The role of persistent identifiers in tracking taxon changes

Andrew C. Jones, Richard J. White, Ewen R. Orme,School of Computer Science,

Cardiff University, UK

{Andrew.C.Jones | R.J.White | E.R.Orme} @cs.cardiff.ac.uk

Jones, White & Orme. Tracking Taxon Changes (TDWG 2009)2

The Catalogue of Life

GSD

GSD

GSD

CAS

Web front-end

Othersoftwareclients ofCatalogue ofLife (e.g.using it as their“taxonomicbackbone”)

Jones, White & Orme. Tracking Taxon Changes (TDWG 2009)3

CoL in use

Jones, White & Orme. Tracking Taxon Changes (TDWG 2009)4

CoL & LSIDs

Jones, White & Orme. Tracking Taxon Changes (TDWG 2009)5

Concepts that stay the same

Sci. name 1Synonyms:

Sci. name 2Sci. name 3Sci. name 4

urn:lsid:catalogueoflife.org:taxon:<uuid 1>:dc

urn:lsid:catalogueoflife.org:taxon:<uuid 1>:ac2009

Dynamic checklist lsid

Annual checklist lsid

KEY:

Sci. name 1Synonyms:

Sci. name 2Sci. name 3Sci. name 4

urn:lsid:catalogueoflife.org:taxon:<uuid 1>:dc

urn:lsid:catalogueoflife.org:taxon:<uuid 1>:ac2010

Jones, White & Orme. Tracking Taxon Changes (TDWG 2009)6

Evolving concepts in dynamic & annual checklist

Sci. name 1Synonyms:

Sci. name 2Sci. name 3Sci. name 4

Sci. name 1Synonyms:

Sci. name 3

Sci. name 2Synonyms:

Sci. name 4

Sci. name 1Synonyms:

Sci. name 3Sci. name 5

Sci. name 2Synonyms:

Sci. name 4

urn:lsid:catalogueoflife.org:taxon:<uuid 1>:dc

urn:lsid:catalogueoflife.org:taxon:<uuid 2>:dc

urn:lsid:catalogueoflife.org:taxon:<uuid 3>:dc

urn:lsid:catalogueoflife.org:taxon:<uuid 4>:dc

urn:lsid:catalogueoflife.org:taxon:<uuid 3>:dc

urn:lsid:catalogueoflife.org:taxon:<uuid 1>:ac2009

urn:lsid:catalogueoflife.org:taxon:<uuid 4>:ac2010

urn:lsid:catalogueoflife.org:taxon:<uuid 3>:ac2010Dynamic checklist lsid

Annual checklist lsid

KEY:

Jones, White & Orme. Tracking Taxon Changes (TDWG 2009)7

Data integration and the CoL

• Two sources of information about species x: Do they refer to the same concept?

• Same persistent identifier If not, how are the concepts related; what can we

infer?• Different persistent identifiers• Needs something like TCS

Jones, White & Orme. Tracking Taxon Changes (TDWG 2009)8

Specimen data & changing concepts

Jones, White & Orme. Tracking Taxon Changes (TDWG 2009)9

Using data associated with changing concepts

Pipistrelluspipistrellussensu stricto

(CommonPipistrelle;45 kHz)

Pipistrelluspygmaeus

(SopranoPipistrelle;55 kHz)

Pipistrellus pipistrellus sensu lato (45 & 55 kHz)(Pre-1999)

Don't know which new species these observations relate to ...

… but still applicable to genus Pipistrellus10

Jones, White & Orme. Tracking Taxon Changes (TDWG 2009)11

Worse still …

• Though CoL taxa have precise circumscription when defined …

• … difficult precisely to know that concept when applying a CoL persistent identifier

• Identification keys for CoL taxa?

Jones, White & Orme. Tracking Taxon Changes (TDWG 2009)12

Capturing taxon concept changes

• Changed persistent identifiers from source databases; or

• Detecting changes by comparison Same synonyms, parent taxon, etc?

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Representing the changes• Persistent identifier metadata

Taxon concept relationships e.g. isCongruentTo; includes; overlaps

• Granularity? Many species changed due to underlying cause, e.g.

splitting a genus? Higher taxa need relationship metadata too

Additional explanatory metadata attached to species (set of relationships between relevant higher taxa)?

Explicit representation of the actions leading to change, e.g. “split”, “merge” & “transfer”?

Jones, White & Orme. Tracking Taxon Changes (TDWG 2009)14

Issues for discussion• Differing perspectives of users, providers (and computer

scientists)

• Need for conventions in describing evolving checklists

• Metadata describing actions, not just set relationships?

• Services to support data integration exploiting persistent identifiers

• When does a concept really change?

Some URLs ...

• 4D4Life project: http://www.4d4life.eu

• 4D4Life questionnaire: http://biodiversity.cs.cf.ac.uk/4d4life/