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Microbe; version 1.0 Package

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

See SAMN02911891 for example record of this type of BioSample.

Name

Microbe.1.0

Description

Use for bacteria or other unicellular microbes when it is not appropriate or advantageous to use MIxS, Pathogen or Virus 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"

sample type

  • Harmonized namesample_type
  • DescriptionSample type, such as cell culture, mixed culture, tissue sample, whole organism, single cell, metagenomic assembly

At Least One Required

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

Organism group

strain

  • Harmonized namestrain
  • Descriptionmicrobial or eukaryotic strain name

isolate

  • Harmonized nameisolate
  • Descriptionidentification or description of the specific individual from which this sample was obtained

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

altitude

  • Harmonized namealtitude
  • DescriptionThe altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.

biomaterial provider

  • Harmonized namebiomaterial_provider
  • Descriptionname and address of the lab or PI, or a culture collection identifier

collected by

  • Harmonized namecollected_by
  • DescriptionName of persons or institute who collected the sample

culture collection

  • Harmonized nameculture_collection
  • DescriptionName of source institute and unique culture identifier. See the description for the proper format and list of allowed institutes, http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier

depth

  • Harmonized namedepth
  • DescriptionDepth is defined as the vertical distance below surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectivly. Depth can be reported as an interval for subsurface samples.

broad-scale environmental context

  • Harmonized nameenv_broad_scale
  • DescriptionAdd terms that identify the major environment type(s) where your sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes e.g.: ┬ámangrove biome [ENVO:01000181]|estuarine biome [ENVO:01000020]

genotype

  • Harmonized namegenotype
  • Descriptionobserved genotype

host tissue sampled

  • Harmonized namehost_tissue_sampled
  • Descriptionname of body site where the sample was obtained from, such as a specific organ or tissue, e.g., tongue, lung. For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON

identified by

  • Harmonized nameidentified_by
  • Descriptionname of the taxonomist who identified the specimen

lab host

  • Harmonized namelab_host
  • DescriptionScientific name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained, e.g., Escherichia coli DH5a, or Homo sapiens HeLa cells

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

mating type

  • Harmonized namemating_type
  • Description

passage history

  • Harmonized namepassage_history
  • DescriptionNumber of passages and passage method

sample size

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

serotype

  • Harmonized nameserotype
  • DescriptionTaxonomy below subspecies; a variety (in bacteria, fungi or virus) usually based on its antigenic properties. Same as serovar and serogroup. e.g. serotype="H1N1" in Influenza A virus CY098518.

serovar

  • Harmonized nameserovar
  • DescriptionTaxonomy below subspecies; a variety (in bacteria, fungi or virus) usually based on its antigenic properties. Same as serovar and serotype. Sometimes used as species identifier in bacteria with shaky taxonomy, e.g. Leptospira, serovar saopaolo S76607 (65357 in Entrez).

specimen voucher

  • Harmonized namespecimen_voucher
  • DescriptionIdentifier for the physical specimen. Use format: "[<institution-code>:[<collection-code>:]]<specimen_id>", eg, "UAM:Mamm:52179". Intended as a reference to the physical specimen that remains after it was analyzed. If the specimen was destroyed in the process of analysis, electronic images (e-vouchers) are an adequate substitute for a physical voucher specimen. Ideally the specimens will be deposited in a curated museum, herbarium, or frozen tissue collection, but often they will remain in a personal or laboratory collection for some time before they are deposited in a curated collection. There are three forms of specimen_voucher qualifiers. If the text of the qualifier includes one or more colons it is a 'structured voucher'. Structured vouchers include institution-codes (and optional collection-codes) taken from a controlled vocabulary maintained by the INSDC that denotes the museum or herbarium collection where the specimen resides, please visit: http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier.

temperature

  • Harmonized nametemp
  • Descriptiontemperature of the sample at time of sampling
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