Taxonomic Synonymy Definition Framework

CHRONOS & GNS Science New Zealand

Douglas Fils, Iain Matcham, Cinzia Cervato, James

Crampton

Why?

www.chronos.org

AKA:Biglobigerinella multispina, Globigerina biforaminata,

Globigerinelloides multispinatus

Globigerinelloides multispinus

FOR TIME CALIBRATION

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

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

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

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

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

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

TSDF

• extended classes • Synonymy

• Synonymy Entry

• TaxanomicName

• A set of supporting properties to define the entries

www.chronos.org

Simple synonymy with Senior Synonym

TSDF• Further

examples

www.chronos.org

Simple synonymy with single Senior and Junior Synonym

TSDF

www.chronos.org

• Multiple Synonymy

• Authors

• Inter-synonymy mapper

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

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

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

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

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

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