Sets

Dictionary v3.0.0 Documentation v2.1.0

Sets are lists of categories and other parts. For example, Collection category set (collectionCatSet) contains a list of the different collection types including: Moore swab, Grab sample, Flow proportional sample, etc.

Sets can have parts that are reused. For example, there are different quality measures for sample collection (e.g. Sample not collected), PCR measures (Inhibition preset), and sequencing measures (Low depth of coverage), but all quality sets share the No quality concerns indicator.

Aggregations

(aggregations). Statistical measures used to report a measure. Each measure reported as a number should be reported with an aggregation. The default aggregation is sin, which corresponds to a single measurement.

• AND Boolean aggregation (andBoo). “AND” aggreation.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Cumulative count (cuCo). The cumulative count of cases of a given disease.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Daily count (daiCo). The daily count of cases of a given disease.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• EpiWeek Mean (epiMean). The mean of all measures taken in one epiweek.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Flow-normalized mean (floMean). Mean measure normalized to wastewater flow.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Geometric mean (gmn). Geometric mean.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• See Header for Aggregation (hAg). An indicator to show in a wide-name that aggregation information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Lower limit of a 95% confidence interval (lowerCI95). Specifies the the lower limit of a 95% confidence interval.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Maximum value (maxVal). Highest value in a range of values for a measure.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Arithmetic mean (me). Arithmetic mean.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Median (med). Median.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Normalized arithmetic mean (menr). Arithmetic mean, normalized.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Minimum value (minVal). Lowest value in a range of values for a measure.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Aggregation not applicable (naAggr). Not applicable for aggregations.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Normalized geometric mean (ngmn). Geometric mean, normalized.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• OR Boolean aggregation (orBoo). “OR” aggreation.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Other aggregation depricated (otherDep). Other aggregation method. Add description to aggregationOther
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• PMMoV- and flow-normalized mean (pmFloMean). Mean measure normalized to amount of PMMoV and wastewater flow.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• PMMoV-normalized mean (pmmovNorm). Mean measure normalized to amount of PMMoV.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Standard deviation (sd). Standard deviation.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Normalized standard deviation (sdn). Standard deviation, normalized.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Single (sin). A value that is not an aggregate measurement (ie. not a mean, median, max or any other) and can be a replicate value.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Standard Error (stEr). The standard error of a series of measurements.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Rolling sum of previous 14 days (sum14). The rolling sum of case counts/some kind of count over the previous 14 days.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Total amount or count - the sum (total). The total number or final count of cases, or other defined metric.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Upper limit of a 95% confidence interval (upperCI95). Specifies the the upper limit of a 95% confidence interval.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Aggregation scales

(aggregationScales). The scale of an aggregation set. Aggregation scales include quantitative and qualitative.

• Aggregation scale not applicable (naAggrScale). Not application for aggregation sets.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Other aggregation scale (othAgg). Specifies an aggregation scale that can’t be described as either “qualitative” or “quantitative”.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Qualitative (qualAggScale). The qualitative aggregation scale.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Quantitative (quantAggScale). The “quantAggScale” aggregation scale.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• See unit (aggregation scales) (seeUnitAggScale). A value for aggregation scale to be used when the aggregation scale depends on that specified in the parts list entry for the unit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Aggregation sets

(aggregationSets). Sets of aggregations. Examples of aggregation sets include logarithm, linear and boolean.

Boolean aggregation set

(booleanAggrSet)Aggreagation set for boolean.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• AND Boolean aggregation (andBoo). “AND” aggreation.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• OR Boolean aggregation (orBoo). “OR” aggreation.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Single (sin). A value that is not an aggregate measurement (ie. not a mean, median, max or any other) and can be a replicate value.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Linear scale aggregation set

(linearAggrSet)The aggregation set that contains all aggregations that exist on the linear scale.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Cumulative count (cuCo). The cumulative count of cases of a given disease.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Daily count (daiCo). The daily count of cases of a given disease.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• EpiWeek Mean (epiMean). The mean of all measures taken in one epiweek.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Flow-normalized mean (floMean). Mean measure normalized to wastewater flow.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Lower limit of a 95% confidence interval (lowerCI95). Specifies the the lower limit of a 95% confidence interval.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Maximum value (maxVal). Highest value in a range of values for a measure.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Arithmetic mean (me). Arithmetic mean.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Median (med). Median.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Normalized arithmetic mean (menr). Arithmetic mean, normalized.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Minimum value (minVal). Lowest value in a range of values for a measure.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• PMMoV- and flow-normalized mean (pmFloMean). Mean measure normalized to amount of PMMoV and wastewater flow.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• PMMoV-normalized mean (pmmovNorm). Mean measure normalized to amount of PMMoV.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Standard deviation (sd). Standard deviation.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Normalized standard deviation (sdn). Standard deviation, normalized.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Single (sin). A value that is not an aggregate measurement (ie. not a mean, median, max or any other) and can be a replicate value.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Standard Error (stEr). The standard error of a series of measurements.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Rolling sum of previous 14 days (sum14). The rolling sum of case counts/some kind of count over the previous 14 days.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Total amount or count - the sum (total). The total number or final count of cases, or other defined metric.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Upper limit of a 95% confidence interval (upperCI95). Specifies the the upper limit of a 95% confidence interval.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Logarithmic scale aggregation set

(logAggrSet)The aggregation set that contains all aggregations that exist on the logarithmic scale (rather than linear or qualitative).
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Flow-normalized mean (floMean). Mean measure normalized to wastewater flow.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Geometric mean (gmn). Geometric mean.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Lower limit of a 95% confidence interval (lowerCI95). Specifies the the lower limit of a 95% confidence interval.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Maximum value (maxVal). Highest value in a range of values for a measure.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Minimum value (minVal). Lowest value in a range of values for a measure.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Normalized geometric mean (ngmn). Geometric mean, normalized.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• PMMoV- and flow-normalized mean (pmFloMean). Mean measure normalized to amount of PMMoV and wastewater flow.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• PMMoV-normalized mean (pmmovNorm). Mean measure normalized to amount of PMMoV.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Single (sin). A value that is not an aggregate measurement (ie. not a mean, median, max or any other) and can be a replicate value.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Standard Error (stEr). The standard error of a series of measurements.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Upper limit of a 95% confidence interval (upperCI95). Specifies the the upper limit of a 95% confidence interval.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Aggregation set not applicable

(naAggrSet)Not application for aggregation sets. Used for parts for which an aggregation set value is not applicable or appropriate.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Aggregation not applicable (naAggr). Not applicable for aggregations.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Other aggregation set

(otherAggrSet)Aggregation set used for unitless measures.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Cumulative count (cuCo). The cumulative count of cases of a given disease.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Daily count (daiCo). The daily count of cases of a given disease.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• EpiWeek Mean (epiMean). The mean of all measures taken in one epiweek.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Flow-normalized mean (floMean). Mean measure normalized to wastewater flow.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Geometric mean (gmn). Geometric mean.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• See Header for Aggregation (hAg). An indicator to show in a wide-name that aggregation information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Lower limit of a 95% confidence interval (lowerCI95). Specifies the the lower limit of a 95% confidence interval.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Maximum value (maxVal). Highest value in a range of values for a measure.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Arithmetic mean (me). Arithmetic mean.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Median (med). Median.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Normalized arithmetic mean (menr). Arithmetic mean, normalized.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Minimum value (minVal). Lowest value in a range of values for a measure.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Aggregation not applicable (naAggr). Not applicable for aggregations.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Normalized geometric mean (ngmn). Geometric mean, normalized.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Standard deviation (sd). Standard deviation.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Normalized standard deviation (sdn). Standard deviation, normalized.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Single (sin). A value that is not an aggregate measurement (ie. not a mean, median, max or any other) and can be a replicate value.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Standard Error (stEr). The standard error of a series of measurements.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Rolling sum of previous 14 days (sum14). The rolling sum of case counts/some kind of count over the previous 14 days.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Total amount or count - the sum (total). The total number or final count of cases, or other defined metric.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Upper limit of a 95% confidence interval (upperCI95). Specifies the the upper limit of a 95% confidence interval.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Attributes

(attributes). Attributes describe the who, where, when, and why of environmental surveillance. There are attributes for domain, specimen, compartment, or table. Attributes are one of the three main components or ways to report environment surviellence data. The other two components are measures and methods.

• Accessions Index ID (accessIndexID). Provisional ID to act as a primary key for each row of the accessions table.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Accession Number in Repository (accessNum). The accession number for the data entry in the given data repository or hosting platform.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Public health action (action). The specific public health action or designation being taken or applied.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Public health action datetime (actionDT). The date and Time of the public health action.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Public Health Action Group ID (actionGrpID). ID used for linking multiple public health actions together for a single action.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Public health action type (actionType). The type of public health action being taken.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Analysis date (aDate). Date the measurement was performed in the lab.
  Status: depreciated. First released: 1.0.0. Last updated: 2.1.0.
• Analysis date end (aDateEnd). Date the measurement or analysis was completed.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Analysis date start (aDateStart). Date the measurement or analysis was started.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Address Line 1 (addL1). Line 1 (the street name, number and direction) for a given address.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Address Line 2 (addL2). Line 2 (the unit number) for a given address.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Address ID (addressID). A unique identifier for an address.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Aggregation scale (aggragationScale). A scale used for an aggregation. Only applicable for measures and units.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Aggregation (aggregation). Statistical measures used to report a measure. Each aggregation has a corresponding value.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Aggregation input (wide table) (aggregationInput). The partID for the aggregation being used in a wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Aggregation name (wide table) (aggregationName). The aggregation referenced for the wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Aggregation set (aggregationSet). The aggregation set for a unit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Alias depreciated (aliasDep). ID of an assay that is the same or similar. A comma separated list.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Alias ID depreciated (aliasIDDep). Alias id
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Access to all org (allOrgs). If this is ‘no’, this data will not be available to any partner organization. If missing, data will be available to the all organizations.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Assay method id default depreciated (amDefDep). Used as default when a new measurement is created for this lab. See ID in AssayMethod table.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Assay ID (asID). Links with the AssayMethod used to perform the analysis. Use instrument.ID for measures that are not viral measures.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Attribute input (wide table) (attributeInput). The partID for the attribute being used in a wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Attribute name (wide table) (attributeName). The attribute referenced for the wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Calculation Type (calcType). A field to explain the purpose/nature of a single calculation/data treatment.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Calculation ID (calculationID). A unique identifier and primary key for every row of the calculations table.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Capital city endonym (capitalEndonym). The name locals use for their country’s capital.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Capital city exonym (capitalExonym). The English name foreigners use for the country’s capital.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• character length (charLength). The number of characters used for the wide names.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• City (city). The city where a site or organization is located; part of the address.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Class (class). A unique identifier for a class, which is akin to a sub-group; it’s a way of grouping parts within a given group. A group can have one or more classes to describe different parts of the class.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Collection Approximate Time Period (collAppxT). The general time period (ie. Morning, afternoon, evening) of sample collection.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Collection Date (time not included) (collDate). Sample collection date, where time is reported in a separate field.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Collection date time (collDT). For grab samples this is the date, time and timezone the sample was taken.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Collection date time end (collDTEnd). For integrated time average samples this is the date, time and timezone the sample was finished being taken.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Collection date time start (collDTStart). For integrated time averaged samples this is the date, time and timezone the sample was started being taken.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Collection number (collNum). The number of subsamples that were combined to create the sample. Use NA for continuous, proportional or passive sampling.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Collection period and number (collNumPer). Composite collection number.period.
  Status: depreciated. First released: 2.0.0. Last updated: 3.0.0.
• Collection period (collPer). Collection period. The time period over which the sample was collected, in hours. Alternatively, use collectionStart and collectionEnd.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sample collection type (collType). The type of collection.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Column name depreciiated (columnNameDep). Name for the column
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Compartment (compartment). The attribute identifying the substance from which where a sample was taken. For more information, see partID = compartment.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Compartment input (wide table) (compartmentInput). The partID for the compartment being used in a wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Compartment name (wide table) (compartmentName). The compartment referenced for the wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Compartment Set Header (compartmentSet). An idenfication of a set of compartments that can be applied for a measure or method.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Contact ID (contactID). A unique identifier for a given contact person.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Contact name (contactName). Contact person or group, for the lab.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Contact phone (coPhone). Contact phone number, for the lab.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Country (country). The country where a site or organization is located; part of the address.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Country endonym (countryEndonym). The name locals use for their country.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Country exonym (countryExonym). The English name foreigners use for the country.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Covid-19 population measurement date (cphDate). date of reporting for covid-19 measure.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Cphd ID (cphid). Unique identifier for the table.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Custody Contact ID (custodyCont). A unique identifier for data custodians.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Data custodian ID (custodyID). The data custodian of a database.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Host Data Repository or Bank (dataHost). The external repository or database/bank in which a sequence (or other external data) is stored.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Dataset creation date (datasetDate). Specifies the date a given dataset was created.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Dataset ID (datasetID). The name of the dataset that stores information for MeasureReport, SampleReport and other reporting tables.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Date (dateDep). Date
  Status: depreciated. First released: 1.0.0. Last updated: 3.0.0.
• Description (descr). A detailed description of a measure, method, or attribute.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Access to details deprecated (detailsDep). More details on the existing confidentiality requirements of this measurement.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Domain (domain). Domain is the highest level of describing of a measure.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Contact email (email). Contact e-mail address, for the lab.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• European Nucleotide Association Mapping Column (enaMap). ENA header
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• European Nucleotide Association (ENA) - notes (enaNotes). ENA notes
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Enumeration for set values (enumeration). The numeric value that corresponds to a given value in a set, defined in the sets table.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• EpiWeek Number (epiWeek). The number of the epi week in which a sample what collected, or to which a measure would apply.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• EpiWeek Start Date (epiWeekStart). Start date of a given epi week. Noted that not all epi weeks use the same start dates, despite being a standard, so including the start dat resolves the possible ambiguity.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Year of the EpiWeek (epiYear). The year in which the epi week is occuring.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Equation (equation). The equation used in the calculation/data treatment.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• File location of polygon (fileLocation). The location of the file containing the geometry of the polygon.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• First name of contact (firstName). Specifies the first name of a given contact.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Fraction analyzed (fraction). Fraction of the sample that is analyzed.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Fraction input (wide table) (fractionInput). The partID for the fraction being used in a wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Fraction name (wide table) (fractionName). The fraction analyzed referenced for the wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Funder contact ID (funderCont). A unique identifier for a funder.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Funding agency ID (funderID). The funding agency of the dataset.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• European Petroleum Survey Group Coordinates (geoEPSG). The unique EPSG code specifying a given geospatial area.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Latitude (geoLat). Geographical location, latitude in decimal coordinates, ie.: (45.424721)
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Longitude (geoLong). Geographical location, longitude in decimal coordinates, ie.: (-75.695000)
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Type of geography (geoType). Type of geography that is represented by the polygon.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Well-known text (geoWKT). Well-known text of the polygon
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Group (group). Unique identifier for a group of measures. Mostly applicable for measures, methods, units, and aggregations.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Health Region for a Site (healthRegion). A free-text variable for listing the health region for a given site.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Version of Data Hosting Platform/Repository (hostVersion). The version of the data repository or hosting platform being used.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Index (index). Index number in case the measurement was taken multiple times.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Instrument ID (instrumentID). A unique identifier for an instrument.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Instrument Type (insType). Type of instrument used to perform the measurement.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Describe other instrument type, if applicable (insTypeOth). Description of the instrument in case it is not listed in instrumentType.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• ISO639-1 (iso6391). The first part of the ISO 639 series of international standards for language codes. Part 1 covers the registration of two-letter codes. There are 183 two-letter codes registered as of June 2021. The registered codes cover the world’s major languages.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ISO639-2B (iso6392B). A set of international standards that lists short codes for language names. These ISO639-2 are the three-letter codes defined in part two (ISO 639-2) of the standard, including the corresponding two-letter (ISO 639-1) codes where they exist. The ‘B’ specifies the bibliographic code (B code).
  Status: depreciated. First released: 2.0.0. Last updated: 3.0.0.
• ISO639-2T (iso6392T). A set of international standards that lists short codes for language names. These ISO639-2 are the three-letter codes defined in part two (ISO 639-2) of the standard, including the corresponding two-letter (ISO 639-1) codes where they exist. The ‘T’ specifies the terminological code (T code).
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ISO639-3 (iso6393). A set of international standards that lists short codes for language names. ISO 639-3 extends the ISO 639-2 alpha-3 codes with an aim to cover all known natural languages.
  Status: depreciated. First released: 2.0.0. Last updated: 3.0.0.
• ISO639-6 (iso6396). A set of international standards that lists short codes for language names. ISO 639-6 builds off ISO639-3 with the use of four-letter codes, and allowing users to differenciate between variants of languages and language families, such as histroical vs. revived versions of languages.
  Status: depreciated. First released: 2.0.0. Last updated: 3.0.0.
• ISO 3166-1 alpha-2 country code (isoCode). The ISO 3166-1 alpha-2 code, a two-letter country code which is also used to create the ISO 3166-2 country subdivision code and the Internet country code top-level domain.
  Status: active. First released: 2.1.0. Last updated: 3.0.0.
• ISO 3166-1 alpha-3 country code (isoCodeX). The ISO 3166-1 alpha-3 code, a three-letter country code which may allow a better visual association between the code and the country names than the 3166-1 alpha-2 code.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• ISO 3166-2 code for country sub-domain (isoZone). The ISO 3166-2 codes for the names of the principal subdivisions (e.g., provinces, states, departments, regions) of all countries coded in ISO 3166-1.
  Status: active. First released: 2.1.0. Last updated: 3.0.0.
• Lab ID default depricated (labDefDep). Used as default when a new sample is created by this reporter. See ID in Lab table.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Lab ID (labID). Unique identifier for a laboratory.
  Status: depreciated. First released: 1.0.0. Last updated: 2.1.0.
• Language ID (lang). Language code for translation purposes. Specifies the langage for each translation, other than the default English. Uses the ISO-6393 code.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Language family (langFam). Specifies the language family of a given language for translation and language tracking purposes.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Language name (langName). Specifies the name of the language in roman alphabet characters for translation and language tracking purposes.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• National language script (langScript). The language(s) and script(s) used for the country’s capital endonyms.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Last edited (lastEdited). The date the entry was last updated.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Last name of contact (lastName). Specifies the last name of a given contact.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Link (li). Link to an external reference that describes the geometry of the polygon.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• License (license). The license of a dataset.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Access to local ha (localHA). If this is ‘no’, the, data will not be available to local health authorities. If missing, data will be available to local health authorities.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Manufacturer (manufacturer). Manufacturer of an instrument.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Measure (measure). A measurement or observation of any substance including a biological, physical or chemical substance.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Measure input (wide table) (measureInput). The partID for the measure being used in a wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Measure license (measureLic). Specifies the access and use licensing for a given single measurement.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Measure name (wide table) (measureName). The measure referenced for the wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Report ID (measureRepID). Unique identifier for a measurement.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Measure set report set ID (measureSetRepID). Unique identifier that links together a group of related measures.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Method (method). A procedure for collecting a sample or performing a measure.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Method input (wide table) (methodInput). The partID for the method being used in a wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Method name (wide table) (methodName). The method referenced for the wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Missingness Set (missingnessSet). Missingness sets for measures, methods or attributes.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Measure, Method, or Attribute Set Header (mmaSet). The set for a measure, method, or attribute. Only applicable for categorical fields, and the categories that populate them.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Model (model). Model number or version of the instrument.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Name (name). Name of a domain, specimen, group, class, attribute, unit, nomeclature or other entity.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• English name for countries (nameEngl). English-language name of a given country.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Official state name (nameOfficial). Official english-language name of a given state.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Native Name (natName). The native name of the language, i.e. what the language is called by its speakers.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• National Center for Biotechnology Information (ncbi). NCBI header
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• NCBI - notes (ncbiNotes). NCBI notes
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Nomenclature (nomenclature). A classification system to report the measure class. Only applicable to variants, mutations, and diseases.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• NORMAN (norman). NORMAN header
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• NORMAN - notes (normanNotes). Norman notes
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Notes (notes). A note used to describe details that are not captured in other attributes
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ISO 3166-1 numeric country code (numCode). The ISO 3166-1 numeric code, a three-digit country code which is identical to that developed and maintained by the United Nations Statistics Division, with the advantage of script (writing system) independence, and hence useful for people or systems using non-Latin scripts.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• National Wastewater Surveillance System (nwss). NWSS header
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• NWSS - notes (nwssNotes). NWSS notes
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• NWSS - process (nwssProcess). NWSS process
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sequence Order (order). The order a single calculation/data treatment takes within the full container pipeline/workflow.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Organization ID (organizationID). A unique identifier for the organization to which the reporter is affiliated.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Organization level (orgLevel). The geographic level of an organization.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Organization sector (orgSector). The sector of an organization
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Organization Type (orgType). Specifies the type or purpose of a given organization.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sample origin (origin). An attribute of a sample specifying the origin.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Original Data Format (originalFormat). The original structure or model used to record and store the data. This helps indicate if data have been transformed or mapped into the ODM structure.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Access to other prov depricated (otherProvDep). If this is ‘no’, this data will not be available to other data providers not listed before. If missing, data will be available to other data providers not listed before
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Parent dataset ID (parDatasetID). The datasetID that is a parent to another datasetID.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Parent sample ID (parent). If this sample has been pooled into one big sample for analysis this indicates the sample of the larger pooled sample.
  Status: depreciated. First released: 1.1.0. Last updated: 2.0.0.
• Parent Site ID (parSiteID). The siteID that is a parent to another siteID; usually the sub-site will be contained in the parentSite.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Part type input (wide table) (partTypeInput). The partID for the part type being used in a wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Part type name (wide table) (partTypeName). The part type being used in a wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Postal or Zip Code (pCode). The zip code or postal code for a given address, specifying a specifc geographic area.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Access to phac (phac). If this is ‘no’, the data will not be available to employees of the Public Health Agency of Canada - PHAC. If missing, data will be available to employees of the Public Health Agency of Canada - PHAC.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Public Health Action ID (phActionID). Unique identifier for public health actions.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PHAGE (phage). PHAGE header
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• PHAGE - notes (phageNotes). PHAGE notes
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Country national phone prefix (phone). International dialing code for the country.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Pipeline ID (pipelineID). A primary key linked to a single measure (may be used multiple times), it is the shorthand for the data transformation pipeline used. Serves as a data pipeline identifier.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Polygon License (poLic). The license for the availability of the polygon shapefile.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Polygon ID (polygonID). Unique identifier for the polygon.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Polygon ID Object (polygonIDObject). The polygon ID Object in a polygon relationship.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Polgygon ID Subject (polygonIDSubject). The polygon ID subject in a polygon relationship.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Polygon relationship ID (polygonRelID). Unique identifier for each row in the polygon relationships table.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Pooled (pooled). Is this a pooled sample, and therefore composed of multiple child samples obtained at different sites
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Type of date for case reporting depreciated (popDateTypeDep). Type of date used for confirmed cases. Typically, report or episode are reported. Onset and test date is not usually reported within aggregate data.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Protocol ID (protocolID). A unique identifier for a given protocol.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Protocol ID container (protocolIDContainer). Unique identifier for the protocol and the steps and other protocols that make it up.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Protocol ID object (protocolIDObj). The object of the relationship between one protocol and another protocol or step, within a given protocol ID container.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Protocol ID subject (protocolIDSub). The subject of the relationship between one protocol and another protocol or step, within a given protocol ID container.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Synthetic ID for the protocolRelationships table (protocolRelationshipsID). A unique, autoincremental ID generated to produce a unique identifier and primary key for each row of the protocolRelationships table.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Protocol version (protocolVersion). Specifies the version of a method set.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Access to prov ha (provHA). If this is ‘no’, this data will not be available to provincial health authorities. If missing, data will be available to provincial health authorities.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Pretreatment description - depreciated (ptDescDep). If preTreatment then describe the treatment that was performed.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Access to public (public). If this is ‘no’, this data will not be available to the public. If missing, data will be available to the public.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Purpose (purpose). The reason the measure or sample was taken.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Quality flag (qualityFlag). A field for reporting any quality concerns - of lack thereof - for a sample or measure.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Quality Indicator Set Header (qualityIndSet). The quality set that corresponds to a given part. Only applicable for samples and measures.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Quality report ID (qualityReportID). A unique identifier for a given quality report.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Date sample recieved (recDate). The date the sample was received at the laboratory for analysis.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Reference link (refLink). Link to the reference material for a part. May link to literature on a method, measure, etc.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Relationship between entities (relationshipID). Attribute for specifying the relationship between a sample subject and object.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Measure relevance end date (relDateEnd). The end date of the relevancy period of a measure - mostly for time-varrying metrics for sites or polygons.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Measure relevance start date (relDateStart). The start date of the relevancy period of a measure - mostly for time-varrying metrics for sites or polygons.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Primary reporting authority ID (repOrg1). The primary or most responsible authority for rountine surveillance reports or findings, or where the site is located.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Secondary reporting authority ID (repOrg2). The secondary, additional or alternative authority for rountine surveillance reports or findings, or where the site is located.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Reportable (reportable). Flag for whether a measure is reportable or not, based on confidence in the measure and methods applied.
  Status: active. First released: 2.0.0. Last updated: 2.1.0.
• Report date (reportDate). The date a measure was reported.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Reporter ID depreciated (reporterIDDep). Unique identifier for the person or organization that is reporting the data.
  Status: depreciated. First released: 1.1.0. Last updated: 2.0.0.
• Report table input (wide table) (reportTableInput). The short name for the listed source table.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Report table name (wide table) (reportTableName). The report table that the wide name calls from.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Replicate Type (repType). Attirbute of a sample, specifying whether the sample is unique, or a replicate. And if it is a replicate, what type of replicate is it?
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Role of contact (role). Specifies the organizational role of a given contact.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sample material (saMaterial). Type of sample.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sample ID (sampleID). Unique identifier for a sample.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Sample ID object (sampleIDObject). Populated by sampleID - this specifies the object of a sample relationship.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sample ID subject (sampleIDSubject). Populated by sampleID - this specifies the subject of a sample relationship.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Synthetic ID for the sampleRelationships table (sampleRelationshipsID). A unique, autoincremental ID generated to produce a unique identifier and primary key for each row of the sampleRelationships table.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Sample shed (sampleShed). A geographic area, physical space, or structure. A sample is taken from a sampleshed for a representative measurement of a substance(s).
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Access to self (self). If this is ‘no’, this data will not be shown on the portal when this reporter logs in. If missing, data will be available to this reporter.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Date sample was sent (sentDate). Date that the sample was sent from the collection site to the lab.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Composite Set ID (setCompID). A composite ID generated by concatennating the ‘setID’ and ‘partID’ of a given row in the sets table. This allows for a unique primary key and robust relational database structure.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Set ID (setID). The unique identifier of a value set.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Severity indicator (severity). An indicator of the severity or seriousness of a quality flag.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sewer network file link depreciated (sewerNetworkFileBLOB). Link to a file that has any detailed information about the sewer network associated with the site (any format).
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Site ID default (siteDef). Used as default when a new sample is created by this reporter. See ID in Site table.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Site ID (siteID). Unique identifier for the location where a sample was taken.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Level of Aggregation of a Sampling Site (siteLevel). Specifies the level of aggregation that occurs at the site - essentially, what size and type of region is represented by the base sewershed. This can be used to pool together or average results across similar sewersheds, and avoid trying to average different scales of sewershed together without a correction for size.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Site measure ID (siteMeasureID). Unique identifier for wide table only. Use when all measures are performed on a single sample.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Site Type (siteType). Type of site or institution where sample was taken.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sewer network file link depreciated 2 (snfl). Link to a file that has any detailed information about the sewer network associated with the site (any format).
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Wide name source (source). The database or table sourced for the wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Source Code (sourceCode). The source code for the calculation/data treatment, more applicable for algorithms/more complex steps.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Source Protocol ID (sourceProtocol). A protocol that served as a basis for another protocol. This may be due to version changes, or a referencing a protocol that was later adapted.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Protocol step source ID (sourceStep). Specifies the protocol step which serves as a basis for a given protocol step.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sovereign status of a country (sovereignty). Sovereign status of a country, indicating which state has the highest jurisdiction over a given territory.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Specimen (specimen). The substance or thing upon which the observation was made.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Specimen input (wide table) (specimenInput). The partID for the specimen being used in a wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Specimen name (wide table) (specimenName). The specimen referenced for the wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Specimen Set Header (specimenSet). An idenfication of a set of specimens that can be applied for a measure or method.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Standard for Data Adjustment (standard). A field where one can categorically record the standard to which something is being standardized (ie. PMMoV, Crassphage, Flow, etc.) or smoothed (ie. bayesian smoothing, central average smoothing, 7-days, time, etc.).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• State, Province, or Region (stateProvReg). The state, province, or region where a site or organization is located; part of the address.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Protocol Step ID (stepID). The unique identifier for a specific protocol step.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Step ID Object (stepIDObj). The object of the relationship between one protocol step and another step or protocol, within a given protocol ID container.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Step ID Subject (stepIDSub). The subject of the relationship between one protocol step and another step or protocol, within a given protocol ID container.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Method step parent ID (stepProvenanceID). A method step that served as a basis for another method step. This may be due to version changes, or a referencing a method set that was later adapted.
  Status: depreciated. First released: 2.0.0. Last updated: 2.0.0.
• Protocol step version (stepVer). Specifies the version of a given protocol step.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sewer network file blob (storTempDef). A file blob that has any detailed information about the sewer network associated with the site (any format).
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Summary (summ). Short description of the assay and how it is different from the other assay methods.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Public health threat targeted by action (threatTarget). The pathogen or variant for which the designation or action is being taken.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Country code top-level domain (tld). The internet top-level domain generally used or reserved for a country, sovereign state, or dependent territory identified with a country code.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Synthetic ID for the translations table (translationID). A unique, autoincremental ID generated to produce a unique identifier and primary key for each row of the translations table.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Treatment ID (treatmentID). A unique identifier for a single calculation/data treatment, a single data treatment identifier.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Type other depreciate2 (tyOtDep2). Description of the site when the site is not listed. See siteType.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Unit (unit). The units of a measurement.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Unit input (wide table) (unitInput). The partID for the unit being used in a wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Unit name (wide table) (unitName). The unit referenced for the wide name.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Unit set (unitSet). An idenfication of a set of units that can be used for a measure or method.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• U site measure ID (uSiteMeasureID). Unique identifier for each measurement for a site.
  Status: depreciated. First released: 2.0.0. Last updated: 2.0.0.
• Coordinated universal time (UTC) zone (utc). UTC – Time zone.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Coordinated universal time (UTC) zone in daylight savings (utcDST). Time zone during Daylight Saving Time.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Value Treatment (valTreat). A field which specifies what kinds of data treatments or the nature of the measurement value.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Value (value). Value of a measure, observation or attribute.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ODM V1 category (version1Category). ODM V1 category
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ODM V1 location (version1Location). ODM V1 location
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ODM V1 table (version1Table). ODM V1 table
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ODM version 1 to 2 changes (version1to2Changes). Changes for part between ODM v1 and V2
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ODM V1 variable (version1Variable). ODM V1 variable
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Specified attribute (wide table) (wideAttribute). Unique identifier for an attribute in a wide table only. 
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Measure identification (wide table) (wideMeasure). Unique identifier for a measure in a wide table only. 
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Wide Name (wideName). Unique identifier for wide table only. Use when all measures are performed on a single sample at the same time and same laboratory. Suggestion: siteID_sampleID_LabID_reportDate_ID.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Wide name type (wideNameType). The type of wide name generated. Possible options are measure, protocol or attribute.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Specified protocol (wide table) (wideProtocol). Unique identifier for a protocol in a wide table only. 
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• World Sphere (W-SPHERE) (wSphere). World Sphere header
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• World Sphere (W-SPHERE) notes (wSphereNotes). W-Shere notes
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• English name of country sub-domains (zoneName). The english-language name for a given country sub-domain.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.

Classes

(classes). A class is a collection of one or more related measures or methods within a group. A group can have one more more classes to describe different parts or the class.

• Alleles class (allele). Measures and methods related to alleles.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Bacteria and Fungus Class (bactFung). Measures and methods relating to bacteria.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Capacity class (capacity). Measures and methods relating to capacity.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Conductivity class (conductivity). Measures and methods related to conductivity.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Database and Data Repository Class (database). Measures and methods related to databases and data repositories.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Dilution Class (dilution). Measures and methods relating to dilutions.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Diseases (human) class (disease). Measure and methods related to disease or infection in humans.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Flow class (flowClass). Measures and methods related to flow.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Gas class (gas). Measures and methods relating to gas and gases.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Humidity class (humid). Measures and methods related to humidity.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Dictionary tables (lookup). Tables to describe and support the ODM dictionary.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Mutations class (mutation). Measures and methods related to mutations.
  Status: depreciated. First released: 2.0.0. Last updated: 2.3.0.
• Mutation panels class (mutationPanel). Measures and methods related to a panel or list of more than one mutation from the same sequence read.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Class not applicable (naClass). Class is not applicable.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Organism (organism). Organism class
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Outbreak class (outbreak). Measures and methods relating to public health outbreaks.
  Status: depreciated. First released: 2.0.0. Last updated: 3.0.0.
• qPCR Class (pcr). Measures and methods relating to qPCR.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• pH class (pHClass). Measures and methods relating to pH.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Physical class (physical). Measures and methods related to generic physical properties.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Population Class (popClass). Measures and methods relating to population (ie. Measures of population, location).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Precipitation class (precipitation). Measures and methods related to precipitation.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Program decription tables (programDescr). Tables used to describe surveillance and testing programs.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Proteins class (protein). Measures and methods related to proteins.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Results tables (results). Tables used to record samples, measures and quality reports.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Genetic sequences class (sequence). Measures and methods related to genetic sequencing.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Software Class (software). Measures and methods related to software.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Speed class (speed). Measures and methods relating to speed.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Standard concentrations class (standardConc). Measures and methods relating to standard conentrations.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Standard curve class (standardCurve). Measures and methods relating to generating or recording a standard curve.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Temperature class (temperature). Measures and methods related to temperatures.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Time class (timeClass). Measures and methods relating to time.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Turburdity class (turbidity). Measures and methods relating to water and wastewater turbidity.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Variants class (variant). Measures and methods relating to variants.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Weather class (weather). Measures and methods relating to weather.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Compartments

(compartments). The substance from which a sample was taken. For example, wastewater has component of “water”. Compartments are attributes of measures, methods, units, and aggregations.

• Air compartment (air). A measure or observation made from a substance in the air.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• See Header for Compartment (hCo). A indicator for wide-names that the compartment information is stored in a separate column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Human compartment (hum). A measure or observation made about a human.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Compartment not applicable (naCompartment). Compartment not applicable.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Surface compartment (surf). A measure or observation made from a substance on a surface.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Water compartment (wat). A measure or observation made from a substance in the water, including wastewater.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Compartment sets

(compartmentSets). Sets of compartments. Compartment sets are used to identify when a measure can be recorded for more than one compartment. For example, SARS-CoV-2 can be measured in people (humans), water, surface, or air.

Air compartment set

(airCompartmentSet)A compartment set for measures and methods in the air compartment.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Air compartment (air). A measure or observation made from a substance in the air.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Air and surface compartment set

(airSurfaceCompartmentSet)A compartment set for measures and methods in the air or surface compartments.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Air compartment (air). A measure or observation made from a substance in the air.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Surface compartment (surf). A measure or observation made from a substance on a surface.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Air and water compartment set

(airWaterCompartmentSet)A compartment set for measures and methods in the air or water compartments.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Air compartment (air). A measure or observation made from a substance in the air.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Any compartment set

(anyCompartmentSet)A compartment set for measures and methods in any compartment.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Air compartment (air). A measure or observation made from a substance in the air.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Surface compartment (surf). A measure or observation made from a substance on a surface.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Water compartment (wat). A measure or observation made from a substance in the water, including wastewater.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Human compartment set

(humanCompartmentSet)A compartment set for measures and methods in the human compartment.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Human compartment (hum). A measure or observation made about a human.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Compartment set not applicable

(naCompartmentSet)Compartment not applicable.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Compartment not applicable (naCompartment). Compartment not applicable.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Surface compartment set

(surfaceCompartmentSet)A compartment set for measures and methods in the surface compartment.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Surface compartment (surf). A measure or observation made from a substance on a surface.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Surface and water compartment set

(surfaceWaterCompartmentSet)A compartment set for measures and methods in the surface or water compartments.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Surface compartment (surf). A measure or observation made from a substance on a surface.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Water compartment (wat). A measure or observation made from a substance in the water, including wastewater.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Water compartment set

(waterCompartmentSet)A compartment set for measures and methods in the water compartment.
Status: active. First Released: 1.0.0. Last updated: 2.0.0.

• Water compartment (wat). A measure or observation made from a substance in the water, including wastewater.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Compartment set for wide names

(wideCompartmentSet)Compartment set for wide names. For wide names.
Status: active. First Released: 2.2.0. Last updated: 3.0.0.

• Air compartment (air). A measure or observation made from a substance in the air.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• See Header for Compartment (hCo). A indicator for wide-names that the compartment information is stored in a separate column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Compartment not applicable (naCompartment). Compartment not applicable.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Surface compartment (surf). A measure or observation made from a substance on a surface.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Water compartment (wat). A measure or observation made from a substance in the water, including wastewater.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Data types

(dataTypes). The data type for a part. Data types used in the ODM include: varchar, booleen, float, category, date, time, datetime, url, email. dataType corresponds the the entry or cell within a data table, most commonly within a report table. If the data entry has a unit, then the dataType corresponds to the unit and the dataType refers to ‘unit’. If the data entry is a category, then the dataType refers to ‘category’. All categories are varchar. Otherwise the dataType is identifed within the part entry. TBA: dataType for dictionary.

• Binary Large Object (BLOB) data type (blob). The data type for Binary Large Object (BLOB) data.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Boolean data type (boolean). The data type for boolean/binary data.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Categorical data type (categorical). The data type for categorical data.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Date data type (date). The data type for date data (does not include time).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Datetime data type (datetime). The data type for date and time data.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Float data type (float). The data type for float data.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Integer data type (integer). The data type for integers.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• See unit (data type) (seeUnitData). The data type entry when the data type for a given entry is specified by the unit used.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Variable character data type (varchar). The data type for variable character data.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Dictionary set type

(dictSets). Sets used to describe and group dictionary tables.

Airport Sheets Set

(airportSheetSet)Worksheets in the full airport surveillance template (list + template). `ODM_template-planes_{version}.xlxs
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Airport lists worksheet (airportLists). Parts lists used to generate airport and airplane data entry templates.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Airport Surveillance Template (airportTemplate). The input template for airport and airplane surveillance in the EU.
  Status: active. First released: 2.0.0. Last updated: 2.1.0.

Contact table set

(contactTableSet)Tables are where measures, methods and attributes are recorded. Tables represent the main entities of the environmental surveillance.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Address table (addresses). The table that contains information about addresses. Addresses can recorded for sites, organizations or contacts (indivduals). The Sites, Organizations, and Contacts tables include a link to the addresses table through Address ID. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Contact table (contacts). The table that contains information about a contact; a person who is the contact of a site or laboratory. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Organization table (organizations). The table that contains information about a laboratory. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sites table (sites). The table that contains information about a site; the location where an environmental sample was taken. The site of an eviromental sample. Information in the site table does not regularly change. Consider using the MeasureReport table if the infomation changes often. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Crosswalk table set

(crosswalkTableSet)Tables used to translate to and from other environmental dictionaries and models.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• European Nucleotide Association Mapping Column (enaMap). ENA header
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• European Nucleotide Association (ENA) - notes (enaNotes). ENA notes
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• National Center for Biotechnology Information (ncbi). NCBI header
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• NCBI - notes (ncbiNotes). NCBI notes
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• NORMAN (norman). NORMAN header
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• NORMAN - notes (normanNotes). Norman notes
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• National Wastewater Surveillance System (nwss). NWSS header
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• NWSS - notes (nwssNotes). NWSS notes
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• NWSS - process (nwssProcess). NWSS process
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• PHAGE (phage). PHAGE header
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• PHAGE - notes (phageNotes). PHAGE notes
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ODM V1 category (version1Category). ODM V1 category
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ODM V1 location (version1Location). ODM V1 location
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ODM V1 table (version1Table). ODM V1 table
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ODM version 1 to 2 changes (version1to2Changes). Changes for part between ODM v1 and V2
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ODM V1 variable (version1Variable). ODM V1 variable
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• World Sphere (W-SPHERE) (wSphere). World Sphere header
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• World Sphere (W-SPHERE) notes (wSphereNotes). W-Shere notes
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Dictionary reference table set

(dictionaryRefTableSet)Reference or look-up tables. For example, the parts table describe all elements of the ODM, including tables, table headers, measures, methods, categories, and units. sets are collections of parts. For example, units can be grouped together in a unitSet. languages and translations support translations.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Countries look-up tables (countries). Look up table for the possible country inputs. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Language Look-up table (languages). Look up table for all languages, used to give structure to the translation table. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Parts Look-up table (parts). Look up table containing all parts in of the data model. Contains all parts, including self-referential parts. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sets look-up table (sets). Look up table for all sets, managing how categorical inputs for various methods and attributes are grouped together. This table manages many-to-many relationships and category recycling within the ODM. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Translation look-up table (translations). Look up table for translations of the description, label, and instruction for all parts. The default language if a translation is not specified is English. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Zones look-up table (zones). Look up table for the possible sub-national region or zone inputs. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.

ERD table set

(erdTableSet)All tables listed in the Entity Relationship Diagram. The full ODM model is commonly referred to as “long” tables as it stores data with one measurement per row.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Address table (addresses). The table that contains information about addresses. Addresses can recorded for sites, organizations or contacts (indivduals). The Sites, Organizations, and Contacts tables include a link to the addresses table through Address ID. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Contact table (contacts). The table that contains information about a contact; a person who is the contact of a site or laboratory. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Countries look-up tables (countries). Look up table for the possible country inputs. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Dataset table (datasets). A report table for capturing details about data’s parental data set and data custodians. Supplying attribution for data collectors. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Instrument table (instruments). The table that contains information about instruments. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Language Look-up table (languages). Look up table for all languages, used to give structure to the translation table. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Measure report table (measures). The table that contains information and details about a given measure. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Measure set report table (measureSets). The table that identifies sets of measures. Examples of measure sets include a set of replicates, dilutions (used to generate a Ct curve) or varients that are identified in a single sample. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Organization table (organizations). The table that contains information about a laboratory. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Parts Look-up table (parts). Look up table containing all parts in of the data model. Contains all parts, including self-referential parts. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Polygon table (polygons). The table that contains information about the geometry of a geographic area. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Protocol relationships table (protocolRelationships). The table that contains the organizational information and details (such as order) about a given protocol, recorded as a series of protocol steps (protocolSteps). Protocols are a group of related protocol steps. For example a protocol step can describe a sample concentration, extraction, inhibition or a measurement. Protocols can include both methodID (a proceedure) and measureIDs (a measure). An example of a method is centrifugation; where the centriguation rotation speed is described as a measure. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Protocols table (protocols). The table for protocols. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Protocol steps table (protocolSteps). The table for collecting metadata on individual steps in a protocol, methodological process, or assay. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Quality reports table (qualityReports). The table for recording the various quality metrics and indicators for samples and measures. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Reporter table depreciated (reportersDep). The table that contains information about a reporter of a sample, method, measure, or attribute. The short name for the table (partID) can be found in the instructions field.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Sample relationships table (sampleRelationships). Table for recording the relationships between samples.Samples can be pooled or split. The sample relationships table holds information on parent-child relationships between samples, and allow for tracking sample lineage for single and pooled samples. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sample report table (samples). The table that contains information about a sample. A sample is defined as a representative volume of wastewater (or other forms of water or liquid), air, or surface area taken from a site.Samples can be combined, split, stored and reused. The Sample relationships (sampleRelationships) is used to describe the relationships between samples. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sets look-up table (sets). Look up table for all sets, managing how categorical inputs for various methods and attributes are grouped together. This table manages many-to-many relationships and category recycling within the ODM. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sites table (sites). The table that contains information about a site; the location where an environmental sample was taken. The site of an eviromental sample. Information in the site table does not regularly change. Consider using the MeasureReport table if the infomation changes often. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Zones look-up table (zones). Look up table for the possible sub-national region or zone inputs. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.

Full dictionary sheets set

(fullDictionarySheetSet)Worksheets in the full Excel dictionary. The full dictionary is ODM_full-dictionary.xlxs </br> Status: active. First Released: 2.0.0. Last updated: 2.0.0. <ul> <li> **Address table** <a href="/parts.html#addresses">(addresses)</a>. The table that contains information about addresses. Addresses can recorded for sites, organizations or contacts (indivduals). The Sites, Organizations, and Contacts tables include a link to the addresses table through Address ID. The short name for the table (partID) can be found in the instructions field. </br>Status: active. First released: 2.0.0. Last updated: 2.0.0. </li> <li> **Contact table** <a href="/parts.html#contacts">(contacts)</a>. The table that contains information about a contact; a person who is the contact of a site or laboratory. The short name for the table (partID) can be found in the instructions field. </br>Status: active. First released: 2.0.0. Last updated: 2.0.0. </li> <li> **Countries look-up tables** <a href="/parts.html#countries">(countries)</a>. Look up table for the possible country inputs. The short name for the table (partID) can be found in the instructions field. </br>Status: active. First released: 2.1.0. Last updated: 2.1.0. </li> <li> **Dataset table** <a href="/parts.html#datasets">(datasets)</a>. A report table for capturing details about data's parental data set and data custodians. Supplying attribution for data collectors. The short name for the table (partID) can be found in the instructions field. </br>Status: active. First released: 2.0.0. Last updated: 2.0.0. </li> <li> **Instrument table** <a href="/parts.html#instruments">(instruments)</a>. The table that contains information about instruments. The short name for the table (partID) can be found in the instructions field. </br>Status: active. First released: 1.0.0. Last updated: 2.0.0. </li> <li> **Language Look-up table** <a href="/parts.html#languages">(languages)</a>. Look up table for all languages, used to give structure to the translation table. The short name for the table (partID) can be found in the instructions field. </br>Status: active. First released: 2.0.0. Last updated: 2.0.0. </li> <li> **List worksheet** <a href="/parts.html#lists">(lists)</a>. Parts lists for template dropdowns and other documentation. </br>Status: active. First released: 2.0.0. Last updated: 2.0.0. </li> <li> **Measure report table** <a href="/parts.html#measures">(measures)</a>. The table that contains information and details about a given measure. The short name for the table (partID) can be found in the instructions field. </br>Status: active. First released: 1.0.0. Last updated: 2.0.0. </li> <li> **Measure set report table** <a href="/parts.html#measureSets">(measureSets)</a>. The table that identifies sets of measures. Examples of measure sets include a set of replicates, dilutions (used to generate a Ct curve) or varients that are identified in a single sample. The short name for the table (partID) can be found in the instructions field. </br>Status: active. First released: 2.0.0. Last updated: 2.0.0. </li> <li> **Organization table** <a href="/parts.html#organizations">(organizations)</a>. The table that contains information about a laboratory. The short name for the table (partID) can be found in the instructions field. </br>Status: active. First released: 1.0.0. Last updated: 2.0.0. </li> <li> **Parts Look-up table** <a href="/parts.html#parts">(parts)</a>. Look up table containing all parts in of the data model. Contains all parts, including self-referential parts. The short name for the table (partID) can be found in the instructions field. </br>Status: active. First released: 2.0.0. Last updated: 2.0.0. </li> <li> **Polygon table** <a href="/parts.html#polygons">(polygons)</a>. The table that contains information about the geometry of a geographic area. The short name for the table (partID) can be found in the instructions field. </br>Status: active. First released: 1.0.0. Last updated: 2.0.0. </li> <li> **Protocol relationships table** <a href="/parts.html#protocolRelationships">(protocolRelationships)</a>. The table that contains the organizational information and details (such as order) about a given protocol, recorded as a series of protocol steps (protocolSteps). Protocols are a group of related protocol steps. For example a protocol step can describe a sample concentration, extraction, inhibition or a measurement. Protocols can include both methodID (a proceedure) and measureIDs (a measure). An example of a method is centrifugation; where the centriguation rotation speed is described as a measure. The short name for the table (partID) can be found in the instructions field. </br>Status: active. First released: 2.0.0. Last updated: 2.0.0. </li> <li> **Protocols table** <a href="/parts.html#protocols">(protocols)</a>. The table for protocols. The short name for the table (partID) can be found in the instructions field. </br>Status: active. First released: 2.0.0. Last updated: 2.0.0. </li> <li> **Protocol steps table** <a href="/parts.html#protocolSteps">(protocolSteps)</a>. The table for collecting metadata on individual steps in a protocol, methodological process, or assay. The short name for the table (partID) can be found in the instructions field. </br>Status: active. First released: 1.0.0. Last updated: 2.0.0. </li> <li> **Quality reports table** <a href="/parts.html#qualityReports">(qualityReports)</a>. The table for recording the various quality metrics and indicators for samples and measures. The short name for the table (partID) can be found in the instructions field. </br>Status: active. First released: 2.0.0. Last updated: 2.0.0. </li> <li> **Sample relationships table** <a href="/parts.html#sampleRelationships">(sampleRelationships)</a>. Table for recording the relationships between samples.Samples can be pooled or split. The sample relationships table holds information on parent-child relationships between samples, and allow for tracking sample lineage for single and pooled samples. The short name for the table (partID) can be found in the instructions field. </br>Status: active. First released: 2.0.0. Last updated: 2.0.0. </li> <li> **Sample report table** <a href="/parts.html#samples">(samples)</a>. The table that contains information about a sample. A sample is defined as a representative volume of wastewater (or other forms of water or liquid), air, or surface area taken from a site.Samples can be combined, split, stored and reused. TheSample relationships` (sampleRelationships) is used to describe the relationships between samples. The short name for the table (partID) can be found in the instructions field.
Status: active. First released: 1.0.0. Last updated: 2.0.0.

Sets look-up table (sets). Look up table for all sets, managing how categorical inputs for various methods and attributes are grouped together. This table manages many-to-many relationships and category recycling within the ODM. The short name for the table (partID) can be found in the instructions field.
Status: active. First released: 2.0.0. Last updated: 2.0.0.

Sites table (sites). The table that contains information about a site; the location where an environmental sample was taken. The site of an eviromental sample. Information in the site table does not regularly change. Consider using the MeasureReport table if the infomation changes often. The short name for the table (partID) can be found in the instructions field.
Status: active. First released: 1.0.0. Last updated: 2.0.0.

Summary worksheet (summary). Summary sheet of the dictionary.xlxs file.
Status: active. First released: 2.0.0. Last updated: 2.0.0.

Translation look-up table (translations). Look up table for translations of the description, label, and instruction for all parts. The default language if a translation is not specified is English. The short name for the table (partID) can be found in the instructions field.
Status: active. First released: 2.0.0. Last updated: 2.0.0.

Wide name table (wideNames). The table for wide names. The short name for the table (partID) can be found in the instructions field.
Status: active. First released: 2.0.0. Last updated: 2.0.0.

Zones look-up table (zones). Look up table for the possible sub-national region or zone inputs. The short name for the table (partID) can be found in the instructions field.
Status: active. First released: 2.1.0. Last updated: 2.1.0.

List set

(listSet)PartTypes that contain categories, sets, or lists. Used to generate documentation.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Aggregations (aggregations). Statistical measures used to report a measure. Each measure reported as a number should be reported with an aggregation. The default aggregation is sin, which corresponds to a single measurement.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Aggregation scales (aggregationScales). The scale of an aggregation set. Aggregation scales include quantitative and qualitative.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Attributes (attributes). Attributes describe the who, where, when, and why of environmental surveillance. There are attributes for domain, specimen, compartment, or table. Attributes are one of the three main components or ways to report environment surviellence data. The other two components are measures and methods.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Classes (classes). A class is a collection of one or more related measures or methods within a group. A group can have one more more classes to describe different parts or the class.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Compartments (compartments). The substance from which a sample was taken. For example, wastewater has component of “water”. Compartments are attributes of measures, methods, units, and aggregations.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Data types (dataTypes). The data type for a part. Data types used in the ODM include: varchar, booleen, float, category, date, time, datetime, url, email. dataType corresponds the the entry or cell within a data table, most commonly within a report table. If the data entry has a unit, then the dataType corresponds to the unit and the dataType refers to ‘unit’. If the data entry is a category, then the dataType refers to ‘category’. All categories are varchar. Otherwise the dataType is identifed within the part entry. TBA: dataType for dictionary.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Domains (domains). There are three domain types: biologic (i.e. Covid-19, chemical (i.e. nitrogen), physical measure (temperature).
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Groups (groups). A collection of related measures. Used primary to group measurements and methods, this helps pare down the drop down list for a given measurement or methods.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Measures (measurements). The attribute to describe a part type of measures. All measures have partType = “measure”.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Methods (methods). Procedures or steps for collecting samples or performing measures. For example, methodExtract is a method that describes the how a sample was extracted.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Missingness (missingness). The part type for missingness values. Only used for the dictionary entries of parts.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Nomenclatures (nomenclatures). A classification system to report the measure class. See partID = nomenclatureID.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Quality indicators (qualityIndicators). A measure of the quality of a reported value or sample. Only used for the dictionary entries of parts.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Specimens (specimens). Measures or observations are taken from three types of substances: populations (humans or geographic areas), samples, sites. See partID = specimentID.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Tables (tables). Tables are where measures, methods and attributes are recorded. Tables represent the main entities of the environmental surveillance. An example of a table is site a collection of attributes such as site name and address to describe where environment samples are taken. PHES-ODM has report tables, but users can create their own tables as well.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Units (units). The unit of the measurement. Every measurement must have a unit. Meaning, units are a mandatory field whenever a measurement is recorded.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Other report table set

(otherReportTableSet)Additional tables that form the full data model.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Dataset table (datasets). A report table for capturing details about data’s parental data set and data custodians. Supplying attribution for data collectors. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Polygon table (polygons). The table that contains information about the geometry of a geographic area. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Protocol table set

(protocolTableSet)Tables holding information on the methods used for sample collection or measurement.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Instrument table (instruments). The table that contains information about instruments. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Protocol relationships table (protocolRelationships). The table that contains the organizational information and details (such as order) about a given protocol, recorded as a series of protocol steps (protocolSteps). Protocols are a group of related protocol steps. For example a protocol step can describe a sample concentration, extraction, inhibition or a measurement. Protocols can include both methodID (a proceedure) and measureIDs (a measure). An example of a method is centrifugation; where the centriguation rotation speed is described as a measure. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Protocols table (protocols). The table for protocols. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Protocol steps table (protocolSteps). The table for collecting metadata on individual steps in a protocol, methodological process, or assay. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Regular reports table set

(regularReportTableSet)Tables used for daily reporting of new measurements and information on sample collection.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Measure report table (measures). The table that contains information and details about a given measure. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sample report table (samples). The table that contains information about a sample. A sample is defined as a representative volume of wastewater (or other forms of water or liquid), air, or surface area taken from a site.Samples can be combined, split, stored and reused. The Sample relationships (sampleRelationships) is used to describe the relationships between samples. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Template Sheet Set

(templateSheetSet)Worksheets in the full generic ODM surveillance template (all tables).
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Address table (addresses). The table that contains information about addresses. Addresses can recorded for sites, organizations or contacts (indivduals). The Sites, Organizations, and Contacts tables include a link to the addresses table through Address ID. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Contact table (contacts). The table that contains information about a contact; a person who is the contact of a site or laboratory. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Dataset table (datasets). A report table for capturing details about data’s parental data set and data custodians. Supplying attribution for data collectors. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Instrument table (instruments). The table that contains information about instruments. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Language Look-up table (languages). Look up table for all languages, used to give structure to the translation table. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• List worksheet (lists). Parts lists for template dropdowns and other documentation.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Measure report table (measures). The table that contains information and details about a given measure. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Measure set report table (measureSets). The table that identifies sets of measures. Examples of measure sets include a set of replicates, dilutions (used to generate a Ct curve) or varients that are identified in a single sample. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Organization table (organizations). The table that contains information about a laboratory. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Parts Look-up table (parts). Look up table containing all parts in of the data model. Contains all parts, including self-referential parts. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Polygon table (polygons). The table that contains information about the geometry of a geographic area. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Protocol relationships table (protocolRelationships). The table that contains the organizational information and details (such as order) about a given protocol, recorded as a series of protocol steps (protocolSteps). Protocols are a group of related protocol steps. For example a protocol step can describe a sample concentration, extraction, inhibition or a measurement. Protocols can include both methodID (a proceedure) and measureIDs (a measure). An example of a method is centrifugation; where the centriguation rotation speed is described as a measure. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Protocols table (protocols). The table for protocols. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Protocol steps table (protocolSteps). The table for collecting metadata on individual steps in a protocol, methodological process, or assay. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Quality reports table (qualityReports). The table for recording the various quality metrics and indicators for samples and measures. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sample relationships table (sampleRelationships). Table for recording the relationships between samples.Samples can be pooled or split. The sample relationships table holds information on parent-child relationships between samples, and allow for tracking sample lineage for single and pooled samples. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sample report table (samples). The table that contains information about a sample. A sample is defined as a representative volume of wastewater (or other forms of water or liquid), air, or surface area taken from a site.Samples can be combined, split, stored and reused. The Sample relationships (sampleRelationships) is used to describe the relationships between samples. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sets look-up table (sets). Look up table for all sets, managing how categorical inputs for various methods and attributes are grouped together. This table manages many-to-many relationships and category recycling within the ODM. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sites table (sites). The table that contains information about a site; the location where an environmental sample was taken. The site of an eviromental sample. Information in the site table does not regularly change. Consider using the MeasureReport table if the infomation changes often. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Domains

(domains). There are three domain types: biologic (i.e. Covid-19, chemical (i.e. nitrogen), physical measure (temperature).

• All domains (allDo). Domain that specifies that it could apply to al domains; biological, chemical, and physical.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Biologic (bio). A living organism or biological substance.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Chemical (che). A chemical compound.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Domain not applicable (naDomain). Not applicable.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Physical property (phy). A physical property or object not characterized by life or chemistry.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Groups

(groups). A collection of related measures. Used primary to group measurements and methods, this helps pare down the drop down list for a given measurement or methods.

• Acinetobacter Group (acinetobacterGrp). A group of measures/methods related to acinebacter bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Adenovirus Group (adenovirusGrp). A group of measures/methods related to Adenoviruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Anti-microbial resistance Group (amrGrp). The group for measures and methods pertaining to anti-microbial resistant microbes (general).
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Anaplasma Group (anaplasmaGrp). A group of measures/methods related to anaplasma bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Astrovirus Group (astrovirusGrp). A group of measures/methods related to astroviruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Babesia or Nuttallia Group (babesiaGrp). A group of measures/methods related to babesia parasites.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Bacteroides Group (bacteroidesGrp). A group of measures/methods related to bacteroides bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Miscellaneous bacteria group (bactMisc). A group of measures/methods related to miscellaneous bacteria.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Beta Coronavirus Group (betaCoronaGrp). A group of measures/methods related to beta coronaviruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Beta-Lactamase Anti-microbial resistance Group (bLacAMRGrp). The group for measures and methods pertaining to beta-lactamase-related anti-microbial resistance.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Borrelia burgdorferi or Lyme Disease Group (borreliaGrp). A group of measures/methods related to Borrelia burgdorferi or Lyme Disease.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Brucella Group (brucellaGrp). A group of measures/methods related to brucella bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Campylobacter Group (campGrp). A group of measures/methods related to campylobacter bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Candida auris Group (cAurisGrp). A group of measures/methods related to Candida auris.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Chikungunya Group (chikungunyaGrp). A group of measures/methods related to chikungunya virus.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Chlamydia Group (chlamydiaGrp). A group of measures/methods related to chlamydia bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Clostridium Group (clostridiumGrp). A group of measures/methods related to clostridium bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Colistin Anti-microbial resistance group (colAMRGrp). The group for measures and methods pertaining to colistin-related anti-microbial resistance.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Collection group (colGrp). A group of measurement-like attributes related to sample collection.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Cryptosporidium Group (cryptosporidiumGrp). A group of measures/methods related to cryptosporidium parasites.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• SARS-CoV-2 Delta Variant Group (deltaGrp). A group of measures/methods related to the SARS-CoV-2 Delta Variant.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Diphtheria Group (diptheriaGrp). A group of measures/methods related to the diptheria bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Escherichia coli group (ecoliGrp). A group of measures/methods related to Escherichia coli bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Enterovirus Group (enterovirusGrp). A group of measures/methods related to enteroviruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Flavivirus (West Nile, Dengue, Zika) Group (flavivirusGrp). A group of measures/methods related to flaviviruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• FLiRT/SLip Variant Group (flirtSLipGrp). The group for measures and methods pertaining to the FLiRT and SLip variants of SARS-CoV-2.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Influenza A Virus Group (fluAGrp). A group of measures/methods related to Influenza A viruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Influenza B Virus Group (fluBGrp). A group of measures/methods related to Influenza B viruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Influenza Virus General Group (fluGrp). A group of measures/methods related to general influenza viruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Gonococcus Group (gonococcusGrp). A group of measures/methods related to gonococcus bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Haemophilus Group (haemophilusGrp). A group of measures/methods related to haemophilus bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Hepatitis Group (hepGrp). A group of measures/methods related to hepatitis viruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Herpes Virus Group (herpesGrp). A group of measures/methods related to herpes viruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• HIV Group (hivGrp). A group of measures/methods related to Human Immunodeficiency Virus (HIV).
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Rhinovirus Group (hrvGrp). A group of measures/methods related to rhinoviruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Integrase Anti-microbial resistance Group (intAMRGrp). The group for measures and methods pertaining to integrase-related anti-microbial resistance.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Klebsiella Group (klebsiellaGrp). A group of measures/methods related to klbsiella bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Legionella Group (legionellaGrp). A group of measures/methods related to legionella bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Lentivirus Group (lentiGrp). A group of measures/methods related to lentiviruses, including viral vectors such as the Puro virus vector.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Listeria Group (listeriaGrp). A group of measures/methods related to listeria bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Plasmodium or Malaria Group (malariaGrp). A group of measures/methods related to plasmodium parasites or malaria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Measurement group (measGrp). A group of measures that cannot be otherwise categorized.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Measles Group (measlesGrp). A group of measures/methods related to the measles virus.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Metabolite Group (metaboliteGrp). A group of measures/methods related to metabolites.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Miscellaneous attribute group (miscAttr). A group of miscellaneous measurement-like attributes.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Miscellaneous measure group (miscMeas). A group of measures that cannot be otherwise categorized.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• MPox Clade I Group (mpoxCldIGrp). A group of measures/methods related to Mpox Clade I (formerly “Monkey Pox”).
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• MPox Clade II Group (mpoxCldIIGrp). A group of measures/methods related to Mpox Clade II (formerly “Monkey Pox”).
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• MPox Group (mpoxGrp). A group of measures/methods related to Mpox (formerly “Monkey Pox”).
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Metapneumovirus Group (mpvGrp). A group of measures/methods related to metapneumoviruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Mumps Group (mumpsGrp). A group of measures/methods related to the mumps virus.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Mycoplasma Group (mycoplasmaGrp). A group of measures/methods related to mycoplasma bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Group not applicable (naGroup). Used when there is no group; ie. group is not applicable.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• SARS-CoV-2 Nimbus Variant Group (nimbusGrp). A group of measures/methods related to the SARS-CoV-2 Nimbus Variant.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Norovirus GI Group (noroGIGrp). A group of measures/methods related to norovirus GI.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Norovirus GII Group (noroGIIGrp). A group of measures/methods related to norovirus GII.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Norovirus Group (noroGrp). A group of measures/methods related to noroviruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• SARS-CoV-2 Omicron Variant Group (omicronGrp). A group of measures/methods related to the SARS-CoV-2 Omicron Variant.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Orthopox Virus Group (orthoGrp). A group of measures/methods related to orthopox viruses (excluding variolla viruses).
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Papilomavirus Group (papilomavirusGrp). A group of measures/methods related to papilomaviruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Parainfluenza Group (parafluGrp). A group of measures/methods related to parainfluenza viruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Bacteriophage Group (phageGrp). A group of measures/methods related to bacteriophages.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• PMMoV Group (pmmovGrp). A group of measures/methods related to the Pepper Mild Mottle Virus (PMMoV).
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Poliovirus Group (polioGrp). A group of measures/methods related to polioviruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Population group (popGrp). A group of measures/methods related to population-level factors.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Processing group (procGrp). A group of measures/methods related to processing samples for analysis.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Pseudomonas Group (pseudomonasGrp). A group of measures/methods related to pseudomonas bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Rickettsia Group (rickettsiaGrp). A group of measures/methods related to ricketsia parasites.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Rotavirus Group (rotavirusGrp). A group of measures/methods related to rotaviruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Respiratory syncytial virus (RSV) Group (rsvGrp). Human Respiratory Syncytial virus (RSV).
  Status: active. First released: 2.0.0. Last updated: 2.1.2.
• Rubella Group (rubellaGrp). A group of measures/methods related to the rubella virus.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Salmonella Group (salmonellaGrp). A group of measures/methods related to salmonella bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Sapovirus Group (sapovirusGrp). A group of measures/methods related to sapoviruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• SARS-CoV-2 (sarsCov2). A group of measures/methods related to the SARS-CoV-2 virus.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Shigella Group (shigellaGrp). A group of measures/methods related to shigella bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Site features group (siteFeat). A group of environmental measures/methods and those pertaining to the features of a site.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Staphylococcus Group (staphGrp). A group of measures/methods related to staphylococcus bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Streptococcus Group (strepGrp). A group of measures/methods related to streptococcus bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Tetracycline Anti-microbial resistance Group (tetAMRGrp). The group for measures and methods pertaining to tetracycline-related anti-microbial resistance.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Treponema Group (treponemaGrp). A group of measures/methods related to treponema bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Trichomonas Group (trichomonasGrp). A group of measures/methods related to trichomonas bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Tuberculosis Group (tuberculosisGrp). A group of measures/methods related to tuberculosis.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Francisella tularensis (tularemia) Group (tularemiaGrp). A group of measures/methods related to Francisella tularensis.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Ureaplasma Group (ureaplasmaGrp). A group of measures/methods related to ureaplasma bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Vancomycin Anti-microbial resistance Group (vanAMRGrp). The group for measures and methods pertaining to vancomycin-related anti-microbial resistance.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Varicella Group (varicellaGrp). A group of measures/methods related to varicella viruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Vibrio Group (vibrioGrp). A group of measures/methods related to vibrio bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Miscellaneous viruses group (virusMisc). A group of measures/methods related to miscellaneous viruses.
  Status: depreciated. First released: 1.0.0. Last updated: 2.2.0.
• Vesicular Stomatitis Virus (VSV) Group (vsvGrp). A group of measures/methods related to Vesicular Stomatitis Virus (VSV).
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Water Quality Group (waterQualityGrp). A group of measures/methods related to water quality.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Yersinia Group (yersiniaGrp). A group of measures/methods related to yersinia bacteria.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.

Measures

(measurements). The attribute to describe a part type of measures. All measures have partType = “measure”. mes

• a1306s delta-variant gene target (a1306s). a1306s delta-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• a1918v delta-variant gene target (a1918v). a1918v delta-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• a2710t omicron-variant gene target (a2710t). a2710t omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• a63t omicron-variant gene target (a63t). a63t omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• a67v omicron-variant gene target (a67v). a67v omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Omicron Variant a67v del69 and del70 mutations (a67vDel69Del70). Omicron Variant a67v mutation mutation, and del 69 and del70 mutations co-occuring
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Absolute humidity (absHum). A measure of the total mass of water vapour present in the air per volume of air.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Acinetobacter (acinetobacter). Acinetobacter
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Adenovirus (F40/41) (adenovirusF40). Adenovirus (F40/41)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Adenovirus 40 (adv40). Adenovirus serotype 40.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Adenovirus 41 (adv41). Adenovirus serotype 41.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Adenovirus F41 Fibre Gene Target (advF41Fibre). Human Adenovirus Group F41 Fiber gene target
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Environmental temperature (airTemp). Environmental temperature.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Alkalinity (alkaline). Measure of alkalinity
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Assay Limit of Detection (LOD) (alod). The minimum level of a target consistently detectable (e.g., with 95% probability) using the assay considering only the amplification and quantification steps of RT-qPCR.
  Status: active. First released: 2.2.0. Last updated: 3.0.0.
• The number of ambiguous bases (Ns) normalized (ambigNs). The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Amplicon Size (ampSize). The length of the amplicon generated by PCR amplification.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Anaplasma phagocytophilum (aPhagocytophilum). Anaplasma phagocytophilum
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Arrival temperature (arTemp). The temperature of a sample upon arrival at the laboratory for analysis.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Astrovirus (astrovirus). Astrovirus
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Babesia (babesia). Babesia
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Borrelia burgdorferi (bBurgdorferi). Borrelia burgdorferi
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• bcov (bcov). Measure of the amount of bovine coronavirus.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Beta (beta). B.1.351
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Cephamycin Beta-Lactamase-Resistance gene target (blaCMY). Cephamycin Beta-Lactamase anti-microbial resistance gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• CTX-M Beta-Lactamase-Resistance gene target (blaCTXM1). CTX-M Beta-Lactamase anti-microbial resistance gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Impenemase (IMP) Beta-Lactamase-Resistance gene target (blaIMP). Impenemase (IMP) Beta-Lactamase anti-microbial resistance gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Klebsiella pneumoniae Carbapenam (KPC) Beta-Lactamase-Resistance gene target (blaKPC). Klebsiella pneumoniae Carbapenam (KPC) Beta-Lactamase anti-microbial resistance gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• New-Delhi Metallo- (NDM) Beta-Lactamase-Resistance gene target (blaNDM). New-Delhi Metallo- (NDM) Beta-Lactamase anti-microbial resistance gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• OXA-type Beta-Lactamase-Resistance gene target (blaOXA48). OXA-type Beta-Lactamase anti-microbial resistance gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• SHV Beta-Lactamase-Resistance gene target (blaSHV). SHV-type Beta-Lactamase anti-microbial resistance gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• TEM Beta-Lactamase-Resistance gene target (blaTEM). TEM-type Beta-Lactamase anti-microbial resistance gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Verone Integron-Encoded Metallo- (VIM) Beta-Lactamase-Resistance-resistance gene target (blaVIM). Verone Integron-Encoded Metallo- (VIM) Beta-Lactamase anti-microbial resistance gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• 5-Day carbonaceous biochemical oxygen demand (bod5c). The quantity of oxygen utilized for the biochemical degradation of organic matter under standard laboratory procedures in five (5) days in the presence of a nitrification inhibitor, expressed in milligrams per litre (mg/l).
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• 5-day total biochemical oxygen demand (bod5t). 5 day total biochemical oxygen demand.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Bovine respiratory syncytial virus group (brsv). Bovine respiratory syncytial virus.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• BRSV-N (brsvN). bovine respiratory syncytial virus capsid protein gene region
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Brucella (brucella). Brucella
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• C28311T Omicron N1 Point Mutation (c2811t). A measure of the C to T point mutation at position 28311 (C28311T) of the N1 probe, present in all Omicron sub-linages.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Caffeine (caff). Caffeine (usually measured as a human fecal chemical indicator)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Calprotectin (Calprotectin). Calprotectin is a calcium- and zinc-binding protein of the S-100 protein family which is mainly found within neutrophils and throughout the human body. The presence of calprotectin in faeces is a consequence of neutrophil migration into the gastrointestinal tissue due to an inflammatory process.
  Status: active. First released: 2.2.0. Last updated: 3.0.0.
• Campylobacter (camp). Campylobacter.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Candida auris (cAuris). The yeast species Candida auris, or C. auris.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Carbonaceous Biochemical Oxygen Demand (cbod). A measure of the amount of oxygen required by microorganisms to break down organic carbon-based compounds in water over a specified period, typically five days at 20°C (CBOD₅). Unlike BOD (Biochemical Oxygen Demand), CBOD excludes oxygen demand from the oxidation of nitrogenous compounds (such as ammonia). It is used to assess organic pollution in wastewater and natural waters.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Carbapenemase-encoding genes (cbp). Carbapenemase-encoding genes.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Clostridium difficile (cDiff). Clostridium difficile
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Corynebacterium diphtheriae (cDip). Corynebacterium diphtheriae
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Centrifugation speed (centSpeed). Centrifugation speed
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Chikungunya virus (CHIKV) (chikv). Chikungunya virus (CHIKV)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Chlamydia (chlamydia). Chlamydia
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Campylobacter jejuni bacteria (cJejuni). Campylobacter jejuni gene target/measurement
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Carbon Dioxide (co2). A measure of an amount or concentraion of carbon dioxide.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Chemical Oxygen Demand (cod). Chemical oxygen demand.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Time from collection to storage (col2Frdg). The amount of time between sample collection and the samples placement in stable storage/refrigeration.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Colistin resistance (colis). Colistin-resistant bacteria.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Concentration measure (conc). Measurement of concentration (generalized) - designed for describing protocols.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Sample volume after concentration (concVol). The total volume of a sample after the concentration step.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Water conductivity (cond). Measurement of conductivity of sample or site.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• consensus genome length (conGenLen). The length of the genome defined by the most common nucleotides at each position.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Covid-19 (cov). Covid-19 infection.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• SARS-CoV-2 measure (cov2Me). Measure the amount of SARS-CoV-2 virus.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• SARS-CoV-2-B.1.1.7 (covB117). Variant B.1.1.7 of the SARS-CoV-2 virus.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• SARS-CoV-2-B.1.351 (covB135). Variant B.1.351 of the SARS-CoV-2 virus.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• SARS-CoV-2-E (covE). SARS-CoV-2 E gene.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• SARS-CoV-2 M Gene target (covM). SARS-CoV-2 M gene (orf5)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2-N1 (covN1). SARS-CoV-2 nucleocapsid gene, allele 1.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• SARS-CoV-2-N2 (covN2). SARS-CoV-2 nucleocapsid gene, allele 2.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• SARS-CoV-2-N200 (covN200). SARS-CoV-2 nucleocapsid gene, amino acids 199-202.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• SARS-CoV-2-N3 (covN3). SARS-CoV-2 nucleocapsid gene, allele 3.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• SARS-CoV-2-P.1 (covP1). Variant P.1 of the SARS-CoV-2 virus.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• SARS-CoV-2-RdRp (covRdrp). SARS-CoV-2 RdRp gene.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• SARS-CoV-2 S Gene Target (covS). S sars-cov-2 gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• SARS-COV-2 5’ UTR Gene target (covUTR5). SARS-COV-2 5’ UTR Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Clostridium perfringens (cPerfrigens). Clostridium perfringens
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• crAssphage-N (cra). crAssphage virus capsid protein gene region
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Creatinine (crea). Creatinine (usually measured as a human fecal chemical indicator)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Cryptosporidium (cryptosporidium). Cryptosporidium
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Circulating vaccine-derived poliovirus type 2 (cVDPV2). Circulating vaccine-derived poliovirus type 2
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Number of cycles (cyNum). The number of cycles of a PCR machine, or any other cycling process.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• D339H Mutation (d339h). The FLiRT/SLip variant mutation D339H.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• d377y delta-variant gene target (d377y). d377y delta-variant mutation gene target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• d3g omicron-variant gene target (d3g). d3g omicron-variant mutation gene target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• d63g delta-variant gene target (d63g). d63g delta-variant mutation gene target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• d796y omicron-variant gene target (d796y). d796y omicron-variant mutation gene target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• d950n delta-variant gene target (d950n). d950n delta-variant mutation gene target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ddcov_e sars-cov-2 gene target (ddcovE). ddcov_e sars-cov-2 mutation gene target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ddcov_n sars-cov-2 gene target (ddcovN). ddcov_n sars-cov-2 mutation gene target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Omicron Variant 142-144 Deletion (del142144). Omicron Variant 142-144 Deletion mutation
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• del143/145  (del143). 143 or 145 deletion omicron-variant mutation gene target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Delta Variant 156-157 Deletion (del156157). Delta Variant 156-157 Deletion mutation
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• del 157/158 (del157). 157 or 158 deletion delta-variant gene target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• del2084/2084  (del2084). 2084 or 2084 deletion omicron-variant mutation gene target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• del212/212  (del212). 212 or 212 deletion omicron-variant mutation gene target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Omicron Variant 142-14431-33 Deletion (del3133). Omicron Variant 142-14431-33 Deletion mutation.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• del3674/3676  (del3674). 3674 or 3676 deletion omicron-variant mutation gene target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• del69/70 (del6970). 69 or 70 deletion omicron-variant mutation gene target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Delta (delta). B.1.617.2
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Dengue Virus Type 1 (den1). Dengue virus, Type 1, general measurement
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Dengue Virus Type 2 (den2). Dengue virus, Type 2, general measurement
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Dengue Virus Type 3 (den3). Dengue virus, Type 3, general measurement
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Dengue Virus Type 4 (den4). Dengue virus, Type 4, general measurement
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Dengue (dengue). Dengue virus, general measurement
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• depth of coverage threshold (depCovThresh). The threshold used as a cut-off for the depth of coverage.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Detected Lineage or Clade Name (detLinClade). The measurement for reporting detected lineage or clade information - used as an “other” for measurements not already captured in the ODM structure.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Dilution factor (dilFact). Specifies the extent to which a sample or aliquot was diluted prioir to analysis.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Point dillutions (dillute). Exact concentration or dillutions for generating a standard curve.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Dissolved oxygen (dissOxy). Measure of dissolved oxygen in liquid medium
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• DNA Fragment Length (dnaFragLen). The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Dengue Virus E Gene (dnvE). Dengue Type 2-specific gene taget.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Dengue Virus NS5 Gene (dnvNS5). Dengue Type 1-specific gene target.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Dengue Virus prM Gene (dnvprM). Dengue Type 3 and 4-specific gene target.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Duration time of a method (duration). The duration of time for a given method as described in protocols.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• e156g delta-variant gene target (e156g). e156g delta-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• e484a omicron-variant gene target (e484a). e484a omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Enteroaggregative Escherichia coli (EAEC) (eaec). Enteroaggregative Escherichia coli (EAEC)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Epstein–Barr virus (EBV) (ebv). Epstein–Barr virus (EBV), formerly known as Human gammaherpesvirus 4
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Escherichia coli (ecoli). Concentration of bacteria that are passed through the faecal excrement of humans, livestock and wildlife
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Enterohemorrhagic Escherichia coli (EHEC) (ehec). Enterohemorrhagic Escherichia coli (EHEC)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Enteroinvasive Escherichia coli (EIEC) (eiec). Enteroinvasive Escherichia coli (EIEC)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Enterovirus (enterovirus). Enterovirus
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Rainfall (envRnF). Rainfall, i.e. amount of precipitation in the form of rain.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Ground snow depth (envSnwD). Total depth of snow on the ground.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Snowfall (envSnwF). Snowfall, i.e. amount of precipitation in the form of snow.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Enteropathogenic Escherichia coli (EPEC) (epec). Enteropathogenic Escherichia coli (EPEC)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Sarbecovirus-specific E sars-cov-2 gene target (eSarbec). Sarbecovirus-specific E sars-cov-2 gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ESBL-encoding genes (esbl). Extended-spectrum beta-lactamase-encoding genes.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Estimated frequency of reads (estFreqReads). Estimated frequency of reads in a sequencing assay
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Enterotoxigenic Escherichia coli (ETEC) (etec). Enterotoxigenic Escherichia coli (ETEC)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• SARS-CoV-2 exoN gene (nsp14) (exoNnsp14). SARS-CoV-2 exoN gene (nsp14)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Extraintestinal pathogenic Escherichia coli (ExPEC) (expec). Extraintestinal pathogenic Escherichia coli (ExPEC)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Extraction Recovery Percent (extractRecov). The percentage of spiked in or endogenous compound used to assess extraction recovery of nucleic acids.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Extraction volume of sample (exvol). Extraction volume of sample.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• F456L Mutation (f456l). The FLiRT/SLip variant mutation F456L.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Male-specific (F+) coliphage - general (fColiphage). Male-specific (F+) coliphage - general
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• F+ DNA coliphage (fDNA). F+ DNA coliphage
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Fecal coliform count (fecalCol). Measure of prevalence of fecal coliform bacteria
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Final volume (finVol). The final volume of a testing solution or sample.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• FLiRT Variants (flirtV). FLiRT is the name given to an entire family of COVID-19 subvariants that are gaining dominance. They’ve evolved from the JN.1 subvariant.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Flow rate (floRate). Wastewater volumetric flow rate at the sample collection location over the 24-hr period during which the sample was collected.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Flow volume (flowVol). Volume of influent.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Influenza virus measure (flu). General influenza virus measure
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Influenza A virus (fluA). Influenza A virus.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Influenza virus A1 (fluA1). Influenza virus A1 type
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Influenza virus A1 and A2 combined (fluA1A2c). Measure of influenza virus A1 and A2 combined, usually due to single fluorescence channel.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• influenza virus A2 (fluA2). influenza virus A2 type
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Influenza virus B (fluB). Influenza virus B type
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Influenza A H5 hemagglutinin gene (fluH5hema). Measure of the H5 hemagglutinin gene from the Highly Pathogenic Avian Influenza Virus (HPAIV), the H5N1 Influenza A Virus (IAV) subtype.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Influenza A M gene (fluIAVm). A measure of the M gene found in Influenza A viruses (IAV). The virus has segmented RNA genome and 7th segment, M gene, encodes 2 proteins. M1 is a matrix protein and M2 is a membrane protein. The M gene may be involved in determining host tropism.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Influenza A N1 neuraminidase gene (fluN1neur). Measure of the N1 neuraminidase gene from the Highly Pathogenic Avian Influenza Virus (HPAIV), the H5N1 Influenza A Virus (IAV) subtype.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• F-Specific RNA bacteriophages (fRNABact). A measure for amount of F-Specific RNA bacteriophages.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• F+ RNA coliphage (fRNAColi). F+ RNA coliphage
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• F-Specific RNA bacteriophages, G2 (frnaG2). A measure for amount of G2 F-Specific RNA bacteriophages.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Field sample temperature (fst). Temperature that the sample is stored at while it is being sampled. This field is mainly relevant for composite samples which are either kept at ambient temperature or refrigerated while being sampled.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Francisella tularensis (fTularensis). Francisella tularensis
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• g215c delta-variant gene target (g215c). g215c delta-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• g339d omicron-variant gene target (g339d). g339d omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• g496s omicron-variant gene target (g496s). g496s omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• g662s delta-variant gene target (g662s). g662s delta-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Gamma (gam). P.1
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• genome completeness (genComplete). The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• H5N1 avian influenza A virus (IAV) (h5n1). General measurement for the Highly Pathogenic Avian Influenza Virus (HPAIV), the H5N1 Influenza A Virus (IAV) subtype.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Haemophilus ducreyi (hDucreyi). Haemophilus ducreyi
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• SARS-CoV-2 hel gene (nsp13) (hel). SARS-CoV-2 hel gene (nsp13)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Hepatitis A (hepA). Hepatitis A
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Hepatitis B (hepB). Hepatitis B
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Hepatitis C (hepC). Hepatitis C
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Hepatitis E (hepE). Hepatitis E
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• hep g armored rna (hepGRna). Measure of the amount Hepatitis G Armored RNA.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• HF183 Bacteriodes 16S (hf183). Human-Specific HF183 Bacteriodes 16S rRNA
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• 5-hydroxyindoleacetic acid (5-HIAA) (hiaa5). A serotonin metaboliteused for normalizing wastewater surveillance signal. Analysis of 5-HIAA is done in clinical settings to assess the possibility of carcinoid syndorme in patients, and used in wastewater analysis to estimate human population numbers. Studies have shown that 5-HIAA can be quanitified in samples from WWTPs, and that measured quantities of this molecule have a positive correlation with the population calculated using hydrochemical parameters, and are also correlated well with the census population measures.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Haemophilus influenzae (hInfluenzae). Haemophilus influenzae
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Human Immunodeficiency Virus (HIV) (hiv). Human Immunodeficiency Virus (HIV)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• See Header for Measure (hMe). An indicator to show in a wide-name that measure information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Human Metapneumovirus (HMPV) (hmpv). Human Metapneumovirus (HMPV)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Human Parainfluenza Virus (HPIV) (hpiv). Human Parainfluenza Virus (HPIV)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Human Papiloma Virus (HPV) (hpv). Human Papiloma Virus (HPV)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Human Rhinovirus (HRV) (hrv). Human Rhinovirus (HRV)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Human Rhinovirus (HRV) A (hrvA). Human Rhinovirus (HRV) A
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Human Rhinovirus (HRV) B (hrvB). Human Rhinovirus (HRV) B
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Human Rhinovirus (HRV) C (hrvC). Human Rhinovirus (HRV) C
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Herpes Simplex Virus (hsv). Herpes Simplex Virus
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• i1566v omicron-variant gene target (i1566v). i1566v omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• i3758v omicron-variant gene target (i3758v). i3758v omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• i82t delta-variant gene target (i82t). i82t delta-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Ibuprofen (ibu). Ibuprofen (usually measured as a human fecal chemical indicator)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Industrial input (indusIn). Percentage of total wastewater input coming from industrial sources.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Influent equilibration (influEqui). Binary indicator for whether a site stores influent wastewater prior to treatment to equilibrate flow rates.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Inhibition measure (inhibMe). Parameter to report whether or not inhibition was detected in the sample.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Omicron Variant ins214epe Insertion (ins214epe). Omicron Variant ins214epe Insertion mutation.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Integrase Class I gene target (integraseCl1). Integrase anti-microbial resistance gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Combined ip2 and ip4 sars-cov-2 gene target (ip2ip4). Combined ip2 and ip4 sars-cov-2 gene target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• JN.1.7 Variant (jn17V). The JN.1.7 variant of SARS-CoV-2, one of the FLiRT variants.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• JN.1 Variant (jn1V). The JN.1 variant is a subvariant of Omicron variant BA.2.86, and contains several mutations that are associated with escape from vaccine-mediated immune protection. The source of the FLiRT variants of SARS-CoV-2.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• k856r omicron-variant gene target (k856r). k856r omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Klebsiella pneumoniae (klebsiellaPneu). Klebsiella pneumoniae
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• KP.1.1 Variant (kp11V). The KP.1.1 variant of SARS-CoV-2, one of the FLiRT variants.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• KP.1 Variant (kp1V). The KP.1 variant of SARS-CoV-2, one of the FLiRT variants.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• KP.2 Variant (kp2V). The KP.2 variant of SARS-CoV-2, one of the FLiRT variants.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• KP.3.1.1 Variant (kp311V). The KP.3.1.1 variant of SARS-CoV-2, one of the FLiRT variants.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• KP.3 Variant (kp3V). The KP.3 variant of SARS-CoV-2, one of the FLiRT variants.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Omicron Variant l24s mutation (l24s). Omicron Variant l24s mutation
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• l452r delta-variant gene target (l452r). l452r delta-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• L455S Mutation (l455s). The FLiRT/SLip variant mutation L455S.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• l981f omicron-variant gene target (l981f). l981f omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Lachnospiraceae (Lachno3) (lachno3). Human-associated bacteria in the family Lachnospiraceae (Lachno3), often used as microbial source tracking markers for human fecal pollution tracking in environmental waters.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Lambda (lamba). C.37
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• LB.1 Variant (lb1V). The LB.1 variant of SARS-CoV-2,similar to other FLiRT variants but with an additional mutation.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Legionella (legionella). Legionella
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Listeria (listeria). Listeria
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Limit of Blank (LOB) (lob). The highest concentration of a target analyte (DNA or RNA) that can be expected in a blank sample (a sample with no target DNA/RNA) while still considering the sample as negative. Defines the upper limit of “noise” or background signal that should not be confused with a true positive.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Limit of detection (LOD) (lod). Limit of detection, ie. the minimum level of a genetic target.
  Status: active. First released: 1.1.0. Last updated: 3.0.0.
• Limit of detection (LOD) - sewage (lodSewa). Limit of detection, ie. the minimum level of a genetic target, for sewage samples.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Limit of quantification (LOQ) (loq). Sample limit of quantification (LOQ) is defined as “the concentration of a target that can be quantified with an acceptable level of precision when present in a sample” (Ahmed et al., 2021).
  Status: active. First released: 1.1.0. Last updated: 3.0.0.
• LP.8.1 Variant (lp81V). The LP.8.1 variant of SARS-CoV-2, a Omicron subvariant of JN.1, and FLiRT variant.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Omicron Variant LPPA24S mutation (lppa24s). Omicron Variant LPPA24S mutation
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Sample Material Characteristics (matChar). A site measurement for describing the qualitative characteristics of the sample material in situ (ie. The material from which the sample is collected.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Concentration Factor (mCF). Concentration Factor (CF) is the degree to which the concentration observed in the final qPCR assay volume has been magnified compared to concentration of the analyte in the original sample (see Box 2.1 Protocol).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• MCR-1.1 Colistin-resistence gene target (mcr11). The MCR-1.1 colistin anti-microbial resistance gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Measles (measles). Measles
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Other Measure (measOth). Other measure, not otherwise specified in measures.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Other Measure Description (meOthDe). Description of other measure (measOtherDesc).
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Effective Sample Size/Volume (mESV). Effective Sample Size/Volume (ESV) is the amount of the original sample size/volume that was actually analyzed in a qPCR reaction (see Box 2.1 Protocol)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Mycoplasma genitalus (mGenitalus). Mycoplasma genitalus
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Murine Hepatitis Virus (mhv). A measure for amount of murine hepatitis viurs.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• minimum post-trimming read length (minPTLength). The threshold used as a cut-off for the minimum length of a read after trimming.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Method Limit of Detection (LOD) (mlod). The minimum level of a target necessary for its consistent detection considering all sample processing steps as in the definition of SLOD), but considering biases attributable to method losses. The MLOD is experimentally determined using a rigorous and iterative testing approach and it is sensitive to the recovery surrogate used and the sample matrix encountered.
  Status: active. First released: 2.2.0. Last updated: 3.0.0.
• Mpox (mpox). The virus known as Mpox, previously also known as Monkey Pox.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Mpox B6R Gene Target (mpxB6R). Human MPox Virus (hMPXV) gene target. Envelope protien gene CDC Assay; selective for MPXV.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Clade I Mpox C3L Gene Target (mpxC3L). Human MPox Virus (hMPXV) Clade I gene target. hMPXV C3L primers and probe detect Clade I viruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Mpox Clade I (mpxClI). The virus known as Mpox, previously also known as Monkey Pox, Clade I virus type.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Mpox Clade II (mpxClII). The virus known as Mpox, previously also known as Monkey Pox, Clade II virus type.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Mpox & Orthopox E9L-NVAR Gene Target (mpxe9lNVAR). Human MPox Virus (hMPXV) gene target for Orthopoxvirus DNA polymerase. CDC Assay detects all hMPXV​ clades and non-variola Orthopox viruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Mpox & Orthopox E9L-OPX3 Gene Target (mpxe9lOPX3). Human MPox Virus (hMPXV) gene target using the generic orthopox virus OPX3. Lower sensitivity for MPox.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Mpox Clade I F3L Gene Target (mpxF3L). Human MPox Virus (hMPXV) Clade I gene target, F3L
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Mpox G2R-G Gene Target (mpxG2RG). Human MPox Virus (hMPXV) gene target using the G2R_G primers and probe which  detects all MPox Virus strains ​.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Mpox G2R-NML Gene Target (mpxG2RNML). Human MPox Virus (hMPXV) gene target using the G2R_NML primers and probe which  detects all MPox Virus strains ​.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Clade II Mpox G2R-WA Gene Target (mpxG2RWA). Human MPox Virus (hMPXV) Clade II gene target, measured with G2R_WA primers and probe to detects Clade II viruses.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Mpox GT Molecular Gene Target (mpxGTmol). Human MPox Virus (hMPXV) gene target - this specific measure and gene target are proprietary to GT Molecular
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Methicillin-resistant Staphylococcus aureus (MRSA) (mrsa). Methicillin-resistant Staphylococcus aureus (MRSA)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• ms2 coliphage (ms2Col). Measure of the amount of ms2 coliphage.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Mycobacterium tuberculosis (mTuberculosis). Mycobacterium tuberculosis
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Mu (mu). B.1.621
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• murine coronavirus (muCo). Measure of the amount of murine coronavirus.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Mumps (mumps). Mumps
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• N sars-cov-2 gene target (n). N sars-cov-2 gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Combined N1 and N2 sars-cov-2 gene target (n1n2). Combined N1 and N2 sars-cov-2 gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Omicron Variant n211i mutation (n211i). Omicron Variant n211i mutation & gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• N50 (n50). The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Omicron Variant n679k mutation (n679k). Omicron Variant n679k mutation & gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Omicron Variant n856k mutation (n856k). Omicron Variant n856k mutation & gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Omicron Variant n969k mutation (n969k). Omicron Variant n969k mutation & gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• NB.1.8.1 variant (Nimbus) (nb181V). The Nimbus variant of SARS-CoV-2 (NB.1.8.1), descendant of the recombinant variant XDV.1.5.1.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• number of base-pairs sequenced (nBPSeq). The number of total base pairs generated by the sequencing process.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• number of contigs (nContig). The number of contigs (contiguous sequences) in a sequence assembly.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Neisseria gonorrhoeae (nGonorrhoeae). Neisseria gonorrhoeae
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Ammonia and Ammonium as Nitrogen (nh3nh4). Ammonia and Ammonium combined concentration, as Nitrogen
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Ammonium Nitrogen (nH4N). Ammonium nitrogen concentration, as N.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• niid_2019-ncov_n sars-cov-2 gene target (niid19). niid_2019-ncov_n sars-cov-2 gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Norovirus (noro). Norovirus.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Norovirus G1 (noroG1). Norovirus genogroup 1
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Norovirus G2 (noroG2). Norovirus genogroup 2
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sarbecovirus-specific N sars-cov-2 gene target (nSarbec). Sarbecovirus-specific N sars-cov-2 gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• SARS-CoV-2 nsp1 Gene target (nsp1 ). SARS-CoV-2 nsp1 Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 nsp10 Gene target (nsp10 ). SARS-CoV-2 nsp10 Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 nsp11 Gene target (nsp11). SARS-CoV-2 nsp11 Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 nsp15 Gene target (nsp15). SARS-CoV-2 nsp15 Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 nsp16 Gene target (nsp16). SARS-CoV-2 nsp16 Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 nsp2 Gene target (nsp2 ). SARS-CoV-2 nsp2 Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 nsp3 Gene target (nsp3 ). SARS-CoV-2 nsp3 Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 nsp4 Gene target (nsp4 ). SARS-CoV-2 nsp4 Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 nsp5 Gene target (nsp5 ). SARS-CoV-2 nsp5 Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 nsp6 Gene target (nsp6 ). SARS-CoV-2 nsp6 Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 nsp7 Gene target (nsp7 ). SARS-CoV-2 nsp7 Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 nsp8 Gene target (nsp8 ). SARS-CoV-2 nsp8 Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 nsp9 Gene target (nsp9 ). SARS-CoV-2 nsp9 Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• number of total reads (nTotRead). The total number of non-unique reads generated by the sequencing process.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Number of NTCs per Run (numNTC). The number of no-template controls included in each PCR instrument run.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• number of unique reads (nUniRead). The number of unique reads generated by the sequencing process.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• coronavirus OC43 (oc43). Measure of the amount of coronavirus OC43.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Omicron BA.1 (omicr1). Omicron B.1.1.529
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Omicron BA.2 (omicr2). Omicron BA.2
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Omicron BA.2.75 (omicr275). Omicron BA.2.75
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Omicron BA.4 (omicr4). Omicron BA.4
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Omicron BA.5 (omicr5). Omicron BA.5
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Orthophosphates (ophos). Ortho-phosphate concentration.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• SARS-CoV-2 orf10 Gene target (orf10). SARS-CoV-2 orf10 Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 orf14 Gene target (orf14). SARS-CoV-2 orf14 Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• ORF1a sars-cov-2 gene target (orf1a). ORF1a sars-cov-2 gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ORF1ab sars-cov-2 gene target (orf1ab). ORF1ab sars-cov-2 gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ORF1b sars-cov-2 gene target (orf1b). ORF1b sars-cov-2 gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• SARS-CoV-2 orf3a Gene target (orf3a). SARS-CoV-2 orf3a Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 orf3b Gene target (orf3b). SARS-CoV-2 orf3b Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 orf6 (ns6) Gene target (orf6). SARS-CoV-2 orf6 (ns6) Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 orf7a Gene target (orf7a). SARS-CoV-2 orf7a Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 orf7b (ns7b) Gene target (orf7b). SARS-CoV-2 orf7b (ns7b) Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 orf8 (ns8) Gene target (orf8). SARS-CoV-2 orf8 (ns8) Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 orf9b Gene target (orf9b). SARS-CoV-2 orf9b Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SARS-CoV-2 orf9c Gene target (orf9c). SARS-CoV-2 orf9c Gene target
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Oxidation reduction potential (ORP) (orp). Oxidation-reduction potential (ORP) measures the ability of a lake or river to cleanse itself or break down waste products, such as contaminants and dead plants and animals.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Variants Other (otherV). Used for reporting variants detected for which a specific measureID doesn’t already exist. The ODM team will periodically migrate collected responses in this category into set measureIDs.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Delta Variant p100l mutation (p100l). Delta Variant p100l mutation & gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Omicron Variant p13l mutation (p13L). Omicron Variant p13l mutation
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Delta Variant p2046l mutation (p2046l). Delta Variant p2046l mutation & gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Delta Variant p2287s mutation (p2287s). Delta Variant p2287s mutation & gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Omicron Variant p3395h mutation (p3395h). Omicron Variant p3395h mutation & gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Delta Variant p681r (p681r). Delta Variant p681r mutation & gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Paraxanthine (PARA) (para). A metabolite of the common central nervous system stimulant caffeine, measred levels of paraxanthine have been found to be less affected by the genetic heterogeneity and population structure than caffeine is, and it may serve as a useful population biomarker in wastewater.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• percent read contamination (percContam). The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• percent Ns across total genome length (percNLength). The percentage of the assembly that consists of ambiguous bases (Ns).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• pH (ph). pH measurement
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Phagetyping Results (phagetype). The phagetyping results from an organism.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Pseudomonas virus phi6 (phi6). Measure of the amount of pseudomonas virus phi6.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Total phosphorous (phos). Total phosphorous
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Total Phosphates (phostot). Total phosphates
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• PHRED quality score (phred). PHRED Quality Score For Sequencing
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Plasmodium (plasmodium). Plasmodium
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Polygon Population (polyPop). An attribute of a polygon, which specifies the population of that polygon. A rough estimate of the number of human residents.
  Status: active. First released: 2.0.0. Last updated: 2.3.0.
• Populated area type (popAreaType). Type of populated area being sample (ie. urban, rural)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Population density (popDensity). Measure of population density of a site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Population Served (popServ). An measure of a site, which specifies the population of/population served by a given site.
  Status: active. First released: 2.0.0. Last updated: 2.3.0.
• Population Served - Interval (popServRange). Population served by a site, when reported as an interval.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PMMoV-CP (ppmv). Pepper mild mottle virus capsid protein gene region
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Precipitation - general (precip). General measure of precipitation, type not specified.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Storage temperature prior to concentration (preConcTemp). The temperature at which a sample was stored between collection and concentration.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Storage time prior to concentration (preConcTime). Length of time for which a sample is stored between collection and concentration.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Storage temperature prior to extraction (preExtractTemp). The temperature at which a sample was stored between concentration and extraction.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Storage time prior to extraction (preExtractTime). Length of time for which a sample is stored between concentration and extraction.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• presampling activity (presampAct). A measure for recording any relevant activities that occur upstream of the sampling source. For example, recording that the river one is sampling from flows through farmland, or that filtration and/or sedimentation occurred at the wastewater treatment plant before the sample was collected.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Pre-sampling weather (preSampWeath). Weather leading up to, but not including, the day of sampling.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Pretreatment (pretreat). Was the sample chemically treated in anyway with the addition of stabilizers or other
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Pseudomonas (pseudomonas). Pseudomonas
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Puro virus (puro). Measure of the amount of puro virus.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Poliovirus type 2 (pv2). Poliovirus type 2
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• q19e omicron-variant gene target (q19e). q19e omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• q493r omicron-variant gene target (q493r). q493r omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• q498r omicron-variant gene target (q498r). q498r omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• q954h omicron-variant gene target (q954h). q954h omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• r203m delta-variant gene target (r203m). r203m delta-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• R346T Mutation (r346t). The FLiRT/SLip variant mutation R346T.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• dPCR Rain Percentage (rainPerc). The percentage of droplets tha fall between the major positive and negative population in digital droplet PCR.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• IP2 rdrp sars-cov-2 gene target (rdrpIP2). IP2 rdrp sars-cov-2 gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• IP4 rdrp sars-cov-2 gene target (rdrpIP4). IP4 rdrp sars-cov-2 gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Recombinant Lineage Variant (recomb). A catch-all measure for viruses of non-specified and recombinant lineages, defined as those virsues wherein viruses of two different parent strains coinfect the same host cell and interact during replication to generate virus progeny that have some genes from both parents. Recombination generally occurs between members of the same virus type (e.g., between two influenza viruses or between two herpes simplex viruses). This is particularly common in the evolution of coronaviruses and sarbecoviruses.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Relative humidity (relHum). The unit of relative humidity, or the air-water mixture. The ratio of the partial pressure of water vapor in the mixture to the equilibrium vapor pressure of water over a flat surface. of pure water at a given temperature.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• replicate number (repNum). The replicate number for a Ct or Cq value - used for specifying out a protocol standard curve.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Rickettsia (rickettsia). Rickettsia
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Ribonuclease P (RNase P) (rnaseP). Ribonuclease P (RNase P) (usually measured as a human fecal indicator)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Rotavirus (rotavirus). Rotavirus
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Respiratory syncytial virus A and B combined (rsvAB). Human Respiratory Syncytial Virus Type A (RSV A) and Type B (RSV B).
  Status: active. First released: 2.1.0. Last updated: 2.1.3.
• Respiratory syncytial virus A (rsvAMe). Human Respiratory Syncytial Virus Type A (RSV A).
  Status: active. First released: 2.1.0. Last updated: 2.1.3.
• Respiratory syncytial virus B (rsvB). Human Respiratory Syncytial Virus Type B (RSV B).
  Status: active. First released: 2.1.0. Last updated: 2.1.3.
• Respiratory syncytial virus (rsvMe). Human Respiratory Syncytial virus (RSV), generic measure.
  Status: active. First released: 2.0.0. Last updated: 2.1.2.
• RSV N-gene (rsvN). Human Respiratory syncytial Virus, N-gene region.
  Status: active. First released: 2.1.3. Last updated: 2.1.3.
• Rubella (rubella). Rubella
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• s2083i omicron-variant gene target (s2083i). s2083i omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• s371l omicron-variant gene target (s371l). s371l omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• s373p omicron-variant gene target (s373p). s373p omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• s375f omicron-variant gene target (s375f). s375f omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• s477n omicron-variant gene target (s477n). s477n omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Salinity (salinity). Measurement of salinity/salt content
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Salmonella (salmonella). Salmonella
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Sample volume (samVol). The volume of a given sample.
  Status: active. First released: 2.2.0. Last updated: 3.0.0.
• Sapovirus (sapovirus). Sapovirus
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• sequence assembly length (seqAssLen). The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Serological Variant (Serovar) (serovar). The serovar of the organism.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Settled solids (settsol). Amount of settled solids from a wastewater sample.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sewage equivalent (sewEq). Equivalent unconcentrated volume of wastewater or mass of sludge in PCR reaction
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Sewage travel time (sewTrTi). A measure of sewage travel time, often approximate, from sewage source to the sampling site.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Shaker aggitation speed (shaker). The speed/aggitation level for a shaker plate/shaker platform.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Shigella (shigella). Shigella
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Sample Limit of Detection (LOD) (slod). The minimum level of a target within a sample that would be consistently detectable considering all sample processing steps, from sample concentration leading up to and including amplification and quantification steps of RT-qPCR. In this Protocol, the SLOD is the concentration factor-adjusted ALOD, which provides a theoretical estimate of the minimum concentration in the original sample that would yield consistent detection of the target, assuming no method losses.
  Status: active. First released: 2.2.0. Last updated: 3.0.0.
• Specific humidity (specHum). Measure for specific humidity, the unit is the ratio of the mass of water vapour and the mass of total air.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Spike Concentration (spikeConc). Concentration of the recovery efficiency target in a spike matrix and recovery assay.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• SARS-CoV-2 Spike gene (orf2) (spikeGene). SARS-CoV-2 Spike gene (orf2)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Shiga-toxin-producing Escheria coli (STEC) (stec). Shiga-toxin-producing Escheria coli (STEC).
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Storage temp (sTemp). Temperature that the sample is stored at in Celsius.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Stercobilin (stercobilin). Stercobilin is a tetrapyrrolic bile pigment and is one end-product of heme catabolism. It is the chemical responsible for the brown color of human feces and was originally isolated from feces in 1932.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Storage time (stoTim). Length of time that a sample was in storage.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Strain ID (strainID). The strain identifier for a given organism.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Streptococcus pneumoniae (strepPneu). Streptococcus pneumoniae
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Sub-variant or lineage (subVar). A unit used to report a specific genetic lineage, or to specify that a reported variant is a sub-variant of another.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sucralose (suc). Sucralose (usually measured as a human fecal chemical indicator)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Surveillance Level (survLevel). The scale or level of surveillance being done at a site. Ie. Is it institutional, is it only for a single building, or is it for a whol municipality.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• t19r delta-variant gene target (t19r). t19r delta-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• t3646a delta-variant gene target (t3646a). t3646a delta-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• t547k omicron-variant gene target (t547k). t547k omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• t9i omicron-variant gene target (t9i). t9i omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• TaqPath N sars-cov-2 gene target (taqpatN). TaqPath N sars-cov-2 mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• TaqPath S sars-cov-2 gene target (taqpatS). TaqPath N sars-cov-2 mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Total Dissolved Solids (TDS) (tds). Total dissolved solids
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Sample temperature (temp). Temperature of the sample measured in degrees Celcius
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Nucleic acid template volume (tempVol). The volume of DNA or RNA template used for PCR.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• TetW Tetracycline-resistance gene target (tetW). The tetW tetracycline anti-microbial resistance gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Total Kjeldahl Nitrogen (tkn). A measure of Total Kjeldahl Nitrogen; ie. the sum of nitrogen bound in organic substances, nitrogen in ammonia (NH3-N) and in ammonium (NH4+-N) in the chemical analysis of soil, water, or waste water.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Total Nitrogen (tn). Total nitrogen concentration, as N.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Treponema pallidum (tPallidum). Treponema pallidum
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Total solids concentration (ts). Total solids concentration
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Total suspended solids (tss). Total suspended solids
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Concentration of total suspended solids (tssConc). Total suspended solids concentration of the wastewater.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Turbidity (turb). A measure for the turbidity of water, or a liquid sample, quanitfying the relative clarity or opcaity of a liquid. Highly indicative of water quality.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Trichomonas vaginalis (tVaginalis). Trichomonas vaginalis
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Tube weight empty (tWeighE). The weight of the tube used for analysis while empty.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Tube weight full (tWeighF). The weight of the tube used for analysis while full of analyte.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Ureaplasma (ureaplasma). Ureaplasma
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Urobilin or urochrome (urobilin). Urobilin or urochrome is the chemical primarily responsible for the yellow color of urine. It is a linear tetrapyrrole compound that, along with the related colorless compound urobilinogen, are degradation products of the cyclic tetrapyrrole heme.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• V1104L Mutation (v1104l). The FLiRT/SLip variant mutation V1104L
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• v2930l delta-variant gene target (v2930l). v2930l delta-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• VanA-A Vancomycin-resistance gene target (vanAA). The VanA-A vancomycin anti-microbial resistance gene target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Vancomycin resistance (vanc). Vancomycin resistant bacteria.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Varicella (varicella). Varicella
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Vibrio (vibrio). Vibrio
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Size in volume (vol). Total volume of water or sludge sampled.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Volatile suspended solids (vss). Volatile suspended solids
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Volatile suspended solids - ignition (vssIg). A water quality measure, captured by via the loss on ignition of the mass of measured total suspended solids. This ignition generally takes place in an oven at a temperature of 550 °C to 600 °C. It represents the amount of volatile matter present in the solid fraction of the measured solution.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Verotoxin-producing Escherichia coli (VTEC) (vtec). Verotoxin-producing Escherichia coli (VTEC)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Wastewater temperature (watTemp). Temperature of the wastewater.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Weather (time of sampling) (weath). A measure for weather captured through qualitative categories; part of a larger suite of weather measures that may be useful when collecting samples from outdoor sources.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• West Nile (westNile). West Nile
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Wind Speed (wind). A measure for wind speed; part of a larger suite of weather measures that may be useful when collecting samples from outdoor sources.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Delta Variant wt214 gene target (wt214). Delta Variant wt214 gene target
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Wastewater treatment plant designed capacity (wwtpCap). A measure for the designed capacity of a wastewater treatment plant, in terms of how much water it was designed to be able to hold and process.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• XEC Variant (xecV). The XEC variant of SARS-CoV-2, a subvariant of the Omicron strain.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• y505h omicron-variant gene target (y505h). y505h omicron-variant mutation gene target
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Yersinia enterocolitica (yEnterocolitica). Yersinia enterocolitica
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Zika (zika). Zika
  Status: active. First released: 2.2.0. Last updated: 2.2.0.

Methods

(methods). Procedures or steps for collecting samples or performing measures. For example, methodExtract is a method that describes the how a sample was extracted. met

• AMR Analysis Software (amrSoft). Software use to analyse bacterial genomes and genes for anti-mocrobial resistance (AMR).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Bacterial testing method (bactMeth). Description of the bacterial testing/detection method.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Lineage- or Clade-analysis Software (cladeAn). Software tool or pipeline for determining the clade or lineage of an organism.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Consensus Sequence Software (conSeqSoft). Software use to run consensus sequence on sequencing analyses.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Deduplication Method (dedup). Sequencing and PCR deduplication method.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Dehosting Method (dehost). Sequencing and PCR dehosting method.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Extraction Blank - Control (extBlank). Binary Y/N indicator for if extraction blank was used as a control for the nucleic acid extraction process.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Nucleic acid extraction method (extraction). Description of the nucleic acid extraction method.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Genomic Target Enrichment (gte). The molecular technique used to selectively capture and amplify specific regions of interest from a genome.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Inhibition method (inhibMeth). Description of the method used to evaluate molecular inhibition.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Library Preparation Kit (libraryKit). The name of the DNA/RNA library preparation kit used to generate the library being sequenced.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Concentration method (methodConc). Description of the method to concentrate a wastewater sample.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Pasteurized sample (pasteur). Binary indicator for whether a sample was pasteurized as part of its processing.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• PCR Action/Activity (pcrAct). Describes a given PCR cycle for delineating more method information.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• PCR method (pcrmeth). Description of the PCR method.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Population assessment method (popAs). Method for assessing the population count for a site/polygon.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Genetic primer (primer). Method ID used for indicating the primer used for a PCR or sequencing assay.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Quaility assurance method (qaqc). Quality assurance and quality control method.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Quality Control Method (qcMethod). Method for quality control or assessment.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Raw Sequence Data Processing Method (rawSeqProc). The software/library/pipeline used to process the raw sequencing data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Sequencing read mapping software name (readMapper). The name of the bioinformatics software tool used to align short DNA or RNA sequence reads (obtained from high-throughput sequencing technologies like Illumina, PacBio, or Oxford Nanopore) to a reference genome or transcriptome.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Resuspension method (resuspension). Describes the method used for resuspending material.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Retained Element (retainedElement). The element retained after centrifugation, filtration, solid separation, etc.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Collection other depreciated (sampleTypeOther). Description for other type of method not listed in collection. depreciated.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Standard curve frequency (scf). A method for specifying the frequecy over which a standard curve (or ‘Master Curve’) is used.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Genetic sequencing script version (scriptVersion). Used to specify the script or script version used to extract summary information (i.e. coverage and mutation frequency statistics, etc.) from the sequencing output.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sequence Assembly Software (seqAss). The name of the software/toolkit/pipeline used for assembling sequences from reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Sequencing Layout (seqLay). The layout of genetic material used in sequencing.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sequencing QC Pipeline (seqQC). The quality control pipeline for sequencing or PCR data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Sequencing selection method (seqSel). The primer sequence selection method used in sequencing.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sequencing Strategy (seqStrat). The sequencing strategy used for an analysis.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Serotyping Method (seroMeth). The method used to determine the serovar.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Shipped on ice (shipOnIce). Was the sample kept cool while being shipped to the lab
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Solid seperation (solidSep). Process used to separate solid and liquid phases of the sample.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Spike material (spikeMat). Material into which the recovery efficiency control target is spiked.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Recovery efficiency spike target (spikeTarget). Method specifying the recovery efficiency control target. This matches on to the the spike material method ID.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Standard Curve Calculation Method (stdCurveMet). Describes the specific approach used for calculating a standard curve.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Sample Storage Medium (stoMed). The medium used to store a sample before final analysis.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Nucelic Acid Template Type (tempType). Specifies whether a PCR or sequencing used RNA or DNA as the template for the reaction.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Type other depreciate (tyOtDep). Description for other type of sample not listed in
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.

Missingness

(missingness). The part type for missingness values. Only used for the dictionary entries of parts.

• Data Not Collected (dnc). A missingness value for when when data was not measured or collected; an analysis not run, etc.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Missing data (miss). A general missingness value for missing data, used when data is not included for an unknown reason.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Not applicable (NA). The field for which the expected value is not a property of the described object.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Not a number (nan). The outcome of a measurement is not a valid number (plus or minus infinity, error, …)
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Not reported (nr). A value could have been recorded, however, it was not.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Null (null). A logical representation of a statement that is neither TRUE nor FALSE.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Restricted data (restrict). Missing data is witheld because it is restricted access.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Undisclosed or Not Provided (undisc). A value has been recorded, however it was not included in the dataset.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Missingness sets

(missingnessSets). Set of missingness values. Examples of missingness sets may include NR or NA esclusive sets, or general all-purpose sets.

General missingness set

(genMissingnessSet)The general set for missingness values.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Data Not Collected (dnc). A missingness value for when when data was not measured or collected; an analysis not run, etc.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Missing data (miss). A general missingness value for missing data, used when data is not included for an unknown reason.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Not applicable (NA). The field for which the expected value is not a property of the described object.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Not a number (nan). The outcome of a measurement is not a valid number (plus or minus infinity, error, …)
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Not reported (nr). A value could have been recorded, however, it was not.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Null (null). A logical representation of a statement that is neither TRUE nor FALSE.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Restricted data (restrict). Missing data is witheld because it is restricted access.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Undisclosed or Not Provided (undisc). A value has been recorded, however it was not included in the dataset.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Not reported, Not applicable missing set

(nrNAMissingnessSet)Not reported, Not applicable missing set.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Not applicable (NA). The field for which the expected value is not a property of the described object.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Not reported (nr). A value could have been recorded, however, it was not.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Measure, method, or attribute sets

(mmaSets). A set of categories. For example, site type has a list of different sites, such as a wastewater treatment plant, a septic tank, or a pumping station. Only used for the dictionary entries of parts.

Public Health Action Type Value Set

(actionTypeSet)A set of valid categories for the public health action type field.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Antimicrobial resistance (AMR) classification (amrClass). A public health action type wherein threat level classification has been done on a strain of antimicrobial resistant (AMR) microbes, and communicated to the public.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Control measure implementation (contMeasImp). A public health action type wherein authorities have begun implementing infection control measures.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Outbreak declaration (outb). Public health action type used to indicate outbreak status. Given that when outbreaks occur, full data on case counts may not be available or completely accurate, using this measure indicates that case counts may be approximate.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Public health advisory (phAdvise). A public health action type wherein a public health advisory is deseminated to the public.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Surveillance alert (survAlert). A public health action type wherein authorities have made a decision about surveillance and communicated the alert.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Threat designation (threatDes). A public health action type wherein a threat level is determined and communicated by authorities.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

All Public Health Actions Set

(allActionsSet)A set of all valid categories for public health action, regardless of action type.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Border closure (borderClos). A measure shutting entry points to limit cross-border movement and disease spread.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Critical priority pathogen (cpp). A microorganism with resistance to multiple drugs and a high threat to human health.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Decreased surveillance (decSurv). Scaling back of monitoring activities, often due to reduced risk.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• De-escalated variant (dev). A given microbial threat has been de-escalated; a de-escalated variant - different institutions may use different criteria for assigning this threat level.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Hand hygiene advisory (handHygAdv). Public guidance promoting handwashing or sanitizing to reduce infection risk.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Stay-at-home order (homeOrder). A directive requiring people to remain at home except for essential activities.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• High priority pathogen (hpp). A resistant organism of serious concern, requiring urgent attention.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Increased surveillance (incSurv). Intensified efforts to monitor disease trends or case counts.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Lockdown (lockdown). Broad restrictions on movement and activities within a region to control disease spread.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Mask mandate (maskMand). A legal requirement for individuals to wear masks in specified settings.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Mask recommendation (maskRec). Guidance encouraging the public to wear masks to reduce disease transmission.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Medium priority pathogen (mpp). A resistant organism of moderate concern, needing ongoing monitoring.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• End of Outbreak (outbEnd). Indicates an outbreak has ended.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Outbreak - on-going (outbOngoing). Indicates an outbreak is on-going.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Declared outbreak or Outbreak start (outbStart). Indicates an outbreak began.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Public health emergency (outbreak) (phEmerg). Indicates a public health emergency from an outbreak.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Quarantine recommendation (quarRec). Advice that individuals exposed to a disease should isolate to prevent spread.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Routine surveillance (routSurv). Standard, ongoing collection of public health data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Resistant strain identified (rsi). Confirmation that a specific microorganism is resistant to one or more antimicrobial agents.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• School closure (schoolClos). Temporary shutdown of educational institutions to prevent disease transmission.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Social distancing measures (socialDist). Policies encouraging or enforcing physical space between individuals in public or private settings.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Targetted surveillance initiated (targSurv). Monitoring focused on a specific population, location, or risk factor.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Travel ban (travBa). A restriction prohibiting travel to or from specific locations.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Travel warning (travWa). A notice advising against travel to certain areas due to health risks.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Change to Vaccine Schedule (vaxSched). A public health advisory has been issued to change the vaccination schedule or roll-out a vaccination campaign in response to a threat.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Variant of concern (voc). A given microbial threat has been deemed a variant of concern - different institutions may use different criteria for assigning this threat level.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Variant of interest (voi). A given microbial threat has been deemed a variant of interest - different institutions may use different criteria for assigning this threat level.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• variant under monitoring (vum). A given microbial threat has been deemed a variant under monitoring - different institutions may use different criteria for assigning this threat level.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Data Adjustment Standard Value Set

(allStandardSet)Set of valid input values for the standard field.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Bayesian Smoothing applied (bayesSmooth). This data treatment smooths the measurement value using bayesian smoothing techniques.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Central average smoothing applied (caSmooth). This data treatment smooths the measurement value using central average smoothing.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Crassphage Standarized (crassStand). This data treatment standardizes the measurement value to concentration levels of crassphage.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• 7-day smoothing of values (day7Smooth). This data treatment smooths the measurement value across 7-days.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Flow Standarized (flowStand). This data treatment standardizes the measurement value to flow rates.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Gaussian distribution stanrdized/Normalized (gauss). Standardize the data to a gaussian/normal distribution, such that the data have a mean of zero and a standard deviation of one.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PMMoV Standarized (pmmovStand). This data treatment standardizes the measurement value to concentration levels of pepper mild mottle virus (PMMoV).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Time standardized (timeStand). This data treatment standardizes the measurement value against time.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Antimicrobial Resistance (AMR) Classification Value Set

(amrClassSet)A set of valid categories for the public health action field, where the action type is ‘antimicrobial resistance (AMR) classification’.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Critical priority pathogen (cpp). A microorganism with resistance to multiple drugs and a high threat to human health.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• High priority pathogen (hpp). A resistant organism of serious concern, requiring urgent attention.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Medium priority pathogen (mpp). A resistant organism of moderate concern, needing ongoing monitoring.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Resistant strain identified (rsi). Confirmation that a specific microorganism is resistant to one or more antimicrobial agents.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

AMR Software Set

(amrSoftSet)The valid set of AMR analysis software categories.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• ABRicate Software (abricate). Software tool for screening bacterial genomes against multiple resistance databases.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• AMRFinderPlus Software (amrFinderPlus). Software tool that was developed by NCBI to detect AMR genes in bacterial genomes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• ARG-ANNOT Annotation Tool (argAnnotSoft). Software annotation tool for antimicrobial resistance genes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• CARD Resistance Gene Identifier (RGI) (cardRGI). Software tool that is a part of the Comprehensive Antibiotic Resistance Database (CARD) used for annotation and prediction of AMR.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• DeepARG Software (deepARG). Software tool that predicts AMR genes using deep learning on metagenomic data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• MetaPhlAn Software (metaPhIAn). Software tool that profiles microbial communities and can provide resistance gene insights.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• ResFinder Tool (resFinderSoft). Software tool that identifies acquired antimicrobial resistance genes in bacterial genomes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• ShortBRED Software (shortBRED). Software tool that screens for known AMR genes in shotgun metagenomic sequencing data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SRST2 Software (srst2). Software tool for analyzing antimicrobial resistance using short read sequences.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• StarAMR Software (starAMR). Software tool that is used to detect AMR genes in genome assemblies.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Bacterial testing method set

(bactMethSet)The set capturing containing all of the valid methods for the bacterial testing method.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Antimicrobial gradient test (agt). A gradient strip test is performed according to the manufacturer’s instructions: a short plastic or paper strip impregnated with antibiotic is placed on inoculated agar. On the standardised 100 mm Petri dish, two strips may be placed, while on the larger 150 mm Petri dish, up to six antibiotics may be tested simultaneously.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Bacterial culture (bacCul). Growing a bacterial culture to test for bacterial presence.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Gram stain (gramSt). After the sample is taken, the Gram stain is colored purple. Then, a solvent is added to the stain. When the solvent combines with bacteria in a sample, the bacteria will either stay purple or turn pink or red. If the bacteria remain purple, they are Gram-positive. If the bacteria turn pink or red, they are Gram-negative.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Growth in enrichment broth (growBroth). The selective cultivation of microorganisms in a nutrient-rich liquid medium to increase their concentration before analysis.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Boolean value set

(booleanSet)Set that contains the valid possible values for a boolean measure (TRUE or FALSE).
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• FALSE (FALSE). Boolean data type = FALSE
  Status: active. First released: 1.0.0. Last updated: 2.3.0.
• TRUE (TRUE). Boolean data type = TRUE
  Status: active. First released: 1.0.0. Last updated: 2.3.0.

Calculation type set

(calcTypeSet)The set of valid inputs for the calculation type field.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Normalization Calculation Type (normalization). A transformation of data to have a mean of zero and a standard deviation of one, commonly used to compare values across different datasets or units.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Predictive Modeling Calculation Type (predictiveModels). A statistical or machine learning approach used to estimate future values or outcomes based on historical data patterns.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Smoothing Calculation Type (smoothing). A technique used to reduce short-term fluctuations in data to better reveal underlying trends or patterns, such as using moving averages or splines.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Standardization Calculation Type (standardization). A method used to scale data to a common range or distribution, often to enable fair comparisons across different variables, time periods, or locations.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Lineage- or Clade-analysis Software Set

(cladeAnSet)Valid category set for lineage or clade analysis software types.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Bayesian Evolutionary Analysis by Sampling Trees (BEAST) Software (beast). A lineage or clade analysis software tool for estimating evolutionary relationships and divergence times in a Bayesian framework.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• ClonalFrameML Software (clonalFrameML). A lineage or clade analysis software tool for reconstructing phylogenetic relationships considering recombination, used in bacterial lineage analysis.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• IQ-TREE Software (iqTree). A lineage or clade analysis software tool for constructing phylogenetic trees with clade support.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• LINEAGE Software (lineage). LINEAGE - Tool for bacterial lineage analysis, often applied to genome sequences in epidemiology.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• mash Software (mash). A lineage or clade analysis software tool for the clustering-based method of lineage and clade analysis, comparing large genomes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• MrBayes Software (mrBayes). A lineage or clade analysis software tool for bayesian inference of phylogeny, used for inferring clade relationships with high accuracy.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Nextstrain Software (nextstrain). A lineage or clade analysis software tool for real-time tracking of pathogen evolution, with tools for clade and lineage analysis.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• OrthoFinder Software (orthoFinder). OrthoFinder - For orthogroup identification and phylogenetic tree building, often useful in evolutionary clade studies.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Pangolin Software (pangolinSoft). A lineage or clade analysis software tool used for lineage assignment in SARS-CoV-2 and other viral genomes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PhyloPhlAn Software (phyloPhIAn). A lineage or clade analysis software tool, specialized in high-resolution phylogenetic analysis, typically used for microbial clade analysis.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PhyloSuite Software (phyloSuite). An integrated platform for sequence alignment, phylogenetic reconstruction, and clade assignment.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PhyML Software (phyML). A lineage or clade analysis software tool that builds phylogenetic trees using maximum likelihood methods, with clade confidence assessments.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• RaxML Software (raxML). A lineage or clade analysis software tool, popular for rapid maximum likelihood-based phylogenetic tree building with clade assignment.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SNAPP Software (snapp). A lineage or clade analysis software tool in BEAST for species delimitation and clade analysis in population genomics.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Statistical Analysis of Metagenomic Profiles (STAMP) Software (stamp). A lineage or clade analysis software tool for analyzing taxonomic profiles and differentiating clades.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• StrainPhlAn Software (strainPhIAb). A lineage or clade analysis software tool within MetaPhlAn for strain-level lineage analysis from metagenomic data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Taxonium Software (taxonium). Taxonium - A scalable tool for viewing and analyzing large phylogenetic trees, including clade annotations.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• TreeTime Software (treeTime). A lineage or clade analysis software tool for phylodynamic analysis, often for molecular clock dating and clade assignment.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Ultrafast Sample placement on Existing tRees (UShER) Software (usher). A lineage or clade analysis software tool that adds new genomes to an existing phylogenetic tree, widely used for SARS-CoV-2 clade assignment.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Collection Approximate Time Period Set

(collAppxSet)The category set of valid inputs for the collGenT attribute field.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Afternoon (aft). Sample was collected in the afternoon, sometime after lunch.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Evening (eve). Sample was collected in the evening, late in the day.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Morning (morn). Sample was collected at some point in the morning, early in the day.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Night (night). Sample was collected at night, between sunset and sunrise.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Sample collection set

(collectSet)Methods for collection samples. Sample collection methods include water, air, and surface. See the attribute Compartment set of the sample collection method.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Area proportional sample (areaPr). An area proportional sample.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Automatic composite sampling (autoComp). A composite sampler which is automated to collect and store multiple wastewater samples across multiple time points.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Automatic sequential sampling (autoSeq). A composite sampler which is automated to collect and combine multiple samples of equal volume taken at a set time interval.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Bag Mediated Filtration (bagFilt). Sample was collected using bag-mediated filtration.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Composite sample - archival (comp). A composite sample, usually generated by an autosampler.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Cone-shaped sampling (cone). Intrument type is a grab sample that has a controlled valve that opens to take a sample from a specific depth, then closes to bring the sample out.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Core sampling (core). Intrument type is a grab sampler that captures a vertical section of the substrate matrix of fecal sludge.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• COSCa ball (cosca). COSCa passive sampling device.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Flow proportional sample (flowPr). A flow proportional composite sample generally collected by an autosampler.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Grab sample (grb). A single large representative grab sample.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Horizontal grab sampling (horGrb). Intrument type is a grab sampler in which the container for the sample is mounted on the end of a rod, which is suitable for collecting discharge from a pipe or truck.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Manual Composite Sample (manComp). Specifies a composite sample where the sub-samples were collected manually.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Moore swab passive sample (moorSw). Moore swab passive sample.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Passive Sample - General (passiveGen). Used to specify a passive sampling method not otherwise specified was used to collect the sample.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Surface swab (surfSw). Surface swab.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Time proportional sample (timePr). A time proportional composite sample generally collected by an autosampler.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Passive (trap) sampling (trap). A composite sampler that passively collects a sample without use of electricity or a battery.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Vacuum sludge sampling (vac). Intrument type is a grab sampler that takes a sample at a designated depth with minimal disturbance to surrounding layers.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Vertical grab sampling (vertGrb). Intrument type is a grab sampler in which the container for the sample is mounted on the end of a rod, which is suitable for collecting waste from a tank.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Volume proportional sample (volPr). A volume proportional sample generally collected by an autosampler.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Consensus Sequence Software Set

(conSeqSoftSet)The valid set of consensus sequencing software categories.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• AliView (aliView). Sequencing software that is a user-friendly alignment editor with consensus sequence options.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Bcftools (bcfTools). Sequencing software that works with SAMtools to call variants and produce consensus sequences from alignments.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• BioEdit (bioEdit). Sequencing software that offers sequence alignment and visualization, used to manually generate consensus sequences.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• BWA (Burrows-Wheeler Aligner) (bwa). BWA (Burrows-Wheeler Aligner). A general-purpose read mapper. A sequencing software that is often used in workflows where generating consensus sequences from mapped reads is required. Includes algorithms like BWA-MEM, optimized for high-quality read mapping. Best for: Whole-genome sequencing (WGS), high-quality alignments.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Clustal Omega (clustalO). Sequencing software that is widely used for multiple sequence alignment and producing consensus sequences.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Emboss Cons (embossCons). Sequencing software that is part of the EMBOSS suite, generates consensus sequences from multiple alignments.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Geneious (geneious). Sequencing software that is popular for sequence assembly, alignment, and consensus sequence generation.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• MAFFT (mafft). Sequencing software that performs multiple sequence alignment, commonly used in consensus sequence generation.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Molecular Evolutionary Genetics Analysis (MEGA) (mega). Sequencing software that provides tools for sequence alignment and consensus sequence extraction.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SAMtools (samTools). Sequencing software that is used with aligned sequence data to generate consensus sequences from BAM files.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SeqMan Pro (Lasergene) (seqManPro). Sequencing software that is for de novo sequence assembly and consensus calling.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SPAdes (spades). Sequencing software that is primarily an assembler, but it can produce contigs that can be used to infer consensus sequences in assemblies.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Ugene (uGene). Sequencing software that offers alignment and consensus sequence generation features.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Control Measure Implementation Value Set

(contMeasImpSet)A set of valid categories for the public health action field, where the action type is ‘control measure implementation’.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Border closure (borderClos). A measure shutting entry points to limit cross-border movement and disease spread.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Stay-at-home order (homeOrder). A directive requiring people to remain at home except for essential activities.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Lockdown (lockdown). Broad restrictions on movement and activities within a region to control disease spread.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Mask mandate (maskMand). A legal requirement for individuals to wear masks in specified settings.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• School closure (schoolClos). Temporary shutdown of educational institutions to prevent disease transmission.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Social distancing measures (socialDist). Policies encouraging or enforcing physical space between individuals in public or private settings.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Data Repository Set

(dataRepoSet)The mma set for all valid input categories for the dataRepo field.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Antibiotic Resistance Genes Database (ARDB) (ardb). An archive for antibiotic resistance genes and associated information.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• BacMet Database (bacMet). Database of antibacterial biocide and metal resistance genes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Comprehensive Antibiotic Resistance Database (CARD) (cardDtbase). Database that provides high-quality reference sequences for resistance genes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• DNA Data Bank of Japan (DDBJ) (ddbj). DNA Data Bank of Japan (DDBJ) archives.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• DDBJ sequence Read Archive (DRA) (dra). The DNA Data Bank of Japan (DDBJ) sequence read archive (DRA).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• European Nucleotide Archive (ENA) (ena). European Nucleotide Archive (ENA).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Enterobase archives (enterobase). Enterobase archives.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• GenBank Archives (genBank). GenBank Archives.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Global Initiative on Sharing All Influenza Data (GISAID) archives (gisaid). Global Initiative on Sharing All Influenza Data (GISAID) archives.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• GitHub (github). GitHub external data storage.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Genome Sequence Archive (GSA) (gsa). Genome Sequence Archive (GSA).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• International Nucleotide Sequence Database Collaboration (INSDC) Archives (insdc). International Nucleotide Sequence Database Collaboration (INSDC) Archives - often includes ENA, NCBI, or DDBJ inputs.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Internal reference (internalRef). Reference an internal (i.e. private) database within the user’s own organization.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• MEGARes database (megares). A comprehensive database of antimicrobial resistance genes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• NCBI’s Pathogen Detection Isolates Browser (ncbiPDIB). Database that tracks AMR in pathogens and provides resistance profiles for pathogens worldwide.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• National Database of Antibiotic Resistant Organisms (NDARO) (ndaro). A database maintained by the USCDC with genomic data on AMR organisms.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Open Science Foundation (OSF) (osf). Open Science Foundation project/data storage.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PATRIC/RAST Database (patricRast). Database that hosts resistance gene annotations within their microbial genome data resources.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• ResFinder Database (resFinderDtbase). nomenclaturre from the National Center for Biotechnology Information
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Sequence Read Archive (SRA) (sra). Sequence Read Archive (SRA).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Zenodo (zenodo). Zenodo open data storage.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Deduplication Method Set

(dedupSet)The valid set of deduplication method categorical inputs.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• bamUtil Dedup (bamUtil). A deduplication method that removes duplicate reads directly from BAM files.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• BWA-MEM with Duplicate Marking (bwaMEM). A deduplication method that is used with SAMtools or Picard to mark duplicates during read mapping.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• BBMap’s Clumpify (clumpify). A deduplication method that groups identical sequences, often used to deduplicate reads efficiently.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• FastUniq (fastUniq). A deduplication method that is specifically designed to remove duplicates in paired-end sequencing data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• MitoZ Deduplication (mitoZ). A deduplication method that is used primarily for mitochondrial genomes but can handle deduplication by read clustering.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Picard MarkDuplicates (picard). A deduplication method within the Picard suite that marks duplicate reads in BAM files based on mapped location.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SAMtools rmdup (samRmdup). A deduplication method that identifies and removes PCR duplicates based on alignment data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SeqKit rmdup (seqKitRmdup). A deduplication method that works within SeqKit for duplicate removal in FASTA/FASTQ files.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Unique Molecular Identifier (UMI) Tagging (umiTag). A deduplication method that adds unique tags to individual DNA fragments, allowing identification and removal of duplicate reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• UMI-tools (umiTools). A deduplication method that is dedicated to deduplicating reads using unique molecular identifiers, especially effective in RNA-seq and single-cell workflows.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Dehosting Method Set

(dehostSet)The valid set of dehosting method categorical inputs.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• BBMap Reformat (bbmapReform). A dehosting software that filters out host sequences by aligning to reference genomes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• BMTagger (bmtagger). A dehosting software developed by NCBI for identifying and removing host sequences based on local alignment.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Bowtie2 (bowtie2). Bowtie2. A general-purpose read mapper. Fast and memory-efficient, commonly used for aligning short reads. Best for: Small genomes, RNA-seq preprocessing. Can also be used as a dehosting software that maps reads against a host reference genome to remove aligned reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Host Subtraction with Bowtie2 & SAMtools (bowtie2XSam). A combined workflow for dehosting where reads mapped to the host are removed from downstream analysis.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• BWA for Host Filtering (bwaHost). A dehosting software that maps reads to a host genome, filtering mapped reads from analysis.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• CLARK (clark). A dehosting software that classifies reads taxonomically, which helps filter out host reads in metagenomic data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• DeconSeq (deconSeq). A dehosting software that is used for dehosting by filtering reads against host reference genomes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• FASTQ Screen (fastqScreen). A dehosting software that checks reads against multiple reference genomes, including host genomes, to remove contamination.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Kraken2 (kraken2). A dehosting software that classifies reads against reference databases, used to filter out host reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• MetaPhlAn Software (metaPhIAn). Software tool that profiles microbial communities and can provide resistance gene insights.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Nucleic Acid Extraction set

(extractSet)set used for storing all the valid category values for the nucleic acid extraction method.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Amicon filter, extract with MP96 (amiMP96). Nucleaic acid extraction, usually used for the liquid fraction of a wastewater sample, using amicon filtration and using an MP96 for final extraction.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Bead beating, extract with MP96 (bbMP96). Nucleaic acid extraction, usually used for solid fraction of a wastewater sample, using bead beating and using an MP96 for final extraction.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Chemagic viral dna/rna 300 kit (chemVir). Nucleic acid extraction performed using the chemagic viral dna/rna 300 kit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• exclusions based sample preparation (ESP) (esp). exclusions based sample preparation (ESP)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• 4s method (extract4s). Nucleic acid extraction performed using the 4s method.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• luminultra wastewater extraction kit (luminWWExtract). luminultra wastewater extraction kit
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• monarch total RNA miniprep kit (new england biolabs) + onestep PCR inhibitor removal kit (zymo) (monarchRNA). monarch total RNA miniprep kit (new england biolabs) + onestep PCR inhibitor removal kit (zymo)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Nuclisens automated magnetic bead extraction kit (nucAuto). Nucleic acid extraction performed using the nuclisens automated magnetic bead extraction kit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• nucleomag (ref. 744220.4) using kingfisher automated instrument (nucKingfish). nucleomag (ref. 744220.4) using kingfisher automated instrument
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Nuclisens manual magnetic bead extraction kit (nucManu). Nucleic acid extraction performed using the nuclisens manual magnetic bead extraction kit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Phenol chloroform (phenCl). Nucleic acid extraction performed using phenol chloroform.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• promega automated tna kit (promAuto). Nucleic acid extraction performed using the promega automated tna kit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• promega ht tna kit (promHt). Nucleic acid extraction performed using the promega ht tna kit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• promega manual tna kit (promManu). Nucleic acid extraction performed using the promega manual tna kit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• promega wastewater large volume tna capture kit (promWW). Nucleic acid extraction performed using the promega wastewater large volume tna capture kit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• qiagen allprep dna/rna kit (qgDNARNA). Nucleic acid extraction performed using the qiagen allprep dna/rna kit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• qiagen ez1 virus mini kit v2.0 (qgEz1). Nucleic acid extraction performed using the qiagen ez1 virus mini kit v2.0.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• qiagen allprep powerfecal dna/rna kit (qgPwrFecal). Nucleic acid extraction performed using the qiagen allprep powerfecal dna/rna kit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• qiagen allprep powerviral dna/rna kit (qgPwrViral). Nucleic acid extraction performed using the qiagen allprep powerviral dna/rna kit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• qiagen powerwater kit (qgPwrWtr). Nucleic acid extraction performed using the qiagen powerwater kit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• qiagen qiaamp buffers with epoch columns (qgQiAmp). Nucleic acid extraction performed using the qiagen qiaamp buffers with epoch columns.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• qiagen rneasy kit (qgRneasy). Nucleic acid extraction performed using the qiagen rneasy kit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• qiagen rneasy powermicrobiome kit (qgRneasyPwr). Nucleic acid extraction performed using the qiagen rneasy powermicrobiome kit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• qiagen allprep dna/rna kit (qiAllprep). qiagen allprep dna/rna kit
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• qiagen qiaamp dsp viral rna mini kit (qiampDSP). qiagen qiaamp dsp viral rna mini kit
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Resuspend COSCa filter collection (resCosca). Nucleic acid extraction via resuspension of a sample collected using the COSCa ball method.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• sciencell viral rna isolation kit (sciencellRNA). sciencell viral rna isolation kit
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• thermo magmax microbiome ultra nucleic acid isolation kit (thermMag). Nucleic acid extraction performed using the thermo magmax microbiome ultra nucleic acid isolation kit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• thermo magmax viral/pathogen nucleic acid isolation kit (thermMagmax). thermo magmax viral/pathogen nucleic acid isolation kit
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• trizol, zymo mag beads w/ zymo clean and concentrator (trizol). Nucleic acid extraction performed using the trizol, zymo mag beads w/ zymo clean and concentrator method.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• trizol, garnet bead beating, alcohol precipitation (trizolEtOH). trizol, garnet bead beating, alcohol precipitation
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• trizol and RNA purification kit (trizolRNA). trizol and RNA purification kit
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• zymo quick-rna viral kit #r1035 (zymo1035). zymo quick-rna viral kit #r1035
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• zymo quick-rna viral 96 kit #r1041 (zymo1041). zymo quick-rna viral 96 kit #r1041
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• zymo environ water rna kit/ zymo environ water rna kit (cat. r2042) (zymoEnv). Nucleic acid extraction performed using the zymo environ water rna kit/ zymo environ water rna kit (cat. r2042).
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• zymo quick-rna fungal/bacterial miniprep #r2014 (zymoQuick). Nucleic acid extraction performed using the zymo quick-rna fungal/bacterial miniprep #r2014 kit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Sample fraction set

(fractionSet)set for the fraction of the sample (solid, liquid, etc.).
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Liquid fraction (liq). Liquid fraction of a sample.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Mixed/homogenized sample (mix). Mixed or homogenized sample or fraction analyzed.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Multiple fraction (mul). Multiple fractions were analyzed separately and aggregated together post-analysis.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Not applicable (NA). The field for which the expected value is not a property of the described object.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Solid fraction (general) (sol). Solid fraction of a sample.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Solid Fraction (Dry) (solDry). Solid fraction of a sample - dry material is analyzed, by drying, baking, etc. of sludge or other solids.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Solid fraction (Wet) (solWet). Solid fraction of a sample - wet material is analyzed, and not dried. Ex. Sludge.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.

Geographic set

(geoTypeSet)set for different type of geographic components.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Sewer Network Health Region (hlthReg). Health region served by the sewer network
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sewer catchment area (swrSet). Sewer catchment area.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Genomic Target Enrichment Methods Set

(gteSet)The set for valid inputs for the Genomic Target Enrichment method.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Hybrid Selection Method (hySel). Selection by hybridization in array or solution for genomic target enrichment.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• rRNA Depletion Method (rnaDepl). Removal of background RNA for the purposes of enriching the genomic target.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Inhibition set

(inhibitionSet)Category set for inhibition methods.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Serial dilution (serialDilution). The serial dilution method for assessing inhibition.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Spike matrix and recovery (spike). The spike matrix and recovery method for assessing inhibition.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Instrument set

(insTypeSet)List of instruments that are used for measures and methods
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Atline Analyzer (aas). Atline analyzer with sampler.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Autosamplers (autoInst). Autosampler instruments, used to automatically collect flow- or time-proportional samples over a period (e.g., ISCO autosamplers).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Fragment analyzers or bioanalyzers (bioanalys). Fragment analyzer or bioanalyzer instruments, used to assess fragment size distribution in libraries.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Centrifuges (centriInst). Centrifuge instruments; separate solids from liquids or concentrate particles.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Digital PCR (dPCR) intruments (dPCRinst). Digital PCR instruments, enables absolute quantification without the need for standard curves (e.g., Bio-Rad QX200).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Temperature and pH probes (enviroInst). Local probe insturments for temperature or pH; allow monitoring of environmental conditions at sites, for example.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Filtration units (filtInst). Filtration instruments; remove large particulates or concentrate targets (e.g., tangential flow filtration).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Flow meters (flowInst). Flow meter instruements; used to measure wastewater flow rates to enable standardization of sample data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Grab samplers (grabInst). Grab sampler instruments; manually collect a single sample at a point in time.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Hand Measurement (hma). Handheld measurement analyzer.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Other instrument (instrumentTypeOther). Type of instrument other than those included in the PHES-ODM.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Library preparation instruments (libPrepInst). Instruments for the preparation of sequencing libraries, e.g., automation platforms like the Illumina NeoPrep.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Magnetic separation racks (magInst). Magnetic separation rack instrument; may be used with magnetic beads for nucleic acid extraction.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Next-Generation Sequencing (NGS) platforms or intruments (ngsInst). Next generation sequencer instruments and platforms.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Lab Analysis (ola). Offline laboratory analysis.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Online Sensor (onse). Online sensor
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• qPCR instruments (quantitative PCR) (qPCRinst). A quantitative PCR instrument, to detect and quantify specific DNA/RNA targets.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• RT-qPCR intruments (rtqPCRinst). Real-time quantitative PCR instruments, used when detecting RNA viruses (an additional a reverse transcription step).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Spectrophotometers or fluorometers (spectroFluoro). Spetrometer and fluorometer instruments; may be used to assess concentration and purity (e.g., NanoDrop™, Qubit™).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Thermal cyclers (thermCyc). A thermal cycler instrument, used to perform temperature-controlled reactions for PCR.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Ultracentrifuges (ultraCentInst). Ultracentrifuge instruments; used for fine-scale separation of particles.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Library Preparation Kit Set

(libraryKitSet)The valid set of categorical values for sequencing library preparation kits.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Accel-NGS 2S Plus DNA Library Kit (accelNGS2Splus). Accel-NGS 2S Plus DNA Library Kit by Swift Biosciences. A library prep kit designed for efficient library prep from fragmented or damaged DNA.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Apollo PrepX Library Preparation Kits (apolloPrepX). Apollo PrepX Library Preparation Kit by Takara Bio. An automated library preparation kit for Illumina sequencing on Apollo systems.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Bioo Scientific NEXTflex Rapid DNA-Seq Kit (biooSci). Bioo Scientific NEXTflex Rapid DNA-Seq Kit by PerkinElmer. A rapid and flexible library prep kit for DNA sequencing on Illumina platforms.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• CleanPlex DNA Library Prep Kit (cleanPlex). CleanPlex DNA Library Prep Kit by Paragon Genomics. A library target enrichment kit optimized for high sensitivity and low input.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Covaris truXTRAC FFPE DNA Library Kit (covarisTruXTRAC). Covaris truXTRAC FFPE DNA Library Kit. A specialized library prep kit for extracting and preparing DNA from FFPE tissue.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Nextera DNA Flex/DNA Prep Library Prep Kit (dnaPrep). Nextera DNA Flex Library Prep Kit, now called DNA Prep, by Illumina. A flexible, transposase-based library prep kit for a wide range of DNA input amounts, suitable for microbial and human DNA.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• EasySeq NGS Targeted Capture Kit (easySeqNGS). EasySeq NGS Targeted Capture Kit by Nimagen. A library preparation kit and targeted capture in one, ideal for small panels.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Illumina DNA Prep with Enrichment (illuminaDNAprep). Illumina DNA Prep with Enrichment by Illumina. A library prep kit that integrates DNA library prep with enrichment for target regions, ideal for targeted sequencing.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• KAPA HyperPrep Kit (kapaHyperPrep). KAPA HyperPrep Kit by Roche. An optimized library prep kit for high-quality libraries from low-input or degraded DNA, commonly used for Illumina platforms.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Ligase-Dependent Library Prep Kits (ligaseDep). Ligase-Dependent Library Prep Kits by Lucigen/Epicentre. A library prep kit suitable for long-read applications and used with Illumina platforms.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• MGIEasy DNA Library Prep Kit (mgiEasy). MGIEasy DNA Library Prep Kit by MGI/BGI. A library prep kit designed for MGI sequencing platforms, offering flexibility in sample input.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• NEBNext Ultra II DNA Library Prep Kit (nebnextUltraII). NEBNext Ultra II DNA Library Prep Kit by New England Biolabs. A high-efficiency library prep kit for low DNA input, ideal for whole-genome and target enrichment.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Nextera XT DNA Library Preparation Kit (nexteraXT). Nextera XT DNA Library Preparation Kit by Illumina. A fast and efficient library prep kit for small genomes and amplicons, uses transposase-based fragmentation.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• QIAseq FX DNA Library Kit (qiaSeqFX). QIAseq FX DNA Library Kit by Qiagen. Alibrary prep kit that uses enzymatic fragmentation, suitable for a variety of applications, including whole-genome sequencing.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SMARTer ThruPLEX Plasma-seq Kit (smarterThruPLEX). SMARTer ThruPLEX Plasma-seq Kit by Takara Bio. A library prep kit optimized for low-input DNA, including cell-free DNA for liquid biopsy studies.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SureSelect XT HS2 DNA Library Preparation Kit (sureSelectXThs2). SureSelect XT HS2 DNA Library Preparation Kit by Agilent. A high-sensitivity library prep kit with target capture capabilities.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Swift 2S Turbo DNA Library Kit (swift2STurbo). Swift 2S Turbo DNA Library Kit by Swift Biosciences. A fast library prep kit workflow with robust performance for low-input DNA.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• ThruPLEX DNA-seq Kit (thruPLEX). ThruPLEX DNA-seq Kit by Takara Bio. A low-input library prep kit with fast, three-step protocol.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• TruSeq DNA PCR-Free Library Prep Kit (truSeqDNA). TruSeq DNA PCR-Free Library Prep Kit by Illumina. A high-quality library prep kit without PCR amplification, reducing bias.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Data license set

(licSet)The set to describe valid categorical values for the licensing fields for measures or datasets.
Status: active. First Released: 2.2.0. Last updated: 2.2.0.

• Academic Free License v3.0 (afl30). The licensing for the measure or data set is managed under the Academic Free License v3.0.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• GNU Affero General Public License v3.0 (agpl30). The licensing for the measure or data set is managed under the GNU Affero General Public License v3.0.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Apache license 2.0 (apache20). The licensing for the measure or data set is managed under the Apache license 2.0.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Artistic license 2.0 (artistic20). The licensing for the measure or data set is managed under the Artistic license 2.0.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• BSD Zero-Clause license (bsd0). The licensing for the measure or data set is managed under the BSD Zero-Clause license.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• BSD 2-clause “Simplified” license (bsd2Clause). The licensing for the measure or data set is managed under the BSD 2-clause “Simplified” license.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• BSD 3-clause “New” or “Revised” license (bsd3Clause). The licensing for the measure or data set is managed under the BSD 3-clause “New” or “Revised” license.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• BSD 3-clause Clear license (bsd3ClauseClear). The licensing for the measure or data set is managed under the BSD 3-clause Clear license.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• BSD 4-clause “Original” or “Old” license (bsd4Clause). The licensing for the measure or data set is managed under the BSD 4-clause “Original” or “Old” license.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Boost Software License 1.0 (bsl10). The licensing for the measure or data set is managed under the Boost Software License 1.0.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Creative Commons Zero v1.0 Universal (cc010). The licensing for the measure or data set is managed under the Creative Commons Zero v1.0 Universal.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Creative Commons Attribution 4.0 (ccby40). The licensing for the measure or data set is managed under the Creative Commons Attribution 4.0.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• CC BY-NC 4.0 license (ccbync40). The licensing for the measure or data set is managed under the Creative Commons 4.0 by-attribution, non-commercial international license.
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• CC BY-NC-SA 4.0 license (ccbyncsa40). The licensing for the measure or data set is managed under the Creative Commons 4.0 by-attribution, non-commercial, and sharealike international license.
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Creative Commons Attribution ShareAlike 4.0 (ccbysa40). The licensing for the measure or data set is managed under the Creative Commons Attribution ShareAlike 4.0.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• CeCILL Free Software License Agreement v2.1 (cecill21). The licensing for the measure or data set is managed under the CeCILL Free Software License Agreement v2.1.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Educational Community License v2.0 (ecl20). The licensing for the measure or data set is managed under the Educational Community License v2.0.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Eclipse Public License 1.0 (epl10). The licensing for the measure or data set is managed under the Eclipse Public License 1.0.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Eclipse Public License 2.0 (epl20). The licensing for the measure or data set is managed under the Eclipse Public License 2.0.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• European Union Public License 1.1 (eupl11). The licensing for the measure or data set is managed under the European Union Public License 1.1.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• European Union Public License 1.2 (eupl12). The licensing for the measure or data set is managed under the European Union Public License 1.2.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• GNU Free Documentation License v1.3 (gfdl13). The licensing for the measure or data set is managed under the GNU Free Documentation License v1.3.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• GNU General Public License v2.0 (gpl20). The licensing for the measure or data set is managed under the GNU General Public License v2.0.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• GNU General Public License v3.0 (gpl30). The licensing for the measure or data set is managed under the GNU General Public License v3.0.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• ISC (isc). The licensing for the measure or data set is managed under the ISC license.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• GNU Lesser General Public License v2.1 (lgpl21). The licensing for the measure or data set is managed under the GNU Lesser General Public License v2.1.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• GNU Lesser General Public License v3.0 (lgpl30). The licensing for the measure or data set is managed under the GNU Lesser General Public License v3.0.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• LaTeX Project Public License v1.3c (lppl13c). The licensing for the measure or data set is managed under the LaTeX Project Public License v1.3c.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• MIT (mit). The licensing for the measure or data set is managed under the MIT license.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• MIT No Attribution (mit0). The licensing for the measure or data set is managed under the MIT no attribution license.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Mozilla Public License 2.0 (mpl20). The licensing for the measure or data set is managed under the Mozilla Public License 2.0.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Microsoft Public License (mspl). The licensing for the measure or data set is managed under the Microsoft Public License.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Mulan Permissive Software License, Version 2 (mulanPSL20). The licensing for the measure or data set is managed under version 2 of the Mulan Permissive Software License.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• University of Illinois/NCSA Open Source License (ncsa). The licensing for the measure or data set is managed under the University of Illinois/NCSA Open Source License.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• SIL Open Font License 1.1 (ofl11). The licensing for the measure or data set is managed under the SIL Open Font License 1.1.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Open license not otherwise described (open). The licensing for the measure or data set is managed under an open license not otherwise described.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Open Software License 3.0 (osl30). The licensing for the measure or data set is managed under the Open Software License 3.0.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• PostgreSQL License (postgreSQL). The licensing for the measure or data set is managed under the PostgreSQL License.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Private data - not for disemination (private). The measure or data set is private data - not for disemination.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• The Unlicense (unlicense). The licensing for the measure or data set is managed under The Unlicense.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• **Do What The F*ck You Want To Public License** (wtfpl). The licensing for the measure or data set is managed under the Do What The F*ck You Want To Public License.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• zLib License (zlib). The licensing for the measure or data set is managed under the zLib License.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.

Sample Material Characteristics Set

(matCharSet)The set for recording the possible valid values for describing the sample material characteristics.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Contamination (contam). The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Fast-flowing (faFlow). A quality of a body of water wherein there is a fast flow.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Fecal-contamination (fecContam). A contamination quality in which fecal matter is a key component of the contamination.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Liquid (liquidMat). Material is liquid, ie. is a state of matter with a definite volume but no fixed shape, adapting to the shape of their container.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Semi-solid (semSol). A state of matter consisting of molecules in a non-rigid structure that can retain its shape and volume but that is not resistant to such change.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Slow-flowing (slFlow). A quality of a body of water wherein there is a slow flow.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Slurry (slur). An quality in which the fluid like material is more viscous due to the suspension of insoluble solid particles.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Solid (solidMat). The state in which a substance has no tendency to flow under moderate stress; resists forces (such as compression) that tend to deform it; and retains a definite size and shape.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Stagnant (stag). A quality of a body of water wherein it has no current or flow.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Treated (treat). A quality which denotes an altered state of an item resulting from purposeful interventions or processes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Untreated (untreat). A quality which denotes an absence of purposeful intervention or processes on an item.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Concentration method set

(methodConcSet)A set a concentration methods.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Aloh3 precipitation (aloh3). Aloh3 precipitation
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Amicon ultrafiltration (amiconUf). Amicon ultrafiltration
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Beef extract flocculation (beeExtractFloc). Beef extract flocculation.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Centricon ultrafiltration (centriconUf). Centricon ultrafiltration.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Ceres nanotrap (ceres). Ceres nanotrap.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Flocculation (floc). The process of aggregating suspended particles into larger clusters (flocs) using coagulants to aid in sedimentation or filtration.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Hollow fiber dead end ultrafiltration (hollowFiberUF). Hollow fiber dead end ultrafiltration
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Innovaprep ultrafiltration (innovaprepUF). Innovaprep ultrafiltration
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Magnetic nanobead binding (magBead). The use of tiny, magnetized beads to selectively capture and isolate biological molecules (e.g., DNA, proteins) in a magnetic field.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• membrane filtration with addition of mgcl3 (memMgCl3). membrane filtration with addition of mgcl3
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Membrane filtration with acidification and mgcl2 (mfAcidmgcl2). Membrane filtration with acidification and mgcl2
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Membrane filtration with acidification and mgcl2, membrane recombined with separated solids (mfAcidmgcl2SS). Membrane filtration with acidification and mgcl2, membrane recombined with separated solids
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Membrane filtration with addition of mgcl2 (mfMgcl2). Membrane filtration with addition of mgcl2
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Membrane filtration with mgcl2 and separated solids (mfMgcl2SS). Membrane filtration with addition of mgcl2, membrane recombined with separated solids
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Membrane filtration with no amendment (mfNoAmend). Membrane filtration with no amendment
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Membrane filtration with no amendment, membrane recombined with separated solids (mfNoAmendSS). Membrane filtration with no amendment, membrane recombined with separated solids
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Membrane filtration with sample acidification (mfSampleAcid). Membrane filtration with sample acidification
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Membrane filtration with sample acidification, membrane recombined with separated solids (mfSampleAcidSS). Membrane filtration with sample acidification, membrane recombined with separated solids
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• No liquid concentration, liquid recombined with separated solids (noliquid). No liquid concentration, liquid recombined with separated solids
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• No Seperation or Concentration (noSep). Denoted that a sample did not undergo a solids separation protocol, or did not undergo a sample concentration protocol.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Polyethyleneglycol (PEG) precipitation (peg). Peg precipitation
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Precipitation (from solution) (prec). The formation of a solid from a dissolved substance in a solution, typically induced by chemical reactions or changes in temperature/pH.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• promega wastewater large volume tna capture kit (promegaLVTNA). promega wastewater large volume tna capture kit
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Skimmed milk flocculation (skimMilkFloc). Skimmed milk flocculation
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Ultracentrifugation (untracent). Ultracentrifugation
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• water concentrating buffer (R2042-1) (watConcBuff). water concentrating buffer (R2042-1)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• zymo environ water rna kit/ zymo environ water rna kit (cat. r2042) (zymoWatRNA). zymo environ water rna kit (cat. r2042)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.

Original Data Format Set

(ogFormSet)The category set for recording the possible original data formats to be recorded in the originalFormat field in the datasets table.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• ENA Format (enaForm). Dataset was originally recorded and/or stored in ENA format.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• NCBI Format (ncbiForm). Dataset was originally recorded and/or stored in NCBI format.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Norman Format (normanForm). Dataset was originally recorded and/or stored in Norman format.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• US-CDC NWSS Format (nwssForm). Dataset was originally recorded and/or stored in the US-CDC’s NWSS format.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Other (or proprietary) Format (otherForm). Dataset was originally recorded and/or stored in a format not otherwise described.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PHA4GE Format (pha4geForm). Dataset was originally recorded and/or stored in PHA4GE format.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PHES-ODM Version 1 Format (phesODMFormV1). Dataset was originally recorded and/or stored in PHES-ODM version 1 format.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PHES-ODM Version 2 Format (phesODMFormV2). Dataset was originally recorded and/or stored in PHES-ODM version 2 format.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PHES-ODM Version 3 Format (phesODMFormV3). Dataset was originally recorded and/or stored in PHES-ODM version 3 format.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• wSphere Format (wSphereForm). Dataset was originally recorded and/or stored in wSphere format.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Organization level set

(orgLevelSet)Categories of organization levels.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Administrative regions (admRegLevel). Administrative regions
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Countries or sovereign states (countryLevel). Countries or sovereign states
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Districts, counties, regions (countyLevel). Districts, counties, regions
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Municipalities or communes (municipalLevel). Municipalities or communes
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Local administrative units or neighborhoods (neighborLevel). Local administrative units or neighborhoods
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Departments, states, or provinces (stateProvLevel). Departments, states, or provinces
  Status: active. First released: 2.0.0. Last updated: 3.0.0.

Organization sector set

(orgSectorSet)Cateogries of organization sectors.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Data collection sector or organization (dataColl). Describes organization who collect compile, analyze, and or manage data as their central focus.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• First Nation (fiNa). Used to categorize a sampleshed that is a First Nation, or on reserve lands.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Health administration or planning agency (healthAdm). Health adminstrative or planning organization.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Laboratory (lab). Laboratory for environmental testing.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Policy and political sector or organization (policy). Describes organizations whose core focus is on policy or political activity.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Public Administration (pubAdm). An organisation type that describes governmental organizations that manage or administer programs.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Public Authority (pubAuth). An organization type describing a public agency with authority over a given domain.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Public health agency (pubHealth). Public health agency.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Research sector or organization (research). Describes organizations whose focus is on research generation.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Utilities sector or organization (utilities). Describes organization that manage or provide utilities services, whether water, gas, heat, etc.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Wastewater Treatment Agency (wta). An organization type that includes those organizations who manage wastewater treatment programs.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Wastewater Treatment Plant Operator (wtpo). An organization type that includes those organizations who run and operate wastewater treatment facilities.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Organization type set

(orgTypeSet)The set for storing organization types.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Academic institution (academ). The category of organization type used for academic institutions or research groups.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Government agency (govt). The category of organization type used for government agencies, programs, or crown-owned bodies.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Private sector (priv). The category of organization type used for private sector or non-profit groups that are not otherwise captured by the academic category.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Sample Origin set

(originSet)The set for storing the valid categorical values of sample origin.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Derived data (derived). Derived data, data that has undergone agregation, standardization, adjustment, or any cleaning prior to reporting.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Field sample (field). Specifies a sample taken from the field; directly collected from an area for testing.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Synthetic sample (synthetic). A synthetic or artificially generated sample.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Outbreak declaration Value Set

(outbreakSet)set for the valid values of the outbreak measure.
Status: active. First Released: 2.0.0. Last updated: 3.0.0.

• End of Outbreak (outbEnd). Indicates an outbreak has ended.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Outbreak - on-going (outbOngoing). Indicates an outbreak is on-going.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Declared outbreak or Outbreak start (outbStart). Indicates an outbreak began.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Public health emergency (outbreak) (phEmerg). Indicates a public health emergency from an outbreak.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

PCR action/activity set

(pcrActSet)The set capturing containing all of the valid methods for the PCR activity cycles.
Status: active. First Released: 2.2.0. Last updated: 2.2.0.

• annealing/extension (anneal). Describes the annealing and/or extension cycle in a PCR process.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• denaturation (denat). Describes the denaturation cycle in a PCR process.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• polymerase activation (pAct). Describes the polymerase activation cycle in a PCR process.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• reverse transcription (rt). Describes the reverse transcription cycle in a PCR process.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.

PCR Method set

(pcrSet)The set capturing containing all of the valid methods for the PCR method.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Digital droplet emulsification PCR (bioRadDdpcr). Describes a PCR analysis done using BioRad’s digital droplet emulsification PCR technology.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Digital Droplet PCR (ddPCR) (ddpcr). Describes a PCR analysis done using digital droplet PCR technology (general).
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Digital PCR (dPCR) (dpcr). Describes a PCR analysis done using digital PCR technology (general).
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Fluidigm digital PCR (fluiDpcr). Describes a PCR analysis done using FluidIGM’s digital PCR technology.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Life technologies digital PCR (ltDpcr). Describes a PCR analysis done using Life Technologies’ digital PCR technology.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• qiagen digital PCR (qgDpcr). Describes a PCR analysis done using Qiagen’s digital PCR technology.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Quantitative Real-Time PCR (qpcr). Real-time PCR, also called ‘quantAggScale’ PCR
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Raindance digital PCR (rainDpcr). Describes a PCR analysis done using Raindance’s digital PCR technology.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Singleplex, probe-based, one-step RT-qPCR (sinProbeOne). Describes a PCR method that is singleplex, probe-based, and one-step RT-qPCR.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.

Public Health Advisory Value Set

(phAdviseSet)A set of valid categories for the public health action field, where the action type is ‘publi health advisory’.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Hand hygiene advisory (handHygAdv). Public guidance promoting handwashing or sanitizing to reduce infection risk.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Mask recommendation (maskRec). Guidance encouraging the public to wear masks to reduce disease transmission.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Quarantine recommendation (quarRec). Advice that individuals exposed to a disease should isolate to prevent spread.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Travel ban (travBa). A restriction prohibiting travel to or from specific locations.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Travel warning (travWa). A notice advising against travel to certain areas due to health risks.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Change to Vaccine Schedule (vaxSched). A public health advisory has been issued to change the vaccination schedule or roll-out a vaccination campaign in response to a threat.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Polygon Relationship Set

(polyRelSet)Value set for polygon relationships.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Child relationship (child). Indicated that this is a sample generated from (an)other sample(s) either because of pooling or sub-sampling.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Co-located relationship (colocated). Second or multiples samples collected at or near (one-half to three feet away) from the same selected sample location to determine local variability of a given analyte. Analytical results from co-located samples can be used to assess site variation, but only in the immediate sampling area. Samples at the same location but using different media (i.e. water and air samples, soil and sediment samples) are also classified as co-located samples.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Neighbouring relationship (neighbour). Locations/polygon are neighbouring eachother.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Overlapping relationship (overlap). Locations/polygon have overlapping portions.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Populated area type set

(popAreaSet)Set of valid values used to describe the type of a populated area.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Rural (rural). Rural populated area type
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Suburban (suburban). Suburban populated area type
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Urban (urban). Urban populated area type
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Population Interval Set

(popIntSet)The collection of categorical inputs for population interval measures.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• <10 people (less10). Fewer than 10 people.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• 10 - 100 people (less100). Between 10 and 100 people.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• 10,000 - 100,000 people (less100k). Between 10,000 and 100,000 people.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• 1,000 - 10,000 people (less10k). Between 1,000 and 10,000 people.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• 100 - 1,000 people (less1k). Between 100 and 1,000 people.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• 100,000 -  1,000,000 people (less1mil). Between 100,000 and 1,000,000 people.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• 1,000,000+ people (more1mil). More than 1,000,000 people.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Population assessment method set

(popMetSet)The set for valid inputs for the population assessment method.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Population census (census). Government or other agency census for determining site/polygon population.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Population count (count). A count of residents for determining site/polygon population.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Review of records (rev). A review of records for determining site/polygon population.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Presampling activity category set

(presampSet)The set of valid input values for reporting pre-sampling activity.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Agricultural activity (agri). Agricultural activity occurred upstream of the sampling site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Healthcare activity (hcAct). Healthcare activity occurred upstream of the sampling site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Animal husbandry (husb). Animal husbandry occurred upstream of the sampling site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Industrial activity (indus). Industrial activity occurred upstream of the sampling site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Wastewater aerobic digestion (wwAerDigest). Wastewater aerobic digestion occurred upstream of the sampling site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Wastewater anaerobic digestion (wwAnaerDigest). Wastewater anaerobic digestion occurred upstream of the sampling site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• wastewater comminution process (wwCominuated). wastewater comminution process occurred upstream of the sampling site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Wastewater sludge removal (wwDesludge). Wastewater sludge removal occurred upstream of the sampling site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Wastewater sludge dewatering (wwDewater). Wastewater sludge dewatering occurred upstream of the sampling site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Wastewater sludge drying (wwDry). Wastewater sludge drying occurred upstream of the sampling site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Wastewater filtration (wwFilt). Wastewater filtration occurred upstream of the sampling site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Wastewater grit removal (wwGrit). Wastewater grit removal occurred upstream of the sampling site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Wastewater microbial treatment (wwMic). Wastewater microbial treatment occurred upstream of the sampling site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Wastewtaer primary sedimentation (wwPriSed). Wastewtaer primary sedimentation occurred upstream of the sampling site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Wastewater screening process (wwScreen). Wastewater screening process occurred upstream of the sampling site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Wastewater secondary sedimentation (wwSecSed). Wastewater secondary sedimentation occurred upstream of the sampling site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Wastewater treatment (wwTrt). Wastewater treatment occurred upstream of the sampling site.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Genetic primer set

(primerSet)The set for genetic primers used in sequencing or PCR assays.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Artic V1 Primer Set (articV1). An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 1.0.0.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Artic V2 Primer Set (articV2). An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 2.0.0.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Use of the articV3 primer (articV3). Initial implementation of an ARTIC bioinformatics platform for nanopore sequencing of nCoV2019 novel coronavirus; Artic Foundation v3 primer.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Use of the articV4 primer (articV4). Artic V4 sequencing primer for VOCs and VOIs.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Artic V4.1 Primer Set (articV41). An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.1.0.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Artic V5 Primer Set (articV500). An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.0.0 which produces amplicons approximately 400bp in length.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Artic V5.1 Primer Set (articV510). An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2with the attributes of version 5.1.0 which produces amplicons approximately 400bp in length.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Artic V5.2 Primer Set, 1200bp (articV520bp1200). An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 1200bp in length.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Artic V5.2 Primer Set, 400bp (articV520bp400). An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 400bp in length.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Artic V5.3.2 Primer Set (articV532). An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.3.2 which produces amplicons approximately 400bp in length.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Bacteroides 16S forward primer (HF183) (ABI) (bact16sABIFor). Bacteroides 16S forward primer (HF183) (ABI)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Bacteroides 16S probe (BacP234) (ABI) (bact16sABIProbe). Bacteroides 16S probe (BacP234) (ABI)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Bacteroides 16S reverse primer (BacR287) (ABI) (bact16sABIRev). Bacteroides 16S reverse primer (BacR287) (ABI)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Sarbeco_E forward primer (IDT) (cdcCovEIDTFor). Sarbeco_E forward primer (IDT)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Sarbeco_E probe (IDT) (cdcCovEIDTProbe). Sarbeco_E probe (IDT)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Sarbeco_E reverse primer (IDT) (cdcCovEIDTRev). Sarbeco_E reverse primer (IDT)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• 2019-nCoV_N1 forward primer (IDT) (cdcCovN1IDTFor). 2019-nCoV_N1 forward primer (IDT)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• 2019-nCoV_N1 probe (IDT) (cdcCovN1IDTProbe). 2019-nCoV_N1 probe (IDT)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• 2019-nCoV_N1 reverse primer (IDT) (cdcCovN1IDTRev). 2019-nCoV_N1 reverse primer (IDT)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• 2019-nCoV_N2 forward primer (IDT) (cdcCovN2IDTFor). 2019-nCoV_N2 forward primer (IDT)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• 2019-nCoV_N2 probe (IDT) (cdcCovN2IDTProbe). 2019-nCoV_N2 probe (IDT)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• 2019-nCoV_N2 reverse primer (IDT) (cdcCovN2IDTRev). 2019-nCoV_N2 reverse primer (IDT)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• 2019-nCoV_N3 forward primer (IDT) (cdcCovN3IDTFor). 2019-nCoV_N3 forward primer (IDT)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• 2019-nCoV_N3 probe (IDT) (cdcCovN3IDTProbe). 2019-nCoV_N3 probe (IDT)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• 2019-nCoV_N3 reverse primer (IDT) (cdcCovN3IDTRev). 2019-nCoV_N3 reverse primer (IDT)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Eden V1 Primer Set (edenV1). An amplicon strategy which was developed by John-Sebastian Eden with primers for SARS-CoV-2 and attributes of version 1.0.0 which produces amplicons approximately 2500bp in length.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Midnight and BC-CDC V1 Primer Set (midnightBCCDCv1). An amplicon strategy which is for SARS-CoV-2 and based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Midnight and BC-CDC V2 Primer Set (midnightBCCDCv2). An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Midnight and BC-CDC V3 Primer Set (midnightBCCDCv3). An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 3.0.0 which produces amplicons approximately 1200bp in length.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Midnight and BC-CDC V4 Primer Set (midnightBCCDCv4). An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 4.0.0 which produces amplicons approximately 1200bp in length.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Midnight scheme V1 Primer Set (midnightV1). An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Midnight scheme V2 Primer Set (midnightV2). An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Midnight scheme V3 Primer Set (midnightV3). An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• New England Biolabs VarSKip V1a Long Primer Set (nebVarSkipV1aLong). An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a long.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• New England Biolabs VarSKip V1a short Primer Set (nebVarSkipV1aShort). An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a short.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• New England Biolabs VarSKip V2a Primer Set (nebVarSkipV2a). An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2a.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• New England Biolabs VarSKip V2b Primer Set (nebVarSkipV2b). An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2b.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PMMV forward primer (ABI) (pmmvABIFor). PMMV forward primer (ABI)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• PMMV probe (ABI) (pmmvABIProbe). PMMV probe (ABI)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• PMMV reverse primer (ABI) (pmmvABIRev). PMMV reverse primer (ABI)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• VSV forward primer (ABI) (vsvABIFor). VSV forward primer (ABI)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• VSV probe (ABI) (vsvABIProbe). VSV probe (ABI)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• VSV reverse primer (ABI) (vsvABIRev). VSV reverse primer (ABI)
  Status: active. First released: 2.2.0. Last updated: 2.2.0.

Protocol Relationships set

(protocolRelSet)set for valid values of relationshipID in the protocolRelationships table. Use only for protocolRelationships table relationshipID.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Is Before (before). Specifies that the object step or protocol occurs before the subject step or protocol in the overall protocol container.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Is concurrent to (concurrent). Specifies that the object step or protocol occurs at the same time as the subject step or protocol in the overall protocol container.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Specifies (specifies). Specifies that the object step or protocol occurs specifies details for the subject step or protocol in the overall protocol container.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Purpose set

(purposeSet)Purpose set for a sample or measure.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Chemical contaminant surveillance (chemSurv). Purpose of sampling/measure is to test for the presence of certain chemicals or chemical contaminants.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Domestic travel hub surveillance (domSurv). A surveillance strategy in which wastewater produced within travel hubs or travel vehicles are monitored, related to domestic travel.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Drug surveillance (drugSurv). Purpose of sampling/measure is to surveil drug use in a population.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Education (education). A measure or sample taken for education or training.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Emergency targetted surveillance program (emergSurv). A targeted surveillance strategy which is considered important and/or urgent.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• International travel hub surveillance (internatSurv). A surveillance strategy in which wastewater produced within travel hubs or travel vehicles are monitored, related to international travel.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Longitudinal, repeat sampling surveillance program (longSurv). A surveillance strategy in which an individual or site is selected to undergo repeat sampling over a defined period of time.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Multiple Purpose (multiple). A measure or sample taken for multiple purposes, not easily captured by the other purpose categories.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Purpose is normalization (norm). The purpose of a measure or sample is for normalization.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Environmental survey or profiling (profil). Purpose of sampling/measure is to record characteristics and profile a given environment.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Provisional report (provisional). A provisional or interm report.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Quality control (qualityControl). A measure or sample taken for the purpose of quality control.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Random sampling surveillance program (randomSurv). A surveillance sampling strategy in which baseline is established at the beginning of a study or project by the selection of sample units via random sampling.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Regular Pathogen Surveillance (regular). A measure or sample taken for surveillance or epidemiology.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Research purposes (researchPurp). Purpose of sampling/measure is for research.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Targeted surveillance program (targetSurv). A surveillance sampling strategy in which an aspired outcome is explicitly stated.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Protocol testing (testing). A measure or sample taken to test a new method. These measures are typically used for internal lab uses and not reported to external partners.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Travel hub surveillance - general (travelSurv). A surveillance strategy in which wastewater produced within travel hubs or travel vehicles are monitored.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Validation study (validationStudy). A meaure or sample taken for a validation study.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Viral passage experiment (viralPass). A research sampling strategy in which samples are selected in order to perform a viral passage experiment.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Wastewater treatment efficiency assessment (wwtpAssess). Purpose of sampling/measure is to assess wastewater treatment efficiency.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Raw Sequence Data Processing Method Set

(rawSeqProcSet)The category set of valid innput values for the software/library/pipeline used to process the raw sequencing data.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• AdapterRemoval (adapterRemoval). A sequencing data processing application that removes adapters and filters reads based on quality and length.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• BayesHammer (from SPAdes) (bayesHammer). A sequencing data processing application that does error correction tool specifically for Illumina reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• BBMap Suite (bbmapSuite). A sequencing data processing application library that includes tools like BBDuk for quality trimming, adapter removal, and quality filtering.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• BWA (Burrows-Wheeler Aligner) (bwa). BWA (Burrows-Wheeler Aligner). A general-purpose read mapper. A sequencing software that is often used in workflows where generating consensus sequences from mapped reads is required. Includes algorithms like BWA-MEM, optimized for high-quality read mapping. Best for: Whole-genome sequencing (WGS), high-quality alignments.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• CD-HIT (cdHIT). A sequencing data processing application that clusters and removes duplicate sequences, useful for dereplication.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Cutadapt (cutadapt). A sequencing data processing application that does adapter removal and trimming tool for high-throughput sequencing data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• DADA2 (dada2). A sequencing data processing application that is primarily used in amplicon sequencing for error correction and generating amplicon sequence variants.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• DeconSeq (deconSeq). A dehosting software that is used for dehosting by filtering reads against host reference genomes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• FASTP (fastp). A sequencing data processing application that combines quality control, adapter trimming, filtering, and error correction.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• FastQC (fastQC). A sequencing data processing quality control tool that provides visual metrics on raw read quality.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• FASTX Toolkit (fastXTools). A sequencing data processing application that provides various functions for FASTQ processing, including quality filtering.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Fqtrim (fqtrim). A sequencing data processing fast tool for adapter removal, quality trimming, and quality control.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• iVar (iVar). A sequencing data processing application that is designed for viral amplicon data, removes primers and can trim low-quality bases.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• KneadData (kneadData). A sequencing data processing pipeline for quality control, including trimming and host decontamination (uses Trimmomatic and Bowtie2).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Minimap2 (minimap2). Minimap2. A general-purpose read mapper, and a sequencing data processing application that is a Fast aligner often used in quality control for host decontamination. A versatile tool for mapping long reads (e.g., PacBio, Nanopore) and short reads. Best for: Large-scale genome or transcriptome assembly.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Porechop (porechop). A sequencing data processing application that is specifically designed for adapter trimming in Oxford Nanopore Technologies data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Prinseq-lite (prinseqLite). A sequencing data processing application that filters sequences based on complexity and removes low-quality reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SAMtools (samTools). Sequencing software that is used with aligned sequence data to generate consensus sequences from BAM files.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• seqtk (seqtk). A lightweight sequencing data toolkit for FASTQ and FASTA manipulation, including trimming and subsampling.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Sickle (sickle). A sequencing data processing application that is a quality-based trimming tool for Illumina data with single-end and paired-end support.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Skewer (skewer). A sequencing data processing application that is a fast tool for adapter trimming and quality trimming in Illumina data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SortMeRNA (sortMeRNA). A sequencing data processing application that is used for ribosomal RNA filtering in metatranscriptomic data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SPAdes (spades). Sequencing software that is primarily an assembler, but it can produce contigs that can be used to infer consensus sequences in assemblies.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Trimmomatic (trimmomatic). A sequencing data processing application that trims adapters and low-quality bases from Illumina sequencing reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• UMI-tools (umiTools). A deduplication method that is dedicated to deduplicating reads using unique molecular identifiers, especially effective in RNA-seq and single-cell workflows.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Sequencing read mapping software set

(readMapperSet)The set of valid input values for the sequence read mapping software.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• BBMap (bbmap). BBMap. A general-purpose read mapper. High-sensitivity aligner for DNA and RNA reads. Best for: Error-prone reads from platforms like Nanopore or PacBio.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• BLASR (Basic Local Alignment with Successive Refinement) (blasr). BLASR (Basic Local Alignment with Successive Refinement). A long-read specific mapper. Optimized for PacBio data. Best for: High-quality long-read alignment.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Bowtie2 (bowtie2). Bowtie2. A general-purpose read mapper. Fast and memory-efficient, commonly used for aligning short reads. Best for: Small genomes, RNA-seq preprocessing. Can also be used as a dehosting software that maps reads against a host reference genome to remove aligned reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• BWA (Burrows-Wheeler Aligner) (bwa). BWA (Burrows-Wheeler Aligner). A general-purpose read mapper. A sequencing software that is often used in workflows where generating consensus sequences from mapped reads is required. Includes algorithms like BWA-MEM, optimized for high-quality read mapping. Best for: Whole-genome sequencing (WGS), high-quality alignments.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Cufflinks (with TopHat integration) (cufflinks). Cufflinks (with TopHat integration). A specialized read mapper. Combines mapping with transcriptome assembly and quantification. Best for: RNA-seq studies with integrated analysis.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• GEM Mapper (gemMapper). GEM Mapper. A specialized read mapper. High-speed and accurate alignment tool for short reads. Best for: Genomic applications with short reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• GMAP (gmap). GMAP. A specialized read mapper. A long-read aligner for genomic mapping.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• GraphMap (graphmap). GraphMap. A long-read specific mapper. Long-read aligner optimized for highly error-prone reads. Best for: De novo assemblies using long-read data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• GSNAP (gsnap). GSNAP. A specialized read mapper. A splice-aware aligner for RNA-seq reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• HISAT2 (hisat2). HISAT2. A general-purpose read mapper. Successor to TopHat, optimized for RNA-seq data with splicing awareness. Best for: Large-scale RNA-seq experiments.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• LAST (Large-Scale Alignment and Search Tool) (last). LAST (Large-Scale Alignment and Search Tool). A long-read specific mapper. Flexible tool for aligning long and error-prone reads. Best for: Comparative genomics with long reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• MapSplice (mapSplice). MapSplice. A specialized read mapper. Designed specifically for spliced alignment of RNA-seq reads. Best for: Transcriptomics with a focus on detecting splice junctions.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Minimap2 (minimap2). Minimap2. A general-purpose read mapper, and a sequencing data processing application that is a Fast aligner often used in quality control for host decontamination. A versatile tool for mapping long reads (e.g., PacBio, Nanopore) and short reads. Best for: Large-scale genome or transcriptome assembly.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• NGMLR (Next-Generation Mapping and Long-Read Alignment) (ngmlr). NGMLR (Next-Generation Mapping and Long-Read Alignment). A long-read specific mapper. Specialized for long-read platforms like PacBio and Nanopore. Best for: Structural variant analysis.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Novoalign (novoalign). Novoalign. A specialized read mapper. Commercial aligner known for high accuracy. Best for: Applications requiring precise alignments.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SMALT (smalt). SMALT. A highly parallelized mapper. High-speed aligner for genomic DNA reads. Best for: Applications requiring flexibility with non-standard parameters.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Snap (snap). Snap. A highly parallelized mapper. Ultrafast, designed for genomic and RNA-seq applications. Best for: Large-scale sequencing projects.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Soap2 (soap2). Soap2. A specialized read mapper. High-throughput short-read mapper. Best for: Alignment of short Illumina reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Soap3 (soap3). Soap3. A specialized read mapper. High-throughput short-read mapper. Best for: Alignment of short Illumina reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• STAR (Spliced Transcripts Alignment to a Reference) (star). STAR (Spliced Transcripts Alignment to a Reference). A general-purpose read mapper. Fast aligner designed for RNA-seq, supports spliced alignment. Best for: Transcriptome data analysis.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Subread (subread). Subread. A general-purpose read mapper. Includes the subread-align algorithm for mapping DNA and RNA reads. Best for: High-throughput data with a balance of speed and accuracy.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• TopHat (tophat). TopHat. A general-purpose read mapper. An older RNA-seq aligner, splicing-aware. Replaced by HISAT2 in most workflows. Best for: Historical RNA-seq studies.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

General Relationship Set

(relSet)set for valid values of relationshipID across all fields and tables.
Status: active. First Released: 2.2.3. Last updated: 2.2.3.

• Is Before (before). Specifies that the object step or protocol occurs before the subject step or protocol in the overall protocol container.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Child relationship (child). Indicated that this is a sample generated from (an)other sample(s) either because of pooling or sub-sampling.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Co-located relationship (colocated). Second or multiples samples collected at or near (one-half to three feet away) from the same selected sample location to determine local variability of a given analyte. Analytical results from co-located samples can be used to assess site variation, but only in the immediate sampling area. Samples at the same location but using different media (i.e. water and air samples, soil and sediment samples) are also classified as co-located samples.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Is concurrent to (concurrent). Specifies that the object step or protocol occurs at the same time as the subject step or protocol in the overall protocol container.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Field sample replicate (fieldReplicate). A sample divided into two or more homogeneous parts.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Laboratory duplicate (labDuplicate). Second (time or more) processing and analysis of sample. Usually for general chemistry or metals analyses.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Laboratory control sample duplicate (lcsd). Known amounts of an analyte or representative compounds are added to a second “clean” matrix (lab water or clean sand) in laboratory. Duplicate of LCS
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Matrix spike duplicate (msd). A known amounts of an analyte or representative compounds are added in the laboratory to a second aliquot of the sample used for matrix spike.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Relationship Not Reported (relNR). A relationship ID used in relationship tables across the ODM when two entities are related or connected in some way, but the actual nature of that relationship is not clear or reported.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Specifies (specifies). Specifies that the object step or protocol occurs specifies details for the subject step or protocol in the overall protocol container.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Replicate Type set

(replicateSet)The set for storing valid categorical values of replicate type.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Biological replicate (bioRep). A biological replicate not otherwise specified - these are parallel measurements of biologically distinct samples that capture random biological variation, which can be a subject of study or a source of noise itself. Biological replicates are important because they address how widely your experimental results can be generalized. They indicate if an experimental effect is sustainable under a different set of biological variables.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Co-located relationship (colocated). Second or multiples samples collected at or near (one-half to three feet away) from the same selected sample location to determine local variability of a given analyte. Analytical results from co-located samples can be used to assess site variation, but only in the immediate sampling area. Samples at the same location but using different media (i.e. water and air samples, soil and sediment samples) are also classified as co-located samples.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Derived sample (derivedSamp). A sample that is derived or made from another sample or material.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Field sample replicate (fieldReplicate). A sample divided into two or more homogeneous parts.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Laboratory duplicate (labDuplicate). Second (time or more) processing and analysis of sample. Usually for general chemistry or metals analyses.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Laboratory control sample duplicate (lcsd). Known amounts of an analyte or representative compounds are added to a second “clean” matrix (lab water or clean sand) in laboratory. Duplicate of LCS
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Matrix spike duplicate (msd). A known amounts of an analyte or representative compounds are added in the laboratory to a second aliquot of the sample used for matrix spike.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• No amplification control (nac). Denotes a no amplification control replicate sample.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Negative experimental control (negCon). A sample or experimental condition where the expected outcome should not occur, intended to check the original sample matrix for contamination, false positives, or unintended effects. An example would be testing for viral RNA or DNA in a sample known to be free of that virus.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• MinusRT (nrt). Denotes a replicate/control sample prepared without reverse transcriptase (RT).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Non-template control (ntc). Denotes a non-template control sample replicate.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• No target present (ntp). Denotes a sample replicate/control with no target present.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Optical calibrator sample (opt). Denotes a sample control or replicate used for optical calibration.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Positive experimental control (posCon). A sample or experimental condition where the expected outcome is known to occur, intended to confirm that the experimental setup is working properly. An example would be a wastewater sample spiked with a known quantity of SARS-CoV-2 virus.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Sampling Event (sampleEvent). In settings where a person goes out and collects multiple samples, but more accurate location data is not recorded, this is used to group samples from that outing, or ‘sampling event’.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Standard sample (std). Denotes a standard sample replicate.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Subsample (General) (subSamp). A general replicate type for a subsample not otherwise defined.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Technical replicate (techRep). A sample that comes from the same biological or environmental source (e.g., the same extracted DNA, the same RNA aliquot, or the same water sample). Helps detect inconsistencies due to pipetting errors, instrument fluctuations, or reagent inconsistencies, rather than biological variation.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Unique sample (unique). A unique sample, not duplicated.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Unknown sample (unkn). Denotes an unknown sample replicate type.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Resuspension method set

(resusSet)The set to describe valid categorical values for the resuspension method.
Status: active. First Released: 2.2.0. Last updated: 2.2.0.

• Elution buffer (elutionBuff). Elution buffer is used to resuspend material.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.

Retained Element Set

(retElSet)The set for enumerating the valid possible values of the retained element method.
Status: active. First Released: 2.2.0. Last updated: 2.2.0.

• Eluate/Resuspended filter material retained (eluate). The eluate fraction, or material resuspended from filtration, is retained after solid separation/centrifugation.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Liquid/Supernatant retained (liquid). The liquid or supernatant is retained after solid separation/centrifugation.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Solids/Pellet retained (solid). The solids or pellet is retained after solid separation/centrifugation.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.

Sample material set

(sampleMatSet)set for the types of material that can be found in a sample.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Air filter (afu). Air filter as part of filtration or circulating unit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Desk or counter (desk). Desk, table, countertop or other flat working surface.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Wastewater Effluent - non-specified (effluNS). Sample material is wastewater effluent - whether primary, secondary or other is unspecified.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Fecal matter (faeces). Fecal matter.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Floor (floor). Floor of a building or room.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Holding tank wastewater (htSam). Wastewater sampled from a holding tank, such as from an airplane or ship
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Water (nww). Non-wastewater, coming from any kind of water body
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Primary clarifier effluent (pEfflu). Effluent obtained after primary clarifiers
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Primary clarifier sludge (pSludge). Sludge produced by primary clarifiers
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Post-grit (pstGrit). Raw wastewater after a treatment plant’s headworks (post grit or removal of large solids at a treatment plant but priort to a primary clarifier)
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Raw sewage at site (rawWW). Wastewater without any form of treatment
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Raw sewage downstream from a site (rawWWdown). Downstream from a site. See partType = rawWWup.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Raw sewage upstream from a site (rawWWup). Upstream from a site. Used when there is not direct access to a site’s wastewater inconjuctiion with downstream sample. For example, if the site is a long-term care home, but ther is not access to the building or property cleanout. Use two sameple, one sample upstream and one sample downstream.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Secondary clarifier effluent (sEfflu). Effluent obtained after secondary clarifiers
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Septic tank wastewater (septage). Wastewater from within a septic tank
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Wastewater Sludge - non-specified (sludgeNS). Sample material is wastewater sludge - whether primary, secondary or other is unspecified.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Secondary clarifier sludge (sSludge). Sludge produced by secondary clarifiers
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Other surface (surface). Surface other than floor or desk.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sewer sediment (swrSed). Sediments obtained in sewer
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Sample relationships set

(sampleRelSet)set for valid values of relationshipID in the sampleRelationships table. Use only for sampleRelationships table relationshipID.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Child relationship (child). Indicated that this is a sample generated from (an)other sample(s) either because of pooling or sub-sampling.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Co-located relationship (colocated). Second or multiples samples collected at or near (one-half to three feet away) from the same selected sample location to determine local variability of a given analyte. Analytical results from co-located samples can be used to assess site variation, but only in the immediate sampling area. Samples at the same location but using different media (i.e. water and air samples, soil and sediment samples) are also classified as co-located samples.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Control sample (control). Denotes a relationship to a primary sample where the object sample serves as a control to the subject sample.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Field sample replicate (fieldReplicate). A sample divided into two or more homogeneous parts.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Laboratory duplicate (labDuplicate). Second (time or more) processing and analysis of sample. Usually for general chemistry or metals analyses.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Laboratory control sample duplicate (lcsd). Known amounts of an analyte or representative compounds are added to a second “clean” matrix (lab water or clean sand) in laboratory. Duplicate of LCS
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Matrix spike duplicate (msd). A known amounts of an analyte or representative compounds are added in the laboratory to a second aliquot of the sample used for matrix spike.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Sequencing script version set

(scriptSet)The set for script versions
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Freyja Script (freyja). Freyja Script for sequencing.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Gromstole 1.0 Script (gromstole). Gromstole 1.0 Script for sequencing.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Sequence Assembly Software Set

(seqAssSet)The valid set of categorical values for sequence assembly software methods.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• ABySS (abyss). A sequencing software that is a scalable de novo assembler for large genomes, designed for distributed computing.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• AllPaths-LG (allpathsLG). A sequencing software that was designed for high-quality assemblies using large, paired-end Illumina data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• ARACHNE (arachne). A sequencing software that is an early assembler optimized for large, complex genomes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Canu (canu). A sequencing software that is a de novo assembler specifically optimized for long-read data from PacBio and Oxford Nanopore.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Celera Assembler (celera). A sequencing software that was initially developed for the Human Genome Project, still used in some workflows for large genomes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• DISCOVAR de novo (discovar). A sequencing software that is an assembler optimized for Illumina data in whole-genome sequencing.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Flye (flye). A sequencing software that is an assembler for long-read data, particularly effective on nanopore sequencing data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• IDBA-UD (idbaUD). A sequencing software that is an iIterative assembler optimized for metagenomics and complex genomic datasets.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Maryland Super Read Celera Assembler (MaSuRCA) (masurca). A sequencing software that is a hybrid assembler that can integrate both short and long reads for high-quality assemblies, and large, complex genomes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• MEGAHIT (megahit). A sequencing software that is a fast and memory-efficient assembler for large metagenomic datasets.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• MetAMOS (metAMOS). A sequencing software that is an automated pipeline for metagenomic assembly and annotation.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Miniasm (miniasm). A sequencing software that is a lightweight assembler for long reads, typically followed by polishing steps.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• NovoPlasty (novoPlasty). A sequencing software that is an assembler tailored for organellar genomes (mitochondrial and chloroplast).
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PEHaplo (pehaplo). A sequencing software that is an assembler that considers heterozygosity in diploid genomes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Platanus (platanus). A sequencing software that is an assembler, optimized for large, diploid genome assemblies, particularly plants.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Redundans (redundans). A sequencing software that is a genome assembler that reduces redundancy, useful for fragmented assemblies.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Shasta (shasta). A sequencing software that is a fast assembler optimized for nanopore long-read data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SOAPdenovo (soapDenovo). A sequencing software that is an assembler for short-read data, suited to large and complex genomes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SPAdes (spades). Sequencing software that is primarily an assembler, but it can produce contigs that can be used to infer consensus sequences in assemblies.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SSAKE (ssake). A sequencing software that is a simple de novo assembler for highly overlapping short reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Trinity (trinity). A sequencing software that is an assembler designed specifically for RNA-seq data, creating transcriptome assemblies.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Unicycler (unicycler). A sequencing software that is a hybrid assembler for bacterial genomes, combining short and long reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Velvet (velvet). A sequencing software that is a de novo assembler optimized for short-read data, often used in microbial genomics.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• WTDBG (aka wtdbg2) (wtdbg2). A sequencing software that is an assembler for long-read data that generates contigs rapidly.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Sequencing Layout set

(seqLaySet)The set for the layout of genetic material used in sequencing
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Mate pair layout (mateLay). Specifies the mate pair layout for a sequencing method.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Paired Layout (pairLay). Specifies the paired layout for a sequencing method
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Single Layout (sinLay). Specifies the single layout for a sequencing method
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Sequencing QC Pipeline Set

(seqQCSet)The category set of valid innput values for the software/library/pipeline used to do quality checks on sequencing or PCR data.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• AfterQC (afterQC). An automated QC pipeline tool for FASTQ data, combining quality assessment and error correction.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Atropos (atropos). A QC pipeline tool for sequencing data that performs adapter trimming and quality filtering with built-in QC reporting.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• BamQC (from Qualimap) (bamQC). A QC pipeline tool for sequencing data that focuses on quality control for mapped data in BAM format, reporting alignment quality.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• BBDuk (from BBTools) (bbduk). A QC pipeline tool for sequencing data that is a part of the BBMap suite, performs filtering and trimming, and generates QC statistics.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Bracken (bracken). A QC pipeline tool for sequencing data and taxonomic profiling that can also be used to identify contamination and assess data quality in metagenomics.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• DecontaMiner (decontaMiner). A QC pipeline tool for sequencing data for contamination detection and removal in NGS datasets, especially useful in clinical samples.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• EAGER (eager). A QC pipeline tool for sequencing data for ancient DNA, providing quality filtering, contamination estimates, and other QC metrics.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• FASTP (fastp). A sequencing data processing application that combines quality control, adapter trimming, filtering, and error correction.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• FastQC (fastQC). A sequencing data processing quality control tool that provides visual metrics on raw read quality.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• FRCbam (frcBam). A QC pipeline tool for sequencing data that assesses read quality and genome assembly quality metrics for high-throughput data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Kraken2 (kraken2). A dehosting software that classifies reads against reference databases, used to filter out host reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• MultiQC (multiQC). A QC pipeline tool for sequencing data that aggregates QC results from multiple sources (e.g., FastQC, SAMtools) into a single report, useful in large pipelines.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• NanoPlot (nanoPlot). A QC pipeline tool for sequencing data that does visualizations for quality assessment of long-read data, particularly from Oxford Nanopore.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• ncov-tools (ncovtools). Tools and plots for perfoming QC on coronavirus sequencing results.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PIQMIe (piqmie). A comprehensive QC and contamination assessment pipeline for metagenomic datasets and sequencing data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PiSeqQC (piSeqQC). A QC pipeline tool for sequencing data for microbiome and metagenomic sequencing data, including quality filtering and contaminant removal.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• preQC (from Meraculous) (preQC). A QC pipeline tool for sequencing data that evaluates data quality before assembly, particularly for large genomes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PRINSEQ (prinseq). A QC pipeline tool for sequencing data for assessing and filtering sequences based on complexity, quality scores, and GC content.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• QC3 (qc3). A comprehensive QC pipeline for NGS sequencing data that provides summary statistics on sequence quality and contamination.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• qProfiler2 (qProfiler2). A QC pipeline tool for sequencing data that produces reports with detailed QC metrics for aligned and unaligned reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SeqKit stats (seqKitStats). Part of SeqKit, a QC pipeline tool for sequencing data that providing a summary of sequence metrics like length, GC content, and quality.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• TrimGalore! (trimGalore). A QC pipeline tool for sequencing data that integrates Cutadapt and FastQC to assess sequence quality and remove adapters in one step.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Sequencing selection method set

(seqSelSet)The set for the selection method used in sequencing
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• PCR Sequencing Selection Method (pcrSeq). Specifies the PCR selection method for sequencing, ie. that a pre-determined primer was used.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Random sequencing selection method (ranSeq). Specifies the random selection method for sequencing
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Sequencing Strategy set

(seqStratSet)The set for the sequencing strategy used for an analysis
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• 16S Ribosomal Gene Sequencing (16rgs). An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Amplicon sequencing (amp). Specifies the amplicon strategy for genetic sequencing
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Whole genome sequencing (wgs). Specifies the whole genome sequencing (WGS) strategy for genetic sequencing
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Whole Metagenome Sequencing (wms). A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Whole Virome Sequencing (wvs). A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Serotyping Method Set

(seroMethSet)The set of categorical inputs for populating the the serotyping method field.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• ARIBA (ariba). ARIBA. Focus: Genotyping, MLST, and serotyping from raw sequencing reads. Applications: Salmonella, Escherichia coli, Klebsiella pneumoniae, and more. Features: Works with custom databases for serotyping and resistance gene identification.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• BIGSdb (Bacterial Isolate Genome Sequence Database) (bigsdb). BIGSdb (Bacterial Isolate Genome Sequence Database). A flexible platform that supports serotyping alongside sequence typing and other typing schemes. Can be customized for various bacterial species, including Neisseria meningitidis.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• CapsuleFinder (capFin). CapsuleFinder Used for typing capsular polysaccharides in a variety of bacteria, especially Escherichia coli and Klebsiella species.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• ChewBBACA (chewBBACA). ChewBBACA. Focus: Core genome MLST (cgMLST) with optional serotyping analysis. Applications: Broad-spectrum bacterial pathogens. Features: Efficient with large datasets and highly customizable.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• ClermonTyping (clermonTyp). ClermonTyping. Focus: MLST and phylogenetic typing for Escherichia coli. Applications: Ideal for epidemiological studies. Features: Combines MLST and phylogroup-specific information.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• CTFinder (ctFinder). CTFinder. Designed for Clostridioides difficile serotyping and subtyping. Identifies capsular polysaccharide synthesis gene clusters to assign serogroups.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Enterobase archives (enterobase). Enterobase archives.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• FastMLST (fastMLST). FastMLST. Focus: Lightweight MLST and serotyping from assembled genomes or raw reads. Applications: Broad bacterial species. Features: Quick and simple, designed for routine use.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• GenoTyphi (genoTyphi). GenoTyphi. Focus: Specific MLST and serotyping for Salmonella Typhi. Applications: Outbreak investigations and epidemiology. Features: Highly specialized for typhoidal Salmonella.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Kaptive (kaptive). Kaptive. Identifies capsular (K) serotypes in Klebsiella pneumoniae and related species using whole-genome sequence data. Useful for studying capsule diversity and epidemiology.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Kraken2 (kraken2). A dehosting software that classifies reads against reference databases, used to filter out host reads.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• MLST (Center for Genomic Epidemiology) (mlst). MLST (Center for Genomic Epidemiology). Focus: Classical MLST and optional serotype determination. Applications: Compatible with curated schemes for various pathogens. Features: Web-based and command-line versions available.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Mykrobe (mykrobe). Mykrobe. Focus: Rapid detection of resistance, MLST, and serotyping. Applications: Mycobacterium tuberculosis and other pathogens. Features: Fast processing and species-specific database compatibility.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Pathogenwatch (pathogenwatch). Pathogenwatch. Focus: Integrates MLST, serotyping, and resistance typing with a user-friendly interface. Applications: Primarily used for Salmonella and Escherichia coli. Features: Combines typing results with interactive visualization.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PBPfinder (pbfinder). PBPfinder. Used for typing and serotyping of Streptococcus pneumoniae through analysis of penicillin-binding proteins and capsular genes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PGAP (Prokaryotic Genome Annotation Pipeline) (pgap). PGAP (Prokaryotic Genome Annotation Pipeline). Focus: Annotation pipeline that integrates MLST and antigen typing. Applications: Broad bacterial pathogens. Features: Provided by NCBI, designed for high-throughput workflows.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Phandango (phandango). Phandango. A visualization tool that integrates serotype predictions with phylogenetic analyses for population studies. Often used alongside other serotyping tools.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Prokka (with serotyping integration) (prokka). Prokka (with serotyping integration) While primarily an annotation tool, Prokka outputs can be paired with databases for identifying serotypes of certain bacterial pathogens.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Prokka + Roary Pipeline (Nextflow) (prokkaRoary). Prokka + Roary Pipeline. Focus: Genome annotation (Prokka) with MLST and serotyping integration via Roary. Applications: Broad compatibility with bacterial pathogens. Features: Facilitates core-genome MLST and accessory gene analysis.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• PubMLST (pubMLST). PubMLST. Focus: Web-based platform for MLST and serotyping analyses. Applications: Neisseria, Campylobacter, Salmonella, and more. Features: Combines curated databases with user-uploaded sequences.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SalmonellaTypeFinder (salTypeFin). SalmonellaTypeFinder A specialized tool for predicting Salmonella serotypes based on genomic data, similar to SeqSero.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SeqSero2 (seqSero2). SeqSero2. Specifically designed for Salmonella serotyping using raw sequence reads, assemblies, or even complete genomes. Provides results based on antigenic formulas or serotype names.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SeqTyping (seqTyping). SeqTyping. Focus: Simultaneous MLST and serotyping for Escherichia coli and Salmonella. Applications: Integrated with bacterial genome typing databases. Features: Compatible with short-read sequencing data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SerotypeFinder (serotypeFin). SerotypeFinder. A web-based tool that predicts serotypes for Escherichia coli and other bacteria by detecting genes encoding O-antigens and H-antigens. Developed by the Center for Genomic Epidemiology.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Salmonella In Silico Typing Resource (SISTR) (sistr). Salmonella In Silico Typing Resource (SISTR). Used for in silico serotyping of Salmonella enterica based on whole-genome sequencing. Combines genomic data with the traditional White-Kauffmann-Le Minor serotyping scheme.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• SRST2 Software (srst2). Software tool for analyzing antimicrobial resistance using short read sequences.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Streptococcus Serotyping Tool (SSI) (SSI). Streptococcus Serotyping Tool (SSI) A web-based platform for serotyping Streptococcus pneumoniae based on capsular polysaccharide synthesis loci.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Statistical Analysis of Metagenomic Profiles (STAMP) Software (stamp). A lineage or clade analysis software tool for analyzing taxonomic profiles and differentiating clades.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Traditional Serotyping methods (tradSero). Traditional Serotyping methods used for serotyping.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Severity set

(sevSet)A set for severity indicators.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• High severity (high). Indicates a very sever quality issue, likely meaning the data should not be reported.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Low severity (low). A marker for low severity
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Mid-level severity (mid). A marker for med-level severity, where there are some concerns.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Sampleshed set

(shedSet)The set for all valid values of sampleshed.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Airplane (airpln). Airplane sample shed category type
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Airport (airport). Airport sample shed category type
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Bus (bus). A large motor vehicle carrying passengers by road, typically one serving the public on a fixed route and for a fare.
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Bus Station (busStat). A terminal where buses arrive and depart.
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Long-term acute care hospital (ccc). Acute care hospitals, or complex contuing care, that provide care for patients with average length of stay longer than 25 days.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Child day care (cdc). Child day care facility.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Clinic (clinic). A medical clinic, may be used to provide treatment, remedial work, and/or instruction.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Commercial facility - not specified (commFacOth). Specifies a site type which is a commercial facility/worksite that is not otherwise captured or described in the geotype set.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Correctional facility (corFcil). Correctional facility
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Higher education domitory or residential building (dorm). Higher education domitory or residential building
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Educational facility (edFac). A school or other educational facility not otherwise specified.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Farm (farm). An aggricultural area, builing, or tract of land. Used for the cultivation of crops or grazing of livestock, including any buildings.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• First Nation (fiNa). Used to categorize a sampleshed that is a First Nation, or on reserve lands.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Healthcare facility (hcf). A building for the provision of healthcare, not otherwise specified.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Hospital (hosptl). Hospital
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Industrial plant (indPl). A factory not otherwise specified - A building or collection of buildings used for manufacturing, building, producing or storing goods, and occaisonally services, and making them into products.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Land-based Transit Hub (landTH). A transport hub is a place where passengers and cargo are exchanged between land-based vehicles and/or between land-based transport modes.
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Long-term care facility (ltcf). A residential healthcare facility that provides 24-medical care. These are also called skilled nursing facilities.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Long-term care - assisted living or retirement home (ltcfAl). A residential facility that provides assistance with daily care but generally does not provide skilled nursing care.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Other long-term care (ltcfO). Other residential facilities that provide daily and/or medical care, but are not defined as nursing home/skilled nursing facilities or assisted living facilities.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Shopping mall (mall). A large commercial complex with multiple retail stores, services, and restaurants.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Meat processing plant (meatPl). A processing plant for slaughtering, processing, packaging, labelling, handling, and storing of food animal carcasses, parts of carcasses, and meat products.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Municipality (municp). A complete municipality, this specifies an entire metropolitan area, either a city, town, etc.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Neighbourhood (neigh). A municipal neighbourhood, this specifies a sub-section of a larger municipality.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Office (office). A workplace where administrative, managerial, or clerical tasks are performed.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Other residential building (orb). Individual residential buildings or institutions not captured in other categories
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Pharmaceutical manufacturing plant (pharmPl). An industrial building in which pharamceutical drugs are synthesised and processed on an industrial scale.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Port or Harbour (port). A harbor is any sheltered body of water where boats or ships may moor or anchor. A port is an installation that has been built around a harbor with facilities for loading and unloading such vessels.
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Refugee camp (refCamp). A temporary, often makeshift shelter for persons displaced by war, political oppression, or for religious beliefs.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Restaurant (restaurant). A commercial establishment that prepares and serves food and beverages to customers.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Road (road). A paved or unpaved pathway designed for vehicular and pedestrian travel.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Roadside (roadside). The area adjacent to a road, including sidewalks, shoulders, or drainage ditches.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• School (school). A school serving students in the kindergarten to 12th grade range
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Ship (ship). A cruise ship or other ship.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Social services shelter (sss). Other type of social services shelter
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Airport terminal (terminal). Airport terminal sample shed category type
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Transport hub - General (tHub). A tansport hub not otherwise specified. i.e. a place where passengers and cargo are exchanged between vehicles or/and between transport modes.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Train (train). A series of railroad cars moved as a unit by a locomotive or by integral motors.
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Transportation vehicle - general (transp). A vehicle, i.e. a mobile machine, transporting people or cargo, of a type not otherwise specified.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Train Station (trStat). A place on a railroad line where trains regularly stop so that passengers can get on or off.
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• University campus (uCampus). Universityor college campus - comprising an entire campus or part of a campus.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Water-based Transit Hub (waterTH). A transport hub is a place where passengers and cargo are exchanged between water-based vehicles and/or between water-based transport modes.
  Status: active. First released: 2.2.3. Last updated: 2.2.3.

Site Level Category Set

(siteLevelSet)The category set containing all valid entries for the siteLevel field.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• A-Tier Region-level Aggregation at Site (aRegLevel). Specifies that a sewershed/site represents an entire region - where region here is an “A-Tier” region and refers to large, dense urban areas made up of multiple overlapping cities/boroughs. This would be a greater metropolitan area.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• B-Tier Region-level Aggregation at Site (bRegLevel). Specifies that a sewershed/site represents an entire region - where region here is an “B-Tier” region, and thus a region within a greater metropolitan area and larger than a single municipality, but smaller than the entire metropolitan area.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Country-level Aggregation at Site (countLevel). Specifies that a sewershed/site represents an entire nation or country.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• First Nation Territory/Métis Settlement-level Aggregation at Site (fnmiLevel). Specifies that a sewershed/site represents the entirety of a First Nations territory or reservation, or a Métis settlement.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Municipality-level Aggregation at Site (muniLevel). Specifies that a sewershed/site represents an entire municipality.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Neighbourhood-level Aggregation at Site (neighLevel). Specifies that a sewershed/site represents an entire neighbourhood, or a zone within a municipaility.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Province-level Aggregation at Site (provLevel). Specifies that a sewershed/site represents a sub-national state, province, or region.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Site set

(siteTypeSet)set for the type of sampling site.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Aeration tank (aerTank). A chamber in wastewater treatment where air is introduced to promote microbial breakdown of organic pollutants.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Bar screen (barScreen). A bar screen is a mechanical device used to remove large solid debris from wastewater or sewage as it enters a treatment plant. It consists of a series of parallel bars or rods, spaced at specific intervals, that allow water to pass through while capturing larger objects. This process prevents damage to downstream equipment and ensures efficient treatment. Bar screens are typically installed at the inlet of wastewater treatment facilities and can be cleaned manually or mechanically, depending on the design and operational requirements.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Body of water (bow). An outdoor accumuation of water either on the surface or beneath the ground, no other additional details specified.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Branch sewer pipleline (bSwrPpl). Specifies a site type that is collection pipe that run lateral to other municpal sewer lines, allowing drainage into the main sewer.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Building cleanout (buildCO). Specifies a site type that is a capped pipe that connects to a building’s main sewer line.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Canal (canal). Artificial watercourse with no flow or a controlled flow used for navigation, drainage or irrigation.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Cesspit (cesspit). Cesspit, cesspool and soak pit in some contexts are terms with various meanings: they are used to describe either an underground holding tank (sealed at the bottom) or a soak pit (not sealed at the bottom). A cesspit can be used for the temporary collection and storage of feces, excreta, or fecal sludge as part of an on-site sanitation system and has some similarities with septic tanks or with soak pits.
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Communitor (communitor). A mechanical device that grinds large solid waste in wastewater into smaller particles to prevent clogging.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Composting toilet (compToi). A self-contained toilet system wherein human waste is designed to be composted. Usually with the addition of secondary materials, like sawdust.
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Sewer (drain) (drain). A pipe that carries water or sewage away from a place, or an opening in a surface that leads to said pipe.
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Estuary, natural water body (estuary). Estuary, natural water body
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Grit chamber (gritCham). A sedimentation basin in wastewater treatment that removes heavy, inorganic particles (e.g., sand, gravel) before biological treatment.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Ground water (grWa). Underground water which is located in pore spaces found in rock or unconsolidated deposits such as soil, clay, or gravel.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Holding tank (htSite). Holding tank
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Influent pump station (infPump). A facility that lifts and transports raw wastewater from collection systems to treatment plants.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Lagoon system (lagoon). Lagoon system for extensive wastewater treatment
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Lake, natural water body (lake). Lake, natural water body
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Latrine (latrine). A toilet or outhouse, especially a communal one in a camp or barracks.
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Major sewer pipeline (mSwrPpl). Major sewer pipeline
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Ocean, natural water body (ocean). Ocean, natural water body
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Odour Control Unit (ocu). Odour Control Unit ventilation extends the life of a sewer by reducing the amount of maintenance the pipeline needs, making management of the network much more efficient. The filters used in the Odour Control Unit and ventilation stacks absorb gases such as hydrogen sulphide, which is a common source of odours from sewerage systems.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Surface water (opWa). An outdoor accumuation of water either on the surface of the earth, no other additional details specified.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Plumbing drain (pluDra). An artificial channel which transports unwanted water or waste liquids away from their source, either to a more useful area, a receptacle, or into sewers or stormwater mains as waste discharge to be released or processed.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Primary clarifer (primClar). A large settling tank that removes solids and floating materials from wastewater before secondary treatment.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Pumping station (pStat). Pumping station
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Reservoir (res). An artificial body of water, often contained by a dam, constructed for the purpose of water storage.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Retention pond (retPond). Retention pond
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• River, natural water body (river). River, natural water body
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sludge dryer (sDryer). A facility or equipment used to reduce moisture content in wastewater sludge for easier handling and disposal.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Sea, natural water body (sea). Sea, natural water body
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Secondary clarifer (secClar). A tank in wastewater treatment that removes biological solids (e.g., microbial flocs) after aeration.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Septic tank (septTnk). Septic tank
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Spring (spr). A surface landform which provides an egress for groundwater or steam to flow out of the ground.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Stabilization pond (stabPnd). Specifies a site type which is a pond designed and built for wastewater treatment to reduce the organic content and remove pathogens from wastewater.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Stream (str). A watercourse which is linear and flows across the solid portion of a planetary surface.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Sewage truck (swgTrck). Sewage truck
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Wastewater Triturator (triturator). The location where wastewater transportation vehicles unload wastewater.
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Upstream sites (upstream). A general site type for upstream wastewater sampling sites.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Well (well). A cylindrical hole, pit, or tunnel drilled or dug down to a depth from which water, oil, or gas can be pumped or brought to the surface.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Wastewater treatment plant (wwtp). A general site type for wastewater treatment plants.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Back-up wastewater treatment site (wwtpBack). Indicates a wastewater treatment plant where multiple labs are or were sampling, and where secondary samples are being taken taken.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Industrial wastewater treatment plant (wwtpInd). Industrial wastewater treatment plant
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Municipal wastewater treatment plant for combined sewage (wwtpMuC). Municipal wastewater treatment plant for combined sewage
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Municipal wastewater treatment plant for sanitary sewage only (wwtpMuS). Municipal wastewater treatment plant for sanitary sewage only
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Solid separation set

(solidSeparationSet)set for the separation of solids.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Centrifugation (cent). Describes solid separation from a wastewater sample via centrifugation. Likely connected to other method steps prior to analysis.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Filtration (filt). Describes solid separation from a wastewater sample via filtration. Proceeds further concentration or analysis of the liquid filtrate.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Gravity settling (graSet). Describes solid separation from a wastewater sample where the sample material is allowed to settle by gravity, and then separated.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• No Seperation or Concentration (noSep). Denoted that a sample did not undergo a solids separation protocol, or did not undergo a sample concentration protocol.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.

Spike material set

(spikeMatSet)set for spikeMat (aterial into which the recovery efficiency control target is spiked).
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Clarified sample (clari). Clarified sample.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Dewatered solids (deso). Dewatered solids.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Lysis buffer (lysi). Lysis buffer.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Raw wastewater (raws). Raw wastes water sample
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Raw post-pasteurized wastewater (rppw). Raw wastewater sample post-pasteurization
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sample concentrate (samConc). Sample concentrate.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Recovery efficiency spike target set

(spikeTargetSet)The set capturing containing all of the valid categories for the recovery efficiency control (or spike) target.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• bcov culture spike target (bcovCul). Cultured bovine coronavirus is used as the recovery efficiency control target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• bcov spike target (unspecified) (bcovGen). The bovine coronavirus (unspecified) is used as the recovery efficiency control target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• bcov vaccine spike target (bcovVac). The bovine coronavirus vaccine is used as the recovery efficiency control target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• brsv culture spike target (brsvCul). Cultured bovine respiratory syncytial virus (BRSV) is used as the recovery efficiency control target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• brsv vaccine spike target (brsvVac). The bovine respiratory syncytial virus (BRSV) vaccine is used as the recovery efficiency control target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Heat inactivated sars-cov-2 virus spike target (heatInacSARS). Heat inactivated SARS-CoV-2 virus is used as the recovery efficiency control target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• hep g armored rna spike target (hepGRnaMat). Hepatitis G armored RNA is used as the recovery efficiency control target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• murine hepatitis virus (MHV) spike target (mhvSpike). Murine hepatitis virus is used as the recovery efficiency control target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• ms2 coliphage spike target (ms2ColMat). ms2 coliphage is used as the recovery efficiency control target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• murine coronavirus spike target (muCoMat). Murine coronavirus is used as the recovery efficiency control target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• oc43 spike target (oc43Mat). Human coronavirus OC43 is used as the recovery efficiency control target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Parapoxvirus Orf Virus Spike Target (parapoxSpike). parapoxvirus // Orf virus is used as the recovery efficiency control target.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• phi6 spike target (phi6Mat). Pseudomonas virus phi6is used as the recovery efficiency control target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Puro virus spike target (puroMat). Puro Virus is used as the recovery efficiency control target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Vesicular stomatitis virus (VSV) target (vsv). Vesicular stomatitis virus is used as the recovery efficiency control target.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Status set

(statusSet)A set for partID = Status to indicate whether a part is in current use or not.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Active (active). Indicator that a part is in current use.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Depreciated (depreciated). Indicator to say that a part is no longer in current use in the model. See partID = status
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Development (development). Indicator that a part is under development use. See partID = status
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Standard Curve Calculation Set

(stdCurveSet)The set capturing containing all of the valid methods for the PCR standard curve calculations.
Status: active. First Released: 2.2.0. Last updated: 2.2.0.

• serial dillution (serDil). Describes a serial dilution process for standard curve generation for PCR.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.

Sample Storage Medium Set

(stoMedSet)The set of valid categorical inputs for the stoMed field.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Amies Transport Medium (atm). A buffer solution/medium that maintains viability of bacteria in wastewater and environmental samples during transport.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Buffered Peptone Water (bpw). A buffer solution/medium used for bacterial enrichment, can also serve as a temporary preservative.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Cary-Blair Transport Medium (cbtm). A buffer solution/medium commonly used for bacterial preservation in stool and wastewater samples.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• DNA/RNA Shield (dnaRNAshield). A stabilizing solution for nucleic acids in samples, including wastewater, protecting against degradation at room temperature.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• 10% Glycerol Solution (glycerol10). 10% Glycerol Solution - Common cryoprotectant for bacterial and viral storage in environmental samples.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Guanidine Thiocyanate (gt). A buffer solution/medium that serves as a strong preservative for viral RNA, commonly used in molecular biology for RNA preservation.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Hank’s Balanced Salt Solution (HBSS) (hbss). Hank’s Balanced Salt Solution (HBSS) - Nutrient-rich buffer that maintains cell and microbial integrity in samples.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Lactated Ringer’s Solution (lrs). A buffer solution/medium sometimes used in combination with other preservatives to stabilize microbial samples.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• No sample storage medium used (none). No sample storage medium used
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Phosphate Buffered Saline (PBS) (pbs). An isotonic solution for general sample preservation, used when immediate freezing is available.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Peptone Water with Glycerol (pwWg). A buffer solution/medium used in environmental sampling, especially for preserving microorganisms.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• RNAlater (rnaLater). A buffer solution/medium the stabilizes RNA and DNA in samples, effective for preserving nucleic acids in wastewater.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Sterile Distilled Water with Sodium Thiosulfate (sDWwST). Sterile Distilled Water with Sodium Thiosulfate - Used to neutralize chlorine for microbiological analysis in wastewater samples.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Skim Milk–Glycerol Medium (smgm). A buffer solution/medium that protects bacteria in environmental samples, preventing freeze-thaw damage.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Sucrose Phosphate Glutamate (SPG) Buffer (spg). A buffer solution/medium that stabilizes viruses, including in wastewater samples, by preventing RNA degradation.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Sodium Thiosulfate Solution (sts). A buffer solution/medium that neutralizes residual chlorine in wastewater samples, ensuring microbial viability.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• TE Buffer (Tris-EDTA) (trisEDTA). A buffer solution/medium that preserves DNA stability in environmental samples.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Tryptic Soy Broth (TSB) (tsb). Tryptic Soy Broth (TSB) - A nutrient-rich medium for bacterial survival, sometimes used for short-term storage.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Universal Transport Medium (UTM) (utm). Universal Transport Medium (UTM) - Used for microbial preservation in various environmental samples, including wastewater.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Viral Transport Medium (VTM) (vtm). A buffer solution/medium the preserves viral samples during transport, commonly used for wastewater viral studies.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Surveillance Alert Value Set

(survAlertSet)A set of valid categories for the public health action field, where the action type is ‘surveillance alert’.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Decreased surveillance (decSurv). Scaling back of monitoring activities, often due to reduced risk.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Increased surveillance (incSurv). Intensified efforts to monitor disease trends or case counts.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Routine surveillance (routSurv). Standard, ongoing collection of public health data.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Targetted surveillance initiated (targSurv). Monitoring focused on a specific population, location, or risk factor.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Surveillance Level Set

(survLevelSet)The list of valid categories for the survLevel measure.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Building-level Surveillance (builLev). Surveillance is done only at the level of a single building.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Community-level Surveillance (communitLev). Surveillance is done at the level of an entire community.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Institution-level Surveillance (instituLev). Surveillance is done at the level of an entire insitution.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Multi-Community-level Surveillance (multiComLev). The scope of the surveillance covers multiple communities.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Table column set

(tableSet)The set for valid inputs in table columns. These categories are used in the parts list for columns named after tables to indicate the position and function of a given part in the entity relationship diagram of the data model.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Composite Key (cK). Composite key for a table.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Foreign key (fK). Foreign key for a table.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Header (header). Header for a table. Also known as a table variable or entiy relationship ‘attribute’.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Input (input). Input for a table. Indicates if a part can be used in a table.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Primary key (pK). Primary key for a table.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Template Set

(tempSet)The organizing set for templates.
Status: active. First Released: 2.2.0. Last updated: 2.2.0.

• DNA Template (dna). Deoxyribonucleic Acid (DNA) template is used for PCR or sequencing work.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• RNA Template (rna). Ribonucleic Acid (RNA) template is used for PCR or sequencing work.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Threat designation Value Set

(threatDesSet)A set of valid categories for the public health action field, where the action type is ‘threat designation’.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• De-escalated variant (dev). A given microbial threat has been de-escalated; a de-escalated variant - different institutions may use different criteria for assigning this threat level.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Variant of concern (voc). A given microbial threat has been deemed a variant of concern - different institutions may use different criteria for assigning this threat level.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Variant of interest (voi). A given microbial threat has been deemed a variant of interest - different institutions may use different criteria for assigning this threat level.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• variant under monitoring (vum). A given microbial threat has been deemed a variant under monitoring - different institutions may use different criteria for assigning this threat level.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Value treatment value set

(valTreatSet)Valid set of values for the value treatment set.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Derived data (derived). Derived data, data that has undergone agregation, standardization, adjustment, or any cleaning prior to reporting.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Estimated data (estimate). Estimated data, data that should be understood to be an estimation, possiblynot taken directly from sample measures.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Predicted data (predicted). Predicted data, data generated by predictove models or algorithims, not taken directly from sample measures.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Raw data (raw). Raw data, without adjustment or additional treatment.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Weather set

(weathSet)A set of the valid qualitative categories for the qualitative weather measure.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Cloudy (cloudy). Qualitative category for the weather measure, specifying an overcast day with no rain.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Foggy (foggy). Qualitative category for the weather measure, specifying a foggy or hazy day.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• No rain (noRain). Qualitative category for the weather measure, specifying no rainfall for a given day.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Rainy (rainy). Qualitative category for the weather measure, specifying a rainy day.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Snowy (snowy). Qualitative category for the weather measure, specifying a snowy day.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Stormy Weather (stormy). Stormy weather
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Sunny (sunny). Qualitative category for the weather measure, specifying a clear and sunny day.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Fraction set for wide names

(wideFractionSet)Fraction set for wide names. For wide names.
Status: active. First Released: 2.2.0. Last updated: 2.2.0.

• See Header for Fraction Analyzed (hFr). An indicator in wide-names to show that information on the fraction analyzed in found under a separate header.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Liquid fraction (liq). Liquid fraction of a sample.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Mixed/homogenized sample (mix). Mixed or homogenized sample or fraction analyzed.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Multiple fraction (mul). Multiple fractions were analyzed separately and aggregated together post-analysis.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Not applicable (NA). The field for which the expected value is not a property of the described object.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Not reported (nr). A value could have been recorded, however, it was not.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Solid fraction (general) (sol). Solid fraction of a sample.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Solid Fraction (Dry) (solDry). Solid fraction of a sample - dry material is analyzed, by drying, baking, etc. of sludge or other solids.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Solid fraction (Wet) (solWet). Solid fraction of a sample - wet material is analyzed, and not dried. Ex. Sludge.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.

Nomenclatures

(nomenclatures). A classification system to report the measure class. See partID = nomenclatureID.

• International Classification of Diseases (icd). Classification system for diseases in humans.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Nomenclature not applicable (naNomenclature). Not applicable.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Nomenclaturre from the NCBI (ncbiNom). Nomenclaturre from the National Center for Biotechnology Information
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• NextClade nomenclature (nextclade). Specifies variant or genetic nomenclature as set out by NextClade.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Pangolin nomenclature (pangolin). Specifies variant or genetic nomenclature as set out by the Phylogenetic Assignment of Named Global Outbreak Lineages (Pangolin).
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• WHO nomenclature (who). Specifies variant or genetic nomenclature as set out by the World Health Organization.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Quality indicators

(qualityIndicators). A measure of the quality of a reported value or sample. Only used for the dictionary entries of parts.

• Sequence Amplification Artifacts (ampliArtifact). Sequence amplification artifacts detected.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Below LOD (beLOD). Measure is below the limit of detection (LOD) for a specific analyte.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Measured levels below LOQ (belowLOQ). Indicates that a measurement detected the analyte, but at levels below the limit of quantification (LOQ).
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Delayed Arrival or Prolonged Transit (delayArriv). A substantial delay (ie. of more than 14 days) between sample collection and the start of analysis.
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Experiment Failed (expFail). PCR experiment failed. No value reported.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• AI - Inhibition present but addressed (flagAI). The original sample was inhibited; however, the inhibition has been addressed through dilution. The reported concentration estimate is the updated result after addressing inhibition.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• B - Trace levels of contamination (flagB). Analytical result may be subject to “trace” levels of contamination; the target analyte was also detected in negative controls on the same run as the sample.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• FI - Inhibition present and unaddressed (flagFI). The original sample was inhibited; however, the inhibition has not been successfully addressed. Therefore, no concentration estimate has been reported.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• J - Weak signal extrapolation (flagJ). Analytical result falls below the lowest concentration of the experiment-specific standard curve but above the y-intercept value; the reported value is based on the extrapolation of the standard curve in the non-linear region.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ND - Non-detect (flagND). No amplification occurred in the reaction; non-detect.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• UJ - Trace signal extrapolation (flagUJ). Observed quantitation cycle is greater than the experiment-specific standard curve intercept value but evidence of clear amplification was present (i.e., “trace” signal observed); the reported value is based on the extrapolation of the standard curve in the non-linear region.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• UQ - Unquantifiable (flagUQ). Unquantifiable, Ct value exceeds the maximum value of the standard curve. There was a detect, but we cannot quantify it with certainty.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sample frozen (frozen). Sample was frozen before analysis or processing
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Low Average Genome Coverage (lAGC). Average coverage of the genome is low/poor.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Low breadth of coverage (lBC). The percentage of the genome covered by reads (the breadth) is low.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Low depth of coverage (lDC). Poor coverage, specifically an insufficient number of reads or too many sequencing reads that are mapped incorrectly.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Leaked sample (leaked). Sample leaked, some volume and material was lost.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Low Coverage of Characteristic Mutations (lowCovMut). Low coverage of characteristic mutations.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Low-quality Sequence (lowQualSeq). Low-quality sequence.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Low Signal-to-Noise Ratio (lowSNRatio). Low signal-to-noise ratio.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Low-volume sample (lowVol). Sample is low-volume, but was run regardless.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Low Percent of Genome Captured (lPGC). Only captured a small/low percentage of the genome.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Multiple issues (mI). Multiple issues have arisen in the sequencing process.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• No quality concerns (noConcern). A flag to indicate there is are no quality concern about the measure or sample.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sample not labelled (noLabel). Sample had no label
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sample missing time stamp (noTime). Sample is missing the autosampler time; incomplete metadata on collection.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• NTC Amplification Detected (ntcAmp). Quality flag for when the non-template control (NTC) still sees amplification - ie. The NTCs in qPCR show a Ct value less than 40, or NTCs in a ddPCR have 3 or more positive droplets.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Control-plate Flag - NTCs (ntcFlag). quality indicator for when there is observed amplicifation in the non-template controls (NTCs) of a PCR reaction.
  Status: depreciated. First released: 2.0.0. Last updated: 3.0.0.
• Value out of range (oor). Value is outside of the allowable range for quality control.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Value is an outlier (out). Value is an outlier and may be of questionable quality.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Quality concerns (qf1). A flag to indicate there is a quality concern, not otherwise sepcified.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sparse coverage (sC). Sequencing shows sparse coverage, ie. numerical breadth of coverage shows as adequate but coverage plots reveal missing genome pieces.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sequence Contaminated (seqContam). Sequence is contaminated.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Read Lengths Shorter Than Expected (shortRead). Read lengths are shorter than expected.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Sample spilled (spill). Sample contents spilled from container.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Wide 95% interval (wI). The 95% interval is too wide, low confidence in results.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sample stored incorrectly (wrongStorage). Sample was stored inappropriately.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sample stored at wrong temperature (wrongTemp). Sample was stored at an inappropriate temperature.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Quality indicator sets

(qualityIndSets). Sets of quality indicators or measures. For example, PCR have a quality measure set.

Generic quality flag set

(genQualitySet)A quality set to specify any generic quality concerns about a measure or sample.
Status: active. First Released: 1.0.0. Last updated: 2.0.0.

• Multiple issues (mI). Multiple issues have arisen in the sequencing process.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• No quality concerns (noConcern). A flag to indicate there is are no quality concern about the measure or sample.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Quality concerns (qf1). A flag to indicate there is a quality concern, not otherwise sepcified.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Measures quality set

(measQualitySet)A quality set for any measure, includes all the quality flag options for any measure. Used as an “any quality set” for measures, but excludes the sample quality flags to avoid confusion and data entry errors.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Below LOD (beLOD). Measure is below the limit of detection (LOD) for a specific analyte.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Measured levels below LOQ (belowLOQ). Indicates that a measurement detected the analyte, but at levels below the limit of quantification (LOQ).
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Delayed Arrival or Prolonged Transit (delayArriv). A substantial delay (ie. of more than 14 days) between sample collection and the start of analysis.
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Experiment Failed (expFail). PCR experiment failed. No value reported.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• AI - Inhibition present but addressed (flagAI). The original sample was inhibited; however, the inhibition has been addressed through dilution. The reported concentration estimate is the updated result after addressing inhibition.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• B - Trace levels of contamination (flagB). Analytical result may be subject to “trace” levels of contamination; the target analyte was also detected in negative controls on the same run as the sample.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• FI - Inhibition present and unaddressed (flagFI). The original sample was inhibited; however, the inhibition has not been successfully addressed. Therefore, no concentration estimate has been reported.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• J - Weak signal extrapolation (flagJ). Analytical result falls below the lowest concentration of the experiment-specific standard curve but above the y-intercept value; the reported value is based on the extrapolation of the standard curve in the non-linear region.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ND - Non-detect (flagND). No amplification occurred in the reaction; non-detect.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• UJ - Trace signal extrapolation (flagUJ). Observed quantitation cycle is greater than the experiment-specific standard curve intercept value but evidence of clear amplification was present (i.e., “trace” signal observed); the reported value is based on the extrapolation of the standard curve in the non-linear region.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• UQ - Unquantifiable (flagUQ). Unquantifiable, Ct value exceeds the maximum value of the standard curve. There was a detect, but we cannot quantify it with certainty.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Low breadth of coverage (lBC). The percentage of the genome covered by reads (the breadth) is low.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Low depth of coverage (lDC). Poor coverage, specifically an insufficient number of reads or too many sequencing reads that are mapped incorrectly.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Multiple issues (mI). Multiple issues have arisen in the sequencing process.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• No quality concerns (noConcern). A flag to indicate there is are no quality concern about the measure or sample.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sample missing time stamp (noTime). Sample is missing the autosampler time; incomplete metadata on collection.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• NTC Amplification Detected (ntcAmp). Quality flag for when the non-template control (NTC) still sees amplification - ie. The NTCs in qPCR show a Ct value less than 40, or NTCs in a ddPCR have 3 or more positive droplets.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Value out of range (oor). Value is outside of the allowable range for quality control.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Value is an outlier (out). Value is an outlier and may be of questionable quality.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Quality concerns (qf1). A flag to indicate there is a quality concern, not otherwise sepcified.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sparse coverage (sC). Sequencing shows sparse coverage, ie. numerical breadth of coverage shows as adequate but coverage plots reveal missing genome pieces.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Wide 95% interval (wI). The 95% interval is too wide, low confidence in results.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

PCR quality set

(pcrQualitySet)Quality set for PCR measures.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Below LOD (beLOD). Measure is below the limit of detection (LOD) for a specific analyte.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Measured levels below LOQ (belowLOQ). Indicates that a measurement detected the analyte, but at levels below the limit of quantification (LOQ).
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Experiment Failed (expFail). PCR experiment failed. No value reported.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• AI - Inhibition present but addressed (flagAI). The original sample was inhibited; however, the inhibition has been addressed through dilution. The reported concentration estimate is the updated result after addressing inhibition.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• B - Trace levels of contamination (flagB). Analytical result may be subject to “trace” levels of contamination; the target analyte was also detected in negative controls on the same run as the sample.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• FI - Inhibition present and unaddressed (flagFI). The original sample was inhibited; however, the inhibition has not been successfully addressed. Therefore, no concentration estimate has been reported.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• J - Weak signal extrapolation (flagJ). Analytical result falls below the lowest concentration of the experiment-specific standard curve but above the y-intercept value; the reported value is based on the extrapolation of the standard curve in the non-linear region.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• ND - Non-detect (flagND). No amplification occurred in the reaction; non-detect.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• UJ - Trace signal extrapolation (flagUJ). Observed quantitation cycle is greater than the experiment-specific standard curve intercept value but evidence of clear amplification was present (i.e., “trace” signal observed); the reported value is based on the extrapolation of the standard curve in the non-linear region.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• UQ - Unquantifiable (flagUQ). Unquantifiable, Ct value exceeds the maximum value of the standard curve. There was a detect, but we cannot quantify it with certainty.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• No quality concerns (noConcern). A flag to indicate there is are no quality concern about the measure or sample.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• NTC Amplification Detected (ntcAmp). Quality flag for when the non-template control (NTC) still sees amplification - ie. The NTCs in qPCR show a Ct value less than 40, or NTCs in a ddPCR have 3 or more positive droplets.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Value out of range (oor). Value is outside of the allowable range for quality control.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Value is an outlier (out). Value is an outlier and may be of questionable quality.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Sample quality set

(sampleQualitySet)Quality set for a sample.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Delayed Arrival or Prolonged Transit (delayArriv). A substantial delay (ie. of more than 14 days) between sample collection and the start of analysis.
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Sample frozen (frozen). Sample was frozen before analysis or processing
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Leaked sample (leaked). Sample leaked, some volume and material was lost.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Low-volume sample (lowVol). Sample is low-volume, but was run regardless.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• No quality concerns (noConcern). A flag to indicate there is are no quality concern about the measure or sample.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sample not labelled (noLabel). Sample had no label
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sample missing time stamp (noTime). Sample is missing the autosampler time; incomplete metadata on collection.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sample spilled (spill). Sample contents spilled from container.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sample stored incorrectly (wrongStorage). Sample was stored inappropriately.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sample stored at wrong temperature (wrongTemp). Sample was stored at an inappropriate temperature.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Sequencing quality set

(seqQualitySet)Quality set for sequencing measures
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Sequence Amplification Artifacts (ampliArtifact). Sequence amplification artifacts detected.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Below LOD (beLOD). Measure is below the limit of detection (LOD) for a specific analyte.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Measured levels below LOQ (belowLOQ). Indicates that a measurement detected the analyte, but at levels below the limit of quantification (LOQ).
  Status: active. First released: 2.2.3. Last updated: 2.2.3.
• Experiment Failed (expFail). PCR experiment failed. No value reported.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Low Average Genome Coverage (lAGC). Average coverage of the genome is low/poor.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Low breadth of coverage (lBC). The percentage of the genome covered by reads (the breadth) is low.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Low depth of coverage (lDC). Poor coverage, specifically an insufficient number of reads or too many sequencing reads that are mapped incorrectly.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Low Coverage of Characteristic Mutations (lowCovMut). Low coverage of characteristic mutations.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Low-quality Sequence (lowQualSeq). Low-quality sequence.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Low Signal-to-Noise Ratio (lowSNRatio). Low signal-to-noise ratio.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Low Percent of Genome Captured (lPGC). Only captured a small/low percentage of the genome.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• No quality concerns (noConcern). A flag to indicate there is are no quality concern about the measure or sample.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sample missing time stamp (noTime). Sample is missing the autosampler time; incomplete metadata on collection.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• NTC Amplification Detected (ntcAmp). Quality flag for when the non-template control (NTC) still sees amplification - ie. The NTCs in qPCR show a Ct value less than 40, or NTCs in a ddPCR have 3 or more positive droplets.
  Status: active. First released: 2.0.0. Last updated: 3.0.0.
• Value out of range (oor). Value is outside of the allowable range for quality control.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Value is an outlier (out). Value is an outlier and may be of questionable quality.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sparse coverage (sC). Sequencing shows sparse coverage, ie. numerical breadth of coverage shows as adequate but coverage plots reveal missing genome pieces.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sequence Contaminated (seqContam). Sequence is contaminated.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Read Lengths Shorter Than Expected (shortRead). Read lengths are shorter than expected.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Wide 95% interval (wI). The 95% interval is too wide, low confidence in results.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Shorthand or Short Name Set Type

(shortSets). Sets used to group together short names for tables or part types in ODM.

Short Name Set

(shrtNameSet)The abbreviated short name used to reference the The table that contains information about addresses. Addresses can recorded for sites, organizations or contacts (indivduals).
Status: active. First Released: 2.2.2. Last updated: 2.2.2.

• Accessions report table Shorthand (ac). The abbreviated short name used to reference the report table for accessions and accessionIDs.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Address table Shorthand (ad). The abbreviated short name used to reference the The table that contains information about addresses. Addresses can recorded for sites, organizations or contacts (indivduals).
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Calculations Table Short Name (cl). The abbreviated short name used to reference the table for recording data on data treatments and calculations applied to measurements and reported values.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Contact table Shorthand (co). The abbreviated short name used to reference the The table that contains information about a contact; a person who is the contact of a site or laboratory.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Countries look-up tables Shorthand (cu). The abbreviated short name used to reference the Look up table for the possible country inputs.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Dataset table Shorthand (ds). The abbreviated short name used to reference the report table for capturing details about data’s parental data set and data custodians. Supplying attribution for data collectors.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Instrument table Shorthand (in). The abbreviated short name used to reference the The table that contains information about instruments.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Language Look-up table Shorthand (la). The abbreviated short name used to reference the Look up table for all languages, used to give structure to the translation table.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Measures Part-type Shorthand (mes). The abbreviated short name used to reference the The attribute to describe a part type of measures. All measures have partType = “measurements”.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Methods part-type Shorthand (met). The abbreviated short name used to reference the Procedures or steps for collecting samples or performing measures.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Measure report table Shorthand (mr). The abbreviated short name used to reference the The table that contains information and details about a given measure
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Measure set report table Shorthand (ms). The abbreviated short name used to reference the The table that identifies sets of measures.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Organization table Shorthand (or). The abbreviated short name used to reference the The table that contains information about a laboratory.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Parts Look-up table Shorthand (pa). The abbreviated short name used to reference the Look up table containing all parts in of the data model.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Public Health Actions Report Table Shortname (pha). The abbreviated short name used to reference the table for recording information on public health actions.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Polygon table Shorthand (po). The abbreviated short name used to reference the The table that contains information about the geometry of a geographic area.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Polygon Relationships Table Short Name (por). The abbreviated short name used to reference the table for recording the relationships between polygons.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Protocol relationships table Shorthand (pr). The abbreviated short name used to reference the The table that contains the organizational information and details (such as order) about a given protocol, recorded as a series of protocol steps (protocolSteps).
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Protocols table Shorthand (pro). The abbreviated short name used to reference the the table that contains the summary information and details about a given protocol.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Protocol steps table Shorthand (ps). The abbreviated short name used to reference the The table for collecting metadata on individual steps in a protocol, methodological process, or assay.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Quality reports table Shorthand (qr). The abbreviated short name used to reference the The table for recording the various quality metrics and indicators for samples and measures.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Sample relationships table Shorthand (sar). The abbreviated short name used to reference the Table for recording the relationships between samples.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Sample report table Shorthand (sas). The abbreviated short name used to reference the The table that contains information about a sample. A sample is defined as a representative volume of wastewater (or other forms of water or liquid), air, or surface area taken from a site.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Sets look-up table Shorthand (se). The abbreviated short name used to reference the Look up table for all sets, managing how categorical inputs for various methods and attributes are grouped together.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Sites table Shorthand (si). The abbreviated short name used to reference the The table that contains information about a site; the location where an environmental sample was taken.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Translation look-up table Shorthand (tr). The abbreviated short name used to reference the Look up table for translations of the description, label, and instruction for all parts.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Wide name table Shorthand (wn). The abbreviated short name used to reference the The table for wide names.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.
• Zones look-up table Shorthand (zo). The abbreviated short name used to reference the Look up table for the possible sub-national region or zone inputs.
  Status: active. First released: 2.2.2. Last updated: 2.2.2.

Specimens

(specimens). Measures or observations are taken from three types of substances: populations (humans or geographic areas), samples, sites. See partID = specimentID.

• See Header for Specimen (hSp). An indicator to show in a wide-name that specimen information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Specimen not applicable (naSpecimen). Non applicable specimen.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Polygon (poly). A measure made on a compartment or property within a polygon.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Population (pop). An measure or observation for a geographic area or population.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sample (sa). A measure made on a compartment or property from a sample of a substance.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Site (sit). A measure made on a compartment or property at a site.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Specimen sets

(specimenSets). Sets of specimens. Specimen sets are used when a measure or attribute can be recorded for more than one specimen.

Any specimen set

(anySpecimenSet)A specimen set that inculdes any specimen.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Polygon (poly). A measure made on a compartment or property within a polygon.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Population (pop). An measure or observation for a geographic area or population.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sample (sa). A measure made on a compartment or property from a sample of a substance.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Site (sit). A measure made on a compartment or property at a site.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Specimen set not applicable

(naSpecimenSet)A specimen set for when specimen/specimen set is not applicable. Use ‘not applicable’ when there is no specimen/set for the part
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Specimen not applicable (naSpecimen). Non applicable specimen.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Polygon or site specimen set

(polySiSpecimenSet)A specimen set that inculdes polygon or site specimen.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Polygon (poly). A measure made on a compartment or property within a polygon.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Site (sit). A measure made on a compartment or property at a site.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Polygon specimen set

(polySpecimenSet)A specimen set that inculdes only a polygon specimen.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Polygon (poly). A measure made on a compartment or property within a polygon.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Population or polygon specimen set

(poPolySpecimenSet)A specimen set that inculdes population or polygon specimen.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Polygon (poly). A measure made on a compartment or property within a polygon.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Population (pop). An measure or observation for a geographic area or population.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Population or sample set

(poSaSpecimenSet)A specimen set that inculdes population or sample specimen.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Population (pop). An measure or observation for a geographic area or population.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sample (sa). A measure made on a compartment or property from a sample of a substance.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Population or site set

(poSiSpecimenSet)A specimen set that inculdes population or site specimen.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Population (pop). An measure or observation for a geographic area or population.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Site (sit). A measure made on a compartment or property at a site.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Population specimen set

(poSpecimenSet)A specimen set that inculdes only a population specimen.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Population (pop). An measure or observation for a geographic area or population.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Sample specimen set

(saSpecimenSet)A specimen set that inculdes only a sample specimen.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Sample (sa). A measure made on a compartment or property from a sample of a substance.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Site or sample specimen set

(siSaSpecimenSet)A specimen set that inculdes site or sample specimen.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Sample (sa). A measure made on a compartment or property from a sample of a substance.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Site (sit). A measure made on a compartment or property at a site.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Site specimen set

(siSpecimenSet)A specimen set that inculdes only a site specimen.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Site (sit). A measure made on a compartment or property at a site.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Speciment set for wide names

(wideSpecimenSet)Speciment set for wide names. For wide names.
Status: active. First Released: 2.2.0. Last updated: 2.2.0.

• See Header for Specimen (hSp). An indicator to show in a wide-name that specimen information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Specimen not applicable (naSpecimen). Non applicable specimen.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Polygon (poly). A measure made on a compartment or property within a polygon.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Population (pop). An measure or observation for a geographic area or population.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sample (sa). A measure made on a compartment or property from a sample of a substance.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Site (sit). A measure made on a compartment or property at a site.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Tables

(tables). Tables are where measures, methods and attributes are recorded. Tables represent the main entities of the environmental surveillance. An example of a table is site a collection of attributes such as site name and address to describe where environment samples are taken. PHES-ODM has report tables, but users can create their own tables as well.

• accessions Table (accessions). Table for recording accession IDs for external data, namely sequences in large sequencing databases and repositories. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Address table (addresses). The table that contains information about addresses. Addresses can recorded for sites, organizations or contacts (indivduals). The Sites, Organizations, and Contacts tables include a link to the addresses table through Address ID. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Calculations Table (calculations). Table for recording data on data treatments and calculations applied to measurements and reported values.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Contact table (contacts). The table that contains information about a contact; a person who is the contact of a site or laboratory. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Countries look-up tables (countries). Look up table for the possible country inputs. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.
• Dataset table (datasets). A report table for capturing details about data’s parental data set and data custodians. Supplying attribution for data collectors. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Instrument table (instruments). The table that contains information about instruments. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Language Look-up table (languages). Look up table for all languages, used to give structure to the translation table. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Measure report table (measures). The table that contains information and details about a given measure. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Measure set report table (measureSets). The table that identifies sets of measures. Examples of measure sets include a set of replicates, dilutions (used to generate a Ct curve) or varients that are identified in a single sample. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Organization table (organizations). The table that contains information about a laboratory. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Parts Look-up table (parts). Look up table containing all parts in of the data model. Contains all parts, including self-referential parts. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Public Health Actions Report Table (phActions). Table for recording information on public health actions. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Polygon Relationships Table (polygonRelationships). Table for recording the relationships between polygons. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.3.0. Last updated: 2.3.0.
• Polygon table (polygons). The table that contains information about the geometry of a geographic area. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Protocol relationships table (protocolRelationships). The table that contains the organizational information and details (such as order) about a given protocol, recorded as a series of protocol steps (protocolSteps). Protocols are a group of related protocol steps. For example a protocol step can describe a sample concentration, extraction, inhibition or a measurement. Protocols can include both methodID (a proceedure) and measureIDs (a measure). An example of a method is centrifugation; where the centriguation rotation speed is described as a measure. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Protocols table (protocols). The table for protocols. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Protocol steps table (protocolSteps). The table for collecting metadata on individual steps in a protocol, methodological process, or assay. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Quality reports table (qualityReports). The table for recording the various quality metrics and indicators for samples and measures. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Reporter table depreciated (reportersDep). The table that contains information about a reporter of a sample, method, measure, or attribute. The short name for the table (partID) can be found in the instructions field.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• Sample relationships table (sampleRelationships). Table for recording the relationships between samples.Samples can be pooled or split. The sample relationships table holds information on parent-child relationships between samples, and allow for tracking sample lineage for single and pooled samples. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sample report table (samples). The table that contains information about a sample. A sample is defined as a representative volume of wastewater (or other forms of water or liquid), air, or surface area taken from a site.Samples can be combined, split, stored and reused. The Sample relationships (sampleRelationships) is used to describe the relationships between samples. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sets look-up table (sets). Look up table for all sets, managing how categorical inputs for various methods and attributes are grouped together. This table manages many-to-many relationships and category recycling within the ODM. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Sites table (sites). The table that contains information about a site; the location where an environmental sample was taken. The site of an eviromental sample. Information in the site table does not regularly change. Consider using the MeasureReport table if the infomation changes often. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Translation look-up table (translations). Look up table for translations of the description, label, and instruction for all parts. The default language if a translation is not specified is English. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Wide name table (wideNames). The table for wide names. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Zones look-up table (zones). Look up table for the possible sub-national region or zone inputs. The short name for the table (partID) can be found in the instructions field.
  Status: active. First released: 2.1.0. Last updated: 2.1.0.

Units

(units). The unit of the measurement. Every measurement must have a unit. Meaning, units are a mandatory field whenever a measurement is recorded.

• Number of active cases (acti). Number of active cases.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Number of active cases by Onset date (actiCaseOn). Number of active cases by onset date.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Number of active cases by episode date (actiEp). Number of active cases by episode date.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Number of active cases by Report date (actiRep). Number of active cases by report date.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Number of active cases by test date (actiTest). Number of active cases by test date.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Breadth of coverage (>=5x depth) (boc). The percentage of the reference genome covered by the sequenced data, to a prescribed read depth greater or equal to 5.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Base-pairs (bps). A base pair (bp) is a unit of measurement in molecular biology that represents a pair of complementary nucleotides in DNA or RNA. The length of DNA sequences is often measured in base pairs.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Episode date of confirmed cases (caseEpDate). Episode date is the earliest of onset, test or reported date for a confirmed case.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Onset date of confirmed cases (caseOnDate). Earliest that symptoms were reported for a confirmed case. This data is often not known and reported. In lieu, episode is used.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Report date of confirmed cases (caseRepDate). Date that the numbers were reported publicly for a confirmed case. Typically, reported data and this measure is most commonly reported and used.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Test date of confirmed cases (caseTestDate). Date that the covid-19 test was performed for a confirmed case.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Degrees Celcius (cel). Degrees Celsius.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Colony Forming Units (cfu). Colony forming units
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• CFU per 100 ml (cfu100). Colony forming units per 100 ml of filtered sample.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Colony forming units per grams total solids (cfugTS). colony forming units per grams total solids (CFU/gTS)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Colony forming units per milliliter (cfumL). colony forming units per milliliter (CFU/mL)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Centimetres (cm). Unit part for the SI unit of centimetres.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Number of confirmed cases (conf). Number of confirmed cases.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Number of confirmed cases by episode date (confEp). Number of confirmed cases of a given disease, totaled by episode date.
  Status: active. First released: 1.0.0. Last updated: 2.2.0.
• Number of confirmed Cases Onset date (confOn). Number of confirmed cases of a given disease, totaled by onset date.
  Status: active. First released: 1.0.0. Last updated: 2.2.0.
• Number of confirmed cases by report date (confRep). Number of confirmed cases of a given disease, totaled by report date.
  Status: active. First released: 1.0.0. Last updated: 2.2.0.
• Number of confirmed cases test date (confTest). Number of confirmed cases of a given disease, totaled by test date.
  Status: active. First released: 1.0.0. Last updated: 2.2.0.
• Gene copies per well (cpWell). Gene or variant copies per well.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Cycle threshold or quantification cycle (Ct or Cq) (ct). Cycle thresholds in a PCR assay.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Cycle threshold per quantification cycle (ctcq). cycle threshold (Ct) / quantification cycle (Cq)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Days (days). A unit for indicating a length of time in days.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Deaths (death). Units for describing a population measure of patients who have died from a given cause.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Detected (det). Substance detected or not detected.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Depth of coverage (doc). The average number of reads representing a given nucleotide in the reconstructed sequence, provided as a value as a fold of coverage.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Efficiency (efficient). The efficiency reported for a standard curve.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Degree Fahrenheit (fah). Unit for temperature, degrees Fahrenheit.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Formazin nephelometric unit (fnu). formazin nephelometric unit (FNU)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Feet (foot). foot (ft)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Gene copies (gc). Gene or variant copies
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Gene copies per copy of crAssphage (gcCrA). Gene or variant copies per copy of crAssphage.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Gene copies per day (gcDay). Unit of measurement of the number of gene copies per day.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• gene copies per day per 100,000 people (gcDay100k). The unit for measures reflecting the gene copies per day per 100,000 people in the population.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Gene copies per gram solids (gCGS). Gene or variant copies per gram solids.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Gene copies per L (gcL). Gene or variant copies per litre.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Gene copies per mL (gcMl). Gene or variant copies per millilitre of solution.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Gene copies per millilitre per 100,000 people (gcMl100k). Unit of measurement of the number of gene copies per millilitre per 100,000 people.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Gene copies per PMMoV copy (gcPpmov). Gene or variant copies per copy of PMMoV.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Gene copies per Reaction (gcRx). Gene or variant copies per reaction in PCR
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Gram per kilogram (gkg). gram per kilogram (g/kg)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Gram per liter (gL). gram per liter (g/L)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Gram per cubic metre (gm3). Density unit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Nitrogen per total solids (gNgTS). nitrogen per total solids (gN/gTS)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Grams per total solids (gPergTS). Grams per total solids (g/gTS)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Orthophosphate per total solids (gPO43gTS). orthophosphate per total solids (gPO43–/gTS)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Orthophosphate as phosphorus per total solids (gPO4PgTS). orthophosphate as phosphorus per total solids (gPO4-P/gTS)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Grams (grams). A unit of mass or weight.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• General Hospital Admissions (hosa). Hospital admissions or patients newly admitted to hospital.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Hospital Census (hosc). Hospital census or the number of people admitted with an ailment.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Hours (hours). A unit for indicating a length of time in hours.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Intensive care unit patients (icu). Units for describing a population measure of patients who are in intensive care due to a given cause.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Inch (inch). inch (in)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Intercept (inter). Intercept value of the calibration curve.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Kilogram per cubic meter (kgm3). Kilogram per cubic meter (kg/m^3)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Kilogram per second (kgS). Kilograms per second.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Kilolitres (kl). Kilolitres of volume
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Litres (l). Litres of volume
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Litres per day (lday). Unit of litres per day, usually for measuring flow.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Liter per hour (lhour). liter per hour (L/h)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Liter per minute (lmin). liter per minute (L/min)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• log10 gene copies per g (log10cpG). Unit for log10 copies per gram
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• log10 gene copies per L (log10cpL). Unit for log10 copies per litre
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• log10 gene copies per mL (log10cpml). Unit for log10 copies per mililitre
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Log10 gene copies per 100 milliliter (log10gc100mL). log10 gene copies per 100 milliliter (log10 GC/100 mL)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Log10 gene copies per nanogram total DNA (log10gcngDNA). log10 gene copies per nanogram total DNA
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• log10 micrograms per g (log10ugG). Unit for log10 micrograms per gram
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• log10 micrograms per L (log10ugL). Unit for log10 micrograms per litre
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Liter per second (lsec). liter per second (L/s)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Cubic metres per day (m3D). Cubic metres per day.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Cubic metres per hour (m3H). Cubic metres per hour.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Cubic meter per minute (m3min). cubic meter per minute (m^3/min)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Cubic metres per second (m3S). Cubic metre per second.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Mega-bases or Mega-base-pairs (megaB). A mega-base (Mb) or mega-base-pair (Mbp) is equal to one million base pairs (1,000,000 bp). It is commonly used to describe the size of genomes or large DNA sequences.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Milliequivalent per liter (meqL). Unit for alkalinity, miliequivalents per litre.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Meter (meter). meter (m)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Millions of gallons per day (MG/D) (mgd). A unit for measuring of design capacity for wastewater treatment plants, represented as millions of gallons per day. Also can be used to measure flow.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Milligrams per litre (mgL). Milligrams per litre.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Milligram per liter of calcium carbonate (mgLCaCO3). Unit for alkalinity, miligram per litre of calcium carbonate.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Milligrams orthophosphate per liter (mgPO43L). milligrams orthophosphate per liter (mg PO43–/L)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Milligrams orthophosphate as phosphorus per liter (mgPO4PL). milligrams orthophosphate as phosphorus per liter (mg PO4-P/L)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Minutes (minutes). A unit for indicating a length of time in minutes.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Millilitres (ml). Millilitres of volume
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Megalitres per day (ML/d) (mld). Megalitres per day.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Millimetres (mm). Unit part for the SI unit of millimetres.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Millimho per centimeter (mmhocm). Millimho per centimeter (mmho/cm)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Months (months). A unit for indicating a length of time in months.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Most probable number per 100 milliliters (mpn100mL). most probable number per 100 milliliter (MPN/100 mL)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Most probable number per milliliter (mpnmL). most probable number per milliliter (MPN/mL)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Metres per second (mps). metres per second.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• MilliSiemen per centimeter (mScm). MilliSiemens per centimeter (mS/cm)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• MilliVolt (mvolt). milliVolt (mV)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Unit not applicable (naUnit). Not appliable for units.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Population of newly vaccinated persons (newVax). Population of newly vaccinated persons
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Nanograms per liter (ngL). nanograms per liter (ng/L)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Nano-molar (nM). the unit of nanomolar.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Number per 100 kilo-base-pairs (nPerKbp). This unit expresses the frequency of an event (such as a mutation, binding site, or feature) per 100,000 base pairs (kbp) of DNA or RNA. It normalizes counts across genomic regions of different lengths, making comparisons more meaningful.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Nephelometric turbidity unit (ntu). Nephelometric Turbidity Units, a unit used in the measurement of turbidity (see “turbidity” under measureIDs).
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Other Unit depricated (otunDep). Other measurement of viral copies or wastewater treatment plant parameter. Add description to UnitOther.
  Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
• PCR Quanitification Cycles (pcrCycles). A count unit of how many Polymerase Chain Reaction (PCR) cycles it took to detect a real signal from a sample. Equivalent to the PCR cycle number at which a sample’s reaction curve intersects the threshold line.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Number of people (peeps). Unit specifying a number of people.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Percent (perc). Percentage.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Percent recovery (percRec). Percent of the surrogate recovery for a recovery efficiency control assay (as a unit).
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Persons for square kilometre (personPerKm). Persons per square kilometre.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Persons per square mile (personPerMile). Persons per square mile.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Population equivalents (popEq). A unit for measuring of design capacity for wastewater treatment plants, represented as the approximate amount of water a signle person would use.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Percent positive (pp). Percent positive of sample measures.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• parts per million (ppm). Parts per million.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Percent positivity rate (pprt). Percent positivity rate of tests conducted within a day in a given region.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Percent primary sludge (pps). Percentage of total solids, for primary sludge.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• parts per thousand (ppt). Parts per thousand.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Proportion of total (prop). Proportion as a precent of total.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Proportion of variant in sample (propV). Proportion of a variant as percent of total variants.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Practical salinity unit (psu). practical salinity unit (PSU)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Number of positive tests (ptot). Number of positive tests conducted within a day in a given region.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• R squared (r2). R-squared value of the calibration curve.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Ratio (ratio). Ratio (unitless)
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Recovered patients (recov). Units for describing a population measure of patients who have recovered from a given disease.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Residents per square kilometre (resPerKm). Residents per square kilometre.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Residents per square mile (resPerMile). Residents per square mile.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Rate per 100,000 (rP100). Units for describing a population measure of a rate of case incidence per 100,000 people of a given disease.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Revolutions per minute (RPM) (rpm). RPM stands for “Revolutions per minute.” This is how centrifuge manufacturers generally describe how fast the centrifuge is going. The rotor, regardless of its size, is revolving at that rate.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Seconds (seconds). The unit of time, seconds.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• slope (slope). Slope value of the calibration curve.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Siemens per meter (sm). Siemens per meter (S/m)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Number of tests performed (test). Number of tests performed.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Micrograms per gram (ugG). Micrograms per gram
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Micrograms per litre (ugL). Micrograms per litre
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Micrograms per milligram (ugmg). Concentration unit of micrograms per milligram.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Micro-litres (uL). The unit of microlitres.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Micromho per centimeter (umhocm). Micromho per centimeter (μmho/cm)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Unitless measure (unitless). A unit for unitless measures, like pH.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Micro-Siemens per centimetre (uSCm). Micro-siemens per centimetre.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Frequency of variants detected (varFreq). A description of the frequency of a variants detected.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Population with 1 dose of vaccine (vax1). The population with exactly 1 dose of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Proportion of population with 1+ vaccine dose(s) (vax1p). Specifies the portion of the population with 1 or more doses of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Population with 1+ dose(s) of vaccine (vax1plus). The population with 1 or more doses of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Population with 2 or more doses of vaccine (vax2). The population with exactly 2 dose of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Proportion of population with 2+ vaccine doses (vax2p). Specifies the portion of the population with 2 or more doses of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Population with 2+ or more doses of vaccine (vax2plus). The population with 2 or more doses of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Population with 3 or more doses of vaccine (vax3). The population with exactly 3 dose of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.0.0. Last updated: 2.2.0.
• Proportion of population with 3+ vaccine doses (vax3p). Specifies the portion of the population with 3 or more doses of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Population with 3+ or more doses of vaccine (vax3plus). The population with 3 or more doses of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Population with 4 or more doses of vaccine (vax4). The population with exactly 4 dose of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Proportion of population with 4+ vaccine doses (vax4p). Specifies the portion of the population with 4 or more doses of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Population with 4+ or more doses of vaccine (vax4plus). The population with 4 or more doses of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Weeks (weeks). A unit of measuring time in weeks, or periods of seven days.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Weight for weight (ww). weight for weight (% w/w)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Relative Centrifugal Force (RCF) or x g units (xg). RCF (Relative Centrifugal Force) denotes the degree of force exerted on a sample. RCF is quantified in multiples of the gravitational acceleration that is standard at the Earth’s surface (x g). Thus, the terms RCF and XG are often used interchangeably in centrifugation protocols.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Years (years). A unit for indicating a length of time in years.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Unit sets

(unitSets). Sets of units. Contains units that are associated with part types such as measures. Sets are lists of input values. Each input value within a set is a part (has a partID) that can be reused between sets. For example, a set A could contain the values of ‘yes’ and ‘no’; and set B could contain the values of ‘yes’, ‘no’, and ‘maybe.’ partTypes with sets include aggregations, compartments, missingness, quality flags, specimens, and units. Measures with categories and dataTypes have their own specific sets (catSetID) because their input values are unique and are not reused.

Absolute humidity unit set

(absHumidUnitSet)Unit set for absolute humidity measurements.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Gram per cubic metre (gm3). Density unit.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.

Alkalinity unit set

(alkalinitySet)Unit set for alkalinity measurements.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Milliequivalent per liter (meqL). Unit for alkalinity, miliequivalents per litre.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Milligrams per litre (mgL). Milligrams per litre.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• parts per million (ppm). Parts per million.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Allele unit set

(alleleUnitSet)Unit set for alleles.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Cycle threshold or quantification cycle (Ct or Cq) (ct). Cycle thresholds in a PCR assay.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Detected (det). Substance detected or not detected.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Depth of coverage (doc). The average number of reads representing a given nucleotide in the reconstructed sequence, provided as a value as a fold of coverage.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Efficiency (efficient). The efficiency reported for a standard curve.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Gene copies per copy of crAssphage (gcCrA). Gene or variant copies per copy of crAssphage.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Gene copies per gram solids (gCGS). Gene or variant copies per gram solids.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Gene copies per mL (gcMl). Gene or variant copies per millilitre of solution.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Gene copies per PMMoV copy (gcPpmov). Gene or variant copies per copy of PMMoV.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Intercept (inter). Intercept value of the calibration curve.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• R squared (r2). R-squared value of the calibration curve.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• slope (slope). Slope value of the calibration curve.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Bacteria unit set

(bacteriaUnitSet)Unit set for bacteria-related measurements.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Colony Forming Units (cfu). Colony forming units
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• CFU per 100 ml (cfu100). Colony forming units per 100 ml of filtered sample.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Colony forming units per grams total solids (cfugTS). colony forming units per grams total solids (CFU/gTS)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Colony forming units per milliliter (cfumL). colony forming units per milliliter (CFU/mL)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Most probable number per 100 milliliters (mpn100mL). most probable number per 100 milliliter (MPN/100 mL)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Most probable number per milliliter (mpnmL). most probable number per milliliter (MPN/mL)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Base-pair unit set

(basePairSet)Unit set for base-pair measurements.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Base-pairs (bps). A base pair (bp) is a unit of measurement in molecular biology that represents a pair of complementary nucleotides in DNA or RNA. The length of DNA sequences is often measured in base pairs.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Mega-bases or Mega-base-pairs (megaB). A mega-base (Mb) or mega-base-pair (Mbp) is equal to one million base pairs (1,000,000 bp). It is commonly used to describe the size of genomes or large DNA sequences.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Number per 100 kilo-base-pairs (nPerKbp). This unit expresses the frequency of an event (such as a mutation, binding site, or feature) per 100,000 base pairs (kbp) of DNA or RNA. It normalizes counts across genomic regions of different lengths, making comparisons more meaningful.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Capacity unit set

(capacityUnitSet)Unit set for capacity measurements.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Millions of gallons per day (MG/D) (mgd). A unit for measuring of design capacity for wastewater treatment plants, represented as millions of gallons per day. Also can be used to measure flow.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Megalitres per day (ML/d) (mld). Megalitres per day.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Population equivalents (popEq). A unit for measuring of design capacity for wastewater treatment plants, represented as the approximate amount of water a signle person would use.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Conductivity unit set

(conductivityUnitSet)Unit set related to conductivity measurements.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Millimho per centimeter (mmhocm). Millimho per centimeter (mmho/cm)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• MilliSiemen per centimeter (mScm). MilliSiemens per centimeter (mS/cm)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Micromho per centimeter (umhocm). Micromho per centimeter (μmho/cm)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Micro-Siemens per centimetre (uSCm). Micro-siemens per centimetre.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Dissolved gas concentration unit set

(dissGasUnitSet)Unit set for carbon dioxide concentrations measurements in water or air.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Milligrams per litre (mgL). Milligrams per litre.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• parts per million (ppm). Parts per million.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.

Electrical potential unit set

(electricPotentSet)Unit set for measurements of electrical potential.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.

Volume flow rate unit set

(flowUnitSet)Unit set for volume flow measurements.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Kilogram per second (kgS). Kilograms per second.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Litres per day (lday). Unit of litres per day, usually for measuring flow.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Liter per hour (lhour). liter per hour (L/h)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Liter per minute (lmin). liter per minute (L/min)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Liter per second (lsec). liter per second (L/s)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Cubic metres per day (m3D). Cubic metres per day.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Cubic metres per hour (m3H). Cubic metres per hour.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Cubic meter per minute (m3min). cubic meter per minute (m^3/min)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Cubic metres per second (m3S). Cubic metre per second.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Millions of gallons per day (MG/D) (mgd). A unit for measuring of design capacity for wastewater treatment plants, represented as millions of gallons per day. Also can be used to measure flow.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Megalitres per day (ML/d) (mld). Megalitres per day.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Genetics unit set

(geneticUnitSet)Unit set for genetic-related measurements.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Breadth of coverage (>=5x depth) (boc). The percentage of the reference genome covered by the sequenced data, to a prescribed read depth greater or equal to 5.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Gene copies per well (cpWell). Gene or variant copies per well.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Cycle threshold or quantification cycle (Ct or Cq) (ct). Cycle thresholds in a PCR assay.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Cycle threshold per quantification cycle (ctcq). cycle threshold (Ct) / quantification cycle (Cq)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Detected (det). Substance detected or not detected.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Depth of coverage (doc). The average number of reads representing a given nucleotide in the reconstructed sequence, provided as a value as a fold of coverage.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Efficiency (efficient). The efficiency reported for a standard curve.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Gene copies (gc). Gene or variant copies
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Gene copies per copy of crAssphage (gcCrA). Gene or variant copies per copy of crAssphage.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Gene copies per day (gcDay). Unit of measurement of the number of gene copies per day.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Gene copies per gram solids (gCGS). Gene or variant copies per gram solids.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Gene copies per L (gcL). Gene or variant copies per litre.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Gene copies per mL (gcMl). Gene or variant copies per millilitre of solution.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Gene copies per millilitre per 100,000 people (gcMl100k). Unit of measurement of the number of gene copies per millilitre per 100,000 people.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Gene copies per PMMoV copy (gcPpmov). Gene or variant copies per copy of PMMoV.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Gene copies per Reaction (gcRx). Gene or variant copies per reaction in PCR
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Intercept (inter). Intercept value of the calibration curve.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• log10 gene copies per g (log10cpG). Unit for log10 copies per gram
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• log10 gene copies per L (log10cpL). Unit for log10 copies per litre
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• log10 gene copies per mL (log10cpml). Unit for log10 copies per mililitre
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Log10 gene copies per 100 milliliter (log10gc100mL). log10 gene copies per 100 milliliter (log10 GC/100 mL)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Log10 gene copies per nanogram total DNA (log10gcngDNA). log10 gene copies per nanogram total DNA
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• log10 micrograms per g (log10ugG). Unit for log10 micrograms per gram
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• log10 micrograms per L (log10ugL). Unit for log10 micrograms per litre
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• PCR Quanitification Cycles (pcrCycles). A count unit of how many Polymerase Chain Reaction (PCR) cycles it took to detect a real signal from a sample. Equivalent to the PCR cycle number at which a sample’s reaction curve intersects the threshold line.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Percent recovery (percRec). Percent of the surrogate recovery for a recovery efficiency control assay (as a unit).
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Proportion of total (prop). Proportion as a precent of total.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Proportion of variant in sample (propV). Proportion of a variant as percent of total variants.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• R squared (r2). R-squared value of the calibration curve.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• slope (slope). Slope value of the calibration curve.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Unit set not applicable

(naUnitSet)Not applicable for unit sets.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Unit not applicable (naUnit). Not appliable for units.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Percent unit set

(percentUnitSet)Unit set for percentages.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Percent (perc). Percentage.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Population density unit set

(popDensUnitSet)Unit set for measures of population density of a site.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Persons for square kilometre (personPerKm). Persons per square kilometre.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Persons per square mile (personPerMile). Persons per square mile.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Residents per square kilometre (resPerKm). Residents per square kilometre.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Residents per square mile (resPerMile). Residents per square mile.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Population unit set

(populationUnitSet)Unit set for hospital-related measurements.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Number of active cases (acti). Number of active cases.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Number of active cases by Onset date (actiCaseOn). Number of active cases by onset date.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Number of active cases by episode date (actiEp). Number of active cases by episode date.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Number of active cases by Report date (actiRep). Number of active cases by report date.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Number of active cases by test date (actiTest). Number of active cases by test date.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Episode date of confirmed cases (caseEpDate). Episode date is the earliest of onset, test or reported date for a confirmed case.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Onset date of confirmed cases (caseOnDate). Earliest that symptoms were reported for a confirmed case. This data is often not known and reported. In lieu, episode is used.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Report date of confirmed cases (caseRepDate). Date that the numbers were reported publicly for a confirmed case. Typically, reported data and this measure is most commonly reported and used.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Test date of confirmed cases (caseTestDate). Date that the covid-19 test was performed for a confirmed case.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Number of confirmed cases (conf). Number of confirmed cases.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Number of confirmed cases by episode date (confEp). Number of confirmed cases of a given disease, totaled by episode date.
  Status: active. First released: 1.0.0. Last updated: 2.2.0.
• Number of confirmed Cases Onset date (confOn). Number of confirmed cases of a given disease, totaled by onset date.
  Status: active. First released: 1.0.0. Last updated: 2.2.0.
• Number of confirmed cases by report date (confRep). Number of confirmed cases of a given disease, totaled by report date.
  Status: active. First released: 1.0.0. Last updated: 2.2.0.
• Number of confirmed cases test date (confTest). Number of confirmed cases of a given disease, totaled by test date.
  Status: active. First released: 1.0.0. Last updated: 2.2.0.
• Deaths (death). Units for describing a population measure of patients who have died from a given cause.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• General Hospital Admissions (hosa). Hospital admissions or patients newly admitted to hospital.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Hospital Census (hosc). Hospital census or the number of people admitted with an ailment.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Intensive care unit patients (icu). Units for describing a population measure of patients who are in intensive care due to a given cause.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Population of newly vaccinated persons (newVax). Population of newly vaccinated persons
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Number of people (peeps). Unit specifying a number of people.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Percent positivity rate (pprt). Percent positivity rate of tests conducted within a day in a given region.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Number of positive tests (ptot). Number of positive tests conducted within a day in a given region.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Recovered patients (recov). Units for describing a population measure of patients who have recovered from a given disease.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Rate per 100,000 (rP100). Units for describing a population measure of a rate of case incidence per 100,000 people of a given disease.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Number of tests performed (test). Number of tests performed.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Population with 1 dose of vaccine (vax1). The population with exactly 1 dose of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Proportion of population with 1+ vaccine dose(s) (vax1p). Specifies the portion of the population with 1 or more doses of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Population with 1+ dose(s) of vaccine (vax1plus). The population with 1 or more doses of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Population with 2 or more doses of vaccine (vax2). The population with exactly 2 dose of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Proportion of population with 2+ vaccine doses (vax2p). Specifies the portion of the population with 2 or more doses of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Population with 2+ or more doses of vaccine (vax2plus). The population with 2 or more doses of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Population with 3 or more doses of vaccine (vax3). The population with exactly 3 dose of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.0.0. Last updated: 2.2.0.
• Proportion of population with 3+ vaccine doses (vax3p). Specifies the portion of the population with 3 or more doses of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Population with 3+ or more doses of vaccine (vax3plus). The population with 3 or more doses of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Population with 4 or more doses of vaccine (vax4). The population with exactly 4 dose of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Proportion of population with 4+ vaccine doses (vax4p). Specifies the portion of the population with 4 or more doses of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Population with 4+ or more doses of vaccine (vax4plus). The population with 4 or more doses of vaccine, with the vaccine specified in the measure field.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.

Precipitation unit set

(precipitationUnitSet)Unit set for percipitation measurements.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Centimetres (cm). Unit part for the SI unit of centimetres.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Feet (foot). foot (ft)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Inch (inch). inch (in)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Meter (meter). meter (m)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Millimetres (mm). Unit part for the SI unit of millimetres.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.

Relative humidity unit set

(relHumidUnitSet)Unit set for relative humidity measurements.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Percent (perc). Percentage.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Salinity unit set

(salinityUnitSet)Unit set for salinity measurements.
Status: active. First Released: 3.0.0. Last updated: 3.0.0.

• Gram per kilogram (gkg). gram per kilogram (g/kg)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Gram per liter (gL). gram per liter (g/L)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• parts per thousand (ppt). Parts per thousand.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Practical salinity unit (psu). practical salinity unit (PSU)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Weight for weight (ww). weight for weight (% w/w)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.

Specific humidity unit set

(specHumidUnitSet)Unit set for specific humidity.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Ratio (ratio). Ratio (unitless)
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Speed Unit Set

(speedUnitSet)Unit set for reporting speeds (centrifugation speed, etc.)
Status: active. First Released: 2.2.0. Last updated: 2.2.0.

• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Metres per second (mps). metres per second.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Revolutions per minute (RPM) (rpm). RPM stands for “Revolutions per minute.” This is how centrifuge manufacturers generally describe how fast the centrifuge is going. The rotor, regardless of its size, is revolving at that rate.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Relative Centrifugal Force (RCF) or x g units (xg). RCF (Relative Centrifugal Force) denotes the degree of force exerted on a sample. RCF is quantified in multiples of the gravitational acceleration that is standard at the Earth’s surface (x g). Thus, the terms RCF and XG are often used interchangeably in centrifugation protocols.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.

Standard concentration unit set

(stdConcentrationUnitSet)Unit set for concentration measurements.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Gram per kilogram (gkg). gram per kilogram (g/kg)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Nitrogen per total solids (gNgTS). nitrogen per total solids (gN/gTS)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Grams per total solids (gPergTS). Grams per total solids (g/gTS)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Orthophosphate per total solids (gPO43gTS). orthophosphate per total solids (gPO43–/gTS)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Orthophosphate as phosphorus per total solids (gPO4PgTS). orthophosphate as phosphorus per total solids (gPO4-P/gTS)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Kilogram per cubic meter (kgm3). Kilogram per cubic meter (kg/m^3)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Milligrams per litre (mgL). Milligrams per litre.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Milligram per liter of calcium carbonate (mgLCaCO3). Unit for alkalinity, miligram per litre of calcium carbonate.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Milligrams orthophosphate per liter (mgPO43L). milligrams orthophosphate per liter (mg PO43–/L)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Milligrams orthophosphate as phosphorus per liter (mgPO4PL). milligrams orthophosphate as phosphorus per liter (mg PO4-P/L)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Nanograms per liter (ngL). nanograms per liter (ng/L)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Nano-molar (nM). the unit of nanomolar.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Percent (perc). Percentage.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• parts per million (ppm). Parts per million.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Percent primary sludge (pps). Percentage of total solids, for primary sludge.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Micrograms per gram (ugG). Micrograms per gram
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Micrograms per litre (ugL). Micrograms per litre
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Micrograms per milligram (ugmg). Concentration unit of micrograms per milligram.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Micro-litres (uL). The unit of microlitres.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.

Temperature unit set

(temperatureUnitSet)Unit set for temperature measurements.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Degrees Celcius (cel). Degrees Celsius.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Degree Fahrenheit (fah). Unit for temperature, degrees Fahrenheit.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.

Time unit set

(timeUnitSet)The unit set for measures of time.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Days (days). A unit for indicating a length of time in days.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Hours (hours). A unit for indicating a length of time in hours.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Minutes (minutes). A unit for indicating a length of time in minutes.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Months (months). A unit for indicating a length of time in months.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Seconds (seconds). The unit of time, seconds.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Weeks (weeks). A unit of measuring time in weeks, or periods of seven days.
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• Years (years). A unit for indicating a length of time in years.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Turbidity unit set

(turbidityUnitSet)Unit set for turbidity measurements.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• Formazin nephelometric unit (fnu). formazin nephelometric unit (FNU)
  Status: active. First released: 3.0.0. Last updated: 3.0.0.
• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Nephelometric turbidity unit (ntu). Nephelometric Turbidity Units, a unit used in the measurement of turbidity (see “turbidity” under measureIDs).
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Unitless unit set

(unitlessUnitSet)Unit set for measurements that does not have units.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.

• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Unitless measure (unitless). A unit for unitless measures, like pH.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Volume unit set

(volumeUnitSet)Unit set of volume measurements.
Status: active. First Released: 1.0.0. Last updated: 2.0.0.

• Grams (grams). A unit of mass or weight.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Kilolitres (kl). Kilolitres of volume
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Litres (l). Litres of volume
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Millilitres (ml). Millilitres of volume
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Millimetres (mm). Unit part for the SI unit of millimetres.
  Status: active. First released: 1.1.0. Last updated: 2.0.0.
• Percent positive (pp). Percent positive of sample measures.
  Status: active. First released: 1.0.0. Last updated: 2.0.0.
• Sub-variant or lineage (subVar). A unit used to report a specific genetic lineage, or to specify that a reported variant is a sub-variant of another.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.
• Micro-litres (uL). The unit of microlitres.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Frequency of variants detected (varFreq). A description of the frequency of a variants detected.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.

Wind speed unit set

(windSpeedUnitSet)Unit set for wind speed measurements.
Status: active. First Released: 1.0.0. Last updated: 2.0.0.

• See Header for Unit (hUn). An indicator to show in a wide-name that unit information is located in a different column.
  Status: active. First released: 2.2.0. Last updated: 2.2.0.
• Metres per second (mps). metres per second.
  Status: active. First released: 2.0.0. Last updated: 2.0.0.