Sets

Dictionary v2.2.3 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 single, 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.
  • 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.
  • Standard Error (stEr). The standard error of a series of measurements.
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Administrative regions (admRegLevel). Administrative regions
    Status: depreciated. First released: 2.0.0. Last updated: 2.1.0.
  • 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.
  • Capital city endonym (capitalEndonym). The name locals use for their country‚Äö√Ñ√¥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‚Äö√Ñ√¥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 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: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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.
  • Countries or sovereign states (countryLevel). Countries or sovereign states
    Status: depreciated. First released: 2.0.0. Last updated: 2.1.0.
  • Districts, counties, regions (countyLevel). Districts, counties, regions
    Status: depreciated. First released: 2.0.0. 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.
  • 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: 2.0.0.
  • Date (date). Date
    Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
  • 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 (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.
  • 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.
  • 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: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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: 2.1.0.
  • 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: 2.1.0.
  • 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‚Äö√Ñ√¥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.
  • Municipalities or communes (municipalLevel). Municipalities or communes
    Status: depreciated. First released: 2.0.0. Last updated: 2.1.0.
  • 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.
  • Local administrative units or neighborhoods (neighborLevel). Local administrative units or neighborhoods
    Status: depreciated. First released: 2.0.0. Last updated: 2.1.0.
  • 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 (normanNote). 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 attrbitutes
    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.
  • 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.
  • 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.
  • 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.
  • Polygon ID (polygonID). Unique identifier for the polygon.
    Status: active. First released: 1.0.0. Last updated: 2.0.0.
  • 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: 2.0.0.
  • 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.
  • Population Served (popServ). An attribute of a site, which specifies the population of/population served by a given site.
    Status: active. First released: 2.0.0. 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.
  • 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.
  • 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 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.
  • Departments, states, or provinces (stateProvLevel). Departments, states, or provinces
    Status: depreciated. First released: 2.0.0. Last updated: 2.1.0.
  • 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.
  • 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.
  • 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 ‚Äö√Ñ√¨ 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 (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.¬¨‚Ć
    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.¬¨‚Ć
    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.¬¨‚Ć
    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 Class (bacteria). 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.
  • 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 (flow). Measures and methods related to flow.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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.
  • 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.
  • 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 (time). Measures and methods relating to time.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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.

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.
  • 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).
    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.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Organization table (organizations). The table that contains information about a laboratory.
    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.
    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 (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 (normanNote). 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.
    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.
    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.
    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.
    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.
    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.
    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).
    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.
    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.
    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.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Instrument table (instruments). The table that contains information about instruments.
    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.
    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
    Status: active. First released: 1.0.0. Last updated: 2.0.0.
  • Measure set report table (measureSets). The table that identifies sets of measures.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Organization table (organizations). The table that contains information about a laboratory.
    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.
    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.
    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).
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Protocols table (protocols). The table for protocols.
    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.
    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.
    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.
    Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
  • Sample relationships table (sampleRelationships). Table for recording the relationships between samples.
    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.
    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.
    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.
    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.
    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
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).
    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.
    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.
    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.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Instrument table (instruments). The table that contains information about instruments.
    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.
    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
    Status: active. First released: 1.0.0. Last updated: 2.0.0.
  • Measure set report table (measureSets). The table that identifies sets of measures.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Organization table (organizations). The table that contains information about a laboratory.
    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.
    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.
    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).
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Protocols table (protocols). The table for protocols.
    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.
    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.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Sample relationships table (sampleRelationships). Table for recording the relationships between samples.
    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.
    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.
    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.
    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.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Wide name table (wideNames). The table for wide names.
    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.
    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.
    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.
    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.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Data types (dataTypes). The data type for a part.
    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.
    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.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Missingness (missingness). The part type for missingness values.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Nomenclatures (nomenclatures). A classification system to report the measure class.
    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.
    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.
    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. There
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Units (units). The unit of the measurement.
    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.
    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.
    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.
    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).
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Protocols table (protocols). The table for protocols.
    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.
    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
    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.
    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).
    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.
    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.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Instrument table (instruments). The table that contains information about instruments.
    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.
    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
    Status: active. First released: 1.0.0. Last updated: 2.0.0.
  • Measure set report table (measureSets). The table that identifies sets of measures.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Organization table (organizations). The table that contains information about a laboratory.
    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.
    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.
    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).
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Protocols table (protocols). The table for protocols.
    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.
    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.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Sample relationships table (sampleRelationships). Table for recording the relationships between samples.
    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.
    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.
    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.
    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
  • 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: depreciated. First released: 2.0.0. Last updated: 2.2.0.
  • 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.
  • Chlamydia Group (chlamydiaGrp). A group of measures/methods related to chlamydia bacteria.
    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.
  • 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.
  • 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 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.
  • 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.
  • 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.
  • 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 (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.
  • 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.

Measures

(measurements). The attribute to describe a part type of measures. All measures have partType = “measure”.
  • a1306s delta-variant gene target (a1306s). a1306s delta-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • a1918v delta-variant gene target (a1918v). a1918v delta-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • a2710t omicron-variant gene target (a2710t). a2710t omicron-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • a63t omicron-variant gene target (a63t). a63t omicron-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • a67v omicron-variant gene target (a67v). a67v omicron-variant 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, 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.
  • 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: 2.2.0.
  • 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.
  • 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.
  • 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¬¨‚Ćquantity¬¨‚Ćof¬¨‚Ćoxygen¬¨‚Ćutilized¬¨‚Ćfor the biochemical¬¨‚Ćdegradation¬¨‚Ćof¬¨‚Ćorganic matter¬¨‚Ćunder¬¨‚Ćstandard¬¨‚Ćlaboratory procedures¬¨‚Ćin five (5) days in the¬¨‚Ćpresence of a¬¨‚Ćnitrification inhibitor,¬¨‚Ćexpressed¬¨‚Ćin¬¨‚Ćmilligrams per litre¬¨‚Ć(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.
  • Clade I Mpox C3L Gene Target (mpxC3L). Human MPox Virus (hMPXV) Clade I gene target. hMPXV C3L primers and‚Äö√Ñ√òprobe‚Äö√Ñ√òdetect Clade I viruses.
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • Caffeine (caff). Caffeine (usually measured as a human fecal chemical indicator)
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • 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.
  • 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.
  • 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-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.
  • 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 gene target.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • d3g omicron-variant gene target (d3g). d3g omicron-variant gene target.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • d63g delta-variant gene target (d63g). d63g delta-variant gene target.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • d796y omicron-variant gene target (d796y). d796y omicron-variant gene target.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • d950n delta-variant gene target (d950n). d950n delta-variant 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 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 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
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • del143/145 (del143). 143 or 145 deletion omicron-variant 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
    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 gene target.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • del212/212 (del212). 212 or 212 deletion omicron-variant 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
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • del3674/3676 (del3674). 3674 or 3676 deletion omicron-variant gene target.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • del69/70 (del6970). 69 or 70 deletion omicron-variant 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 (dengue). Dengue
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • 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.
  • 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 gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • e484a omicron-variant gene target (e484a). e484a omicron-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Mpox & Orthopox E9L-NVAR Gene Target (mpxe9lNVAR). Human MPox Virus (hMPXV) gene target for Orthopoxvirus DNA polymerase. CDC Assay detects all hMPXV‚Äö√Ñ√£ 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.
  • Enteroaggregative Escherichia coli (EAEC) (eaec). Enteroaggregative Escherichia coli (EAEC)
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • Epstein‚Äö√Ñ√¨Barr virus (EBV) (ebv). Epstein‚Äö√Ñ√¨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.
  • Extraintestinal pathogenic Escherichia coli (ExPEC) (expec). Extraintestinal pathogenic Escherichia coli (ExPEC)
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • 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.
  • F+ DNA coliphage (fDNA). F+ DNA coliphage
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • 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.
  • 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 gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Mpox G2R-G Gene Target (mpxG2RG). Human MPox Virus (hMPXV) gene target using the G2R_G primers and‚Äö√Ñ√òprobe which ‚Äö√Ñ√òdetects all MPox Virus strains‚Äö√Ñ√ò‚Äö√Ñ√£.
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • 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.
  • g339d omicron-variant gene target (g339d). g339d omicron-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • g496s omicron-variant gene target (g496s). g496s omicron-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • g662s delta-variant gene target (g662s). g662s delta-variant 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.
  • 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.
  • Influenza A H5 hemagglutinin gene (h5hema). 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.
  • 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.
  • 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 gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • i3758v omicron-variant gene target (i3758v). i3758v omicron-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • i82t delta-variant gene target (i82t). i82t delta-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Influenza A M gene (iavM). 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.
  • 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
    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 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.
  • 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 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 gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Lambda (lamba). C.37
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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 detection (LOD) (lod). Limit of detection, ie. the minimum level of a genetic target.
    Status: active. First released: 1.1.0. Last updated: 2.0.0.
  • 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: 2.0.0.
  • Limit of quantification (LOQ) (loq). Loq
    Status: active. First released: 1.1.0. Last updated: 2.0.0.
  • Omicron Variant LPPA24S mutation (lppa24s). Omicron Variant LPPA24S mutation
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • 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.
  • 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.
  • 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: 2.2.0.
  • 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.
  • 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.
  • Influenza A N1 neuraminidase gene (n1neur). 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.
  • Omicron Variant n211i mutation (n211i). Omicron Variant n211i mutation & gene target.
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • 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.
  • Neisseria gonorrhoeae (nGonorrhoeae). Neisseria gonorrhoeae
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Outbreak (outb). Measure 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: 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 recovery (percRec). Percent of the surrogate recovery for a recovery efficiency control assay.
    Status: active. First released: 1.0.0. Last updated: 2.0.0.
  • pH (ph). pH measurement
    Status: active. First released: 1.1.0. Last updated: 2.0.0.
  • 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.
  • PMMoV-CP (ppmv). Pepper mild mottle virus capsid protein gene region
    Status: active. First released: 1.0.0. Last updated: 2.0.0.
  • 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.
  • 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 gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • q493r omicron-variant gene target (q493r). q493r omicron-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • q498r omicron-variant gene target (q498r). q498r omicron-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • q954h omicron-variant gene target (q954h). q954h omicron-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • r203m delta-variant gene target (r203m). r203m delta-variant 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.
  • 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.
  • 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 gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • s371l omicron-variant gene target (s371l). s371l omicron-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • s373p omicron-variant gene target (s373p). s373p omicron-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • s375f omicron-variant gene target (s375f). s375f omicron-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • s477n omicron-variant gene target (s477n). s477n omicron-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Salmonella (salmonella). Salmonella
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • Sapovirus (sapovirus). Sapovirus
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • 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.
  • S sars-cov-2 gene target (sGene). S sars-cov-2 gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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: 2.2.0.
  • 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.
  • 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.
  • Storage time (stoTim). Length of time that a sample was in storage.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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.
  • t19r delta-variant gene target (t19r). t19r delta-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • t3646a delta-variant gene target (t3646a). t3646a delta-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • t547k omicron-variant gene target (t547k). t547k omicron-variant gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • t9i omicron-variant gene target (t9i). t9i omicron-variant 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 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 gene target
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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.
  • 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 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 ¬¨‚àûC to 600 ¬¨‚àûC. 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 (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.
  • y505h omicron-variant gene target (y505h). y505h omicron-variant 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.
  • SARS-CoV-2 S Gene Target (covS). S sars-cov-2 gene target
    Status: active. First released: 2.2.3. Last updated: 2.2.3.
  • Dengue Virus NS5 Gene (dnvNS5). Dengue Type 1-specific gene target.
    Status: active. First released: 2.2.3. Last updated: 2.2.3.
  • Dengue Virus E Gene (dnvE). Dengue Type 2-specific gene taget.
    Status: active. First released: 2.2.3. Last updated: 2.2.3.
  • Dengue Virus prM Gene (dnvprM). Dengue Type 3 and 4-specific gene target.
    Status: active. First released: 2.2.3. Last updated: 2.2.3.
  • Mpox Clade I F3L Gene Target (mpxF3L). Human MPox Virus (hMPXV) Clade I gene target, F3L
    Status: active. First released: 2.2.3. Last updated: 2.2.3.
  • 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: 2.2.3. Last updated: 2.2.3.
  • 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: 2.2.3. Last updated: 2.2.3.
  • 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: 2.2.3. Last updated: 2.2.3.
  • 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: 2.2.3. Last updated: 2.2.3.
  • Mpox Clade I (mpxClI). The virus known as Mpox, previously also known as Monkey Pox, Clade I virus type.
    Status: active. First released: 2.2.3. Last updated: 2.2.3.
  • Mpox Clade II (mpxClII). The virus known as Mpox, previously also known as Monkey Pox, Clade II virus type.
    Status: active. First released: 2.2.3. Last updated: 2.2.3.
  • Dengue Virus Type 1 (den1). Dengue virus, Type 1, general measurement
    Status: active. First released: 2.2.3. Last updated: 2.2.3.
  • Dengue Virus Type 2 (den2). Dengue virus, Type 2, general measurement
    Status: active. First released: 2.2.3. Last updated: 2.2.3.
  • Dengue Virus Type 3 (den3). Dengue virus, Type 3, general measurement
    Status: active. First released: 2.2.3. Last updated: 2.2.3.
  • Dengue Virus Type 4 (den4). Dengue virus, Type 4, general measurement
    Status: active. First released: 2.2.3. Last updated: 2.2.3.
  • Male-specific (F+) coliphage - general (fColiphage). Male-specific (F+) coliphage - general
    Status: active. First released: 2.2.3. Last updated: 2.2.3.

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.
  • 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.
  • Inhibition method (inhibMeth). Description of the method used to evaluate molecular inhibition.
    Status: active. First released: 1.0.0. Last updated: 2.0.0.
  • 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.
  • PCR sequencingsSelection 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: 2.0.0.
  • 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.
  • 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.
  • Sequencing Layout (seqLay). The layout of genetic material used in sequencing.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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.
  • 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.
  • 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.
  • 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.
  • Undisclosed (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.
  • 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.
  • Undisclosed (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.

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: 2.0.0.
  • TRUE (TRUE). Boolean data type = TRUE
    Status: active. First released: 1.0.0. Last updated: 2.0.0.

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.
  • Composite sample - archival (comp). A composite sample, usually generated by an autosampler.
    Status: active. First released: 1.0.0. Last updated: 2.0.0.
  • 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.
  • 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.
  • 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.

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.
  • 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.
  • 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 (sol). Solid fraction of a sample.
    Status: active. First released: 1.0.0. Last updated: 2.0.0.

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.

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.
  • 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.
  • 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.

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.

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.
  • 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.
  • 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.
  • 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.

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: depreciated. First released: 2.0.0. Last updated: 2.1.0.
  • Countries or sovereign states (countryLevel). Countries or sovereign states
    Status: depreciated. First released: 2.0.0. Last updated: 2.1.0.
  • Districts, counties, regions (countyLevel). Districts, counties, regions
    Status: depreciated. First released: 2.0.0. Last updated: 2.1.0.
  • Municipalities or communes (municipalLevel). Municipalities or communes
    Status: depreciated. First released: 2.0.0. Last updated: 2.1.0.
  • Local administrative units or neighborhoods (neighborLevel). Local administrative units or neighborhoods
    Status: depreciated. First released: 2.0.0. Last updated: 2.1.0.
  • Departments, states, or provinces (stateProvLevel). Departments, states, or provinces
    Status: depreciated. First released: 2.0.0. Last updated: 2.1.0.

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.
  • 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 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.

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 sample (derived). A sample that is derived or made from another sample or material.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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 set

(outbreakSet)set for the valid values of the outbreak measure.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.
  • Outbreak End (outbEnd). Indicates an outbreak has ended.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Outbreak - on-going (outbOngoing). Indicates an outbreak is on-going.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Outbreak start (outbStart). Indicates an outbreak began.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.

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 methodID.
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 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.

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.
  • 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.
  • 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 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 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 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 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 reverse primer (IDT) (cdcCovN3IDTRev). 2019-nCoV_N3 reverse primer (IDT)
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • PMMV forward primer (ABI) (pmmvABIFor). PMMV forward primer (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 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.
  • Education (education). A measure or sample taken for education or training.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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.
  • 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.
  • Regular (regular). A measure or sample taken for surveillance or epidemiology.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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.
  • Validation study (validationStudy). A meaure or sample taken for a validation study.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.

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 sample (colocated). Second or multiples samples collected at same location but different time (water, air) or at a nearby location (soil, sediment). Sent blind to laboratory.
    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.
  • 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.
  • Co-located sample (colocated). Second or multiples samples collected at same location but different time (water, air) or at a nearby location (soil, sediment). Sent blind to laboratory.
    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.
  • Unique sample (unique). A unique sample, not duplicated.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.

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.
  • 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: 2.2.3. Last updated: 2.2.3.
  • 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: 2.2.3. Last updated: 2.2.3.
  • 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: 2.2.3. Last updated: 2.2.3.
  • 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: 2.2.3. Last updated: 2.2.3.
  • 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: 2.2.3. Last updated: 2.2.3.
  • 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.
  • 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: 2.2.3. Last updated: 2.2.3.
  • 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: 2.2.3. Last updated: 2.2.3.
  • 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.
  • Passive (trap) sampling (trap). A composite sampler that passively collects a sample without use of electricity or a battery.
    Status: active. First released: 2.2.3. Last updated: 2.2.3.
  • 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: 2.2.3. Last updated: 2.2.3.
  • 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: 2.2.3. Last updated: 2.2.3.

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 sample (colocated). Second or multiples samples collected at same location but different time (water, air) or at a nearby location (soil, sediment). Sent blind to laboratory.
    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.

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.

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 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 sequencingsSelection 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: 2.0.0.
  • 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.
  • 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.

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.
  • 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.
  • 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.
  • Hospital (hosptl). Hospital
    Status: active. First released: 1.0.0. Last updated: 2.0.0.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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: 2.2.3. Last updated: 2.2.3.
  • 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: 2.2.3. Last updated: 2.2.3.
  • 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.

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.
  • 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.
  • 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 A 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 = “measure”.
    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.
  • 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.
  • 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 for protocols.
    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.
  • Summary worksheet Shorthand (su). The abbreviated short name used to reference the Summary sheet of the dictionary.xlxs file.
    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.

Site set

(siteTypeSet)set for the type of sampling site.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.
  • 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.
  • 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.
  • Holding tank (htSite). Holding tank
    Status: active. First released: 1.0.0. Last updated: 2.0.0.
  • Lagoon system (lagoon). Logoon 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.
  • Pumping station (pStat). Pumping station
    Status: active. First released: 1.0.0. Last updated: 2.0.0.
  • 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.
  • Sea, natural water body (sea). Sea, natural water body
    Status: active. First released: 1.0.0. Last updated: 2.0.0.
  • Septic tank (septTnk). Septic tank
    Status: active. First released: 1.0.0. Last updated: 2.0.0.
  • 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.
  • 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.
  • 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.
  • Concentration measure (conc). Measurement of concentration (generalized) - designed for describing protocols.
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • 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.

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.

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.
  • 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.

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.
  • 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.

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.
  • 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.
  • 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.

Quality indicators

(qualityIndicators). A measure of the quality of a reported value or sample. Only used for the dictionary entries of parts.
  • 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.
  • 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 ‚Äö√Ñ√∫trace‚Äö√Ñ√π 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., ‚Äö√Ñ√∫trace‚Äö√Ñ√π 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 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-volume sample (lowVol). Sample is low-volume, but was run regardless.
    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 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: 2.0.0.
  • 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.
  • 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.
  • 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.

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 ‚Äö√Ñ√∫trace‚Äö√Ñ√π 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., ‚Äö√Ñ√∫trace‚Äö√Ñ√π 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: 2.0.0.
  • 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.
  • 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 ‚Äö√Ñ√∫trace‚Äö√Ñ√π 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., ‚Äö√Ñ√∫trace‚Äö√Ñ√π 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: 2.0.0.
  • 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.
  • 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.
  • Experiment Failed (expFail). PCR experiment failed. No value reported.
    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.
  • 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: 2.0.0.
  • 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.
  • 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.

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.
  • 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.
  • 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.

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.

Tables

(tables). Tables are where measures, methods and attributes are recorded. Tables represent the main entities of the environmental surveillance. There 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.
  • Address table (addresses). The table that contains information about addresses. Addresses can recorded for sites, organizations or contacts (indivduals).
    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.
    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.
    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.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Instrument table (instruments). The table that contains information about instruments.
    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.
    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
    Status: active. First released: 1.0.0. Last updated: 2.0.0.
  • Measure set report table (measureSets). The table that identifies sets of measures.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Organization table (organizations). The table that contains information about a laboratory.
    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.
    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.
    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).
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Protocols table (protocols). The table for protocols.
    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.
    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.
    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.
    Status: depreciated. First released: 1.0.0. Last updated: 2.0.0.
  • Sample relationships table (sampleRelationships). Table for recording the relationships between samples.
    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.
    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.
    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.
    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.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Wide name table (wideNames). The table for wide names.
    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.
    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 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 Onset date (actiOn). Number of active cases by onset 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). Positions with read depth greater or equal to 5.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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.
  • CFU per 100 ml (cfu). Colony forming units per 100 ml of filtered sample.
    Status: active. First released: 1.1.0. 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.
  • 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.
  • 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.
  • 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 sequencing read depth.
    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 per 100,000 people (gcD100). 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 PMMoV copy (gcPpmov). Gene or variant copies per copy of PMMoV.
    Status: active. First released: 1.0.0. Last updated: 2.0.0.
  • Gram per cubic metre (gm3). Density unit.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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.
  • Intercept (inter). Intercept value of the calibration curve.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • 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.
  • 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 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.
  • 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 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.
  • Milligrams per litre (mgL). Milligrams per litre.
    Status: active. First released: 1.1.0. Last updated: 2.0.0.
  • 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.
  • Months (months). A unit for indicating a length of time in months.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Metres per second (mps). metres per second.
    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.
  • Population of newly vaccinated persons (newVax). Population of newly vaccinated persons
    Status: active. First released: 2.0.0. Last updated: 2.0.0.
  • Nano-molar (nM). the unit of nanomolar.
    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.
  • 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.
  • Percent (perc). Percentage.
    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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

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 sequencing read depth.
    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 day per 100,000 people (gcD100). 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 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.
  • 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.
  • CFU per 100 ml (cfu). Colony forming units per 100 ml of filtered sample.
    Status: active. First released: 1.1.0. Last updated: 2.0.0.

Capacity unit set

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

Volume flow rate unit set

(flowUnitSet)Unit set for volume flow measurements.
Status: active. First Released: 2.0.0. Last updated: 2.0.0.
  • Kilogram per second (kgS). Kilograms per second.
    Status: active. First released: 1.0.0. Last updated: 2.0.0.
  • 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 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). Positions with read depth greater or equal to 5.
    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 sequencing read depth.
    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 per 100,000 people (gcD100). 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 PMMoV copy (gcPpmov). Gene or variant copies per copy of PMMoV.
    Status: active. First released: 1.0.0. Last updated: 2.0.0.
  • Intercept (inter). Intercept value of the calibration curve.
    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.
    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.

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 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

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.
  • 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.
  • Percent (perc). Percentage.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.

Specific humidity unit set

(specHumidUnitSet)Unit set for specific humidity.
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.

Speed Unit Set

(speedUnitSet)Unit set for reporting speeds (centrifugation speed, etc.)
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.
  • Milligrams per litre (mgL). Milligrams per litre.
    Status: active. First released: 1.1.0. Last updated: 2.0.0.
  • Nano-molar (nM). the unit of nanomolar.
    Status: active. First released: 2.2.0. Last updated: 2.2.0.
  • 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 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.

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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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: depreciated. First Released: 1.0.0. Last updated: 2.0.0.
  • Metres per second (mps). metres per second.
    Status: active. First released: 2.0.0. Last updated: 2.0.0.