Pathogen: clinical or host-associated; version 1.0 Package

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

See SAMN02928182 for example record of this type of BioSample.

Name

Description

Clinical or host-associated pathogen

Mandatory Attributes

collected by

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

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"

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".

host disease

• Harmonized namehost_disease
• DescriptionName of relevant disease, e.g. Salmonella gastroenteritis. Controlled vocabulary, http://bioportal.bioontology.org/ontologies/1009 or http://www.ncbi.nlm.nih.gov/mesh

isolation source

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

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.

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

Optional Attributes

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

genotype

• Harmonized namegenotype
• Descriptionobserved genotype

host age

• Harmonized namehost_age
• DescriptionAge of host at the time of sampling

host description

• Harmonized namehost_description
• DescriptionAdditional information not included in other defined vocabulary fields

host disease outcome

• Harmonized namehost_disease_outcome
• DescriptionFinal outcome of disease, e.g., death, chronic disease, recovery

host disease stage

• Harmonized namehost_disease_stage
• DescriptionStage of disease at the time of sampling

host health state

• Harmonized namehost_health_state
• DescriptionInformation regarding health state of the individual sampled at the time of sampling

host sex

• Harmonized namehost_sex
• DescriptionGender or physical sex of the host

host subject id

• Harmonized namehost_subject_id
• Descriptiona unique identifier by which each subject can be referred to, de-identified, e.g. #131

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

passage history

• Harmonized namepassage_history
• DescriptionNumber of passages and passage method

pathotype

• Harmonized namepathotype
• DescriptionSome bacterial specific pathotypes (example Eschericia coli - STEC, UPEC)

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.

subgroup

• Harmonized namesubgroup
• DescriptionTaxonomy below subspecies; sometimes used in viruses to denote subgroups taken from a single isolate.

subtype

• Harmonized namesubtype
• DescriptionUsed as classifier in viruses (e.g. HIV type 1, Group M, Subtype A).