1 / 17

Taxonomic Synonymy Definition Framework CHRONOS & GNS Science New Zealand

Douglas Fils, Iain Matcham, Cinzia Cervato, James Crampton. Taxonomic Synonymy Definition Framework CHRONOS & GNS Science New Zealand. Why?. AKA: Biglobigerinella multispina, Globigerina biforaminata, Globigerinelloides multispinatus. Globigerinelloides multispinus. FOR TIME CALIBRATION.

shayla
Download Presentation

Taxonomic Synonymy Definition Framework CHRONOS & GNS Science New Zealand

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Douglas Fils, Iain Matcham, Cinzia Cervato, James Crampton Taxonomic Synonymy Definition FrameworkCHRONOS & GNS Science New Zealand

  2. Why? AKA: Biglobigerinella multispina, Globigerina biforaminata, Globigerinelloides multispinatus Globigerinelloides multispinus FOR TIME CALIBRATION www.chronos.org

  3. Needs • Simple method to address current need to exchange synonymy in a standards/future aware method • Encode taxonomic synonymy • Transport these synonymy between sites and applications (Neptune, FRED, ForamDB, CONOP9, XQE, TIS, etc.) via web services and ReST • Associate taxonomic synonymy (Senior & Junior synonyms) with opinions and authorities www.chronos.org

  4. retrieving junior synonym records for a currently displayed senior synonym taxon_link_junior.sql • foramdb_neptune_link • record_number • taxon_id • foramdb_neptune_link • record_number • taxon_id • synonym_status=‘j’ • chkNeptune • chkTaxon • chkTaxonStatus • tcretaceous_all_species • record_number • data • tcretaceous_all_species • record_number • data

  5. retrieving senior synonym records for a currently displayed junior synonym taxon_link_senior.sql • foramdb_neptune_link • record_number • taxon_id • synonym_status=‘j’ • foramdb_neptune_link • record_number • taxon_id • chkNeptune • chkTaxon • chkTaxonStatus • tcretaceous_all_species • record_number • data • tcretaceous_all_species • record_number • data

  6. Benefits • Global taxonomic synonymy network • Bio-diversity studies • Digital Taxonomic Dictionaries • Paleo-climate issues • Method to embed data into web sites to enable semantic web adoption Science Efforts: - MicroPaleo - FormaDB - Andrill - others www.chronos.org

  7. TSDF is not • A way to automatically create synonymy • Dangerous as a means to AUTOMATICALLY generate input for CONOP9 or as a means to get to LOC's • Due to this, these types of documents may imply a need for an educational QA/QC process on creating and transporting these files www.chronos.org

  8. TSDF Description • Based on RDF/SKOS • Relation based • Extension of the SKOS framework • XML (ADBC, DarwinCore, Taxon Concept Schema) vs RDF • No controlled vocabulary initially involved • does not carry morphology or other “data” that might require a vocabulary (more relations based) • pseudo vocabulary derived from taxon name super set and current SKOS terms www.chronos.org

  9. TSDF • extended classes • Synonymy • Synonymy Entry • TaxanomicName • A set of supporting properties to define the entries Simple synonymy with Senior Synonym www.chronos.org

  10. TSDF • Further examples Simple synonymy with single Senior and Junior Synonym www.chronos.org

  11. TSDF • Multiple Synonymy • Authors • Inter-synonymy mapper www.chronos.org

  12. Application of TSDF • Provide Something: • Virtual “master” taxonomy dictionaries • A digital Taxonomic dictionary can be mashed up on the fly (an extension of the current taxon info mash up concept) • semantic web services for discovery www.chronos.org

  13. Exchanging TSDF • Unique Identifier methods used to designate taxa from contributing sources (LSID, URI) • Synonymy requests answered by SOAP or ReST interfaces (services based approach) • various parameters could be used (not set) • Document centric approach (TSDF returned) www.chronos.org

  14. Embedding TSDF • microformats approach (simple semantics) • TSDF is not a microformat, but follows its principles • solve a specific problem • start as simple as possible • design for humans first, machines second • reuse building blocks from widely adopted standards • modularity / embeddability • enable and encourage decentralized development, content, services www.chronos.org

  15. Planning for Displaying and Browsing of TSDF • Looking at the efforts of Simile (MIT) and SWED • Faceted Browsing • Fresnel syntax • Horus / Longwell • Welkin • Enhance community effortslike those of stratigraphy.net www.chronos.org

  16. TSDF mash-ups • Gateway to allow resources like GNS Science NZ, S.net, CHRONOS, Paleobiology and others to contribute to mash-ups and other dynamic taxonomy systems • Change logs to track synonymy evolution (no pun intended) • syndication efforts (TSDF -> RSS) • Cross cutting formats (TSDF <-> FOAF <->other) www.chronos.org

  17. Conclusion • Joint effort between CHRONOS and GNS Science New Zealand • Address current need to exchange synonymy between sites and applications for defined applications • Defined with • future extensibility in mind • to be an extensible long term effort www.chronos.org

More Related