Methods data
Records type and descriptions of methods used for sampling, extraction, fractionation and analysis
Source:vignettes/methods_data.qmd
Introduction
Methodology can significantly affect measured values, and this information is vital to understanding the overall environmental context. In the Methods data table, we classify methodology into four categories:
- Sampling protocol: how were physical samples or information collected from the environment?
- Extraction protocol: how was a substance of interest (analyte) extracted from its matrix?
- Fractionation protocol: what fraction of the analyte was analysed? how was this fraction obtained?
- Analytical protocol: what analytical techniques were used to determine the quantity of analyte in the sample?
These methodologies are structured for the collection of data on chemicals stressors, which reflects the dominant use case of the format so far. Extension to cover a greater range of non-chemical stressors is planned for future versions.
Currently no external ontology or taxonomy is used for methodology. The Chemical Methods Ontology (CMO) may be appropriate, and we will continue to review its progress to determine the appropriate form of any harmonisation.
The Methods table is a metadata table that is transformed before being linked to the Measurements table. Because it is assumed that each measurement will typically have a sampling, extraction, fractionation, and analytical protocol associated with it, the measurements table has a foreign key for each type of methdology that references the relevant Protocol ID.
initialise_methods_tibble()
#> # A tibble: 0 × 5
#> # ℹ 5 variables: PROTOCOL_ID <chr>, CAMPAIGN_NAME <chr>,
#> # PROTOCOL_CATEGORY <chr>, PROTOCOL_NAME <chr>, PROTOCOL_COMMENT <chr>Variables
Protocol ID
PROTOCOL_ID - string, free, mandatory
A short, terse identifier for the protocol. This is used as a primary key for Methods data and a foreign key in the Sampling Protocol, Extraction Protocol, Fractionation Protocol, and Analytical Protocol columns. Measurements data.
Protocol IDs are automatically generated based on the protocol type, short name, campaign name, and, in cases where more than one of a type of technique is used per campaign, sequence number. This is theoretically vulnerable to colisions, and a hashed or serial key would be safer, but this is not anticipated to be a problem at the current scale of use at the format. Additionally, it is far easier to read and intepret for humans.
generate_protocol_id(
protocol_type = "Analytical Protocol",
protocol_name = "ICP-MS",
sequence_number = 1,
campaign_name = "Test_Campaign"
)
#> [1] "A01_ICPMS_TestCampai"Campaign Name
CAMPAIGN_NAME - string, free, mandatory
A short, terse identifier for the campaign. Foreign key referenced from Campaign data, used to generate Protocol ID.
Protocol Category
PROTOCOL_CATEGORY - string, controlled vocabulary, mandatory
The category of protocol/method (Sampling, Extraction, Fractionation, Analytical).
protocol_categories_vocabulary()
#> [1] "Sampling Protocol" "Fractionation Protocol" "Extraction Protocol"
#> [4] "Analytical Protocol"Protocol Name
PROTOCOL_NAME - string, controlled vocabulary, mandatory
The consensus name (short and long) of a protocol or method used in sampling. Options are currently based on the aquatic ecotoxicology domain, but will be extended and harmonised with relevant ontologies and taxonomies as practical.
sampling_protocols_vocabulary()
#> # A tibble: 22 × 3
#> Protocol_Type Short_Name Long_Name
#> <chr> <chr> <chr>
#> 1 Sampling Protocol Not relevant Not relevant
#> 2 Sampling Protocol Not reported Not reported
#> 3 Sampling Protocol Point Point sampling
#> 4 Sampling Protocol Composite Composite sampling
#> 5 Sampling Protocol Trawl Trawl sampling
#> 6 Sampling Protocol Grab Grab sampling
#> 7 Sampling Protocol Core Core sampling
#> 8 Sampling Protocol Seine net Seine net sampling
#> 9 Sampling Protocol Electrofishing Electrofishing
#> 10 Sampling Protocol Plankton net Plankton net sampling
#> # ℹ 12 more rows
extraction_protocols_vocabulary()
#> # A tibble: 19 × 3
#> Protocol_Type Short_Name Long_Name
#> <chr> <chr> <chr>
#> 1 Extraction Protocol Not relevant Not relevant
#> 2 Extraction Protocol Not reported Not reported
#> 3 Extraction Protocol None No extraction
#> 4 Extraction Protocol Methanol Methanol extraction
#> 5 Extraction Protocol Dichloromethane Dichloromethane extrac…
#> 6 Extraction Protocol SPE Isolute Env+ Solid phase extraction…
#> 7 Extraction Protocol Membrane filtration 0.45um Membrane filtration th…
#> 8 Extraction Protocol Membrane filtration 0.2um Membrane filtration th…
#> 9 Extraction Protocol Membrane filtration Membrane filtration
#> 10 Extraction Protocol Filtration Filtration
#> 11 Extraction Protocol Microwave-assisted acid digestion Microwave-assisted aci…
#> 12 Extraction Protocol Acid digestion Acid digestion
#> 13 Extraction Protocol Pressurised liquid Pressurised liquid ext…
#> 14 Extraction Protocol Ultrasonic Ultrasonic extraction
#> 15 Extraction Protocol Soxhlet Soxhlet extraction
#> 16 Extraction Protocol QuEChERS Quick easy cheap effec…
#> 17 Extraction Protocol Accelerated solvent Accelerated solvent ex…
#> 18 Extraction Protocol Sequential extraction Sequential extraction …
#> 19 Extraction Protocol Other Other
fractionation_protocols_vocabulary()
#> # A tibble: 19 × 3
#> Protocol_Type Short_Name Long_Name
#> <chr> <chr> <chr>
#> 1 Fractionation Protocol Not relevant Not relevant
#> 2 Fractionation Protocol Not reported Not reported
#> 3 Fractionation Protocol Total Total fraction
#> 4 Fractionation Protocol Particles Particulate fraction
#> 5 Fractionation Protocol Colloidal Colloidal fraction
#> 6 Fractionation Protocol LMM Low molecular mass fraction
#> 7 Fractionation Protocol Aqueous Aqueous fraction
#> 8 Fractionation Protocol Filtered 0.45um Filtered through 0.45 micrometer me…
#> 9 Fractionation Protocol Filtered 0.2um Filtered through 0.2 micrometer mem…
#> 10 Fractionation Protocol Dissolved Dissolved fraction
#> 11 Fractionation Protocol Filtered Filtered fraction
#> 12 Fractionation Protocol Acid extractable Acid extractable fraction
#> 13 Fractionation Protocol Reducible Reducible fraction
#> 14 Fractionation Protocol Oxidisable Oxidisable fraction
#> 15 Fractionation Protocol Residual Residual fraction
#> 16 Fractionation Protocol Bioavailable Bioavailable fraction
#> 17 Fractionation Protocol Free ion Free ion activity
#> 18 Fractionation Protocol Size fractionated Size fractionated
#> 19 Fractionation Protocol Other Other
analytical_protocols_vocabulary()
#> # A tibble: 15 × 3
#> Protocol_Type Short_Name Long_Name
#> <chr> <chr> <chr>
#> 1 Analytical Protocol Not relevant Not relevant
#> 2 Analytical Protocol Not reported Not reported
#> 3 Analytical Protocol GC-MS Gas chromatography mass spectrometry
#> 4 Analytical Protocol LC-MS Liquid chromatography mass spectromet…
#> 5 Analytical Protocol LC-MS/MS Liquid chromatography tandem mass spe…
#> 6 Analytical Protocol GC-MS/MS Gas chromatography tandem mass spectr…
#> 7 Analytical Protocol UPLC Ultra performance liquid chromatograp…
#> 8 Analytical Protocol ICP-MS Inductively coupled plasma mass spect…
#> 9 Analytical Protocol ICP-OES Inductively coupled plasma optical em…
#> 10 Analytical Protocol AAS Atomic absorption spectroscopy
#> 11 Analytical Protocol XRF X-ray fluorescence spectroscopy
#> 12 Analytical Protocol Ion chromatography Ion chromatography
#> 13 Analytical Protocol Spectrophotometry Spectrophotometry
#> 14 Analytical Protocol Fluorescence Fluorescence spectroscopy
#> 15 Analytical Protocol Other Other
# call all of the above functions bound into a single table
# protocol_options_vocabulary()Protocol Comment
PROTOCOL_COMMENT - string, free, optional
Space for the recording of any additional notes or comments about the method deemed relevant. As information on the specific equipment or more detailed protocols may also be useful, users are encouraged to copy relevant text verbatim from the source.