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Metagenome or environmental; version 1.0 Package

You can download package details in xml format or as an Excel spreadsheet.

Name

Metagenome.environmental.1.0

Description

Use for metagenomic and environmental samples when it is not appropriate or advantageous to use MIxS packages.

Mandatory Attributes

collection date

  • Harmonized namecollection_date
  • Descriptionthe date on which the sample was collected; date/time ranges are supported by providing two dates from among the supported value formats, delimited by a forward-slash character; collection times are supported by adding "T", then the hour and minute after the date, and must be in Coordinated Universal Time (UTC), otherwise known as "Zulu Time" (Z); supported formats include "DD-Mmm-YYYY", "Mmm-YYYY", "YYYY" or ISO 8601 standard "YYYY-mm-dd", "YYYY-mm", "YYYY-mm-ddThh:mm:ss"; e.g., 30-Oct-1990, Oct-1990, 1990, 1990-10-30, 1990-10, 21-Oct-1952/15-Feb-1953, 2015-10-11T17:53:03Z; valid non-ISO dates will be automatically transformed to ISO format

geographic location

  • Harmonized namegeo_loc_name
  • DescriptionGeographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps"

latitude and longitude

  • Harmonized namelat_lon
  • DescriptionThe geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W

At Least One Required

In each group below at least one of listed attributes is required.

Source group

host

  • Harmonized namehost
  • DescriptionThe natural (as opposed to laboratory) host to the organism from which the sample was obtained. Use the full taxonomic name, eg, "Homo sapiens".

isolation source

  • Harmonized nameisolation_source
  • DescriptionDescribes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.

Optional Attributes

reference for biomaterial

  • Harmonized nameref_biomaterial
  • DescriptionPrimary publication or genome report

relationship to oxygen

  • Harmonized namerel_to_oxygen
  • DescriptionIs this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments, eg, aerobe, anaerobe, facultative, microaerophilic, microanaerobe, obligate aerobe, obligate anaerobe, missing, not applicable, not collected, not provided, restricted access

sample collection device or method

  • Harmonized namesamp_collect_device
  • DescriptionMethod or device employed for collecting sample

sample material processing

  • Harmonized namesamp_mat_process
  • DescriptionProcessing applied to the sample during or after isolation

sample size

  • Harmonized namesamp_size
  • DescriptionAmount or size of sample (volume, mass or area) that was collected

source material identifiers

  • Harmonized namesource_material_id
  • Descriptionunique identifier assigned to a material sample used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples.
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