Requirements of a Taxonomy Database Tcl-DB a Prototype

Outline 1.Requirements Hierarchy Alternative Search Terms: Synonyms and Vernaculars Alternative Spellings Alternative Classifications 2.Tcl-DB Prototype System Tcl-DB Structure 2NF 3.Extensibile: Adding a new data source e.g. NCBI 4.Tcl-DB: UID Tracking 5.Tcl-DB: Stats 6.Utility and Further Work

1. Hierarchy

2. Alternative Search Terms: Synonyms and Vernaculars

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

4. Alternative Classifications:

Tcl-DB Prototype System. Proposed Architecture

Tcl-DB: Logical Structure

Tcl-DB Physical Database Structure

Assertion: Resolving the M:M with an association entity

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;

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

Tcl-DB: 2NF

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

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

Step 2: Move names from view to Tcl schema

Step 3: Fill the nodes table in tcl schema

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

Tcl-DB: UID Tracking after name data load: 1.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 2.Update name and give all new names a NID 3.Update name give all names their original NID 4.Refresh the NID_view

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

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?