Model organism or animal; version 1.0 Package

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

See SAMN02905883 for example record of this type of BioSample.

Name

Description

Use for multicellular samples or cell lines derived from common laboratory model organisms, e.g., mouse, rat, Drosophila, worm, fish, frog, or large mammals including zoo and farm animals.

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"

sex

• Harmonized namesex
• Descriptionphysical sex of sampled organism

tissue

• Harmonized nametissue
• DescriptionType of tissue the sample was taken from.

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

breed

• Harmonized namebreed
• Descriptionbreed name - chiefly used in domesticated animals or plants

cultivar

• Harmonized namecultivar
• Descriptioncultivar name - cultivated variety of plant

ecotype

• Harmonized nameecotype
• Descriptiona population within a given species displaying genetically based, phenotypic traits that reflect adaptation to a local habitat, e.g., Columbia

Age/stage group

age

• Harmonized nameage
• Descriptionage at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees

development stage

• Harmonized namedev_stage
• DescriptionDevelopmental stage at the time of sampling.

Optional Attributes

biomaterial provider

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

birth date

• Harmonized namebirth_date
• Description

birth location

• Harmonized namebirth_location
• Description

breeding history

• Harmonized namebreeding_history
• Description

breeding method

• Harmonized namebreeding_method
• Description

cell line

• Harmonized namecell_line
• DescriptionName of the cell line.

cell subtype

• Harmonized namecell_subtype
• Description

cell type

• Harmonized namecell_type
• DescriptionType of cell of the sample or from which the sample was obtained.

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

death date

• Harmonized namedeath_date
• Description

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

disease stage

• Harmonized namedisease_stage
• Descriptionstage of disease at the time of sampling.

genotype

• Harmonized namegenotype
• Descriptionobserved genotype

growth protocol

• Harmonized namegrowth_protocol
• Description

health state

• Harmonized namehealth_state
• DescriptionHealth or disease status of sample at time of collection

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

phenotype

• Harmonized namephenotype
• DescriptionPhenotype of sampled organism. For Phenotypic quality Ontology (PATO) (v1.269) terms, please see http://bioportal.bioontology.org/visualize/44601

sample type

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

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.

storage conditions

• Harmonized namestore_cond
• Descriptionexplain how and for how long the soil sample was stored before DNA extraction.

stud book number

• Harmonized namestud_book_number
• Description

treatment

• Harmonized nametreatment
• Description