Experience from Mapping Existing Models to the Transfer Schema

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Experience from Mapping Existing Models to the
Transfer Schema

• Robert Kukla

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Introduction

• Three test databases
• ITIS (plants part)
• Berlin Model (mosses/higher plants)
• Taxonomer (fishes)
• Imported into mySQL
• Java program to generate XML
• Three main aspects
• Identifying concepts
• Extracting relationships
• Concept details
• No CharacterCircumscription, SpecimenCircumscripti
  on
• No hybrids as implications are not fully
  understood

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ITIS

• Integrated Taxonomic Information System
• authoritative taxonomic information
• Continuously evolving
• New records get added
• Existing records get updated (!)
• 331886 taxonomic units (97741 plants) - 206649
  concepts
• Most explored DB

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ITIS - Identifying Concepts

• ITIS own concepts (type revision)
• taxonomic unit
• usage accepted
• Synonyms (type referenced)
• usage not accepted
• referenced from synonym table
• Vernaculars (type vernacular)
• from vernacular table

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ITIS Extracting Relationships

• Concept Circumscription
• parent_tsn field
• Synonymy Relationships
• Explicit synonyms
• Vernaculars
• Lineage Relationships
• to concept of same name according to different
  publication

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ITIS concept details

• Names
• up to 4 epithets (only 3 used) plus 4 category
  indicators to be interpreted depending on rank
• authorTeam from separate table
• NameSimple calculated
• Publications
• Multiple publication per taxon_unit
• Not completely atomised - compromise

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Berlin Model - Mosses/(German Higher Plants)

• Database of Taxonomic Concepts
• Records will not change
• Explicit concept relationships (name-) synonymy
• 24368 concepts 24368 concepts

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Berlin Model - Identifying Concepts

• From table pTaxon

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Taxonomer

• Relational data model for managing information
  relevant to taxonomic research
• Records get added not changed
• Assertion mention of a taxonomic name in the
  taxonomic literature
• Protonym taxonomic name in the context of its
  first publication
• Relationships between assertions
• 36305 assertions 14971 concepts

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Taxonomer - Identifying Concepts

• Concepts (typereferenced)
• from table tbl_Assertions
• ReliabilityID gt 4 (4-revision, 5 original/new
  combination)

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Taxonomer extracting relationships

• ConceptCircumscription
• ParentAssertionID
• Relationships
• Table not populated

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Taxonomer concept details

• Number of fields in the database suggested a
  complexity that was not supported by the data
  (not all fields filled)
• Atomised name difficult to recreate as only
  terminal epithet is stored omitted it
• Use of cheat fields for NameSimple
• Large number of AccordingTo (gt4000)
• Publication data transferred 11

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Technical Aspects

• Database consistency e.g.
• getting all publication records
• no relationships to non-existant concepts
• Charset
• assume windows-1252 code page
• Slow!
• indexes essential
• fewer queries with big result sets faster
• Recursive approach is more suitable for wrapper
• guarantees small, consistent subset

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Mapping software

• Universal transformation software to convert
  relational data to XML (XMlizer)
• Often GUI based filling in a skeleton XML file
• Relate a single query (table or join) to
  collection of XML nodes
• Map fields from that query to attributes or child
  elements of the XML node
• Problems
• No mechanism to use multiple sources (queries)
  for one
• No conditional transformation
• No splitting of fields
• Limited merging of fields
• Write our own universal mapping software
• addresses first 2 problems

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Conclusion

• Conversion of legacy data is possible but
• information missing
• information will be lost
• Data in original DB is open to interpretation so
  expert should be consulted
• Required computing resources should not be
  underestimated