the role of persistent identifiers in tracking taxon changes andrew c. jones, richard j. white, ewen...

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?

Jones, White & Orme. Tracking Taxon Changes (TDWG 2009)13

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/