The role of persistent identifiers in tracking taxon changes Andrew C. Jones, Richard J. White, Ewen R. Orme, School of Computer Science, Cardiff University,

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Presentation transcript:

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 |

Jones, White & Orme. Tracking Taxon Changes (TDWG 2009)2 The Catalogue of Life GSD CAS Web front-end Other software clients of Catalogue of Life (e.g. using it as their “taxonomic backbone”)

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 1 Synonyms: Sci. name 2 Sci. name 3 Sci. name 4 urn:lsid:catalogueoflife.org: taxon: :dc urn:lsid:catalogueoflife.org: taxon: :ac2009 Dynamic checklist lsid Annual checklist lsid KEY: Sci. name 1 Synonyms: Sci. name 2 Sci. name 3 Sci. name 4 urn:lsid:catalogueoflife.org: taxon: :dc urn:lsid:catalogueoflife.org: taxon: :ac2010

Jones, White & Orme. Tracking Taxon Changes (TDWG 2009)6 Evolving concepts in dynamic & annual checklist Sci. name 1 Synonyms: Sci. name 2 Sci. name 3 Sci. name 4 Sci. name 1 Synonyms: Sci. name 3 Sci. name 2 Synonyms: Sci. name 4 Sci. name 1 Synonyms: Sci. name 3 Sci. name 5 Sci. name 2 Synonyms: Sci. name 4 urn:lsid:catalogueoflife.org: taxon: :dc urn:lsid:catalogueoflife.org: taxon: :dc urn:lsid:catalogueoflife.org: taxon: :dc urn:lsid:catalogueoflife.org: taxon: :dc urn:lsid:catalogueoflife.org: taxon: :dc urn:lsid:catalogueoflife.org: taxon: :ac2009 urn:lsid:catalogueoflife.org: taxon: :ac2010 urn:lsid:catalogueoflife.org: taxon: :ac2010 Dynamic 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 Pipistrellus pipistrellus sensu stricto (Common Pipistrelle; 45 kHz) Pipistrellus pygmaeus (Soprano Pipistrelle; 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 Pipistrellus 10

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: 4D4Life questionnaire: