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Table 3: Descriptions and allowable criteria for each field header in the data matrix part of
the Biota template for the IRBAS database
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
location_name
unitless
varchar
Yes
name of the location sampled within the site (a unique
identifier that follows naming convention rules)
DoeJ_RiverData_SiteA_1
As per the location_names listed in the Site template:
site_name, underscore, your location name (with no spaces
between characters)
sample_name
unitless
varchar
Yes
name of the sample replicate (a unique identifier that follows
naming convention rules)
DoeJ_RiverData_SiteA_1_biota_AI_38585_1
location_name, type of template ('biota' = flora or fauna),
underscore, type of biota (AI = aquatic benthic invertebrates;
AIH = aquatic hyporheic invertebrates; AID = aquatic drift
invertebrates; GI = groundwater invertebrates; TI = terrestrial
invertebrates, TV = terrestrial vertebrates; NFAV = non-fish
aquatic vertebrates; PP = phytoplankton; BA = benthic algae;
B = bacteria; AMP = aquatic macrophytes; TP = terrestrial
plants; other), underscore, date of sample in generic code,
underscore, sample identifier (replicate number or letter, e.g.
1, 2, 3, a, b, c) all with no spaces between characters. For
example: LeighC_GulfRivers_FUM_1_biota_AI_38585_1
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
sampling_date_start
DD/MM/YYYY
varchar
Yes
date sampling began for this sample
DD/MM/YYYY
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
sampling_date_end
DD/MM/YYYY
varchar
Yes
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
date sampling ended for this sample
DD/MM/YYYY
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
sampling_season
unitless
varchar
Yes
season of sampling based on the date (month) in which
sampling was conducted, using the meteorological seasons
only (starting on the 1st day of Dec, Mar, Jun, Sep) and
according to southern or northern hemisphere location
winter, spring, summer, autumn
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
Biota Data Matrix HEADER:
UNIT
TYPE
Leave blank if this is same date as the start date BUT DO NOT
DELETE THE COLUMN
water_state
unitless
varchar
Yes
water state of sampling location across entire width of wetted
or active channel
wet = lentic or flowing, dry = no surface water, unknown =
unknown
wet
flow_state
unitless
varchar
Yes
flow state of sampling location across entire width of wetted
or active channel
no flow = lentic, flow = flowing, dry = dry (no water),
unknown = unknown
no flow
biota_type
unitless
varchar
MANDATORY
DEFINITION
UNIVERSE of data cell entry
Yes
group of organisms sampled
fish, aquatic invertebrates, terrestrial invertebrates,
terrestrial vertebrates, non-fish aquatic vertebrates,
phytoplankton, benthic algae, bacteria, aquatic macrophytes,
terrestrial vegetation, other
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
sampling_strategy
unitless
varchar
Yes
overall strategy (design) used to locate samples of this type
random, haphazard, systematic, stratified, stratified random,
stratified haphazard, stratified systematic, NA, entire location
Describes how were the positions of individual samples within
a location chosen
sampling_strategy_coverage
unitless
varchar
Yes
strategy used to collect samples of this type
patch-weighted composite-habitat sample, habitat specific
sample, depth-integrated profile sample, depth-specific
sample
Provides additional information to that provided in
"sampling_strategy"
sampling_strategy_treatment
unitless
varchar
Yes
experimental treatment subjected or applicable to samples of
this type
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
flow cessation, drying out, nutrient addition, control
Leave blank if this does not apply to your data BUT DO NOT
DELETE THE COLUMN
Biota Data Matrix HEADER:
UNIT
sampling_protocol
unitless
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
varchar
Yes
method (including equipment) used to collect samples of this
type
dipnet, kicknet, gill net, fykenet, drift net, leaf pack,
colonisation trap, electrofishing, pit-fall trapping, plankton
net, emergence trap, butterfly net, Schindler-Patalas sampler,
Bou-Rouch pump, vacuum pump, freeze-corer, Surber
sampler, Hess sampler, seine net, three-pass depletion seine
net, floating pan, NA
Write "NA" if none of the listed protocol methods apply to
your sample type. AND DO NOT DELETE THE COLUMN
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
sampling_protocol_mesh_size
m
integer
Yes
mesh size if net used to collect sample
from 0 to 10000
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
sampling_zone
unitless
varchar
Yes
the general type of environment ('zone') in which the sample
was taken
riparian zone, hyporheic zone, benthic zone, water column,
groundwater, other
UNIVERSE of data cell entry
Leave blank if this does not apply e.g. nets were not used BUT
DO NOT DELETE THE COLUMN
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
sampling_habitat
unitless
varchar
Yes
type of habitat(s) sampled to collect this type of sample
main channel, open water, edge, rifle, pool, run, backwater,
floodplain, riparian zone, dry bed, macrophyte bed, snags,
composite
NAL INSTRUCTIONS
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
number_samples
unitless
integer
Yes
number of individual samples from which the data
corresponding to this sample is derived (1 when the sample is
a unique replicate, >1 when the sample data is a mean of
multiple replicates)
from 1 to 100
quantitative_sampling_depth
m
float
Yes
quantitative depth in water, soil or sediment at which sample
was taken (from the water surface for water samples, from
the bed or soil surface if sediment or soil samples)
from 0 to 100
Leave blank if this does not apply to your data BUT DO NOT
DELETE THE COLUMN
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
qualitative_sampling_depth
unitless
varchar
Yes
qualitative depth at which sample was taken
surface, bottom, complete depth profile, NA
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
area_sampled
m2
integer
Yes
area from which one sample was obtained
from 0 to 1000
Write "NA" if the allowable options do not apply to your data
BUT DO NOT DELETE THE COLUMN
Leave blank if this does not apply to your data BUT DO NOT
DELETE THE COLUMN
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
volume_sampled
m3
integer
Yes
volume from which one sample was obtained
from 0 to 1000
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
time_per_sample
minutes
float
Yes
time taken to obtain one sample
from 0 to 300000
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
type_of_abundance_data
unitless
varchar
Yes
type of abundance data
density = number/m2, arealrate = number/m2/d, volumetric =
number/m3, volrate = number/m3/d, count = number per
sample, biomass = mg per sample, occurence = 0 or 1;
controlled count$integer = count up to a maximum
predefined number of individuals, replace "integer" with the
relevant predefined number; all 0 = known absence (leave
blank if not a real absence)
count
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
Biota Data Matrix HEADER:
UNIT
TYPE
MANDATORY
DEFINITION
UNIVERSE of data cell entry
EXAMPLES of data cell entry
NAMING
CONVENTION/COMMENTS/ADDITIO
NAL INSTRUCTIONS
Leave blank if this does not apply to your data BUT DO NOT
DELETE THE COLUMN
Leave blank if this does not apply to your data BUT DO NOT
DELETE THE COLUMN
e.g. Allodessus$larva
see ‘type_of_abundance_data’
float
Yes
‘abundance’ of the taxon identified in the sample
The following columns and rows of the biota template data
matrix contain the taxon names of flora/ fauna and their
‘abundances’ (counts or biomass data, or densities, or
presences/absences of the taxa) – essentially a taxon by
sample matrix where columns are the taxa, the rows are the
samples, and the cells contain the ‘abundance’ data. You
must create the headers (taxon names) for these columns
yourself, and enter the ‘abundances’ under each taxon name
(i.e. column) in the relevant sample row.
Use the following naming convention for taxon names:
Header name (the name of the taxon) followed by optional
qualifiers if you want to indicate life stage information
(written with no spaces between characters). Optional
qualifiers are: adult, larva (for larva or nymphs), pupa, or YOY
(for young of the year). E.g. Allodessus$larva. In cases of
unnamed/unclassified identifications and in terms of levels of
taxonomic resolution (e.g. you have a taxon or taxa identified
and counted as Allodessus sp. or Allodessus spp.) you must
only use the known and accepted name: i.e. in this case, enter
the taxon at the generic level of resolution using the name
Allodessus only (delete any sp. or spp. terms in your dataset),
followed by an optional life stage qualifier if known.