.4.4</a>). The resulting merged dataset was formatted for ingest into the i5k Workspace and GenBank databases, resulting in <em>Halyomorpha halys</em> Official Gene Set (OGS) v1.0. </p>
<p>Halyomorpha Official Gene Set halhal_OGSv1.1 is a minor update of halhal_OGSv1.0: Alias attributes were added to all manually annotated cathepsin models; six models from contaminated scaffolds were removed; and notes were added to 3 models located on possibly contaminated scaffolds. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Halymorpha halys Official Gene Set OGSv1.2.</p> <p>File Name: halhal_OGSv1.2.tar.gz</p><p>Resource Description: The attached tar.gz archive (halhal_OGSv1.2.tar.gz) contains the following files:</p>
<p>halhal_OGSv1.2.gff. Gff3 of all gene predictions of Halymorpha halys genome annotations OGSv1.2
halhal_OGSv1.2_CDS.fa. CDS sequences of Halymorpha halys genome annotations OGSv1.2
halhal_OGSv1.2_pep.fa. Amino acid sequences of Halymorpha halys genome annotations OGSv1.2
halhal_OGSv1.2_trans.fa. Transcript sequences of Halymorpha halys genome annotations OGSv1.2
readme. Readme file describing Halymorpha halys genome annotations OGSv1.2</p>
<p></p></li></ul><p></p>
|
| num_resources |
1
|
| num_tags |
14
|
| title |
Halyomorpha halys Official Gene Set v1.2
|