MIGS: eukaryote, human-oral; version 6.0 Package

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

See SAMN02909964 for example record of this type of BioSample.

Name

Environmental Package

Description

Use for eukaryotic genomic sequences. Organism must have lineage Eukaryota.

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

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]

local-scale environmental context

• Harmonized nameenv_local_scale
• DescriptionAdd terms that identify environmental entities having causal influences upon the entity at time of sampling, multiple terms can be separated by pipes, e.g.:  shoreline [ENVO:00000486]|intertidal zone [ENVO:00000316]

environmental medium

• Harmonized nameenv_medium
• DescriptionAdd terms that identify the material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. Multiple terms can be separated by pipes e.g.: estuarine water [ENVO:01000301]|estuarine mud [ENVO:00002160]

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".

isolation and growth condition

• Harmonized nameisol_growth_condt
• DescriptionPMID or url for isolation and growth condition specifications

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

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

Optional Attributes

observed biotic relationship

• Harmonized namebiotic_relationship
• DescriptionFree-living or from host (define relationship)

chemical administration

• Harmonized namechem_administration
• Descriptionlist of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v1.72), please see http://bioportal.bioontology.org/visualize/44603

collection method

• Harmonized namecollection_method
• DescriptionProcess used to collect the sample, e.g., bronchoalveolar lavage (BAL)

estimated size

• Harmonized nameestimated_size
• DescriptionEstimated size of genome

ethnicity

• Harmonized nameethnicity
• Descriptionethnicity of the subject

extrachromosomal elements

• Harmonized nameextrachrom_elements
• DescriptionPlasmids that have significance phenotypic consequence

host age

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

host body mass index

• Harmonized namehost_body_mass_index
• Descriptionbody mass index of the host, calculated as weight/(height)squared

host body product

• Harmonized namehost_body_product
• Descriptionsubstance produced by the host, e.g. stool, mucus, where the sample was obtained from

host body temperature

• Harmonized namehost_body_temp
• Descriptioncore body temperature of the host when sample was collected

host diet

• Harmonized namehost_diet
• Descriptiontype of diet depending on the sample for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types

host disease

• Harmonized namehost_disease
• DescriptionName of relevant disease, e.g. Salmonella gastroenteritis. Controlled vocabulary, http://bioportal.bioontology.org/ontologies/1009 or http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/mesh

host family relationship

• Harmonized namehost_family_relationship
• Description

host genotype

• Harmonized namehost_genotype
• Description

host height

• Harmonized namehost_height
• Descriptionthe height of subject

host last meal

• Harmonized namehost_last_meal
• Descriptioncontent of last meal and time since feeding; can include multiple values

host occupation

• Harmonized namehost_occupation
• Descriptionmost frequent job performed by subject

host phenotype

• Harmonized namehost_phenotype
• Description

host pulse

• Harmonized namehost_pulse
• Descriptionresting pulse of the host, measured as beats per minute

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

observed host symbionts

• Harmonized namehost_symbiont
• DescriptionThe taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host

host taxonomy ID

• Harmonized namehost_taxid
• DescriptionNCBI taxonomy ID of the host, e.g. 9606

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

host total mass

• Harmonized namehost_tot_mass
• Descriptiontotal mass of the host at collection, the unit depends on host

medication code

• Harmonized nameihmc_medication_code
• Descriptioncan include multiple medication codes

isolation source

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

medical history performed

• Harmonized namemedic_hist_perform
• Descriptionwhether full medical history was collected

miscellaneous parameter

• Harmonized namemisc_param
• Descriptionany other measurement performed or parameter collected, that is not listed here

negative control type

• Harmonized nameneg_cont_type
• DescriptionThe substance or equipment used as a negative control in an investigation, e.g., distilled water, phosphate buffer, empty collection device, empty collection tube, DNA-free PCR mix, sterile swab, sterile syringe

nose/mouth/teeth/throat disorder

• Harmonized namenose_mouth_teeth_throat_disord
• Descriptionhistory of nose/mouth/teeth/throat disorders; can include multiple disorders

number of replicons

• Harmonized namenum_replicons
• DescriptionNumber of replicons in nuclear genome

Omics Observatory ID

• Harmonized nameomics_observ_id
• DescriptionA unique identifier of the omics-enabled observatory (or comparable time series) your data derives from. This identifier should be provided by the OMICON ontology; if you require a new identifier for your time series, contact the ontology's developers. Information is available here: https://github.com/GLOMICON/omicon. This field is only applicable to records which derive from an omics time-series or observatory.

organism count

• Harmonized nameorganism_count
• Descriptiontotal count of any organism per gram or volume of sample,should include name of organism followed by count; can include multiple organism counts

oxygenation status of sample

• Harmonized nameoxy_stat_samp
• Descriptionoxygenation status of sample

pathogenicity

• Harmonized namepathogenicity
• DescriptionTo what is the entity pathogenic

perturbation

• Harmonized nameperturbation
• Descriptiontype of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types

ploidy

• Harmonized nameploidy
• DescriptionPloidy level of genome (eg., haploid, diploid)

positive control type

• Harmonized namepos_cont_type
• DescriptionThe substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive

propagation

• Harmonized namepropagation
• Descriptionphage: lytic/lysogenic/temperate/obligately lytic; plasmid: incompatibility group; eukaryote: asexual/sexual

reference for biomaterial

• Harmonized nameref_biomaterial
• DescriptionPrimary publication or genome report

sample collection device or method

• Harmonized namesamp_collect_device
• DescriptionMethod or device employed for collecting sample

sample material processing

• Harmonized namesamp_mat_process
• DescriptionProcessing applied to the sample during or after isolation

sample salinity

• Harmonized namesamp_salinity
• Description

sample size

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

sample storage duration

• Harmonized namesamp_store_dur
• Description

sample storage location

• Harmonized namesamp_store_loc
• Description

sample storage temperature

• Harmonized namesamp_store_temp
• Description

sample volume or weight for DNA extraction

• Harmonized namesamp_vol_we_dna_ext
• Descriptionvolume (mL) or weight (g) of sample processed for DNA extraction

source material identifiers

• Harmonized namesource_material_id
• Descriptionunique identifier assigned to a material sample used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples.

subspecific genetic lineage

• Harmonized namesubspecf_gen_lin
• DescriptionInformation about the genetic distinctness of the lineage (eg., biovar, serovar)

temperature

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

time since last toothbrushing

• Harmonized nametime_last_toothbrush
• Descriptionspecification of the time since last toothbrushing

trophic level

• Harmonized nametrophic_level
• DescriptionFeeding position in food chain (eg., chemolithotroph)