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qiita-spots / qiita

Qiita - A multi-omics databasing effort
http://qiita.microbio.me
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NCBI taxonomy documentation #1869

Closed cuttlefishh closed 8 years ago

cuttlefishh commented 8 years ago

Suggest the following changes to https://qiita.ucsd.edu/static/doc/html/tutorials/prepare-information-files.html#required-fields-for-ebi-submission:

ackermag commented 8 years ago

Luke we have had to change unspecified (blank) to :Taxon_id 256318 and scientific_name: metagenome. This is required by EBI and ratified by EBI. For all blanks I am using: Env_biome: urban biome env_feature: research facility env_material (not env_matter): sterile water env_package: misc environment Gail

On Thu, Jun 23, 2016 at 5:39 PM, Luke Thompson notifications@github.com wrote:

Suggest the following changes to https://qiita.ucsd.edu/static/doc/html/tutorials/prepare-information-files.html#required-fields-for-ebi-submission :

  • Place taxon_id and scientific_name together. It's strange that description is between them.
  • Provide a link to the NCBI taxonomy site: http://www.ncbi.nlm.nih.gov/taxonomy
  • Description for taxon_id: NCBI taxon ID for the sample. Should indicate metagenome being investigated. Examples: 410658 for soil metagenome, 749906 for gut metagenome, 412755 for marine sediment metagenome, 408172 for marine metagenome (seawater), or 449393 for freshwater metagenome. If unspecified use 408169.
  • Description for scientific_name: Common name for the provided NCBI taxon ID (must match taxon_id above). Examples: soil metagenome, gut metagenome, marine sediment metagenome, marine metagenome.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/biocore/qiita/issues/1869, or mute the thread https://github.com/notifications/unsubscribe/AB69gNd5rpcuk9NgdMV17U4pKHyCarExks5qOydagaJpZM4I9Xj_ .

Gail Ackermann Knight Lab UCSD glackermann@ucsd.edu ackermag@ucsd.edu

antgonza commented 8 years ago

Thanks @cuttlefishh and @ackermag, I think this info is important and should be in the documentation.

cuttlefishh commented 8 years ago

Thanks Gail. The blank requirements for taxon_id and scientific_name can go in those descriptions. The blank requirements for env fields can go in those descriptions. I can make these changes and issue a PR. Can someone point me to the website code?