Tables for animals

SUSPECIES table

Below we show the proportion of fill rows (blue) and frequency of variables across the suspecies DB broken per species type (i.e. amphibians, fishes, birds, mammals, insects, reptiles). Site, site visit variables, trapping effort (sutrap) species name and type are excluded as it is a given that these variables need to be included when present. Broadly the tables can be broken into species type and type of sampling (opportunistic and survey-based). We identified 23 variavles, most variables are self-explanatory and vocabularies can easily be created for them. It would be important to go through a review process with data owners to choose variables to be included.

These tables contain two FOI’s, animal occurrences (for opportunistic method) or animal individuals for the rest

Properties identified

The following properties have been identified for the animal observations in the SUSPECIES TABLE. The definition for properties which already existed in TERN’s global vocabulary have been left in blank. Properties in the LENGTHNR column have been separated into length parameters by pivoting the LENGTH (as values) and LENGTHNR (as column names) columns.

column in BDBSA	type of property	label	definition	source
STRATANR	observation	animal observation height	The height at which the animal was observed, not the average vegetation height of the quadrat.
MACROHABNR	observation	animal habitat description	Description of the habitat where the animal(s) are found.
SPECIESTYPE	attribute	animal group	Group of one or more populations of an organism or organisms seen to form a unit.
NUMOBSERVED	observation	number of indvidual animals		http://linked.data.gov.au/def/tern-cv/42aa8f4e-4815-4a4b-976a-4443cc605fbc
MICROHABNR	attribute	animal relative habitat position	The relative position of animal(s) in the habitat they were found.
SEX	observation	sex		http://linked.data.gov.au/def/tern-cv/05cbf534-c233-4aa8-a08c-00b28976ed36
TEATS	observation	lactating status	Lactating status of teats
VAGINA	observation	vaginal condition	The morphological condition of the vagina (i.e. perforated or not-perforated).
POUCH	observation	animal pouch condition	The morphology of the marsupial pouch.
NUMPOUCH	observation	number of youngs in pouch	Number of young animal inside pouch
TESTES	observation	animal testes condition	The morphology of male reproductive organ (i.e. scrotal and abdominal).
WEIGHT	observation	body mass	The mass of an animal
SNOUT	observation	snout length	Lenght of the projection on the anterior part of the face that includes the nose or nose and mouth
ISGRAVID	observation	gravid state	An organism containing a developing embryo, fetus, or unborn offspring within the body
LENGTH	observation	body length	The distance from point to point along the longest axis of the body of an organism.
LENGTHMETHOD	attribute
ACTIVITY	attribute	animal activity
PLANTEDRELEASED	observation	released status	Indicates whether an animal has been released in the wild.
NUMNIGHTS	attribute	sampling duration		http://linked.data.gov.au/def/tern-cv/20d4e292-adc1-4585-8f81-c2a0e92eacab
NUMELLIOTTRAPA	attribute	number of elliot traps	The total number of elliot traps in a sample.
NUMELLIOTNIGHTS	attribute	sampling duration
NUMPITTRAPA	attribute	number of pitfall traps
NUMPITNIGHTS	attribute	sampling duration
NUMCAGETRAPA	attribute	number of cage traps	The total number of cage traps in a sample.
NUMCAGENIGHTS	attribute	sampling duration
ISHARPTRAP	attribute	harp trap used	Whether a harp trap was used for animal trapping.
ISMISTNET	attribute	mist nest used	Whether a mist net was used for animal trapping.
ISHAIRTUBE	attribute	hair trap used	Whether a hair trap was used for animal detection.
ISBATDETECTOR	attribute	bat detector used	Whether a bat detector was used for bats.
BAITTRAPNUM	attribute	number of bait traps	The total number of bait traps used to sample.
DIPNETHRS	attribute	dip net sampling duration	Duration of the dip net sampling event.
PIVOT LENGTHNR and LENGTH columns	observation	animal length	The distance from point to point along the longest axis of the body of an organism.
PIVOT LENGTHNR and LENGTH columns	observation	snout to venth length	Length from the tip of the snout to the most posterior opening of the cloacal slit (vent).
PIVOT LENGTHNR and LENGTH columns	observation	tail length	The distance from point to point along the longest axis of the appendage at the caudal end of the vertebral column.
PIVOT LENGTHNR and LENGTH columns	observation	disc length	The length from the tip of snout to the junction of the tail and pelvic fins in rays.
PIVOT LENGTHNR and LENGTH columns	observation	mantle length	The standard measure of length in coleoid cephalopods. In decapodiforms ML is measured along the dorsal midline from the mantle margin to the posterior tip of the body, excluding long tails. In octopodiforms ML is measured from a line joining the midpoint of the eyes rather than the anterior mantle margin since the latter is obscured by the head/mantle fusion.
PIVOT LENGTHNR and LENGTH columns	observation	invertebrate carapace length	Measurement in a straight line from the ridge between the two largest spines above the eyes, back to the rear edge of the carapace.
PIVOT LENGTHNR and LENGTH columns	observation	turtle carapace length	Length of the turtles carapace. This can be measured in 3 ways: 1. SCL minimum: from the notch at the anterior of the carapace to the notch at the posterior end of the carapace where the last 2 marginal scutes meet. 2. SCL n-t: from the notch at the anterior of the carapace to the tip of the last posterior marginal scute. Usually measured to whichever scute is longer. 3. SCL maximum: from the anterior edge of the carapace to the tip of the last posterior marginal scute. Usually measured to whichever scute is longer.
PIVOT LENGTHNR and LENGTH columns	observation	fork length	The length of a fish from the tip of its nose to the middle caudal fin rays.
PIVOT LENGTHNR and LENGTH columns	observation	lower jaw fork length	The length of a fish as measured from the tip of its lower jaw to the fork of the tail.
PIVOT LENGTHNR and LENGTH columns	observation	pes length	The length of a pes (i.e. foot).
PIVOT LENGTHNR and LENGTH columns	observation	head Length	The distance from point to point along the longest axis of the portion of the body containing the brain and organs of sight, hearing, taste, and smell.
PIVOT LENGTHNR and LENGTH columns	observation	forearm length	The length of the forearm from the elbow to the wrist.
PIVOT LENGTHNR and LENGTH columns	observation	carapace length	Measurement in a straight line of the carapace.

Tables per species type

The analyses have been broken into tables per species type, as many methods and parameters are species-specific.

Invertebrate

There are 1,064 rows, from those 1,063 are opportunistic and only one is survey-based (probably a misclassification).

Column name	Proportion of empty rows

Column name	Proportion of empty rows
SITEID	0.412594
VISITNR	0.0
VISITDATE	0.0
QUADSITE	0.99906015
PATCHID	0.0
METHODNR	0.0
SITETYPE	0.0
species_name	0.0
NUMOBSERVED	0.0
SPCOMM	0.0028195488
ISCERTAIN	0.0
RECSTATUSCODE	0.0
LENGTH	0.9567669
LENGTHMETHOD	0.9567669
ACTIVITY	0.91917294
PLANTEDRELEASED	0.0

Birds

There are 2,766,896 observations, from those 2,361,902 are opportunistic and 404,994 are survey-based.

Column name	Proportion of empty rows

Column name	Proportion of empty rows
SITEID	0.6974667
VISITNR	0.0
VISITDATE	0.0
QUADSITE	0.84456664
PATCHID	0.0
METHODNR	0.0
STRATANR	0.9468667
MACROHABNR	0.95743334
SITETYPE	0.0
species_name	0.0
NUMOBSERVED	0.0
MICROHABNR	0.9484
TISSUE	0.99983335
SPCOMM	0.33786666
ISCERTAIN	0.0
SEX	0.99976665
RECSTATUSCODE	0.0
SIGHTINGNR	0.3885
ACTIVITY	0.9782
PLANTEDRELEASED	0.0

Amphibians

There are 47,820 rows, from those 44,331 are opportunistic, and 3,489 come from survey methods.

Column name	Proportion of empty rows

Column name	Proportion of empty rows
SITEID	0.7898
VISITNR	0.0
VISITDATE	0.0
QUADSITE	0.9271
PATCHID	0.0
SITETYPE	0.0
LINENR	0.971
METHODNR	0.0
STRATANR	0.9884667
MACROHABNR	0.9906333
species_name	0.0
NUMOBSERVED	0.0
MICROHABNR	0.99036664
TISSUE	0.9862
SPCOMM	0.1218
ISCERTAIN	0.0
SEX	0.99883336
WEIGHT	0.99633336
SNOUT	0.9999
RECSTATUSCODE	0.0
SIGHTINGNR	0.2451
LENGTH	0.99483335
LENGTHMETHOD	0.99483335
PLANTEDRELEASED	0.0

Mammals

There are 347,403 rows, 267,996 are from opportunistic methods, and 79,407 are from survey-based methods.

Column name	Proportion of empty rows

Column name	Proportion of empty rows
SITEID	0.6694
VISITNR	0.0
VISITDATE	0.0
QUADSITE	0.7693
PATCHID	0.0
LINENR	0.9212667
METHODNR	0.0
STRATANR	0.9755
MACROHABNR	0.9762
SITETYPE	0.0
species_name	0.0
NUMOBSERVED	0.0
MICROHABNR	0.9842
TISSUE	0.9752
SPCOMM	0.45576668
ISCERTAIN	0.0
SEX	0.8231
TEATS	0.9784333
VAGINA	0.9754
POUCH	0.9845333
NUMPOUCH	0.9989333
TESTES	0.9635
WEIGHT	0.8860667
RECSTATUSCODE	0.0
SIGHTINGNR	0.66496664
LENGTH	0.95606667
LENGTHMETHOD	0.95603335
ACTIVITY	0.99986666
PLANTEDRELEASED	0.0

Fish

There are 278,914 rows, 278,913 are from opportunistic sightings, and 1 from survey-based methods (probably a misclassification).

Column name	Proportion of empty rows

Column name	Proportion of empty rows
SITEID	0.30493334
VISITNR	0.0
VISITDATE	0.0
PATCHID	0.0
METHODNR	0.0
SITETYPE	0.0
species_name	0.0
NUMOBSERVED	0.0
SPCOMM	0.6362333
ISCERTAIN	0.0
SEX	0.98066664
WEIGHT	0.94516665
RECSTATUSCODE	0.0
LENGTH	0.14366667
LENGTHMETHOD	0.14366667
ACTIVITY	0.9757
PLANTEDRELEASED	0.0

Reptiles

There are 194,895 rows, 138,916 are from opportunistic sighting 55,979 are from survey-based methods

Column name	Proportion of empty rows

Column name	Proportion of empty rows
SITEID	0.64203334
VISITNR	0.0
VISITDATE	0.0
QUADSITE	0.7113
PATCHID	0.0
LINENR	0.8857667
METHODNR	0.0
STRATANR	0.89306664
MACROHABNR	0.88766664
species_name	0.0
NUMOBSERVED	0.0
MICROHABNR	0.9098667
TISSUE	0.9263
SPCOMM	0.4187
ISCERTAIN	0.0
SEX	0.9584
WEIGHT	0.9628
SNOUT	0.97833335
ISGRAVID	0.99866664
RECSTATUSCODE	0.0
LENGTH	0.9457
LENGTHMETHOD	0.9457
PLANTEDRELEASED	0.0

SUVERTPRESENCE

This table contains 22,967 observations about animal occurrence inferrred by different methods (e.g. presence of dung, tracks, burrows). As such this dataset can be modelled as an animal occurrence with a single parameter (animal type).

BDBSA Dataset Integration