C07: Find a pathogen by keyword

This query enables a search of all pathogens using a keyword as input. The resulting concepts could be used in query C09 to identify diseases caused by a certain pathogen.

Input:
 Parameter  Example  Mandatory  Notes
 Keyword for pathogen  'Trypanosoma'  Yes Keyword should be placed in a single quote
 As of date  Sysdate  No Valid record as of specific date. Current date – sysdate is a default

Sample query run:
The following is a sample run of the query to list all pathogens specified using a keyword as input. The sample parameter substitutions are highlighted in blue.
SELECT   C.concept_id       Pathogen_Concept_ID,
         C.concept_name     Pathogen_Concept_Name,
         C.concept_code     Pathogen_concept_code,
         C.concept_class    Pathogen_concept_class,
         C.concept_level    Pathogen_Concept_Level,
         C.vocabulary_id    Pathogen_Concept_Vocab_ID,
         V.vocabulary_name  Pathogen_Concept_Vocab_Name
FROM    vocabulary.concept     C, 
        vocabulary.vocabulary  V
WHERE   LOWER(C.concept_class) = 'organism'
AND     INSTR(LOWER(C.concept_name), LOWER('Trypanosoma')) > 0
AND     C.vocabulary_id        = V.vocabulary_id
AND     sysdate BETWEEN C.valid_start_date AND C.valid_end_date 
Output:
Output field list:
 Field  Description
 Pathogen_Concept_ID  Concept ID of SNOMED-CT pathogen concept
 Pathogen_Concept_Name  Name of SNOMED-CT pathogen concept with keyword entered as input
 Pathogen_Concept_Code  Concept Code of SNOMED-CT pathogen concept
 Pathogen_Concept_Class  Concept class of SNOMED-CT pathogen concept
 Pathogen_Concept_Level  Concept level of SNOMED-CT pathogen concept
 Pathogen_Vocab_ID  Vocabulary ID of the vocabulary from which the pathogen concept is derived from (1 for SNOMED-CT)
 Pathogen_Vocab_Name  Name of the vocabulary from which the pathogen concept is derived from (SNOMED-CT)

Sample output record:
 Field  Value
 Pathogen_Concept_ID  4085768
 Pathogen_Concept_Name  Trypanosoma brucei
 Pathogen_Concept_Code  243659009
 Pathogen_Concept_Class  Organism
 Pathogen_Concept_Level  0
 Pathogen_Vocab_ID  1
 Pathogen_Vocab_Name  SNOMED-CT
Comments