General Comments
MedDRA Vocabulary load source files
The design and implementation of the LexEVS 6.1 MedDRA Vocabulary Loader assumes the user has access to MedDRA ASCII source files which can be purchased from: MedDRA MSSO
Overview
The current implementation of the LexEVS 6.1 MedDRA Vocabulary Loader will load all information contained within the ASCII load source files. Two root nodes are created, one for the SMQ root node and one for the SOC root node.
LexGrid Objects Created
The following describes LexGrid Objects created. Values extracted from MedDRA tables are in bold using the syntax: <tablename>.<fieldname>
Root Nodes
- SOC
- SMQ
Coding Scheme
CodingSchemeName | “MedDRA” |
FormalName: | “MedDRA-16.0” |
CodingSchemeURI | |
DefaultLanguage | “en” |
RepresentsVersion | medra_release.version |
LocalNameAsReference | “MedDRA” |
EntityDescription | “Medical Dictionary for Regulatory Activities” |
Copyright | “THIS DATA IS COVERED BY A COPYRIGHT” |
Hierarchy |
|
Hierarchy.LocalID | “is_a” |
Hierarchy.AssociationName | “hasSubtype” |
Hierarchy.RootCode | “@” |
Hierarchy.ForwardNavigable | True |
Entities – System Organ Class (SOC)
EntityCode: | soc.soc_code |
EntityDescription: | soc.soc_name |
isActive: | true |
| Presentation |
|
Presentation.PropertyName | “T-1” |
Presentation.Value | soc.soc_name |
Presentation.RepresentationalForm | “OS” |
Presentation.IsPreferred | True |
Property |
|
Property.PropertyName | “P-1” |
Property.Value | intl_ord.intl_ord |
Property |
|
Property.PropertyName | “P-2” |
Property.Value | soc.soc_abbrev |
Entities - High Level Group Term (HLGT)
EntityCode: | hlgt.hlgt_code |
EntityDescription: | hlgt.hlgt_name |
isActive: | true |
Presentation |
|
Presentation.PropertyName | “T-1” |
Presentation.Value | hlgt.hlgt_name |
Presentation.RepresentationalForm | “HG” |
Presentation.IsPreferred | true |
Entities - High Level Term (HLT)
EntityCode | hlt.hlt_code |
EntityDescription | hlt.hlt_name |
isActive | true |
Presentation |
|
Presentation.PropertyName | “T-1” |
Presentation.Value | hlt.hlt_name |
Presentation.RepresentationalForm | “HT” |
Presentation.IsPreferred | true |
Entities - Preferred Term (PT)
EntityCode | pt.pt_code |
EntityDescription | pt.pt_name |
isActive | true |
Presentation |
|
Presentation.PropertyName | “T-1” |
Presentation.Value | pt.pt_name |
Presentation.RepresentationalForm | “PT” |
Presentation.IsPreferred | true |
Presentation (exists if an LLT with duplicate ID exists) |
|
Presentation.PropertyName | “T-2” |
Presentation.Value | llt.llt_name |
Presentation.RepresentationalForm | “LT” |
Presentation.IsPreferred | false |
Property |
|
Property.PropertyName | “PSOC” |
Property.Value | pt.pt_soc_code |
Following properties exist if PT is listed in table smq_content
Property |
|
Property.PropertyName | “SMQ:term level” |
Property.Value | smq_content.term_level |
Property |
|
Property.PropertyName | “SMQ:term scope” |
Property.Value | smq_content.term_scope |
Property |
|
Property.PropertyName | “SMQ:term category” |
Property.Value | smq_content.term_category |
Property |
|
Property.PropertyName | “SMQ:term weight” |
Property.Value | smq_content.term_weight |
Property |
|
Property.PropertyName | “SMQ:term status” |
Property.Value | smq_content.term_status |
Property |
|
Property.PropertyName | “SMQ:term addition version” |
Property.Value | smq_content.term_addition_version |
Property |
|
Property.PropertyName | “SMQ:term last modified version” |
Property.Value | smq_content.term_last_modified_version |
Entities - Lower Level Term (LLT)
EntityCode | llt.llt_code |
EntityDescription | llt.llt_name |
isActive | true |
Presentation |
|
Presentation.PropertyName | “T-1” |
Presentation.Value | llt.llt_name |
Presentation.RepresentationalForm | “LT” |
Presentation.IsPreferred | true |
Following properties exist if LLT is listed in table smq_content
Property |
|
Property.PropertyName | “SMQ:term level” |
Property.Value | smq_content.term_level |
Property |
|
Property.PropertyName | “SMQ:term scope” |
Property.Value | smq_content.term_scope |
Property |
|
Property.PropertyName | “SMQ:term category” |
Property.Value | smq_content.term_category |
Property |
|
Property.PropertyName | “SMQ:term weight” |
Property.Value | smq_content.term_weight |
Property |
|
Property.PropertyName | “SMQ:term status” |
Property.Value | smq_content.term_status |
Property |
|
Property.PropertyName | “SMQ:term addition version” |
Property.Value | smq_content.term_addition_version |
Property |
|
Property.PropertyName | “SMQ:term last modified version” |
Property.Value | smq_content.term_last_modified_version |
Entities - Standard MedDRA Query (SMQ)
EntityCode | smq_list.smq_code |
EntityDescription | smq_list.smq_name |
isActive | True |
Presentation |
|
Presentation.PropertyName | “T-1” |
Presentation.Value | smq_list.smq_name |
Presentation.RepresentationalForm | “SMQ” |
Presentation.IsPreferred | true |
Comment |
|
Comment.PropertyName | “Name” |
Comment.Value | smq_list.smq_name |
Comment |
|
Comment.PropertyName | “Code” |
Comment.Value | smq_list.smq_code |
Comment |
|
Comment.PropertyName | “Level” |
Comment.Value | smq_list.smq_level |
Comment |
|
Comment.PropertyName | “Description” |
Comment.Value | smq_list.smq_description |
Comment |
|
Comment.PropertyName | “Source” |
Comment.Value | smq_list.smq_source |
Comment |
|
Comment.PropertyName | “Note” |
Comment.Value | smq_list.smq_note |
Comment |
|
Comment.PropertyName | “MedDRA Dictionary Version” |
Comment.Value | smq_list.MedDRA_version |
Comment |
|
Comment.PropertyName | “Status” |
Comment.Value | smq_list.status |
Comment |
|
Comment.PropertyName | “Algorithm” |
Comment.Value | smq_list.smq_algorithm |
Relations
--- | Association | Source | Target |
|---|---|---|---|
Soc_hlgt | “hasSubtype” | soc_hlgt.soc_code | soc_hlgt.hlgt_code |
Hlgt_hlt | “hasSubtype” | hlgt_hlt.hlgt_code | hlgt_hlt.hlt_code |
Hlt_pt | “hasSubtype” | hlt_pt.hlt_code | hlt_pt.pt_code |
Llt1 | “hasSubtype” | llt.pt_code | llt.llt_code |
Smq_content | “hasSubtype” | smq_content.smq_code | term_code2 |
- Created only if llt_code does not duplicate a pt_code
- May be a pt_code or an llt_code
Mapping of MedDRA tables to LexGrid Coding Scheme
Meddra_release
MedDRA Table | MedDRA field | LexEVS Object | LexEVS field |
|---|---|---|---|
meddra_release | version | CodingScheme | RepresentsVersion |
Meddra_release | Language | --- | --- |
Meddra_history_english
MedDRA Table | MedDRA field | LexEVS Object | LexEVS field |
|---|---|---|---|
Meddra_history_english | Term_code | --- | --- |
Meddra_history_english | Term_name | --- | --- |
Meddra_history_english | Term_addition_version | --- | --- |
Meddra_history_english | Term_type | --- | --- |
Meddra_history_english | Action | --- | --- |
Mdhier
MedDRA Table | MedDRA field | LexEVS Object | LexEVS field |
|---|---|---|---|
Mdhier | Pt_code | --- | --- |
Mdhier | Hlt_code | --- | --- |
Mdhier | Hlgt_code | --- | --- |
Mdhier | Soc_code | --- | --- |
Mdhier | Pt_name | --- | --- |
Mdhier | Hlt_name | --- | --- |
Mdhier | Hlgt_name | --- | --- |
Mdhier | Soc_name | --- | --- |
Mdhier | Soc_abbrev | --- | --- |
Mdhier | Pt_soc_code | --- | --- |
Mdhier | Primary_soc_fg | --- | --- |
Intl_ord
MedDRA Table | MedDRA field | LexEVS Object | LexEVS field |
|---|---|---|---|
Intl_ord | Intl_ord_code | Entity | Property.Value |
Intl_ord | Soc_code |
|
|
Soc
MedDRA Table | MedDRA field | LexEVS Object | LexEVS field |
|---|---|---|---|
Soc | Soc_code | Entity | EntityCode |
Soc | Soc_name | Entity Entity | EntityDescription Presentation.Value |
Soc | Soc_abbrev | Entity | Presentation.Value |
Soc_hlgt
MedDRA Table | MedDRA field | LexEVS Object | LexEVS field |
|---|---|---|---|
Soc_hlgt | Soc_code | AssociationPredicate | AssociationSource |
Soc_hlgt | Hlgt_code | AssociationPredicate | AssociationTarget |
Hlgt
MedDRA Table | MedDRA field | LexEVS Object | LexEVS field |
|---|---|---|---|
Hlgt | Hlgt_code | Entity | EntityCode |
Hlgt | Hlgt_name | Entity Entity | EntityDescription Presentation.Value |
Hlgt_hlt
MedDRA Table | MedDRA field | LexEVS Object | LexEVS field |
|---|---|---|---|
Hlgt_hlt | Hlgt_code | AssociationPredicate | AssociationSource |
Hlgt_hlt | Hlt_code | AssociationPredicate | AssociationTarget |
Hlt
MedDRA Table | MedDRA field | LexEVS Object | LexEVS field |
|---|---|---|---|
Hlt | Hlt_code | Entity | EntityCode |
Hlt | Hlt_name | Entity Entity | EntityDescription Presentation.Value |
Hlt_pt
MedDRA Table | MedDRA field | LexEVS Object | LexEVS field |
|---|---|---|---|
Hlt_pt | Hlt_code | AssociationPredicate | AssociationSource |
Hlt_pt | Pt_code | AssociationPredicate | AssociationTarget |
Pt
MedDRA Table | MedDRA field | LexEVS Object | LexEVS field |
|---|---|---|---|
Pt | Pt_code | Entity | EntityCode |
Pt | Pt_name | Entity Entity | EntityDescription Presentation.Value |
Pt | Pt_soc_code | Entity | Property.Value |
Llt
MedDRA Table | MedDRA field | LexEVS Object | LexEVS field |
|---|---|---|---|
Llt | Llt_code | Entity AssociationPredicate | EntityCode AssociationTarget |
Llt | Llt_name | Entity Entity | EntityDescription Presentation.Value |
Llt | Pt_code | AssociationPredicate | AssociationSource |
Llt | Llt_currency | --- | --- |
Smq_list
MedDRA Table | MedDRA field | LexEVS Object | LexEVS field |
|---|---|---|---|
Smq_list | Smq_code | Entity Entity | EntityCode Comment.Value |
Smq_list | Smq_name | Entity Entity Entity | EntityDescription Presentation.Value Comment.Value |
Smq_list | Smq_level | Entity | Comment.Value |
Smq_list | Smq_description | Entity | Comment.Value |
Smq_list | Smq_source | Entity | Comment.Value |
Smq_list | Smq_note | Entity | Comment.Value |
Smq_list | MedDRA_version | Entity | Comment.Value |
Smq_list | Status | Entity | Comment.Value |
Smq_list | Smq_algorithm | Entity | Comment.Value |
Smq_content
MedDRA Table | MedDRA field | LexEVS Object | LexEVS field |
|---|---|---|---|
Smq_content | Smq_code | AssociationPredicate | AssociationSource |
smq_content | Term_code | AssociationPredicate | AssociationTarget |
Smq_content | Term_level | Entity | Property.Value |
Smq_content | Term_scope | Entity | Property.Value |
Smq_content | Term_category | Entity | Property.Value |
Sqm_content | Term_weight | Entity | Property.Value |
Smq_content | Term_status | Entity | Property.Value |
Smq_content | Term_addition_version | Entity | Property.Value |
Smq_content | Term_last_modified_version | Entity | Property.Value |
Error Messages
File expected is missing
0 - error - Thu May 23 13:10:26 CDT 2013 - Following files are MISSING in directory provided:
/C:/Users/m113216/Desktop/MedDRA/TestData/Missing PT File/pt.asc
-
1 - fatal - Thu May 23 13:10:26 CDT 2013 - Failed while running the conversion - null
Load process finished - Thu May 23 13:10:26 CDT 2013
Errors Logged: true
Warnings Logged: false
End State: failed
Multiple files expected is missing
0 - error - Thu May 23 13:11:29 CDT 2013 - Following files are MISSING in directory provided:
/C:/Users/m113216/Desktop/MedDRA/TestData/Missing Mult Files/meddra_release.asc
/C:/Users/m113216/Desktop/MedDRA/TestData/Missing Mult Files/mdhier.asc
/C:/Users/m113216/Desktop/MedDRA/TestData/Missing Mult Files/smq_list.asc
/C:/Users/m113216/Desktop/MedDRA/TestData/Missing Mult Files/soc.asc
/C:/Users/m113216/Desktop/MedDRA/TestData/Missing Mult Files/pt.asc
/C:/Users/m113216/Desktop/MedDRA/TestData/Missing Mult Files/soc_hlgt.asc
/C:/Users/m113216/Desktop/MedDRA/TestData/Missing Mult Files/smq_content.asc
-
1 - fatal - Thu May 23 13:11:29 CDT 2013 - Failed while running the conversion - null
Load process finished - Thu May 23 13:11:29 CDT 2013
Errors Logged: true
Warnings Logged: false
End State: failed
File is empty
0 - error - Thu May 23 13:12:14 CDT 2013 - Following files are EMPTY in directory provided:
/C:/Users/m113216/Desktop/MedDRA/TestData/Empty HLT File/hlt.asc
-
1 - fatal - Thu May 23 13:12:14 CDT 2013 - Failed while running the conversion - null
Load process finished - Thu May 23 13:12:14 CDT 2013
Errors Logged: true
Warnings Logged: false
End State: failed
File missing a data field
0 - info - Thu May 23 13:14:40 CDT 2013 - Checking validity of data imported. -
1 - error - Thu May 23 13:14:40 CDT 2013 - ERROR in data imported from file (row 0): hlgt.asc -
2 - error - Thu May 23 13:14:40 CDT 2013 - <REQUIRED>: hlgt_code: null
<REQUIRED>: hlgt_name: null
<IGNORED>: htgt_whoart_code: null
<IGNORED>: hlgt_harts_code: null
<IGNORED>: hlgt_costart_sym: null
<IGNORED>: hlgt_icd9_code: null
<IGNORED>: hlgt_icd9cm_code: null
<IGNORED>: hlgt_icd10_code: null
<IGNORED>: hlgt_jart_code: null
-
3 - info - Thu May 23 13:14:40 CDT 2013 - Completed mapping. Now saving to database -
4 - fatal - Thu May 23 13:14:41 CDT 2013 - Failed while running the conversion - org.LexGrid.LexBIG.Exceptions.LBParameterException: The URN and the version must be populated.
Load process finished - Thu May 23 13:14:41 CDT 2013
Errors Logged: true
Warnings Logged: false
End State: failed
