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MIMAG: metagenome-assembled genome; version 6.0 Package

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

Name

MIMAG.6.0

Environmental Package

No 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 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"

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

Optional Attributes

collection method

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

derived from

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

experimental factor

  • Harmonized nameexperimental_factor
  • DescriptionVariable aspect of experimental design

metagenome source

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

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.

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

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 size

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

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.
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