Queries for Phenoscape UI demo'ed at SICB, Boston in Jan 2009
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
SELECT \* FROM node_link_node_with_pred_and_source WHERE
pred_uid LIKE '%PHENOSCAPE:exhibits%' AND object_uid LIKE
'%TAO:0001510%';
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
SELECT \* FROM node_link_node_with_pred_and_source WHERE
pred_uid LIKE '%oboInOwl:inSubset%' AND node_uid LIKE '%PATO:0000467%';
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
SELECT \* FROM node_link_node_with_pred_and_source WHERE
node_uid LIKE '%PATO:0000467%' AND pred_uid LIKE '%OBO_REL:is_a%';
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
SELECT \* FROM node_link_node_with_pred_and_source WHERE
object_uid LIKE '%TAO:0001510%' AND pred_uid LIKE '%OBO_REL:is_a%';
Execution
- Time: 162 ms
- Rows returned: 2
