Download Implementing SNOMED CT in a Relational Database

IE0X) ModuleEWebinar_Handout
2016-11-16
Implementing
SNOMED CT in a
Relational
Database
Using SNOMED CT in a Relational Database
1. Download database management system
▪ MySQL Community Edition: https://www.mysql.com/products/community/
2. Download RF2 release files
3. Create empty tables
▪ Choose relevant release files
▪ Use RF2 file structure with appropriate indexes and keys
▪ Replace logical datatypes with corresponding physical datatypes
4. Load RF2 release files into tables
▪ Choose relevant release file type (full, snapshot, delta)
5. Create and load Transitive Closure
▪ Create Transitive Closure file from RF2 Relationship Snapshot file
▪ Create Transitive Closure table and load rows from TC file
6. Create views or queries (as required)
▪ Predefine commonly used queries for reuse
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IE0X) ModuleEWebinar_Handout
2016-11-16
Supporting Resources on eLearning Server
▪ MySQL Import for RF2 Full Release
▪ MySQL_database_loader.pdf
▪ Instructions on downloading MySQL and running script
▪ rf2_import_full_template.sql
▪ Creates tables, imports RF2 files, indexes and generates
a range of views, including some linked views that are useful
for viewing particular types of data.
▪ Transitive Closure Script
▪ SnomedCt_Elearning_Transitive_Closure_Script_20150907.pdf
▪ Instructions on using the Transitive Closure script
▪ transitiveClosureRf2Snap.pl
▪ Create transitive closure file from RF2 Snapshot relationship file
▪ rf2_import_tc_template.sql
▪ Creates table and imports transitive closure file
Example MySQL Database
Tables created include:
Row Counts in 2016-07-31 SNOMED CT International Release Files
Table
Full
sct2_concept
535,885
Snapshot
427,350
Snapshot Active
321,901
sct2_description
1,567,797
1,281,845
1,103,969
sct2_relationship
4,790,636
2,538,888
970,938
sct2_relationship (|is a|)
-
-
477,202
ss_transclose
-
-
5,515,515
sct2_refset_c
3,578,834
3,048,236
2,608,835
Note also
snomedct.config
▪ Used to configure snapshot date and language (active = 1)
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IE0X) ModuleEWebinar_Handout
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Example MySQL Database
▪ View Prefixes
▪
▪
▪
▪
sva - Snapshot view for latest date
soa - Snapshot view for latest date - optimised
svx - Snapshot view for specified* date (*in config table)
sox - Snapshot view for specified* date – optimised
▪ View Suffixes
▪
▪
▪
▪
▪
▪
_fsn - view of descriptions that are fully specified names**
_pref - the preferred synonyms**
_synall - all acceptable synonyms**
_rel_child_(fsn|pref) – FSN or PT** of children
_rel_parent_(fsn|pref) – FSN or PT** of parents
_rel_def_(fsn|pref) – FSN or PT** of definition
* Snapshot date selected in active row of config table
** Preferred in language selected in active row of config table
Example MySQL Database
Tables/Views used in following queries:
▪ snomedct.sva_synall – all synonyms in config language
▪ snomedct.sva_pref – preferred synonyms in config language
▪ snomedct.ss_transclose – transitive closure
▪ snomedct.sva_relationship – latest snapshot of relationships
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Example MySQL Database - Queries
1. Create a query to:
Find the active concepts with an ‘acceptable’ synonym containing
the words “disorder” and “lung”
SELECT conceptId, term
FROM snomedct.sva_synall
WHERE MATCH (term) AGAINST
('+disorder +lung' IN BOOLEAN MODE)
AND conceptId IN (SELECT id
FROM snomedct.sva_concept
WHERE active = 1)
ORDER BY length (term)
Result count: 14
Example MySQL Database - Queries
2. Create a query to:
Find the Preferred Term of concept with id “19829001”
SELECT conceptId, term
FROM snomedct.sva_pref
WHERE conceptId = 19829001
Result count: 1
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Example MySQL Database - Queries
3. Create a query to:
Select the “< 19829001 | disorder of lung |”
SELECT tc.subtypeId, pt.term
FROM snomedct.ss_transclose as tc, snomedct.sva_pref as pt
WHERE tc.supertypeId = 19829001
AND pt.conceptId = tc.subtypeId
ORDER BY pt.term
Result count: 997
Example MySQL Database - Queries
4. Create a query to:
Select the “< 19829001 | disorder of lung |:
116676008 | associated morphology | = 79654002 | edema |”
SELECT tc.subtypeId, pt.term
FROM snomedct.ss_transclose as tc,
snomedct.sva_pref as pt
WHERE tc.supertypeId = 19829001
AND pt.conceptId = tc.subtypeId
AND tc.subtypeId IN
(SELECT sourceId FROM snomedct.sva_relationship as r
WHERE r.active = 1 AND r.typeId = 116676008
AND r.destinationId = 79654002)
ORDER BY pt.term
Result count: 19
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Example MySQL Database - Queries
5. Create a query to:
Select the “< 19829001 | disorder of lung |:
116676008 | associated morphology | = << 79654002 | edema |”
SELECT tc.subtypeId, pt.term
FROM snomedct.ss_transclose as tc, snomedct.sva_pref as pt
WHERE tc.supertypeId = 19829001
AND pt.conceptId = tc.subtypeId AND tc.subtypeId IN
(SELECT sourceId FROM snomedct.sva_relationship as r
WHERE r.active = 1 AND r.typeId = 116676008
AND (r.destinationId = 79654002 OR r.destinationId IN
(SELECT tc2.subtypeID
FROM snomedct.ss_transclose as tc2
WHERE tc2.supertypeId = 79654002)))
ORDER BY pt.term
Result count: 28
Example MySQL Database - Queries
6. Create a query to:
Select the “< 404684003 | clinical finding |:
363698007 | finding site | = << 39057004 | pulmonary valve |,
116676008 | associated morphology | = << 415582006 |stenosis|”
SELECT tc.subtypeId, pt.term
FROM snomedct.ss_transclose as tc, snomedct.sva_pref as pt
WHERE tc.supertypeId = 404684003 AND pt.conceptId = tc.subtypeId
AND tc.subtypeId IN (SELECT sourceId FROM snomedct.sva_relationship as r
WHERE r.active = 1 AND r.typeId = 363698007
AND (r.destinationId = 39057004 OR r.destinationId IN
(SELECT tc2.subtypeID FROM snomedct.ss_transclose as tc2
WHERE tc2.supertypeId = 39057004 )))
AND tc.subtypeId IN (SELECT sourceId FROM snomedct.sva_relationship as r
WHERE r.active = 1 AND r.typeId = 116676008
AND (r.destinationId = 415582006 OR r.destinationId IN
(SELECT tc2.subtypeID FROM snomedct.ss_transclose as tc2
WHERE tc2.supertypeId = 415582006 )))
Result count: 22
ORDER BY pt.term
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