The file biota_data.csv contains the contaminant and biological effect data in biota used to construct the National Performance Framework Clean Seas Indicator 2020. The data are also used to make regional assessments of status and trends in Scottish waters for selected contaminant and biological effect groups in biota. The data are a subset of the cleaned and processed data used in the 2020 assessment of the UK's Clean Seas Environment Monitoring Programme (CSEMP) and were extracted from the MERMAN database on 30 March 2022.

The file is UTF-8-BOM encoded so can be read directly into Excel, or into R using the function read.csv with the argument fileEncoding = “UTF-8-BOM”.

The variables in the file are:

series
Description: timeseries identifier
Unit:
Type: categorical
Levels: 2488
Notes:
* identifies the data (typically a station / contaminant / species / matrix combination) that were grouped together into a timeseries and modelled to assess status and trends
* the identifier links to the data and results in the 2020 CSEMP assessment

biogeographic_region
Description: biogeographic assessment region
Unit:
Type: categorical
Levels: Northern North Sea, Irish Sea, Minches & Western Scotland, Scottish Continental Shelf
Note: these regions are the Scottish component of the biogeographic regions used for Charting Progress 2 and for UK MS reporting purposes. There are 5 regions in Scottish waters, but there are no stations in the Atlantic North-West Approaches because it is difficult to sample. The Northern North Sea, Minches and Western Scotland and Irish Sea (Clyde & Solway) are used in the Clean Seas Indicator. The Scottish Continental Shelf is not used in the Indicator because it is difficult to get sufficient spatial coverage for regional assessments for both biota and sediment.

station
Description: monitoring station
Unit:
Type: categorical
Levels: 100
Note:

latitude
Description: station latitude
Unit: decimal degrees
Type: continuous
Range: 54.75, 61.10
Note: this is a nominal position: sampling occurs in a pre-defined area broadly centred on this position

longitude
Description: station longitude
Unit: decimal degrees
Type: continuous
Range: -7.05, 1.20
Note: this is a nominal position: sampling occurs in a pre-defined area broadly centred on this position

MSTAT
Description: type of monitoring station
Unit:
Type: categorical
Levels: B, RH, IH
Note: baseline (B), reference (RH) or impacted (IH)

WLTYP
Description: station typography
Unit:
Type: categorical
Levels: Estuary, Coast, Open Sea
Note:

monitoring_year
Description: monitoring year
Unit:
Type: discrete
Range: 1999, 2019
Note: for some data suppliers, monitoring is in winter and e.g. sampling in December 2018 and January 2019 would be regarded as having come from the same monitoring year

sample_id
Description: sample identifier
Unit:
Type: categorical
Levels: 8782
Note: data from different matrices (e.g. LI and MU) in the same fish have different sample_ids

sample_date
Description: sampling date
Unit:
Type: discrete
Range: 1999-01-17, 2019-08-29
Note:

sample_time
Description: sampling time
Unit:
Type: continuous
Range: 00:00:00, 23:29:00
Note:

sample_latitude
Description: sampling latitude
Unit: decimal degrees
Type: continuous
Range: 54.67, 61.01
Note:

sample_longitude
Description: sampling longitude
Unit: decimal degrees
Type: continuous
Range: -7.03, 1.22
Note:

species
Description: species
Unit:
Type: categorical
Levels: 6
Note:
* Gadus morhua: AphiaID = 126436
* Limanda limanda: AphiaID = 127139
* Mytilus edulis: AphiaID = 140480
* Nucella lapillus: AphiaID = 140403
* Platichthys flesus: AphiaID = 127141
* Pleuronectes platessa: AphiaID = 127143

sex
Description: sex
Unit:
Type: categorical
Levels: F, I, M, X
Note: see ICES reference codes for SEXCO

matrix
Description: sample matrix
Unit:
Type: categorical
Levels: BI, LI, LIS9, MU, SB
Note: see ICES reference codes for MATRX

determinand_group
Description: contaminant or biological effect group
Unit:
Type: categorical
Levels: Metals, PAH parent compounds, PAH metabolites, Polybrominated diphenyl ethers, Polychlorinated biphenyls, Imposex, Biological effects (other)
Note:

determinand
Description: contaminant or biological effect
Unit:
Type: categorical
Levels: 48
Notes:
* see ICES reference codes for PARAM
* data submitted as CHRTR and VDSI have been relabelled as CHR and VDS respectively

metoa
Description: method of chemical analysis
Unit:
Type: categorical
Levels: 17
Note: see ICES reference codes for METOA

basis
Description: basis on which the measurement is expressed
Unit:
Type: discrete
Levels: dry weight (D), lipid weight (L) or wet weight (W)
Note:

unit
Description: unit of the concentration measurement and its uncertainty
Unit:
Type: discrete
Levels: pmol/min/mg protein, st, ug/kg, ug/ml
Note:

concentration
Description: concentration of contaminant or equivalent for biological effects
Unit: see unit column
Type: continuous
Range: 0, 2084754
Note:

qflag
Description: less-than qualifier for the concentration measurement
Unit:
Type: categorical
Levels: "", D, <
Notes:

• "" (a blank or missing value) indicates a non-censored measurement
• D indicates the measurement is left-censored at the limit of detection; i.e. the measurement is below the limit of detection, but it is not known by how much; the limit of detection is given in the concentration column
• Q indicates the measurement is left-censored at the limit of quantification; i.e. the measurement is below the limit of quantification, but it is not known by how much; the limit of quantification is given in the concentration column
• < indicates the measurement is left-censored by an unspecified censoring criterion (which could be the limit of detection or quantification); the value of the censoring criterion is given in the concentration column

uncertainty
Description: uncertainty in the concentration measurement
Unit: see unit column
Type: continuous
Range: 0.0013, 171829
Note: analytical uncertainty expressed as the standard deviation; not applicable to some biological effects measurements

LNMEA
Description: mean length
Unit: cm
Type: continuous
Range: 0.42, 84
Note: length of monitoring organism, or mean length if several individuals were pooled; there are unit errors in these data, so the data should be used with caution

DRYWT
Description: dry weight of the sample
Unit: %
Type: continuous
Range: 7.73, 35.6
Note: all values are above the limit of detection

DRYWT_uncertainty
Description: uncertainty in the dry weight measurement
Unit: %
Type: continuous
Range: 0.61, 2.1
Note: analytical uncertainty expressed as the standard deviation

LIPIDWT
Description: lipid weight of the sample
Unit: %
Type: continuous
Range: 0.1, 56.2
Note: all values are above the limit of detection

LIPIDWT_uncertainty
Description: uncertainty in the lipid weight measurement
Unit: %
Type: continuous
Range: 0.019, 5.95
Note: analytical uncertainty expressed as the standard deviation

noinp
Description: number of individuals pooled in the sample
Unit: nr
Type: discrete
Range: 1, 159
Note:

FEMALEPOP
Description: % of the sample that are females
Unit: %
Type: continuous
Range: 17, 100
Note: used to model imposex data when submitted as a pooled sample