Taxonomic Synonymy Definition Framework CHRONOS & GNS Science New Zealand
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Taxonomic Synonymy Definition Framework
CHRONOS & GNS Science New Zealand
Douglas Fils, Iain Matcham, Cinzia Cervato, James
Crampton
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Why?
www.chronos.org
AKA:Biglobigerinella multispina, Globigerina biforaminata,
Globigerinelloides multispinatus
Globigerinelloides multispinus
FOR TIME CALIBRATION
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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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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
retrieving junior synonym records for a currently displayed senior synonym
taxon_link_junior.sql
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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
retrieving senior synonym records for a currently displayed junior synonym
taxon_link_senior.sql
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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
www.chronos.org
Science Efforts:- MicroPaleo- FormaDB- Andrill- others
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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
www.chronos.org
Simple synonymy with Senior Synonym
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TSDF• Further
examples
www.chronos.org
Simple synonymy with single Senior and Junior Synonym
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TSDF
www.chronos.org
• Multiple Synonymy
• Authors
• Inter-synonymy mapper
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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 efforts
like those of stratigraphy.netwww.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 -> RSS)
• Cross cutting formats (TSDF <-> FOAF <->other)
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