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The ALA Taxonomic Index

Dagstuhl Down Under 2021

Doug Palmer

28 September 2021

The ALA is made possible by contributions from its many partners. It receives support through the Australian Government through the National Collaborative Research Infrastructure Strategy (NCRIS) and is hosted by CSIRO.

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Government

Museums & herbaria

Science agencies & universities

Indigenous Ecological Knowledge holders

NGOs & community groups

Industry

Citizen scientists

Data types & services

Species occurrence records

Dataset metadata

National checklists & taxonomies

Environmental layers

Images & sounds

Spatial classifications

…and more

Powered by ALA

MERIT: Dept Agriculture, Water & the Environment

International Living Atlases

The Tracks App

Flora of Australia

WA Government: IBSA

…and more

User applications

Search & download data

Species list tool

Explore Your Area

Australia’s natural history collections

…and more

Data partners

Australian National Insect Collection, CSIRO

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What does the ALA do?

Collect (biology) occurrence records

Thing
Time
Place

Extend the records

Standardisation

“The ides of March in the 68^th year of the reign of Queen Elizabeth II” → 2021-03-15

Annotation

State: New South Wales → country: Australia

Put them in a data cube
Provide services and UIs to use the data cube

Speed of response is important to allow exploration

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The Thing Part

Usually a scientific name

Osphranter rufus – Red Kangaroo

Match onto a taxon concept

Species = Osphranter rufus (Desmarest, 1822)
Genus = Osphranter Gould, 1842
Family = Macropodidae
Order = Diprotodontia
Class = Mammalia
Phylum = Chordata
Kingdom = Animalia

Subclass = Marsupialia

The author who said “this goes here”

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Taxonomy

The tree of life
A place for everything

And everything in its place

One of the great scientific endeavours
Multiple taxonomies

By genotype
By phenotype (traditional taxonomy)

Used by the ALA

By operational taxonomic unit (OTU)
By the Celestial Emporium of Benevolent Knowledge
There are as many taxonomies as taxonomists

https://today.duke.edu/2015/09/treeoflife

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What Taxonomy Actually Looks Like

Goscinny and Uderzo, Asterix the Gaul

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Search and Information

Biodiversity Information Explorer (BIE)
Human-oriented
As much information as possible

Taxonomy

Synonyms
Vernacular names

Distribution
Images
Imported information
Links to source information

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Name Matching

During occurrence record processing
Standardisation

Attempt to work out the “correct” taxon
Follow synonyms

Macropus rufus → Osphranter rufus

Annotation

Fill out higher-order taxonomy

Kingdom = Animalia

Spot problems

excluded species aka ”you think it’s this but you’re wrong!”

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Vernacular Names

AKA Common Names
Imprecise

Wombat

Vombatus ursinus
Lasiorhinus latifrons

Blue Gum

Eucalyptus globulus subsp. globulus
Eucalyptus globulus subsp. bicostata
Eucalyptus leucoxylon subsp. Megalocarpa

Box Jellyfish

Who knows?

Local

Gymnorhina tibicen telonocua

Piping Shrike in South Australia
White-backed Magpie elsewhere

Variable and contextual

Bull, cow, heifer, calf
Prickly pear (plant), Indian fig (fruit)

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Indigenous Ecological Knowledge

From the ALA’s point of view, a form of vernacular name

Potentially a different taxonomy

Subject to Traditional Knowledge (TK) and Biocultural (BC) Labels

https://localcontexts.org/labels/traditional-knowledge-labels/
Define specific conditions for sharing and using the names
Can be used as retroactive moral conditions

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TK Culturally Sensitive

https://localcontexts.org/label/tk-culturally-sensitive/

BC Research Use

https://localcontexts.org/label/bc-research-use/

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How the ALA gets taxonomy

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AusFungi

AusMoss

AFD

APNI/APC

NZOR

CAAB

CoL

More …

Authorities

AusFungi

AusMoss

AFD

APNI/APC

NZOR

CAAB

CoL

More …

Preprocessing

Large Taxon Collider

Combined Taxonomy

Indexer

Search (BIE)

Matching Index

Name Matching

Merging

Indexing

Use

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Issues with Building

Update Frequency

Some sources update daily
But it takes a long time to

Assemble an index
QA
Deploy
Reprocess

Is this reference data or just another sort of data?

Contradictions

The Large Taxon Collider (LTC) picks winners based on relative authority
A Frankentaxonomy

Nobody said, “this makes sense”

Attribution

Links to overall data source
Individual links to taxa (and variants) – if available
Licenced under CC-BY

But TK labels may include extra restrictions

Presentation title | Presenter name

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Is this a Vocabulary?

It looks SKOS-ifiable

But biological taxonomy has its own traditions

Unique terms

A taxon identifier is unique

Because we make it so
But not (always) a URI

A scientific name is unique within a nomenclatural code
Well …

Homonyms (eg Abelia in botanical and zoological codes)
Pro-parte synonyms
Misapplications and exclusions
Historical oddities (this has been going for over 200 years)

Unstable

By necessity

Presentation title | Presenter name

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FAIR – Current State

Findable

Entire taxonomies are persistent, retrievable and have an identifier.
Individual taxa move about under fire and scientific names may be associated with different identifiers, some persistent, some not.

Accessible

Taxonomies are available as Darwin Core Archives (DwCA) from the ALA archives.

Interoperable

DwCAs are structured using Darwin Core(DwC) and Global Biodiversity Information Framework (GBIF) vocabularies and standards.
Internal vocabularies (taxonomic and nomenclatural status, taxonomic rank, nomenclatural code etc.) are documented but not easily discoverable.

Reusable

Pre-processing sources may abandon some data to convert the source into DwCA format.
The Large Taxon Collider retains original source data and variants and appends provenance statements to adjusted taxa.
Licencing is almost CC-BY

Presentation title | Presenter name

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Thank you

Doug Palmer�Atlas of Living Australia

t +61 2 6218 3432

e Doug.Palmer@csiro.au

The ALA is made possible by contributions from its many partners. It receives support through the Australian Government through the National Collaborative Research Infrastructure Strategy (NCRIS) and is hosted by CSIRO.