Queries for Phenoscape UI demo'ed at SICB, Boston in Jan 2009

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This page documents the queries implemented to retrieve data for the Anatomy Web Services module of the Phenoscape project, which was demonstrated at the SICB Workshop in Boston, MA in Jan 2009.

Query details

These queries correspond to the queries Q1~Q4 detailed in the Queries page. The anatomical feature being searched for is TAO:0001510 (Basihyal Cartilage)

Query 1 (Q1)

This query retrieves the phenotypes from the database that are composed from the anatomical feature as one of their components. These retrieved phenotypes are parsed to retrieve the qualities associated with the anatomical feature being searched for. These retrieved qualities are input to query Q2

SQL

<javascript> SELECT * FROM node_link_node_with_pred_and_source WHERE pred_uid LIKE '%PHENOSCAPE:exhibits%' AND object_uid LIKE '%TAO:0001510%'; </javascript>

Execution

  • Time : 145 Milliseconds
  • Rows Returned: 25

Query 2 (Q2)

For each Quality that is retrieved by Q1, this query Q2 is executed to determine if it is an attribute or a value. A lookup table is populated to avoid redundant queries. This example is using PATO:0000467 (present in normal numbers in the organism)

SQL

<javascript> SELECT * FROM node_link_node_with_pred_and_source WHERE pred_uid LIKE '%oboInOwl:inSubset%' AND node_uid LIKE '%PATO:0000467%'; </javascript>

Execution

  • Time: 286 milliseconds
  • Rows returned: 485

Query 3 (Q3)

If the results from Q2 show the Quality is a Value, then this query Q3 is executed to find out the Attribute

SQL

<javascript> SELECT * FROM node_link_node_with_pred_and_source WHERE node_uid LIKE '%PATO:0000467%' AND pred_uid LIKE '%OBO_REL:is_a%'; </javascript>

Execution

  • Time: 199 milliseconds
  • Rows returned: 685

Notes on Queries Q2 and Q3

  • Queries Q2 and Q3 return many more rows than anticipated because they use wildcard matches. Therefore rows containing only the search term (PATO:0000467) and also the rows containing phenotypes containing the search term (PATO:0000467^inheres_in:...) are returned
  • The attribute is determined by this query Q3 because the reasoner adds all the transitive is_a relationships between the search term and its super attributes and all these inferred rows are retrieved by Q3
  • Q2 and Q3 are executed several times. An attribute-value lookup table is populated from the results of the earlier executions. If the value being searched for is found to be mapped to a specific attribute in the lookup table, the attribute is retrieved directly from the lookup table and the executions of database queries Q2 and Q3 are avoided. Coupled with connection, query execution, and data transfer times, this leads to significant time savings.

Query 4 (Q4)

The sub anatomical features for the given anatomical feature are retrieved in this query. Here, we search for the sub anatomical features of TAO:0001510 (basihyal cartilage). This query, if started with a TAO feature, will often retrieve a corresponding ZFA feature (if the DbXref link has been asserted). For every feature retrieved by the query, the process described above starts off again.

SQL

<javascript> SELECT * FROM node_link_node_with_pred_and_source WHERE object_uid LIKE '%TAO:0001510%' AND pred_uid LIKE '%OBO_REL:is_a%'; </javascript>

Execution

  • Time: 162 ms
  • Rows returned: 2