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 |
|