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