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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. The role of persistent identifiers in tracking taxon changes. The Catalogue of Life. GSD. Web front-end. GSD. Other software

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The role of persistent identifiers in tracking taxon changes

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  1. 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 The role of persistent identifiers in tracking taxon changes

  2. The Catalogue of Life GSD Web front-end GSD Other software clients of Catalogue of Life (e.g. using it as their “taxonomic backbone”) CAS GSD 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 urn:lsid:catalogueoflife.org: taxon:<uuid 1>:dc urn:lsid:catalogueoflife.org: taxon:<uuid 1>:dc Sci. name 1 Synonyms: Sci. name 2 Sci. name 3 Sci. name 4 Sci. name 1 Synonyms: Sci. name 2 Sci. name 3 Sci. name 4 urn:lsid:catalogueoflife.org: taxon:<uuid 1>:ac2009 urn:lsid:catalogueoflife.org: taxon:<uuid 1>:ac2010 KEY: Dynamic checklist lsid Annual checklist lsid Jones, White & Orme. Tracking Taxon Changes (TDWG 2009)

  6. Evolving concepts in dynamic & annual checklist urn:lsid:catalogueoflife.org: taxon:<uuid 1>:dc urn:lsid:catalogueoflife.org: taxon:<uuid 2>:dc urn:lsid:catalogueoflife.org: taxon:<uuid 4>:dc Sci. name 1 Synonyms: Sci. name 2 Sci. name 3 Sci. name 4 Sci. name 1 Synonyms: Sci. name 3 Sci. name 1 Synonyms: Sci. name 3 Sci. name 5 urn:lsid:catalogueoflife.org: taxon:<uuid 4>:ac2010 urn:lsid:catalogueoflife.org: taxon:<uuid 1>:ac2009 urn:lsid:catalogueoflife.org: taxon:<uuid 3>:dc urn:lsid:catalogueoflife.org: taxon:<uuid 3>:dc Sci. name 2 Synonyms: Sci. name 4 Sci. name 2 Synonyms: Sci. name 4 KEY: urn:lsid:catalogueoflife.org: taxon:<uuid 3>:ac2010 Dynamic checklist lsid Annual checklist lsid Jones, White & Orme. Tracking Taxon Changes (TDWG 2009)

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

  8. Jones, White & Orme. Tracking Taxon Changes (TDWG 2009) Specimen data & changing concepts

  9. Jones, White & Orme. Tracking Taxon Changes (TDWG 2009) Using data associated with changing concepts Pipistrellus pipistrellus sensu lato (45 & 55 kHz) (Pre-1999) Pipistrellus pipistrellus sensu stricto (Common Pipistrelle; 45 kHz) Pipistrellus pygmaeus (Soprano Pipistrelle; 55 kHz)

  10. Don't know which new species these observations relate to ... … but still applicable to genus Pipistrellus 10

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

  12. Jones, White & Orme. Tracking Taxon Changes (TDWG 2009) Capturing taxon concept changes • Changed persistent identifiers from source databases; or • Detecting changes by comparison • Same synonyms, parent taxon, etc?

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

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

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