Biota data
Where relevant, records biota species, tissue, life stage, and gender
Source:vignettes/biota_data.qmd
Introduction
Where biota are sampled, it becomes important to capture considerable additional information. Species, tissue type, gender, lifestage, and other factors can considerably affect exposure to pollutants, and thus this information is important to put their occurence in its full context.
The Biota table is an intermediate table that extends the Samples data table where biota compartments are selected. Otherwise, this element of the data entry workflow is skipped as irrelevant.
initialise_biota_tibble()
#> # A tibble: 0 × 14
#> # ℹ 14 variables: SAMPLE_ID <chr>, SITE_CODE <chr>, PARAMETER_NAME <chr>,
#> # ENVIRON_COMPARTMENT <chr>, ENVIRON_COMPARTMENT_SUB <chr>,
#> # MEASURED_CATEGORY <chr>, SAMPLING_DATE <chr>, SUBSAMPLE <chr>,
#> # SPECIES_GROUP <chr>, SAMPLE_SPECIES <chr>, SAMPLE_TISSUE <chr>,
#> # SAMPLE_SPECIES_LIFESTAGE <chr>, SAMPLE_SPECIES_GENDER <chr>,
#> # BIOTA_COMMENT <chr>Variables
Sample ID
SAMPLE_ID - String, free, mandatory
Transcribed from Sample ID in the Samples data.
Site Code
SITE_CODE - String, free, mandatory
Transcribed from Site Code in the Samples data.
Parameter Name
PARAMETER_NAME - String, free, mandatory
Transcribed from Parameter Name in the Samples data.
Environmental Compartment
ENVIRON_COMPARTMENT - String, controlled, mandatory
Transcribed from Environmental Compartment in the Samples data.
Environmental Sub-Compartment
ENVIRON_COMPARTMENT_SUB - String, controlled, mandatory
Transcribed from Environmental Sub-Compartment in the Samples data.
Measured Category
MEASURED_CATEGORY - String, controlled, mandatory
Transcribed from Measured Category in the Samples data.
Sampling Date
SAMPLING_DATE - String, free, mandatory
Transcribed from Sampling Date in the Samples data.
Subsample
SUBSAMPLE - String, free, mandatory
Transcribed from Subsample in the Samples data.
Species Group
SPECIES_GROUP - String, controlled, mandatory
The rough grouping of species the biota belongs to. This classification is not strictly taxonomic but rather reflects the categories typically used in ecotoxicology. Both species group and name (below) are taken from the EPA’s ECOTOX Knowledgebase and cover approximately 13,000 of the species most used in the field. Where this is insufficent, a species name can be added manually.
In future, we hope to incorporate a more exhaustive species taxonomy or resource.
Controlled Vocabulary
species_groups_vocabulary()
#> [1] "All" "Algae" "Amphibians" "Bacteria"
#> [5] "Birds" "Crustaceans" "Ecosystem" "Fish"
#> [9] "Fungi" "Insects/Spiders" "Invertebrates" "Mammals"
#> [13] "Molluscs" "Moss/Hornworts" "Plants" "Reptiles"
#> [17] "Worms" "Other"Sample Species
SAMPLE_SPECIES - String, controlled, mandatory
The consensus binomial scientific name of the species sampled. As above, both species group and name (below) are taken from the EPA’s ECOTOX Knowledgebase and cover approximately 13,000 of the species most used in the field. Where this is insufficent, a species name can be added manually.
Controlled Vocabulary
species_names_vocabulary()
#> # A tibble: 29,562 × 4
#> SPECIES_COMMON_NAME SPECIES_NAME SPECIES_KINGDOM SPECIES_GROUP
#> <chr> <chr> <chr> <chr>
#> 1 Fathead Minnow Pimephales promelas Animalia Fish
#> 2 Bluegill Lepomis macrochirus Animalia Fish
#> 3 Brook Trout Salvelinus fontinalis Animalia Fish
#> 4 Rainbow Trout Oncorhynchus mykiss Animalia Fish
#> 5 Water Flea Daphnia magna Animalia Crustaceans
#> 6 Scud Gammarus lacustris Animalia Crustaceans
#> 7 Scud Gammarus fasciatus Animalia Crustaceans
#> 8 Water Flea Daphnia pulex Animalia Crustaceans
#> 9 Diatom Nitzschia linearis Chromista Algae
#> 10 Green Crab Carcinus maenas Animalia Crustaceans
#> # ℹ 29,552 more rowsSample Tissue
SAMPLE_TISSUE - String, controlled, mandatory
The tissue type sampled from biota. The controlled vocabulary for this variable is currently very much non-exhaustive. This will be replaced by harmonisation with an existing tissue ontology as practical.
Controlled Vocabulary
tissue_types_vocabulary()
#> [1] "Not reported" "Not relevant"
#> [3] "Whole body" "Total soft tissues"
#> [5] "Muscle" "Liver"
#> [7] "Kidney" "Fat/Adipose"
#> [9] "Skin" "Bone"
#> [11] "Pyloric caeca" "Body wall"
#> [13] "Brain" "Heart"
#> [15] "Lung" "Gill"
#> [17] "Gonad" "Shell"
#> [19] "Carapace" "Digestive Gland"
#> [21] "Mantle" "Blood"
#> [23] "Egg" "Larva"
#> [25] "Leaf" "Root"
#> [27] "Stem" "Fruit"
#> [29] "Seed" "Brown meat"
#> [31] "Shoot tips" "Disc skeleton"
#> [33] "Echinoid corona" "Bile"
#> [35] "Plant tissue" "Shoot tip"
#> [37] "Total soft tissues minus gonads" "Other"Sample Species Lifestage
SAMPLE_SPECIES_LIFESTAGE - String, controlled, mandatory
The lifestage of an organism at time of sampling. As above, this is currently somewhat restrictive but will be extended and harmonised as practical.
Controlled Vocabulary
lifestage_vocabulary()
#> [1] "Not reported" "Not relevant" "Adult" "Juvenile" "Larva"
#> [6] "Embryo" "Egg" "Seedling" "Mature" "Young"
#> [11] "Mixed" "Other"Sample Species Gender
SAMPLE_SPECIES_GENDER - String, controlled, mandatory
The gender or sex of a sampled organism. May be harmonised as needed.
Controlled Vocabulary
gender_vocabulary()
#> [1] "Not reported" "Not relevant" "Male" "Female"
#> [5] "Mixed" "Hermaphrodite" "Other"Biota Comment
BIOTA_COMMENT - String, free, optional
Space for the recording of any additional notes or comments about the sampled organism deemed relevant.