Content Comparison

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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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_suspeciessuspeciesY

Code Block
JOIN bdbsa.supatch sp ON sv."PATCHID" = sp."PATCHID" join bdbsa.suspecies spp on sv."VISITNR" = spp."VISITNR"

...

survey based data for plant populations which are observed on plots
survey based data for plant individuals which are observed on plots
opportunistic samples of plant occurrences that are plot-less
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

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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

Code Block

select "PATCHID" , sv."VISITNR" , "VISITDATE" ,
 "ISFIRESCARS" , "LASTFIREYEAR" , "ISFIREYRCERTAIN" ,
 sv."STRFORMATIONNR", lstr."STRFORMATIONDESC", 
 lstr."STRLIFEFORMNR" ,lstr."PROJFOLCOVERNR"
 from bdbsa.suvisit sv
 join bdbsa.lustrformation lstr ON lstr."STRFORMATIONNR" = sv."STRFORMATIONNR"

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:

Filter to only voucher containing AD in the museumherbmnr column
Generate unique record number (http://rs.tdwg.org/dwc/terms/recordNumber ) using prefix and vouchernr.
create specimen_holder column. Value is State Herbarium of South Australia
museumherbmnr corresponds to state catalogue number. ALA use also this field, but adds a space between alphabetic and numeric characters
Scientific name is the concatenation of following flsp columns fl."GENUS",fl."SP",
fl."ISP1RANK" , fl."ISP1" , fl."SPAUTHOR"
Get values from DETERMINERNR1 for the determiner column. The values for observer are outside the database see excel sheet at bottom of this list
NOTICE that DETERMINEDATE is not the same as the collection date that happened during VISITDATE

View file

name	bdbsa-data-returns-template-gen.xlsx

See code below for guidance

Code Block

select sp."SITEID", sp."QUADSITE", sp."PATCHID", sv."VISITNR", sv."VISITDATE", 
 svo."PREFIX", svo."VOUCHERNR",--unique identifiers
 svo."MUSEUMHERBMNR", --used by ALA
-- svo."VOUCHERTYPE",svo."SPSEQNR", spp."SPECIESNR", 
 fl."GENUS",fl."SP",
 fl."ISP1RANK" , fl."ISP1" , fl."SPAUTHOR", 
 svo."DETERMINERNR1" , --svo."DETERMINERNR2", determiner 2 is not used
 svo."DETERMINEDATE", --svo."ACCURACYCODE",--this is for the date
 svo."VOUCHERCOMM" 
 from bdbsa.suvoucher svo
 join bdbsa.suspecies spp on spp."SPSEQNR" =svo."SPSEQNR" and
  spp."VISITNR" = svo."VISITNR" 
 join bdbsa.flsp fl on spp."SPECIESNR" = fl."SPECIESNR"
 join bdbsa.suvisit sv on sv."VISITNR" =svo."VISITNR" 
 join bdbsa.supatch sp on sp."PATCHID" = sv."PATCHID" 
 where substring("MUSEUMHERBMNR" , '[A-Z]{1,}') = 'AD'
 order by "VOUCHERTYPE"

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

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

Code Block

--CREATE TABLE bdbsa.analysis_length AS
SELECT "VISITNR", "SPECIESTYPE","SPSEQNR","NSXCODE","LENGTHMETHOD", "LENGTH"
from bdbsa.suspecies s
where ("LENGTHMETHOD" is not null and "LENGTH" is not null);
--drop TABLE if exists bdbsa.analysis_length;

select distinct "LENGTHMETHOD"
from bdbsa.analysis_length
ORDER  BY 1;

SELECT concat("VISITNR", '_', "SPECIESTYPE",'_',"SPSEQNR",'_',"NSXCODE")as row_id,"VISITNR", "SPECIESTYPE","SPSEQNR","NSXCODE","LENGTHMETHOD", "LENGTH" 
    FROM   bdbsa.analysis_length
    ORDER  BY 5;
   
   
--CREATE EXTENSION IF NOT EXISTS tablefunc;
--create table bdbsa.analyses_length_wide as   
SELECT *
FROM   crosstab(
   $$SELECT concat("VISITNR", '_', "SPECIESTYPE",'_',"SPSEQNR",'_',"NSXCODE") as row_id,"VISITNR", "SPECIESTYPE","SPSEQNR","NSXCODE","LENGTHMETHOD", "LENGTH" 
    FROM   bdbsa.analysis_length
    ORDER  BY 5$$  
  , $$select distinct "LENGTHMETHOD"
from bdbsa.analysis_length
ORDER  BY 1$$
   ) AS ("row_id" text,"VISITNR" float8, "SPECIESTYPE" text,"SPSEQNR" float8, "NSXCODE" text,
   "total_length" float8,
   "svlength" float8, "tail_length" float8,"disc_length" float8,
   "mantlelength" float8, "carapace_length" float8, "fork" float8,
   "lowerjawfork" float8,"pes_length" float8,"head_length" float8,
   "forearm_length" float8);
--drop TABLE if exists bdbsa.analyses_length_wide;

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 :

Code Block

join bdbsa.analyses_length_wide alw on alw."VISITNR"= spp."VISITNR" and alw."SPECIESTYPE"= spp."SPECIESTYPE" and alw."SPSEQNR" = spp."SPSEQNR" and alw."NSXCODE" =spp."NSXCODE"
left join bdbsa.sutrap str on str."VISITNR" = spp."VISITNR"
left join bdbsa.suvisit sv on sv."VISITNR" = spp."VISITNR" 
JOIN bdbsa.supatch sp ON sp."PATCHID" = sv."PATCHID"
where (spp."SPECIESTYPE" = 'M')

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

Code Block

from suspecies spp
join bdbsa.analyses_length_wide alw on alw."VISITNR"= spp."VISITNR" and alw."SPECIESTYPE"= spp."SPECIESTYPE" and alw."SPSEQNR" = spp."SPSEQNR" and alw."NSXCODE" =spp."NSXCODE"
left join bdbsa.sutrap str on str."VISITNR" = spp."VISITNR"
left join bdbsa.suvisit sv on sv."VISITNR" = spp."VISITNR" 
JOIN bdbsa.supatch sp ON sp."PATCHID" = sv."PATCHID"
where spp."SPECIESTYPE" = 'F';

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

Code Block

from suspecies spp
join bdbsa.analyses_length_wide alw on alw."VISITNR"= spp."VISITNR" and alw."SPECIESTYPE"= spp."SPECIESTYPE" and alw."SPSEQNR" = spp."SPSEQNR" and alw."NSXCODE" =spp."NSXCODE"
left join bdbsa.sutrap str on str."VISITNR" = spp."VISITNR"
left join bdbsa.suvisit sv on sv."VISITNR" = spp."VISITNR" 
JOIN bdbsa.supatch sp ON sp."PATCHID" = sv."PATCHID"
where spp."SPECIESTYPE" = 'R';

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:

Code Block

str."FYKENETHRS", str."BAITTRAPHRS", str."BAITTRAPNUM", str."DIPNETHRS"
from suspecies spp
join bdbsa.analyses_length_wide alw on alw."VISITNR"= spp."VISITNR" and alw."SPECIESTYPE"= spp."SPECIESTYPE" and alw."SPSEQNR" = spp."SPSEQNR" and alw."NSXCODE" =spp."NSXCODE"
left join bdbsa.sutrap str on str."VISITNR" = spp."VISITNR"
left join bdbsa.suvisit sv on sv."VISITNR" = spp."VISITNR" 
JOIN bdbsa.supatch sp ON sp."PATCHID" = sv."PATCHID"
where spp."SPECIESTYPE" = 'A';

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:

Code Block

from suspecies spp
join bdbsa.analyses_length_wide alw on alw."VISITNR"= spp."VISITNR" and alw."SPECIESTYPE"= spp."SPECIESTYPE" and alw."SPSEQNR" = spp."SPSEQNR" and alw."NSXCODE" =spp."NSXCODE"
left join bdbsa.sutrap str on str."VISITNR" = spp."VISITNR"
left join bdbsa.suvisit sv on sv."VISITNR" = spp."VISITNR" 
JOIN bdbsa.supatch sp ON sp."PATCHID" = sv."PATCHID"
where spp."SPECIESTYPE" = 'I';

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:

Code Block

JOIN bdbsa.supatch sp ON sv."PATCHID" = sp."PATCHID" 
join bdbsa.suspecies spp on sv."VISITNR" = spp."VISITNR"
join bdbsa.vssp vs on vs."NSXCODE" = spp."NSXCODE"
full join bdbsa.sutrap str on str."VISITNR" = sv."VISITNR"
where (spp."SPECIESTYPE" = 'B')

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

For mammals, the following joins and logic are required

Code Block

FROM bdbsa.suvisit sv JOIN bdbsa.supatch sp ON sv."PATCHID" = sp."PATCHID"  
join bdbsa.suspecies spp on sv."VISITNR" = spp."VISITNR" 
join bdbsa.vssp vs on vs."NSXCODE" = spp."NSXCODE" 
full join bdbsa.sutrap str on str."VISITNR" = sv."VISITNR" 
where (spp."SPECIESTYPE" = 'M' and
 "TEATS" is null 
and "VAGINA" is null 
and "POUCH" is null
and "TESTES" is null
and "WEIGHT" is null
and "NUMPOUCH" is null
and "LENGTH" is null)

Convert 'none detected' value in NUMOBSERVED to 0
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

The following logic is required for fish

Code Block

from suspecies spp
left join bdbsa.sutrap str on str."VISITNR" = spp."VISITNR"
left join bdbsa.suvisit sv on sv."VISITNR" = spp."VISITNR" 
left JOIN bdbsa.supatch sp ON sp."PATCHID" = sv."PATCHID"
where (spp."SPECIESTYPE" = 'F' and "LENGTH" is null and "WEIGHT" is null);

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

For Reptiles

The following logic/joins are required

Code Block

from suspecies spp
left join bdbsa.sutrap str on str."VISITNR" = spp."VISITNR"
left join bdbsa.suvisit sv on sv."VISITNR" = spp."VISITNR" 
JOIN bdbsa.supatch sp ON sp."PATCHID" = sv."PATCHID"
where (spp."SPECIESTYPE" = 'R' and "LENGTH" is null and "WEIGHT" is null);

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

The following logic and joins are required

Code Block

from suspecies spp
left join bdbsa.sutrap str on str."VISITNR" = spp."VISITNR"
left join bdbsa.suvisit sv on sv."VISITNR" = spp."VISITNR" 
left JOIN bdbsa.supatch sp ON sp."PATCHID" = sv."PATCHID"
where (spp."SPECIESTYPE" = 'A' and "LENGTH" is null and "WEIGHT" is null);

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

The following logic and joins are required

Code Block

from suspecies spp
left join bdbsa.sutrap str on str."VISITNR" = spp."VISITNR"
left join bdbsa.suvisit sv on sv."VISITNR" = spp."VISITNR" 
left JOIN bdbsa.supatch sp ON sp."PATCHID" = sv."PATCHID"
where (spp."SPECIESTYPE" = 'I' and "LENGTH" is null and "WEIGHT" is null);

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

Version	Old Version 14	New Version Current
Changes made by	Habacuc FM (Unlicensed)	Habacuc FM (Unlicensed)
Saved on	01 Jul 2022	23 Aug 2022

Versions Compared

Key

SUSPECIES for plants

NUMOBSERVED column

Columns from other tables shared across FOI’s

suoverstorey table ingestion

Plant community and vegetation disturbance ingestion

Plant functional type ingestion

Voucher ingestion

SUSPECIES for animals

NUMOBSERVED column

Individuals

Occurrence