Overview of BDBSA data model

Below is the overview of the alignment between TERN and BDBSA. The alignment will be broken by collection type, starting with plant records on the survey collection (appended with “SU” on tables). Individual data models and preprocessing steps will be displayed below.

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Relationship diagram for BDBSA Collection

SUSPECIES for plants

This single table contains all of the survey- and opportunistic-based measurements on plants and animals.

For filtering the records into survey and observation-based the following joins are needed, table name convention would be tern_survey_suspeciesY

For getting the full scientific name

Preingestion processing of targeted tables

The SUSPECIES table combines three different FOI’s and data types for plants:

1. survey based data for plant populations which are observed on plots

2. survey based data for plant individuals which are observed on plots

3. opportunistic samples of plant occurrences that are plot-less

4. All records need to be filtered by ISCERTAIN = Y

Because of this and rows in the mapping have a 1:1 relationship with an FoI (i.e. a parameter cannot belong to more than one FoI), the data will be separated into three tables for processing: survey-plant population, survey-plant individual and opportunistic-plant occurrence.

NUMOBSERVED column

This column whenever present will be separated into two variables:

NUMOBSERVED: all numeric values >0 will be kept in NUMOBSERVED. 0 values and Non-numeric values will be transformed to NULL values

PRESENCE: This column will have two values “none detected“ and “present”. The “present” value will be all numeric values > 0 in the NUMOBSERVED column as well as the several, present but not countedand Present but not counted values. “none detected” will be all the 0 and none detected values in the NUMOBSERVED column.

Columns from other tables shared across FOI’s

suplantlfstage has to be join to the suspecies table

This table contains two parameters that are shared across plant opportunistic, population and individual FOI’s.

Notice that the following column need to be created for occurrence, individuals and populations

“LIFESTAGECODE”. The following conversion needs to be done for the “LIFESTAGECODE” included in the database

1. DE category has to be converted to D

2. N category has to be converted to V

3. SP needs to be converted to X

4. RE to V (Note while the RE category can become either Vegetative or Regenerating the plants listed as RE in the Database only contain many herbaceous annual species suggesting that they must be in a vegetative state, N of record under RE = 15)

Survey columns individuals

1. Select data for survey only

2. Select data for individuals using DBH as key

3 . For individuals the following variables from the suspecies table will be ingested:

PLANTEDRELEASED_individual, CROWN_EXTENT_PERC, CROWN_EXTENT_SCORE, CROWN_DENSITY_PERC, CROWN_DENSITY_SCORE, DBH, NEW_TIP_GROWTH, EPICORMIC_GROWTH, EXTENT_REPRODUCTION, MISTLETOE_LOAD, LEAF_DIE_OFF, LEAF_DAMAGE, EXTENT_BARK_CRACKING

Notice that the following columns need to be created for both individuals and populations “PLANTEDRELEASED” and species_name columns into “PLANTEDRELEASED_tree” and “species_name_tree”and “PLANTEDRELEASED_population” and “species_name_population”

4. The scientific name of the species comes from matchin the NSXCODE column from suspecies to flvnonsynnotren table.

Opportunistic columns

1. Select data for opportunistic only

Opportunistic records may or may not have a site name (parent site). These records do not belong to a quadrat. All of these records have been assigned a “PATCHID” however a site sensu TERN data ontology does not exist. In terms of the ontology, these records are plot-less

2. For these FOI, a “tern_opportunistic_suspecies” data has to be created and the following columns from the suspecies table need to be included:

NUMOBSERVED,PLANTEDRELEASED_occurence and species_occurrence

3. LOCMETHODNR and RELIABNR are attributes of the coordinates. In the first case it is an instrument that varies by latitude,longitude combination. In the second case is a reliability value for the coordinates that comes in a lookuptable lureliab

4. Only two site attributes have enough information for this ingestion: GENLOC, LOCCOMM. PROPERTY and VISITCOMM may also be added but more than 76% are null.

suoverstorey table ingestion

This table describes the characteristics of overstorey stratum (woody species). For the ingetion a new column called stratum_category needs to be created and filled with the correct stratum, in this case “overstorey” value.

Plant community and vegetation disturbance ingestion

The dataset for plant communities is spread across couple of tables for ingesting this data the folloing merge is needed

Only the following variables will be mapped:

LASTFIREYEAR (note that ? values need to be remapped to Y)

ISFIREYRCERTAIN (note that ? values need to be remapped to Y)

STRFORMATIONNR

Plant functional type ingestion

The data for plant functional type is on a single table, suplantassemb, with only two parameters. This table does not need pre-processing.

Voucher ingestion

Vouchered specimens are in the suvoucher sheet. The following is necessary:

1. Filter to only voucher containing AD in the museumherbmnr column

2. Generate unique record number (http://rs.tdwg.org/dwc/terms/recordNumber ) using prefix and vouchernr.

3. create specimen_holder column. Value is State Herbarium of South Australia

4. museumherbmnr corresponds to state catalogue number. ALA use also this field, but adds a space between alphabetic and numeric characters

5. Scientific name is the concatenation of following flsp columns fl."GENUS",fl."SP",
   fl."ISP1RANK" , fl."ISP1" , fl."SPAUTHOR"

6. Get values from DETERMINERNR1 for the determiner column. The values for observer are outside the database see excel sheet at bottom of this list

   1.  

7. NOTICE that DETERMINEDATE is not the same as the collection date that happened during VISITDATE

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See code below for guidance

SUSPECIES for animals

The suspecies tables for animals will be divided into individuals, populations and occurrences per animal group.

NUMTRAP columns, columns with the following syntax NUMXXXXTRAPA and NUMXXXXTRAPB need to be added by trap type by row, e.g. NUMELLIOTTRAP AS sum(NUMELLIOTTRAPA, NUMELLIOTTRAPB).

These variables are stored at the site-visit level. However, they apply only to particular animal groups,i.e. not all NUMTRAP columns apply to all animal observations done during a site visit. Also create dipnetused variable where the value is YES when DIPNETHRS is not null.

All records have to be filtered by ISCERTAIN = Y

NUMOBSERVED column

This column whenever present will be separated into two variables:

NUMOBSERVED: all numeric values >0 will be kept in NUMOBSERVED. 0 values and Non-numeric values will be transformed to NULL values

PRESENCE: This column will have two values “none detected“ and “present”. The “present” value will be all numeric values > 0 in the NUMOBSERVED column as well as the several, present but not countedand Present but not counted values. “none detected” will be all the 0 and none detected values in the NUMOBSERVED column.

Individuals

1. Pivot length and lengthmethod columns

First, the length and length method have to be pivot to a wider format.

Expand (pivot wider) column LENGTHNR as column names and LENGTH column as values to fill these columns. The column names for the LENTHNR column are below, as well as an example of the query:

1 body length
10 snout to vent length (does not need to be ingested as it already exist as SNOUT)
12 tail Length
14 mantle Length
15 invertebrate carapace length (if species type I)

15 turtle carapace length (if species type R)

2 fork length
3 lower jaw Fork Length
5 PES Length
6 Head Length
7 Forearm Length

2. For individuals the following joins and logic are required, this step differs across species. Invertebrates and birds are excluded as they only comprise 3 records for this FOI.

For mammals :

1. TEATS column: Values in category 3 need to be lumped into category 2.

2. TESTES column: Values in category 3 need to be lumped into category 2.

3. Variables to be ingested are the following (note: NUMOBSERVED is not ingested as this FOI by definition is one individual): METHODNR, species_name, tail_length, pes_length, forearm_length, SPCOMM, SEX, TEATS, VAGINA, POUCH, TESTES, WEIGHT, PLANTEDRELEASED, NUMNIGHTS, NUMELLIOTTRAPA, NUMELLIOTNIGHTS, NUMPITTRAPA, NUMPITNIGHTS, NUMCAGETRAPA, NUMCAGENIGHTS, ISHARPTRAP, ISMISTNET, NUMELLIOTTRAPB, NUMPITTRAPB, NUMCAGETRAPB, ISHAIRTUBE, ISBATDETECTOR

For birds: there are no individuals.

For fish:

The following tables are needed:

Variables to be ingested are as follow:

species_name, METHODNR, SPCOMM, SEX, WEIGHT, ACTIVITY, PLANTEDRELEASED, total_length, disc_length, fork, lowerjawfork, FYKENETDUR, FYKENETNR, BAITTRAPHRS, BAITTRAPNUM

For reptiles:

The following tables are needed

1. Variables to be ingested are the following: METHODNR, STRATANR, MACROHABNR, MICROHABNR, SPCOMM, SEX, WEIGHT, ISGRAVID, PLANTEDRELEASED, total_length, SNOUT, tail_length, turtle_carapace_length, NUMNIGHTS, NUMELLIOTTRAP, NUMELLIOTNIGHTS, NUMPITTRAP, NUMPITNIGHTS, NUMCAGETRAP, NUMCAGENIGHTS, ISHARPTRAP, ISMISTNET, FYKENETDUR, FYKENETNR

For amphibian:

The following tables are needed:

The following variables need to be ingested: METHODNR, SPCOMM, SEX, WEIGHT, PLANTEDRELEASED, total_length, svlength, fork, FYKENETDUR, FYKENETNR

For invertebrates:

The following tables are needed:

The following variables need to be ingested: METHODNR, SPCOMM, ACTIVITY, PLANTEDRELEASED, total_length, mantle_length, carapace_length, FYKENETDUR, FYKENETNR, BAITTRAPHRS, BAITTRAPNUM

Occurrence

For birds the following join is needed:

and the following columns will be ingested:

METHODNR, species_name, STRATANR, NUMOBSERVED, MICROHABNR, MACROHABNR, SPCOMM, SEX, ACTIVITY, PLANTEDRELEASED, NUMNIGHTS, NUMELLIOTTRAP, NUMELLIOTNIGHTS, NUMPITTRAP, NUMPITNIGHTS, NUMCAGETRAP, NUMCAGENIGHTS, ISHARPTRAP, ISMISTNET, ISHAIRTUBE, ISBATDETECTOR

Most of the variables after PLANTEDRELEASEDmay be removed, this needs to be confirmed.

For mammals

1. For mammals, the following joins and logic are required

2. Convert 'none detected' value in NUMOBSERVED to 0

3. The following variables are to be ingested STRATANR, MACROHABNR, species_name, NUMOBSERVED, MICROHABNR, SPCOMM, SEX, ACTIVITY, PLANTEDRELEASED, NUMNIGHTS, NUMELLIOTTRAP, NUMELLIOTNIGHTS, NUMPITTRAP, NUMPITNIGHTS, NUMCAGETRAP, NUMCAGENIGHTS, ISHARPTRAP, ISMISTNET, ISHAIRTUBE, ISBATDETECTOR

For Fish

1. The following logic is required for fish

2. The following variables will be ingested: species_name, NUMOBSERVED, PRESENCE, SPCOMM, SEX, ACTIVITY, PLANTEDRELEASED, FYKENETDUR, FYKENETNR, BAITTRAPHRS, BAITTRAPNUM

For Reptiles

1. The following logic/joins are required

2. The following variables will be ingested: STRATANR, METHODNR, MACROHABNR, MICROHABNR, MACROHABNR, species_name, NUMOBSERVED, PRESENCE, SPCOMM, SEX, ISGRAVID, PLANTEDRELEASED, NUMNIGHTS, NUMELLIOTTRAP, NUMELLIOTNIGHTS, NUMPITTRAP, NUMPITNIGHTS, NUMCAGETRAP, NUMCAGENIGHTS

For Amphibians

1. The following logic and joins are required

2. The following variables will be ingested: NUMOBSERVED, METHODNR, STRATANR, MACROHABNR, MICROHABNR, SPCOMM, PLANTEDRELEASED, NUMNIGHTS, NUMELLIOTTRAP, NUMELLIOTNIGHTS, NUMPITTRAP, NUMPITNIGHTS, NUMCAGETRAP, NUMCAGENIGHTS, FYKENETDUR, FYKENETNR, BAITTRAPHRS, BAITTRAPNUM, DIPNETHRS, dipnetused

For Invertebrates

1. The following logic and joins are required

2. The following variables will be ingested: NUMOBSERVED, METHODNR, SPCOMM, ACTIVITY, PLANTEDRELEASED, NUMNIGHTS, NUMELLIOTTRAP, NUMELLIOTNIGHTS, NUMPITTRAP, NUMPITNIGHTS, NUMCAGETRAP, NUMCAGENIGHTS, FYKENETDUR, FYKENETNR, BAITTRAPHRS, BAITTRAPNUM, DIPNETHRS