Improving data sharing & re-use
at the Atlas of Living Australia

Martin Westgate

I acknowledge the Traditional Owners of the lands on which I live and work, the Ngunnawal people, and pay my respects to Elders past and present.

/outline

/outline

/galah	getting data
/events	survey data
/galaxias	publishing data

/galah

Data from GBIF nodes in R & Python

Global	gbif.org
UK	nbn.org.uk
France	openobs.mnhn.fr
Australia	ala.org.au
Sweden	biodiversitydata.se
Spain	gbif.es
Brazil	sibbr.gov.br
Portugal	gbif.pt
Austria	biodiversityatlas.at
Estonia	elurikkus.ee
Guatemala	snib.conap.gob.at

Number of records

library(galah)

galah_call() |>
  filter(genus == "Perameles",
         basisOfRecord == "HumanObservation") |>
  count() |>
  collect()

# A tibble: 1 × 1
  count
  <int>
1 36610

Download records

galah_call() |>
  filter(genus == "Perameles",
         year == 2024,
         basisOfRecord == "HumanObservation") |>
  collect() |>
  slice_head(n = 3)

--

# A tibble: 3 × 8
  recordID        scientificName taxonConceptID decimalLatitude decimalLongitude
  <chr>           <chr>          <chr>                    <dbl>            <dbl>
1 061ecc74-8b63-… Perameles nas… https://biodi…           -28.4             154.
2 1012b15b-5275-… Perameles nas… https://biodi…           -28.2             153.
3 19fd1821-8ffd-… Perameles gun… https://biodi…           -42.9             147.
# ℹ 3 more variables: eventDate <dttm>, occurrenceStatus <chr>,
#   dataResourceName <chr>

Number of species

galah_call(type = "species") |>
  filter(genus == "Perameles",
         basisOfRecord == "HumanObservation") |>
  count() |>
  collect()

# A tibble: 1 × 1
  count
  <int>
1     6

Species lists

galah_call(type = "species") |>
  filter(genus == "Perameles",
         basisOfRecord == "HumanObservation") |>
  collect()

# A tibble: 6 × 10
  species_guid            species author kingdom phylum class order family genus
  <chr>                   <chr>   <chr>  <chr>   <chr>  <chr> <chr> <chr>  <chr>
1 https://biodiversity.o… Perame… Geoff… Animal… Chord… Mamm… Pera… Peram… Pera…
2 https://biodiversity.o… Perame… Thoma… Animal… Chord… Mamm… Pera… Peram… Pera…
3 https://biodiversity.o… Perame… Gray,… Animal… Chord… Mamm… Pera… Peram… Pera…
4 https://biodiversity.o… Perame… Quoy … Animal… Chord… Mamm… Pera… Peram… Pera…
5 https://biodiversity.o… Perame… Spenc… Animal… Chord… Mamm… Pera… Peram… Pera…
6 https://biodiversity.o… Perame… Gray,… Animal… Chord… Mamm… Pera… Peram… Pera…
# ℹ 1 more variable: vernacular_name <chr>

Comparing packages

/galah

/ALA4R

/rgbif

galah_call() |>
  filter(species == "Eucalyptus gunnii",
         basisOfRecord == "LivingSpecimen") |>
  select(decimalLatitude, decimalLongitude) |>
  collect()

occurrences(
  fq = "basis_of_record:LivingSpecimen",
  taxon = "taxon_name:\"Eucalyptus gunnii\"",
  fields = c("latitude","longitude"),
  qa = "none")

occ_download(
  pred(species, "Eucalyptus gunnii"),
  pred(basisOfRecord, "LivingSpecimen"))

/events

Survey data

Crinia signifera	32
Paracrinia haswelli	9
Uperoleia tyleri	12
Limnodynastes dumerilli	3
Limnodynastes peronii	5
Limnodynases tasmaniensis	19
Litoria jervisiensis	1
Litoria freycineti	0
Litoria nudidigitus	0
Litoria peronii	5

Home

Time series

Survey details

API

graphQL syntax:

{
  "predicate": {
    "type": "and",
    "predicates": [
      {
        "type": "and",
        "predicates": [
          {
            "type": "equals",
            "key": "year",
            "value": "2023"
          },
          {
            "type": "in",
            "key": "stateProvince",
            "values": [
              "Australian Capital Territory"
            ]
          }
        ]
      }
    ]
  },
  "limit": 50,
  "offset": 0
}

galah syntax:

galah_call(type = "events") |>
  filter(year == 2023,
         stateProvince == "Australian Capital Territory") |>
  collect()

NOTE: Not implemented yet!!!!!

/galaxias

Data publication

OccurrenceID	123456
eventDate	2024-02-07T00:00:00Z
decimalLatitude	145.25
decimalLongitude	-35.25
basisOfRecord	humanObservation
scientificName	Litoria peronii
taxonRank	species
recordedBy	Martin Westgate
occurrenceStatus	present
individualCount	1

Building an archive

df <- read_csv("my_data.csv")
metadata <- read_md("my_metadata.qmd")

archive <- dwca() |>
  add_occurrences(df) |>
  add_metadata(metadata)

then:

• build() - construct a DwCA zip file
• check() - run tests to check for DwC compliance
• publish() - send your data to the ALA publication API

/summary

/thanks

The ALA Science & Decision Support Team are:

• Shandiya Balasubramaniam
• Amanda Buyan
• Dax Kellie
• Juliet Seers
• Olivia Torresan
• Callum Waite
• Martin Westgate

These slides were made with Quarto &:

• dplyr
• galah
• ggiraph
• ggplot2
• ozmaps
• sf
• tibble