MIMAG: metagenome-assembled genome, symbiont-associated; version 6.0 Package

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

Name

Environmental Package

Description

Use for metagenome-assembled genome sequences produced using computational binning tools that group sequences into individual organism genome assemblies starting from metagenomic data sets. Organism cannot contain the term 'metagenome'. Use the MIUVIG package for virus genomes. Before creating BioSamples for prokaryotic and eukaryotic MAGs, please read and follow the MAG submission instructions at https://www.ncbi.nlm.nih.gov/genbank/wgsfaq/#metagen.

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

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 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"

host dependence

• Harmonized namehost_dependence
• DescriptionType of host dependence for the symbiotic host organism to its host., e.g., facultative, obligate

host life stage

• Harmonized namehost_life_stage
• Descriptiondescription of host life stage

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

symbiotic host organism life cycle type

• Harmonized namesym_life_cycle_type
• DescriptionType of life cycle of the symbiotic host species (the thing being sampled). Simple life cycles occur within a single host, complex ones within multiple different hosts over the course of their normal life cycle, e.g., complex life cycle, simple life cycle

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.

duration of association with the host

• Harmonized nameassociation_duration
• DescriptionTime spent in host of the symbiotic organism at the time of sampling; relevant scale depends on symbiotic organism and study

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)

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.

derived from

• Harmonized namederived_from
• DescriptionIndicates when one BioSample was derived from another BioSample. Value should include BioSample accession number(s) (SAMNxxxxxxxx).

elevation

• Harmonized nameelev
• DescriptionThe elevation of the sampling site as measured by the vertical distance from mean sea level.

experimental factor

• Harmonized nameexperimental_factor
• DescriptionVariable aspect of experimental design

gravidity

• Harmonized namegravidity
• Descriptionwhether or not subject is gravid, and if yes date due or date post-conception, specifying which is used

host age

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

host body habitat

• Harmonized namehost_body_habitat
• Descriptionoriginal body habitat where the sample was obtained from

host body product

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

host cellular location

• Harmonized namehost_cellular_loc
• DescriptionThe localization of the symbiotic host organism within the host from which it was sampled, e.g., intracellular, extracellular

host color

• Harmonized namehost_color
• Descriptionthe color of host

host common name

• Harmonized namehost_common_name
• DescriptionThe natural language (non-taxonomic) name of the host organism, e.g., mouse

host dry mass

• Harmonized namehost_dry_mass
• Descriptionmeasurement of dry mass

host family relationship

• Harmonized namehost_family_relationship
• Description

host genotype

• Harmonized namehost_genotype
• Description

host growth conditions

• Harmonized namehost_growth_cond
• Descriptionliterature reference giving growth conditions of the host

host height

• Harmonized namehost_height
• Descriptionthe height of subject

host infra specific name

• Harmonized namehost_infra_specific_name
• Descriptiontaxonomic information subspecies level

host infra specific rank

• Harmonized namehost_infra_specific_rank
• Descriptiontaxonomic rank information below subspecies level, such as variety, form, rank etc.

host length

• Harmonized namehost_length
• Descriptionthe length of subject

host number individual

• Harmonized namehost_number
• DescriptionNumber of symbiotic host individuals pooled at the time of collection

observed coinfecting organisms in host of host

• Harmonized namehost_of_host_coinf
• DescriptionThe taxonomic name of any coinfecting organism observed in a symbiotic relationship with the host of the sampled host organism, e.g. where a sample collected from a host trematode species (A) which was collected from a host_of_host fish (B) that was also infected with a nematode (C), the value here would be (C) the nematode {species name} or {common name}. Multiple co-infecting species may be added in a comma-separated list. For listing symbiotic organisms associated with the host (A) use the term Observed host symbiont

host of the symbiotic host disease status

• Harmonized namehost_of_host_disease
• DescriptionList of diseases with which the host of the symbiotic host organism has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text

host of the symbiotic host local environmental context

• Harmonized namehost_of_host_env_loc
• DescriptionFor a symbiotic host organism the local anatomical environment within its host may have causal influences. Report the anatomical entity(s) which are in the direct environment of the symbiotic host organism being sampled and which you believe have significant causal influences on your sample or specimen. For example, if the symbiotic host organism being sampled is an intestinal worm, its local environmental context will be the term for intestine from UBERON (http://uberon.github.io/)

host of the symbiotic host environemental medium

• Harmonized namehost_of_host_env_med
• DescriptionReport the environmental material(s) immediately surrounding the symbiotic host organism at the time of sampling. This usually will be a tissue or substance type from the host, but may be another material if the symbiont is external to the host. We recommend using classes from the UBERON ontology, but subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483) may also be used. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS. Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g., air, water, blood) and not discrete, countable entities (e.g., intestines, heart)

host of the symbiotic host family relationship

• Harmonized namehost_of_host_fam_rel
• DescriptionFamilial relationship of the host of the symbiotic host organisms to other hosts of symbiotic host organism in the same study; can include multiple relationships

host of the symbiotic host genotype

• Harmonized namehost_of_host_geno
• DescriptionObserved genotype of the host of the symbiotic host organism

host of the symbiotic host gravidity

• Harmonized namehost_of_host_gravid
• DescriptionWhether or not the host of the symbiotic host organism is gravid, and if yes date due or date post-conception, specifying which is used

host of the symbiotic host infra-specific name

• Harmonized namehost_of_host_infname
• DescriptionTaxonomic name information of the host of the symbiotic host organism below subspecies level

host of the symbiotic host infra-specific rank

• Harmonized namehost_of_host_infrank
• DescriptionTaxonomic rank information about the host of the symbiotic host organism below subspecies level, such as variety, form, rank

host of the symbiotic host common name

• Harmonized namehost_of_host_name
• DescriptionCommon name of the host of the symbiotic host organism

host of the symbiotic host phenotype

• Harmonized namehost_of_host_pheno
• DescriptionPhenotype of the host of the symbiotic host organism. For phenotypic quality ontology (PATO) terms, see http://purl.bioontology.org/ontology/pato

host of the symbiotic host subject id

• Harmonized namehost_of_host_sub_id
• DescriptionA unique identifier by which each host of the symbiotic host organism subject can be referred to, de-identified, e.g. #H14

host of the symbiotic host taxon id

• Harmonized namehost_of_host_taxid
• DescriptionNCBI taxon id of the host of the symbiotic host organism

host of the symbiotic host total mass

• Harmonized namehost_of_host_totmass
• DescriptionTotal mass of the host of the symbiotic host organism at collection, the unit depends on the host

host phenotype

• Harmonized namehost_phenotype
• Description

host sex

• Harmonized namehost_sex
• DescriptionGender or physical sex of the host

host shape

• Harmonized namehost_shape
• Descriptionmorphological shape of host

host specificity

• Harmonized namehost_specificity
• DescriptionLevel of specificity of symbiont-host interaction, e.g., family-specific, generalist, genus-specific, species-specific

host subject id

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

host substrate

• Harmonized namehost_substrate
• Descriptionthe growth substrate of the host

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

metagenome source

• Harmonized namemetagenome_source
• Descriptiondescribes the original source of a metagenome assembled genome (MAG). Examples: soil metagenome, gut metagenome

miscellaneous parameter

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

mode of transmission

• Harmonized namemode_transmission
• DescriptionThe process through which the symbiotic host organism entered the host from which it was sampled, e.g., horizontal:castrator, horizontal:directly transmitted, horizontal:micropredator, horizontal:parasitoid, horizontal:trophically transmitted, horizontal:vector transmitted, vertical

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

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

perturbation

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

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

reference for biomaterial

• Harmonized nameref_biomaterial
• DescriptionPrimary publication or genome report

relationship to oxygen

• Harmonized namerel_to_oxygen
• DescriptionIs this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments, eg, aerobe, anaerobe, facultative, microaerophilic, microanaerobe, obligate aerobe, obligate anaerobe, missing, not applicable, not collected, not provided, restricted access

route of transmission

• Harmonized nameroute_transmission
• DescriptionDescription of path taken by the symbiotic host organism being sampled in order to establish a symbiotic relationship with the host (with which it was observed at the time of sampling) via a mode of transmission (specified in mode_transmission), e.g., environmental:faecal-oral, transplacental, vector-borne:vector penetration

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
• Descriptionthe amount of salt dissolved within the collected sample

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 solution

• Harmonized namesamp_store_sol
• DescriptionSolution within which sample was stored, if any

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

size fraction selected

• Harmonized namesize_frac
• DescriptionFiltering pore size used in sample preparation, e.g., 0-0.22 micrometer

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.

host of the symbiont role

• Harmonized namesymbiont_host_role
• DescriptionRole of the host in the life cycle of the symbiotic organism, e.g., accidental, dead-end, definitive, intermediate, paratenic, reservoir, single host

temperature

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

type of symbiosis

• Harmonized nametype_of_symbiosis
• DescriptionType of biological interaction established between the symbiotic host organism being sampled and its respective host, e.g., commensalistic, mutualistic, parasitic