Taxonomic Synonymy Definition Framework CHRONOS

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Taxonomic Synonymy Definition FrameworkCHRONOS
GNS Science New Zealand

• Douglas Fils, Iain Matcham, Cinzia Cervato, James
  Crampton

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Why?
AKA Biglobigerinella multispina, Globigerina
biforaminata, Globigerinelloides multispinatus
Globigerinelloides multispinus
FOR TIME CALIBRATION
www.chronos.org
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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
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retrieving junior synonym records for a
currently displayed senior synonym taxon_link_ju
nior.sql

• foramdb_neptune_link
• record_number
• taxon_id

• foramdb_neptune_link
• record_number
• taxon_id
• synonym_statusj

• chkNeptune
• chkTaxon
• chkTaxonStatus

• tcretaceous_all_species
• record_number
• data

• tcretaceous_all_species
• record_number
• data

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retrieving senior synonym records for a
currently displayed junior synonym taxon_link_se
nior.sql

• foramdb_neptune_link
• record_number
• taxon_id
• synonym_statusj

• foramdb_neptune_link
• record_number
• taxon_id

• chkNeptune
• chkTaxon
• chkTaxonStatus

• tcretaceous_all_species
• record_number
• data

• tcretaceous_all_species
• record_number
• data

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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
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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
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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
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TSDF

• extended classes
• Synonymy
• Synonymy Entry
• TaxanomicName
• A set of supporting properties to define the
  entries

Simple synonymy with Senior Synonym
www.chronos.org
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TSDF

• Further examples

Simple synonymy with single Senior and Junior
Synonym
www.chronos.org
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TSDF

• Multiple Synonymy
• Authors
• Inter-synonymy mapper

www.chronos.org
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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
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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
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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
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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
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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 -gt RSS)
• Cross cutting formats (TSDF lt-gt FOAF lt-gtother)

www.chronos.org
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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