209 lines
12 KiB
XML
209 lines
12 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
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<BioSamplePackages>
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<Package>
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<Name>Virus.1.0</Name>
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<DisplayName>Virus; version 1.0</DisplayName>
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<ShortName>Viral</ShortName>
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<EnvPackage/>
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<EnvPackageDisplay/>
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<NotAppropriateFor>wgs_single;wgs_batch;wgs_diploid</NotAppropriateFor>
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<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.</Description>
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<Example>SAMN02927319</Example>
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<TemplateHeader># This is a submission template for batch deposit of 'Virus; version 1.0' samples to the NCBI BioSample database (https://www.ncbi.nlm.nih.gov/biosample/).
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# See SAMN02927319 for an example record of this type of BioSample (https://www.ncbi.nlm.nih.gov/biosample/SAMN02927319).
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# Fields with an asterisk (*) are mandatory. Your submission will fail if any mandatory fields are not completed. If information is unavailable for any mandatory field, please enter 'not collected', 'not applicable' or 'missing' as appropriate.
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# All other fields are optional. Leave optional fields empty if no information is available.
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# You can add any number of custom fields to fully describe your BioSamples, simply include them in the table.
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# CAUTION: Be aware that Excel may automatically apply formatting to your data. In particular, take care with dates, incrementing autofills and special characters like / or -. Doublecheck that your text file is accurate before uploading to BioSample.
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# TO MAKE A SUBMISSION:
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# 1. Complete the template table (typically in Excel, or another spreadsheet application)
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# 2. Save the worksheet as a Text (Tab-delimited) file - use 'File, Save as, Save as type: Text (Tab-delimited)'
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# 3. Upload the file on the 'Attributes' tab of the BioSample Submission Portal at https://submit.ncbi.nlm.nih.gov/subs/biosample/.
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# 4. If you have any questions, please contact us at biosamplehelp@ncbi.nlm.nih.gov.</TemplateHeader>
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<Attribute use="mandatory" group_name="Organism">
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<Name>isolate</Name>
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<HarmonizedName>isolate</HarmonizedName>
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<Description>identification or description of the specific individual from which this sample was obtained</Description>
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<Format>
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<Description/>
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</Format>
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</Attribute>
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<Attribute use="either_one_mandatory" group_name="Host">
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<Name>host</Name>
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<HarmonizedName>host</HarmonizedName>
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<Description>The natural (as opposed to laboratory) host to the organism from which the sample was obtained. Use the full taxonomic name, eg, "Homo sapiens".</Description>
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<Format>
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<Description>None</Description>
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</Format>
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</Attribute>
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<Attribute use="either_one_mandatory" group_name="Host">
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<Name>lab host</Name>
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<HarmonizedName>lab_host</HarmonizedName>
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<Description>Scientific 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</Description>
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<Format>
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<Description>None</Description>
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</Format>
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</Attribute>
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<Attribute use="mandatory">
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<Name>collection date</Name>
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<HarmonizedName>collection_date</HarmonizedName>
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<Description>the 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</Description>
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<Format>
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<Description>{timestamp}</Description>
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</Format>
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</Attribute>
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<Attribute use="mandatory">
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<Name>geographic location</Name>
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<HarmonizedName>geo_loc_name</HarmonizedName>
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<Description>Geographical origin of the sample; use the appropriate name from this list https://www.insdc.org/submitting-standards/geo_loc_name-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"</Description>
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<Format>
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<Description>{term}:{term}:{text}</Description>
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</Format>
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</Attribute>
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<Attribute use="mandatory">
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<Name>isolation source</Name>
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<HarmonizedName>isolation_source</HarmonizedName>
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<Description>Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.</Description>
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<Format>
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<Description>None</Description>
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</Format>
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</Attribute>
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<Attribute use="optional">
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<Name>altitude</Name>
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<HarmonizedName>altitude</HarmonizedName>
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<Description>The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.</Description>
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<Format>
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<Description>{float} m</Description>
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</Format>
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</Attribute>
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<Attribute use="optional">
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<Name>biomaterial provider</Name>
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<HarmonizedName>biomaterial_provider</HarmonizedName>
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<Description>name and address of the lab or PI, or a culture collection identifier</Description>
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<Format>
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<Description/>
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</Format>
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</Attribute>
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<Attribute use="optional">
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<Name>collected by</Name>
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<HarmonizedName>collected_by</HarmonizedName>
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<Description>Name of persons or institute who collected the sample</Description>
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<Format>
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<Description>None</Description>
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</Format>
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</Attribute>
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<Attribute use="optional">
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<Name>culture collection</Name>
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<HarmonizedName>culture_collection</HarmonizedName>
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<Description>Name 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</Description>
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<Format>
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<Description>None</Description>
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</Format>
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</Attribute>
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<Attribute use="optional">
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<Name>depth</Name>
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<HarmonizedName>depth</HarmonizedName>
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<Description>Depth 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.</Description>
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<Format>
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<Description>{float} m</Description>
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</Format>
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</Attribute>
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<Attribute use="optional">
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<Name>disease</Name>
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<HarmonizedName>disease</HarmonizedName>
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<Description>list 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</Description>
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<Format>
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<Description>{term}</Description>
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</Format>
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</Attribute>
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<Attribute use="optional">
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<Name>broad-scale environmental context</Name>
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<HarmonizedName>env_broad_scale</HarmonizedName>
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<Description>Add 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]
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</Description>
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<Format>
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<Description>{term}</Description>
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</Format>
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</Attribute>
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<Attribute use="optional">
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<Name>genotype</Name>
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<HarmonizedName>genotype</HarmonizedName>
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<Description>observed genotype</Description>
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<Format>
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<Description>{text}</Description>
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</Format>
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</Attribute>
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<Attribute use="optional">
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<Name>host tissue sampled</Name>
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<HarmonizedName>host_tissue_sampled</HarmonizedName>
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<Description>name 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</Description>
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<Format>
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<Description>None</Description>
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</Format>
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</Attribute>
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<Attribute use="optional">
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<Name>identified by</Name>
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<HarmonizedName>identified_by</HarmonizedName>
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<Description>name of the taxonomist who identified the specimen</Description>
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<Format>
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<Description/>
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</Format>
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</Attribute>
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<Attribute use="optional">
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<Name>latitude and longitude</Name>
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<HarmonizedName>lat_lon</HarmonizedName>
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<Description>The 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</Description>
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<Format>
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<Description>{float} {float}</Description>
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</Format>
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</Attribute>
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<Attribute use="optional">
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<Name>passage history</Name>
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<HarmonizedName>passage_history</HarmonizedName>
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<Description>Number of passages and passage method</Description>
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<Format>
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<Description>None</Description>
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</Format>
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</Attribute>
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<Attribute use="optional">
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<Name>sample size</Name>
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<HarmonizedName>samp_size</HarmonizedName>
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<Description>Amount or size of sample (volume, mass or area) that was collected</Description>
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<Format>
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<Description>{float} {unit}</Description>
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</Format>
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</Attribute>
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<Attribute use="optional">
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<Name>serotype</Name>
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<HarmonizedName>serotype</HarmonizedName>
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<Description>Taxonomy 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.</Description>
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<Format>
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<Description>None</Description>
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</Format>
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</Attribute>
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<Attribute use="optional">
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<Name>specimen voucher</Name>
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<HarmonizedName>specimen_voucher</HarmonizedName>
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<Description>Identifier 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.</Description>
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<Format>
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<Description>None</Description>
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</Format>
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</Attribute>
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<Attribute use="optional" group_name="Organism">
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<Name>strain</Name>
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<HarmonizedName>strain</HarmonizedName>
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<Description>microbial or eukaryotic strain name</Description>
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<Format>
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<Description/>
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</Format>
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</Attribute>
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<Attribute use="optional">
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<Name>temperature</Name>
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<HarmonizedName>temp</HarmonizedName>
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<Description>temperature of the sample at time of sampling</Description>
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<Format>
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<Description>{float} {unit}</Description>
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</Format>
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</Attribute>
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</Package>
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</BioSamplePackages>
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