MIMAG: metagenome-assembled genome, water; version 6.0 Package
You can download package details in xml format or as an Excel spreadsheet.
Name
MIMAG.water.6.0Environmental Package
waterDescription
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
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.
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
alkalinity
- Harmonized namealkalinity
- Descriptionalkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate
alkalinity method
- Harmonized namealkalinity_method
- DescriptionMethod used for alkalinity measurement
alkyl diethers
- Harmonized namealkyl_diethers
- Descriptionconcentration of alkyl diethers
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.
aminopeptidase activity
- Harmonized nameaminopept_act
- Descriptionmeasurement of aminopeptidase activity
ammonium
- Harmonized nameammonium
- Descriptionconcentration of ammonium
atmospheric data
- Harmonized nameatmospheric_data
- Descriptionmeasurement of atmospheric data; can include multiple data
bacterial production
- Harmonized namebac_prod
- Descriptionbacterial production in the water column measured by isotope uptake
bacterial respiration
- Harmonized namebac_resp
- Descriptionmeasurement of bacterial respiration in the water column
bacterial carbon production
- Harmonized namebacteria_carb_prod
- Descriptionmeasurement of bacterial carbon production
biomass
- Harmonized namebiomass
- Descriptionamount of biomass; should include the name for the part of biomass measured, e.g. microbial, total. can include multiple measurements
bishomohopanol
- Harmonized namebishomohopanol
- Descriptionconcentration of bishomohopanol
bromide
- Harmonized namebromide
- Descriptionconcentration of bromide
calcium
- Harmonized namecalcium
- Descriptionconcentration of calcium
carbon/nitrogen ratio
- Harmonized namecarb_nitro_ratio
- Descriptionratio of amount or concentrations of carbon to nitrogen
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
chloride
- Harmonized namechloride
- Descriptionconcentration of chloride
chlorophyll
- Harmonized namechlorophyll
- Descriptionconcentration of chlorophyll
collection method
- Harmonized namecollection_method
- DescriptionProcess used to collect the sample, e.g., bronchoalveolar lavage (BAL)
conductivity
- Harmonized nameconduc
- Descriptionelectrical conductivity of water
density
- Harmonized namedensity
- Descriptiondensity of sample
derived from
- Harmonized namederived_from
- DescriptionIndicates when one BioSample was derived from another BioSample. Value should include BioSample accession number(s) (SAMNxxxxxxxx).
diether lipids
- Harmonized namediether_lipids
- Descriptionconcentration of diether lipids; can include multiple types of diether lipids
dissolved carbon dioxide
- Harmonized namediss_carb_dioxide
- Descriptionconcentration of dissolved carbon dioxide
dissolved hydrogen
- Harmonized namediss_hydrogen
- Descriptionconcentration of dissolved hydrogen
dissolved inorganic carbon
- Harmonized namediss_inorg_carb
- Descriptiondissolved inorganic carbon concentration
dissolved inorganic nitrogen
- Harmonized namediss_inorg_nitro
- Descriptionconcentration of dissolved inorganic nitrogen
dissolved inorganic phosphorus
- Harmonized namediss_inorg_phosp
- Descriptionconcentration of dissolved inorganic phosphorus
dissolved organic carbon
- Harmonized namediss_org_carb
- Descriptionconcentration of dissolved organic carbon
dissolved organic nitrogen
- Harmonized namediss_org_nitro
- Descriptiondissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2
dissolved oxygen
- Harmonized namediss_oxygen
- Descriptionconcentration of dissolved oxygen
downward PAR
- Harmonized namedown_par
- Descriptionvisible waveband radiance and irradiance measurements in the water column
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
fluorescence
- Harmonized namefluor
- Descriptionraw or converted fluorescence of water
glucosidase activity
- Harmonized nameglucosidase_act
- Descriptionmeasurement of glucosidase activity
light intensity
- Harmonized namelight_intensity
- Descriptionmeasurement of light intensity
magnesium
- Harmonized namemagnesium
- Descriptionconcentration of magnesium
mean friction velocity
- Harmonized namemean_frict_vel
- Descriptionmeasurement of mean friction velocity
mean peak friction velocity
- Harmonized namemean_peak_frict_vel
- Descriptionmeasurement of mean peak friction velocity
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
n alkanes
- Harmonized namen_alkanes
- Descriptionconcentration of n-alkanes; can include multiple n-alkanes
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
nitrate
- Harmonized namenitrate
- Descriptionconcentration of nitrate
nitrite
- Harmonized namenitrite
- Descriptionconcentration of nitrite
nitrogen
- Harmonized namenitro
- Descriptionconcentration of nitrogen (total)
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.
organic carbon
- Harmonized nameorg_carb
- Descriptionconcentration of organic carbon
organic matter
- Harmonized nameorg_matter
- Descriptionconcentration of organic matter
organic nitrogen
- Harmonized nameorg_nitro
- Descriptionconcentration of organic nitrogen
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
particulate organic carbon
- Harmonized namepart_org_carb
- Descriptionconcentration of particulate organic carbon
particulate organic nitrogen
- Harmonized namepart_org_nitro
- Descriptionconcentration of particulate organic nitrogen
perturbation
- Harmonized nameperturbation
- Descriptiontype of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types
petroleum hydrocarbon
- Harmonized namepetroleum_hydrocarb
- Descriptionconcentration of petroleum hydrocarbon
pH
- Harmonized nameph
- DescriptionpH measurement
phaeopigments
- Harmonized namephaeopigments
- Descriptionconcentration of phaeopigments; can include multiple phaeopigments
phosphate
- Harmonized namephosphate
- Descriptionconcentration of phosphate
phospholipid fatty acid
- Harmonized namephosplipid_fatt_acid
- Descriptionconcentration of phospholipid fatty acids; can include multiple values
photon flux
- Harmonized namephoton_flux
- Descriptionmeasurement of photon flux
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
potassium
- Harmonized namepotassium
- Descriptionconcentration of potassium
pressure
- Harmonized namepressure
- Descriptionpressure to which the sample is subject, in atmospheres
primary production
- Harmonized nameprimary_prod
- Descriptionmeasurement of primary production
redox potential
- Harmonized nameredox_potential
- Descriptionredox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential
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
salinity
- Harmonized namesalinity
- Descriptionsalinity measurement
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 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
silicate
- Harmonized namesilicate
- Descriptionconcentration of silicate
size fraction selected
- Harmonized namesize_frac
- DescriptionFiltering pore size used in sample preparation, e.g., 0-0.22 micrometer
size-fraction lower threshold
- Harmonized namesize_frac_low
- DescriptionRefers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample
size-fraction upper threshold
- Harmonized namesize_frac_up
- DescriptionRefers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample
sodium
- Harmonized namesodium
- Descriptionsodium concentration
soluble reactive phosphorus
- Harmonized namesoluble_react_phosp
- Descriptionconcentration of soluble reactive phosphorus
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.
sulfate
- Harmonized namesulfate
- Descriptionconcentration of sulfate
sulfide
- Harmonized namesulfide
- Descriptionconcentration of sulfide
suspended particulate matter
- Harmonized namesuspend_part_matter
- Descriptionconcentration of suspended particulate matter
temperature
- Harmonized nametemp
- Descriptiontemperature of the sample at time of sampling
tidal stage
- Harmonized nametidal_stage
- Descriptionstage of tide
total depth of water column
- Harmonized nametot_depth_water_col
- Descriptionmeasurement of total depth of water column
total dissolved nitrogen
- Harmonized nametot_diss_nitro
- Descriptiontotal dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen
total inorganic nitrogen
- Harmonized nametot_inorg_nitro
- Descriptiontotal inorganic nitrogen content
total nitrogen
- Harmonized nametot_nitro
- Descriptiontotal nitrogen content of the sample
total particulate carbon
- Harmonized nametot_part_carb
- Descriptiontotal particulate carbon content
total phosphorus
- Harmonized nametot_phosp
- Descriptiontotal phosphorus concentration, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus. Can also be measured without filtering, reported as phosphorus
turbidity
- Harmonized nameturbidity
- Descriptionturbidity measurement
water current
- Harmonized namewater_current
- Descriptionmeasurement of magnitude and direction of flow within a fluid