Wastewater

Mandatory Attributes Optional Attributes

Mandatory Attributes

Collection date

• Harmonized name: collection_date

• Description: the 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 name: env_broad_scale

• Description: Add 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 name: env_local_scale

• Description: Add 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 name: env_medium

• Description: Add 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 name: geo_loc_name

• Description: Geographical 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"

Latitude and longitude

• Harmonized name: lat_lon

• Description: The 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

NCBI Taxonomy ID

• Description: NCBI’s taxonomy identifier of the organism for this sample. The NCBI taxonomy ID can be found at https://www.ncbi.nlm.nih.gov/taxonomy/. Enter 32644 (which is a taxonomy ID for unidentified organisms) for the following or similar cases: (1) when NCBI taxonomy ID is not available because NCBI taxonomy does not yet cover the organism, (2) when metagenome or environmental sample was used, whose organismal composition is unknown in advance

• Example: 9606 (for Homo sapiens), 452680 (for Pseudomonas sp. UK4)

Organism

• Description: The most descriptive organism name for this sample (to the species, if possible). In the case of a new species, provide the desired organism name. In the case of unidentified species, choose the appropriate Genus and include ‘sp.’, e.g. “Escherichia sp.”. When sequencing a genome from a non-metagenomic source, include a strain or isolate name too, e.g. “Pseudomonas sp. UK4”

• Example: Homo sapiens, Pseudomonas sp. UK4

Sample name

• Description: A name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every sample name from a single submitter must be unique within a single BioProject

Optional Attributes

Alkalinity

• Harmonized name: alkalinity

• Description: alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate

Biochemical oxygen demand

• Harmonized name: biochem_oxygen_dem

• Description: a measure of the relative oxygen-depletion effect of a waste contaminant

Chemical administration

• Harmonized name: chem_administration

• Description: list 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 name: chem_oxygen_dem

Collection method

• Harmonized name: collection_method

• Description: Process used to collect the sample, e.g., bronchoalveolar lavage (BAL)

Depth

• Harmonized name: depth

• Description: Depth 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

• Description: Indicates when one BioSample was derived from another BioSample. Value should include BioSample accession number(s)

• Example: SAMN00000001, KAS24095074

Efficiency percent

• Harmonized name: efficiency_percent

• Description: percentage of volatile solids removed from the anaerobic digestor

Emulsions

• Harmonized name: emulsions

• Description: amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types

Gaseous substances

• Harmonized name: gaseous_substances

• Description: amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances

Industrial effluent percent

• Harmonized name: indust_eff_percent

• Description: percentage of industrial effluents received by wastewater treatment plant

Inorganic particles

• Harmonized name: inorg_particles

• Description: concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles

Isolation source

• Harmonized name: isolation_source

• Description: Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.

Miscellaneous parameter

• Harmonized name: misc_param

• Description: any other measurement performed or parameter collected, that is not listed here

Negative control type

• Harmonized name: neg_cont_type

• Description: The 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 name: nitrate

• Description: concentration of nitrate

Omics Observatory ID

• Harmonized name: omics_observ_id

• Description: A 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 name: org_particles

• Description: concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.

Organism count

• Harmonized name: organism_count

• Description: total 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 name: oxy_stat_samp

• Description: oxygenation status of sample

Perturbation

• Harmonized name: perturbation

• Description: type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types

pH

• Harmonized name: ph

• Description: pH measurement

Phosphate

• Harmonized name: phosphate

• Description: concentration of phosphate

Positive control type

• Harmonized name: pos_cont_type

• Description: The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive

Pretreatment

• Harmonized name: pre_treatment

• Description: the process of pre-treatment removes materials that can be easily collected from the raw wastewater

Primary treatment

• Harmonized name: primary_treatment

• Description: the 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 name: reactor_type

• Description: anaerobic 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 name: ref_biomaterial

• Description: Primary publication or genome report

Relationship to oxygen

• Harmonized name: rel_to_oxygen

• Description: Is 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 name: samp_collect_device

• Description: Method or device employed for collecting sample

Sample material processing

• Harmonized name: samp_mat_process

• Description: Processing applied to the sample during or after isolation

Sample salinity

• Harmonized name: samp_salinity

• Description: the amount of salt dissolved within the collected sample

Sample size

• Harmonized name: samp_size

• Description: Amount or size of sample (volume, mass or area) that was collected

Sample storage duration

• Harmonized name: samp_store_dur

• Description:

Sample storage location

• Harmonized name: samp_store_loc

Sample storage temperature

• Harmonized name: samp_store_temp

Sample volume or weight for DNA extraction

• Harmonized name: samp_vol_we_dna_ext

• Description: volume (mL) or weight (g) of sample processed for DNA extraction

Secondary treatment

• Harmonized name: secondary_treatment

• Description: the process for substantially degrading the biological content of the sewage

Sewage type

• Harmonized name: sewage_type

• Description: type of wastewater treatment plant as municipial or industrial

Size fraction selected

• Harmonized name: size_frac

• Description: Filtering pore size used in sample preparation, e.g., 0-0.22 micrometer

Sludge retention time

• Harmonized name: sludge_retent_time

• Description: the time activated sludge remains in reactor

Sodium

• Harmonized name: sodium

• Description: sodium concentration

Soluble inorganic material

• Harmonized name: soluble_inorg_mat

• Description: concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.

Soluble organic material

• Harmonized name: soluble_org_mat

• Description: concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.

Source material identifiers

• Harmonized name: source_material_id

• Description: unique 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 name: suspend_solids

• Description: concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter, etc,; can include multiple substances

Temperature

• Harmonized name: temp

• Description: temperature of the sample at time of sampling

Tertiary treatment

• Harmonized name: tertiary_treatment

• Description: the process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment

Total nitrogen

• Harmonized name: tot_nitro

• Description: total nitrogen content of the sample

Total phosphate

• Harmonized name: tot_phosphate

• Description: total amount or concentration of phosphate

Wastewater type

• Harmonized name: wastewater_type

• Description: the origin of wastewater such as human waste, rainfall, storm drains, etc.