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.
|
|
|
|
|
|
/assumptions
- building models requires data
- modelled observations should be alike
- code is good (for precision and reproducibility)
/outline
/darwin-core
|
standardising data |
/galah
|
getting data |
/galaxias
|
publishing data |
/quality
|
checking data |
darwin-core
standardising data
/darwin-core
concept
|
|
|
|
| place | time | taxon |
/darwin-core
archives
|
|
|
|
| events | occurrences | multimedia |
|
|
|
| metadata | schema |
galah
getting data
/galah
count records
/galah
download records
# A tibble: 3 × 9
recordID scientificName taxonConceptID decimalLatitude decimalLongitude
<chr> <chr> <chr> <dbl> <dbl>
1 00002663-22ac-… Perameles nas… https://biodi… -29.7 153.
2 0018c6f9-e772-… Perameles nas… https://biodi… -32.3 152.
3 001a72f5-009f-… Perameles nas… https://biodi… -32.3 152.
# ℹ 4 more variables: eventDate <dttm>, basisOfRecord <chr>,
# occurrenceStatus <chr>, dataResourceName <chr>/galah
count species
/galah
download species
# A tibble: 7 × 11
species species_name scientific_name_auth…¹ taxon_rank kingdom phylum class
<chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 https://b… Perameles n… Geoffroy, 1804 species Animal… Chord… Mamm…
2 https://b… Perameles g… Gray, 1838 species Animal… Chord… Mamm…
3 https://b… Perameles f… Gray, 1841 species Animal… Chord… Mamm…
4 https://b… Perameles p… Thomas, 1923 species Animal… Chord… Mamm…
5 https://b… Perameles b… Quoy & Gaimard, 1824 species Animal… Chord… Mamm…
6 https://b… Perameles e… Spencer, 1897 species Animal… Chord… Mamm…
7 https://b… Perameles n… Thomas, 1922 species Animal… Chord… Mamm…
# ℹ abbreviated name: ¹scientific_name_authorship
# ℹ 4 more variables: order <chr>, family <chr>, genus <chr>,
# vernacular_name <chr>/galah
- tidyverse syntax
- clear & accessible
- multiple data sources
/galah
| Location | URL |
|---|---|
| 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 |
galaxias
publishing data
/galaxias
- set up a project
- match data to darwin core terms
- add metadata
- validate and publish
/galaxias
using darwin core terms
/galaxias
using darwin core terms
/galaxias
adding metadata
# A tibble: 50 × 4
level label text attributes
<int> <chr> <chr> <list>
1 1 Eml <NA> <named list>
2 2 Dataset <NA> <lgl [1]>
3 3 Alternate Identifier 0101d74b-afc2-3b0f-817c-dc350d2a6fe4 <lgl [1]>
4 3 Alternate Identifier 10.15468/14jd9g <lgl [1]>
5 3 Alternate Identifier 0645ccdb-e001-4ab0-9729-51f1755e007e <lgl [1]>
6 3 Alternate Identifier https://collections.ala.org.au/publi… <lgl [1]>
7 3 Title NSW BioNet Atlas <lgl [1]>
8 3 Creator <NA> <lgl [1]>
9 4 Organization Name Department of Planning, Industry and… <lgl [1]>
10 3 Metadata Provider <NA> <lgl [1]>
# ℹ 40 more rows/galaxias
adding metadata
[1] "<h1 schemaLocation=eml://ecoinformatics.org/eml-2.1.1 http://rs.gbif.org/schema/eml-gbif-profile/1.1/eml-gbif-profile.xsd system=ALA-Registry scope=system lang=en xmlns:d=eml://ecoinformatics.org/dataset-2.1.0 xmlns:eml=eml://ecoinformatics.org/eml-2.1.1 xmlns:xsi=http://www.w3.org/2001/XMLSchema-instance xmlns:dc=http://purl.org/dc/terms/>Eml</h1>"
[2] ""
[3] "## Dataset"
[4] ""
[5] "### Alternate Identifier"
[6] ""
[7] "0101d74b-afc2-3b0f-817c-dc350d2a6fe4"
[8] ""
[9] "### Alternate Identifier"
[10] ""
[11] "10.15468/14jd9g"
[12] ""
[13] "### Alternate Identifier"
[14] ""
[15] "0645ccdb-e001-4ab0-9729-51f1755e007e"
[16] ""
[17] "### Alternate Identifier"
[18] ""
[19] "https://collections.ala.org.au/public/show/dr368"
[20] ""
[21] "### Title"
[22] ""
[23] "NSW BioNet Atlas"
[24] ""
[25] "### Creator"
[26] ""
[27] "#### Organization Name"
[28] ""
[29] "Department of Planning, Industry and Environment representing the State of New South Wales"
[30] ""
[31] "### Metadata Provider"
[32] ""
[33] "#### Organization Name"
[34] ""
[35] "Department of Planning, Industry and Environment representing the State of New South Wales"
[36] ""
[37] "### Associated Party"
[38] ""
[39] "#### Organization Name"
[40] ""
[41] "Atlas of Living Australia"
[42] ""
[43] "#### Address"
[44] ""
[45] "##### Delivery Point"
[46] ""
[47] "CSIRO Ecosystems Services"
[48] ""
[49] "##### City"
[50] ""
[51] "Canberra"
[52] ""
[53] "##### Administrative Area"
[54] ""
[55] "ACT"
[56] ""
[57] "##### Postal Code"
[58] ""
[59] "2601"
[60] ""
[61] "##### Country"
[62] ""
[63] "Australia"
[64] ""
[65] "#### Electronic Mail Address"
[66] ""
[67] "info@ala.org.au"
[68] ""
[69] "#### Role"
[70] ""
[71] "distributor"
[72] ""
[73] "#### Organization Name"
[74] ""
[75] "Office of Environment & Heritage"
[76] ""
[77] "#### Role"
[78] ""
[79] "originator"
[80] ""
[81] "### Pub Date"
[82] ""
[83] "2026-05-12"
[84] ""
[85] "### Language"
[86] ""
[87] "English"
[88] ""
[89] "### Abstract"
[90] ""
[91] "#### Para"
[92] ""
[93] "Records from DPIE's NSW BioNet Atlas database of flora and fauna sightings. Includes records from other custodians such as the National Herbarium of NSW, Forests NSW, Australian Bird and Bat Banding Scheme and the Australian Museum."
[94] ""
[95] "### Intellectual Rights"
[96] ""
[97] "#### Para"
[98] ""
[99] "<h5 url=https://creativecommons.org/licenses/by/4.0/>Ulink</h5>"
[100] ""
[101] "###### Citetitle"
[102] ""
[103] "Creative Commons Attribution (International) (CC-BY 4.0 (Int) 4.0)"
[104] ""
[105] "###### Citetitle"
[106] ""
[107] "Creative Commons Attribution (International) (CC-BY 4.0 (Int) 4.x)"
[108] ""
[109] "### Distribution"
[110] ""
[111] "#### Online"
[112] ""
[113] "##### Url"
[114] ""
[115] "https://collections.ala.org.au/public/show/dr368"
[116] ""
[117] "### Contact"
[118] ""
[119] "#### Organization Name"
[120] ""
[121] "Atlas of Living Australia"
[122] ""
[123] "#### Address"
[124] ""
[125] "##### Delivery Point"
[126] ""
[127] "CSIRO Ecosystems Services"
[128] ""
[129] "##### City"
[130] ""
[131] "Canberra"
[132] ""
[133] "##### Administrative Area"
[134] ""
[135] "ACT"
[136] ""
[137] "##### Postal Code"
[138] ""
[139] "2601"
[140] ""
[141] "##### Country"
[142] ""
[143] "Australia"
[144] ""
[145] "#### Electronic Mail Address"
[146] ""
[147] "info@ala.org.au"
[148] ""
[149] "## Additional Metadata"
[150] ""
[151] "### Metadata"
[152] ""
[153] "#### Gbif"
[154] ""
[155] "##### Date Stamp"
[156] ""
[157] "2026-05-12T10:00:13"
[158] ""
[159] "##### Hierarchy Level"
[160] ""
[161] "dataset"
[162] ""
[163] "##### Citation"
[164] ""
[165] "BioNet Species Sightings occurrence data held by the NSW Office of Environment and Heritage (OEH). The BioNet repository holds data from a number of sources and custodians. (Accessed through ALA Data Portal,<Date of Access>)."
[166] "" /galaxias
adding metadata
{xml_node}
<Dataset>
[1] <Alternate Identifier>0101d74b-afc2-3b0f-817c-dc350d2a6fe4</Alternate Id ...
[2] <Alternate Identifier>10.15468/14jd9g</Alternate Identifier>
[3] <Alternate Identifier>0645ccdb-e001-4ab0-9729-51f1755e007e</Alternate Id ...
[4] <Alternate Identifier>https://collections.ala.org.au/public/show/dr368</ ...
[5] <Title>NSW BioNet Atlas</Title>
[6] <Creator>\n <Organization Name>Department of Planning, Industry and Env ...
[7] <Metadata Provider>\n <Organization Name>Department of Planning, Indust ...
[8] <Associated Party>\n <Organization Name>Atlas of Living Australia</Orga ...
[9] <Pub Date>2026-05-12</Pub Date>
[10] <Language>English</Language>
[11] <Abstract>\n <Para>Records from DPIE's NSW BioNet Atlas database of flo ...
[12] <Intellectual Rights>\n <Para>\n <Ulink>\n <Citetitle>Creative ...
[13] <Distribution>\n <Online>\n <Url>https://collections.ala.org.au/publ ...
[14] <Contact>\n <Organization Name>Atlas of Living Australia</Organization ...quality
checking data
/quality
automatic checks
/quality
automatic checks
| spatial | missing georeference information |
| taxonomic | missing taxon rank |
| observation | occurrence status inferred from count |
| temporal | first of month |
/quality
next steps
- assertions audit
- error-type classification
- ‘event’ data
/thanks
The ALA Science & Decision Support Team are:
- Shandiya Balasubramaniam
- Amanda Buyan
- Dax Kellie
- Juliet Seers
- Olivia Torresan
- Martin Westgate
https://labs.ala.org.au
These slides were made with Quarto, R, and:
- dplyr
- forcats
- ggplot2
- lubridate
- ozmaps
- readr
- scales
- sf
- tibble
Martin Westgate | Atlas of Living Australia