Transcript Document 7282945

Taxonomic Synonymy
Definition Framework
CHRONOS & GNS Science
New Zealand
Douglas Fils, Iain Matcham,
Cinzia Cervato, James
Crampton
Why?
AKA:
Biglobigerinella multispina,
Globigerina biforaminata,
Globigerinelloides
multispinatus
Globigerinelloides
multispinus
FOR TIME CALIBRATION
www.chronos.org
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
retrieving junior synonym records for a
currently displayed senior synonym
taxon_link_junior.sql
foramdb_neptune_link
•record_number
•taxon_id
foramdb_neptune_link
chkNeptune
•record_number
•taxon_id
•synonym_status=‘j’
•chkTaxon
•chkTaxonStatus
tcretaceous_all_species
tcretaceous_all_species
•record_number
•data
•record_number
•data
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
chkNeptune
•record_number
•taxon_id
•chkTaxon
•chkTaxonStatus
tcretaceous_all_species
tcretaceous_all_species
•record_number
•data
•record_number
•data
Benefits
•
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Global taxonomic synonymy network
Science Efforts:
Bio-diversity studies
- MicroPaleo
Digital Taxonomic Dictionaries - FormaDB
- Andrill
Paleo-climate issues
- others
Method to embed data into web sites to
enable semantic web adoption
www.chronos.org
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
Simple synonymy with Senior
Synonym
www.chronos.org
TSDF
• Further
examples
Simple synonymy with single Senior
and Junior Synonym
www.chronos.org
TSDF
• Multiple
Synonymy
• Authors
• Intersynonymy
mapper
www.chronos.org
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.net
www.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