Entrez

Entrez query syntax

Nicknames based on the Entrez wrapper generally require the use of a special function. The Entrez wrapper must translate the SQL query into a query that the Entrez API will understand and not all elements of a standard SQL where clause can be so translated.

The schema description tables for datasets that make use of the Entrez wrapper include two extra columns:
  • The 'Q' column designates that a given field can be used when searching an Entrez table.
    • One queries such a column using a request containing a clause or clauses containing the 'CONTAINS' function, as in: 
    SELECT * FROM NCBI.PMARTICLES 
WHERE
   ( ENTREZ.CONTAINS( ARTICLETITLE, 'drosophila') = 1 )
    or 
    SELECT AUTHORLIST, ARTICLETITLE FROM NCBI.PMARTICLES 
WHERE
   ( ENTREZ.CONTAINS( ARTICLETITLE, 'drosophila') = 1 ) 
   AND
   ( ENTREZ.CONTAINS( AUTHORLIST, 'Kaufmann OR Ito') = 1 )
    or 
    SELECT * FROM NCBI.GBSEQ 
WHERE
   ( ENTREZ.CONTAINS( ORGANISM, 'drosophila') = 1 ) 
   AND 
   ( ENTREZ.CONTAINS( SEQLENGTH, '25' ) = 1 )
    or 
    SELECT PRIMARYACCESSION, SEQLENGTH, DEFINITION, SEQUENCE 
FROM NCBI.GBSEQ
WHERE ( ENTREZ.CONTAINS( ORGANISM, 'HUMAN') = 1 ) 
      AND 
      ( ENTREZ.CONTAINS( DEFINITION, 'JAK3' ) = 1 )

    or 

    SELECT PMID, AUTHORLIST, ARTICLETITLE FROM NCBI.PMARTICLES 
WHERE
  ( ENTREZ.CONTAINS(AUTHORLIST, 'kaufmann OR ito') = 1 )
  AND
  (
     ( ENTREZ.CONTAINS (ARTICLETITLE, 'drosophila') = 1 )
     OR
     ( ENTREZ.CONTAINS(ABSTRACT, 'drosophila OR "fruit fly"') = 1 )
  )
  • The 'F' column designates for a given column that a query that uses the standard relational predicates '=' or 'IN' will be translated into a similar Entrez predicate. Otherwise, the predicate will be applied in the DB2 engine.
NOTE: If an Entrez nickname has no search terms designated in the 'Q' column, then information can only be retrieved from that nickname by joining it to another nickname that does have a search term listed in the 'Q' column.