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Requirements of a Taxonomy Database Tcl-DB a Prototype

Requirements of a Taxonomy Database Tcl-DB a Prototype. Outline Requirements Hierarchy Alternative Search Terms: Synonyms and Vernaculars Alternative Spellings Alternative Classifications Tcl-DB Prototype System Tcl-DB Structure 2NF Extensibile: Adding a new data source e.g. NCBI

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Requirements of a Taxonomy Database Tcl-DB a Prototype

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  1. Requirements of a Taxonomy DatabaseTcl-DB a Prototype

  2. Outline • Requirements • Hierarchy • Alternative Search Terms: Synonyms and Vernaculars • Alternative Spellings • Alternative Classifications • Tcl-DB Prototype System • Tcl-DB Structure • 2NF • Extensibile: Adding a new data source e.g. NCBI • Tcl-DB: UID Tracking • Tcl-DB: Stats • Utility and Further Work

  3. 1. Hierarchy

  4. 2. Alternative Search Terms: Synonyms and Vernaculars

  5. 3. Alternative Spellings: Caenorabditis elegans, C elegans and Caenorhabditis elegans  

  6. 4. Alternative Classifications:

  7. Tcl-DB Prototype System. Proposed Architecture

  8. Tcl-DB: Logical Structure

  9. Tcl-DB Physical Database Structure

  10. Assertion: Resolving the M:M with an association entity

  11. Node: Hierarchical Queries Nested Set, Path and Connect by >select count(name_id) from node start with name_id = ‘100891' connect by prior name_id = parent_name_id; >select count(name_id) from node where path like '/%'; >select count(name_id) from node where left_id between 1 and 9290;

  12. synonym_name and vernacular: subtypes,multi-valued attributes or weak entities

  13. Tcl-DB: 2NF

  14. Tcl-DB: Procedures, Packages and Functions: Adding a new data source e.g. NCBI

  15. Step 1: Build Views, what names are already in the database

  16. Step 2: Move names from view to Tcl schema

  17. Step 3: Fill the nodes table in tcl schema

  18. Step 4: fill synonym_name table in tcl schema Step 5: fill vernacular table in tcl schema

  19. Tcl-DB: UID Tracking • after name data load: • Run two joins on name and nids_mv • Nids – name_id when the name_text exist • Null – name_id when the name_text not exist • Update name and give all new names a NID • Update name give all names their original NID • Refresh the NID_view

  20. Tcl-DB: Utility and Further Work • Computing Interesting Stats: • How much overlap between ITIS and NCBI? • How many names unique to NCBI? • How many of these are binomials Vs ‘environmental sample 256’ • How many of these names can be matched allowing for 1 – 3 letter mismatches. • NCBI taxonomy – data quality, Integrity and Usability? • Transitively closing the Synonyms Table and Vernacular Table • Building an interface. • Spell checkers

  21. Lots of Questions?How do we use this to build taxonomically aware databases?How about updates to the data?Database links , Web services, Simple DB Cross References?Use Genbank Model?Open to Suggestions/Ideas!Do we need to think about:PhyloCode?Type Specimens?

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