Parameters data
Records data on stressors (chemical, radiation, etc.), quality measurements
Source:vignettes/parameters_data.qmd
Introduction
The parameters table collects information on stressors, quality parameters, and any other scalar properties measured in the context of adverse environmental effect.
initialise_parameters_tibble()
#> # A tibble: 0 × 10
#> # ℹ 10 variables: PARAMETER_TYPE <chr>, PARAMETER_TYPE_SUB <chr>,
#> # MEASURED_TYPE <chr>, PARAMETER_NAME <chr>, PARAMETER_NAME_SUB <chr>,
#> # INCHIKEY_SD <chr>, PUBCHEM_CID <int>, CAS_RN <chr>, ENTERED_BY <chr>,
#> # PARAMETER_COMMENT <chr>It is expected that most relevant studies will be collecting data on chemical pollutants in the environment. Non-chemicals are accomodated by the format, but they cannot necessarily be as well-characterised as chemicals, where we are able to take advantage of the high-quality infrastructure developed by chemists.
Variables
Parameter Type
PARAMETER_TYPE - string, controlled, mandatory
Parameter type is divided into five classifications and two missing data values. This classification requires a degree of subjective judgement. What makes a chemical a stressor versus a quality parameter is not always clear. However, we anticipate that in most cases this will be uncontroversial. Where this is not the case stressors can still be identified by name/id.
Controlled Vocabulary
parameter_types_vocabulary()
#> [1] "Not relevant" "Stressor" "Quality parameter"
#> [4] "Normalisation" "Background" "Ecological Indicator"
#> [7] "Other""Not relevant" - Use when a type is not applicable to the measured scalar.
"Stressor" - Chemical, physical or biological agent causing stress.
"Quality parameter" - Water/environmental quality parameter.
"Normalisation" - Parameter used for normalising other measurements.
"Background" - Natural background level of a parameter.
"Ecological Indicator" - Parameter is an indicator or metric of ecological concern.
"Other" - Parameter belongs to another category. Please note in comments field.
Parameter Sub-type
PARAMETER_TYPE_SUB - string, controlled, mandatory
Parameter Sub-type is a further subdivision of Parameter Type. The majority of subtypes are chemical classifications from the ChemOnt/ClassyFire chemical taxonomy; other subtypes are intended for use with quality parameters, stressors measured as mixtures, or other cases where additional details are needed. Existing parameters in the format are already assigned a subtype, new parameters should be assigned to a relevant subtype.
Controlled Vocabulary
parameter_types_sub_vocabulary()
#> Warning: `prepend()` was deprecated in purrr 1.0.0.
#> ℹ Please use append(after = 0) instead.
#> ℹ The deprecated feature was likely used in the eDataDRF package.
#> Please report the issue to the authors.
#> [1] "Not relevant"
#> [2] "Not reported"
#> [3] "Other"
#> [4] "Acetylides"
#> [5] "Alkaloids and derivatives"
#> [6] "Allenes"
#> [7] "Benzenoids"
#> [8] "Carbon"
#> [9] "Conductivity"
#> [10] "Dissolved oxygen"
#> [11] "Homogeneous metal compounds"
#> [12] "Homogeneous non-metal compounds"
#> [13] "Hydrocarbon derivatives"
#> [14] "Hydrocarbons"
#> [15] "Inorganic salts"
#> [16] "Lignans, neolignans and related compounds"
#> [17] "Lipids and lipid-like molecules"
#> [18] "Miscellaneous inorganic compounds"
#> [19] "Mixed metal/non-metal compounds"
#> [20] "Mixture"
#> [21] "Nucleosides, nucleotides, and analogues"
#> [22] "Nutrient"
#> [23] "Organic 1,3-dipolar compounds"
#> [24] "Organic acids and derivatives"
#> [25] "Organic nitrogen compounds"
#> [26] "Organic oxygen compounds"
#> [27] "Organic Polymers"
#> [28] "Organic salts"
#> [29] "Organohalogen compounds"
#> [30] "Organoheterocyclic compounds"
#> [31] "Organometallic compounds"
#> [32] "Organophosphorus compounds"
#> [33] "Organosulfur compounds"
#> [34] "pH"
#> [35] "Phenylpropanoids and polyketides"
#> [36] "Salinity"
#> [37] "Temperature"
#> [38] "Total organic carbon"
#> [39] "Turbidity"Parameter Name
PARAMETER_NAME - string, controlled, mandatory
Parameter name records the reported name of a measured parameter. In the majority of cases this will be a short-form conventional chemical name; these are, as above taken from ChemOnt/ClassyFire. To maximise standardisation we recommend use of the existing available names rather than entering new ones; this may require some manual validation of CAS codes, InChIKeys, etc.
Parameter name is currently used as the primary key for the Parameters data table and a foreign key in the Samples and Measurements tables.
Controlled Vocabulary
parameters_vocabulary() |> dplyr::slice_head(n = 20)
#> # A tibble: 20 × 9
#> PARAMETER_TYPE PARAMETER_NAME PARAMETER_TYPE_SUB MEASURED_TYPE CAS_RN
#> <chr> <chr> <chr> <chr> <chr>
#> 1 Quality parameter pH pH Physical par… <NA>
#> 2 Quality parameter Dissolved oxygen Dissolved oxygen Concentration 7782-…
#> 3 Quality parameter Temperature Temperature Physical par… <NA>
#> 4 Quality parameter Conductivity Conductivity Physical par… <NA>
#> 5 Quality parameter Salinity Salinity Physical par… <NA>
#> 6 Quality parameter Turbidity Turbidity Physical par… <NA>
#> 7 Quality parameter Total organic carb… Total organic car… Concentration <NA>
#> 8 Quality parameter Alkalinity Other Concentration <NA>
#> 9 Quality parameter Hardness Other Concentration <NA>
#> 10 Quality parameter Chlorophyll a Other Concentration 479-6…
#> 11 Quality parameter Total suspended so… Other Concentration <NA>
#> 12 Quality parameter Biochemical oxygen… Other Concentration <NA>
#> 13 Quality parameter Chemical oxygen de… Other Concentration <NA>
#> 14 Quality parameter Nitrate Nutrient Concentration 14797…
#> 15 Quality parameter Nitrite Nutrient Concentration 14797…
#> 16 Quality parameter Ammonia Nutrient Concentration 7664-…
#> 17 Quality parameter Total nitrogen Nutrient Concentration <NA>
#> 18 Quality parameter Phosphate Nutrient Concentration 14265…
#> 19 Quality parameter Total phosphorus Nutrient Concentration <NA>
#> 20 Quality parameter Redox potential Other Physical par… <NA>
#> # ℹ 4 more variables: PUBCHEM_CID <int>, INCHIKEY_SD <chr>, ENTERED_BY <chr>,
#> # PARAMETER_NAME_SUB <chr>Parameter Sub-Name
PARAMETER_NAME_SUB - string, controlled, optional
In some cases it may be necessarily to identify parameters at a finer level of detail than is permitted by the above fields - for example, individual wavelengths of ionising radiation. In this case the Parameter Sub-Name field should be used; otherwise it can be left blank.
InChIKey
INCHIKEY_SD - string, free, optional
The IUPAC International Chemical Identifier (InChI) is a widely used chemical identifier based on the molecular structure of a chemical. The InChIKey is a 27-character string of letters and seperator characters (e.g., for ethanol: LFQSCWFLJHTTHZ-UHFFFAOYSA-N) and has become the a gold-standard chemical identifier. As not all parameters are chemicals, this field has been left as optional, but where chemicals are quantified, it is strongly preferred that an InChIKey be made available.
PubChem CID
PUBCHEM_CID - integer, free, optional
The PubChem database uses an internal identifier known as the PubChem Compound Identifier. This is an integer accession number. InChIKeys are strongly preferred for identification, but a PubChem CID can be included if desired for cross-referencing.
CAS Registry Number
CAS_RN- string, free, optional
The Americal Chemical Society maintains an extensive registry of chemicals. CAS Registry Numbers are widely used to identify individual chemicals. In some cases, a single substance may have more than one CAS, and not all substances will have a CAS assigned. InChIKeys are strongly preferred for identification, but a CAS RN can be included if desired for cross-referencing.
Entered By
ENTERED_BY - string, free, mandatory
The name or email address of the user entering data. As many parameters are included as part of the format, this will only be needed if a new parameter is added.
Parameter Comment
PARAMETER_COMMENT - string, free, optional
Space for the recording of any additional notes or comments about the parameter deemed relevant.