Requirements of a Taxonomy Database

Tcl-DB a Prototype

Outline1. 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. NCBI4. Tcl-DB: UID Tracking5. Tcl-DB: Stats6. Utility and Further Work

1. Hierarchy

2. Alternative Search Terms: Synonyms and Vernaculars

3. Alternative Spellings: Caenorabditis elegans, C elegansand 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 QueriesNested 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

Kingdom

KINGDOM_ID

NAME_ID NAME_TEXT SOURCE_ID

Rank

RANK_ID

RANK_NAME SOURCE_ID

ASSERTION

PK ASSERTION_ID

I2,I1 NAME_IDI1 SOURCE_IDI1 DBSOURCE_ID AID NID RANK_ID KINGDOM_ID

ASSERTION

PK ASSERTION_ID

I1,I2 NAME_IDI1 SOURCE_IDI1 DBSOURCE_ID AID NID RANK KINGDOM

Adding a new data source e.g. NCBITcl-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 schemaStep 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 TableBuilding 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?