MIMS: metagenome/environmental, wastewater; version 6.0 Package

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

See SAMN02911905 for example record of this type of BioSample.

Name

Environmental Package

Description

Use for environmental and metagenome sequences. Organism must be a metagenome, where lineage starts with unclassified sequences and scientific name ends with 'metagenome'.

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"

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

biochemical oxygen demand

• Harmonized namebiochem_oxygen_dem
• Descriptiona measure of the relative oxygen-depletion effect of a waste contaminant

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

chemical oxygen demand

• Harmonized namechem_oxygen_dem
• Descriptiona measure of the relative oxygen-depletion effect of a waste contaminant

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.

efficiency percent

• Harmonized nameefficiency_percent
• Descriptionpercentage of volatile solids removed from the anaerobic digestor

emulsions

• Harmonized nameemulsions
• Descriptionamount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types

gaseous substances

• Harmonized namegaseous_substances
• Descriptionamount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances

industrial effluent percent

• Harmonized nameindust_eff_percent
• Descriptionpercentage of industrial effluents received by wastewater treatment plant

inorganic particles

• Harmonized nameinorg_particles
• Descriptionconcentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles

isolation source

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

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

nitrate

• Harmonized namenitrate
• Descriptionconcentration of nitrate

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 particles

• Harmonized nameorg_particles
• Descriptionconcentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.

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

pH

• Harmonized nameph
• DescriptionpH measurement

phosphate

• Harmonized namephosphate
• Descriptionconcentration of phosphate

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

pretreatment

• Harmonized namepre_treatment
• Descriptionthe process of pre-treatment removes materials that can be easily collected from the raw wastewater

primary treatment

• Harmonized nameprimary_treatment
• Descriptionthe process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed

reactor type

• Harmonized namereactor_type
• Descriptionanaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage

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 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

secondary treatment

• Harmonized namesecondary_treatment
• Descriptionthe process for substantially degrading the biological content of the sewage

sewage type

• Harmonized namesewage_type
• Descriptiontype of wastewater treatment plant as municipial or industrial

size fraction selected

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

sludge retention time

• Harmonized namesludge_retent_time
• Descriptionthe time activated sludge remains in reactor

sodium

• Harmonized namesodium
• Descriptionsodium concentration

soluble inorganic material

• Harmonized namesoluble_inorg_mat
• Descriptionconcentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.

soluble organic material

• Harmonized namesoluble_org_mat
• Descriptionconcentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.

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.

suspended solids

• Harmonized namesuspend_solids
• Descriptionconcentration of substances including a wide variety of material, such as silt, decaying plant and animal matter, etc,; can include multiple substances

temperature

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

tertiary treatment

• Harmonized nametertiary_treatment
• Descriptionthe process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment

total nitrogen

• Harmonized nametot_nitro
• Descriptiontotal nitrogen content of the sample

total phosphate

• Harmonized nametot_phosphate
• Descriptiontotal amount or concentration of phosphate

wastewater type

• Harmonized namewastewater_type
• Descriptionthe origin of wastewater such as human waste, rainfall, storm drains, etc.