Evaluating Queries Expressed over GDB and GSDB

Query 1:

Find the protein kinase genes on chromosome X.

The first query generates the following OPM_AL query against HGD:

SELECT displayName, accessionID, mapElements.map.chromosome.displayName
FROM   Gene
WHERE  mapElements.map.chromosome.displayName = "X";

and the GSDB query:

SELECT products.name, genes.gdb_xref
FROM   Feature
WHERE  products.name MATCH "%kinase%";

leaving the condition Feature.genes.gdb_xref = HGD:Gene.accessionID to be tested by the local query engine.

Query 2:

Find sequenced regions on chromosome 17 with length greater than 100,000.

The second query generates the OPM_QL queries for HGD:

SELECT map.chromosome,  segment 
FROM   MapElement
WHERE  map.chromosome = "17";

and

SELECT dBObject,  externalDB.displayName, accessionID 
FROM   SequenceLink
WHERE  externalDB.displayName = "GSDB"

and the following query for GSDB:

SELECT accession_number, sequences.length
FROM   Entry
WHERE  sequences.length > 10000;

Query 3:

Find the sequences of ESTs mapped between 4q21.1 - 21.2.

The first part of the third query already only concerns a single class, MapElement of the HGD database, and may therefore be directly rewritten as an OPM_QL query.

The second part of the query gives rise to the HGD queries:

SELECT displayName, isExpressed, mapElements.map.chromosome.displayName,
       mapElements.sortCoord 
FROM   Amplimer
WHERE  isExpressed = "Yes"
AND    mapElements.map.chromosome.displayName = "4"
AND    mapElements.sortCoord >= START_COORD
AND    mapElements.sortCoord <= END_COORD;

and

SELECT dbObject, externalDB.displayName, accessionID 
FROM   SequenceLink
WHERE  externalDB.displayName = "GSDB";

and the GSDB query:

SELECT accession_number, sequences.length
FROM   Entry;