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Virus; version 1.0 Package

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

See SAMN02927319 for example record of this type of BioSample.

Name

Virus.1.0

Description

Use for all virus samples not directly associated with disease. Viral pathogens should be submitted using the Pathogen: Clinical or host-associated pathogen package.

Mandatory Attributes

isolate

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

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"

isolation source

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

At Least One Required

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

Host 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".

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

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.

disease

  • Harmonized namedisease
  • Descriptionlist of diseases diagnosed; can include multiple diagnoses. the value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology), free text for non-human. For DO terms, please see http://gemina.svn.sourceforge.net/viewvc/gemina/trunk/Gemina/ontologies/gemina_symptom.obo?view=log

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.:  mangrove 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

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

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.

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.

strain

  • Harmonized namestrain
  • Descriptionmicrobial or eukaryotic strain name

temperature

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