./src/pipeline.sh --help
outputs:
map.mdctn-dose-units-drugmap.MDCTN-genRxCUIs-genNames-subRxCUIs-subNames
inputs:
- -t med-targets Tab-delimited, manually curated list of interesting drugs, paired to their most generic RxCUI [config/map.medTarget-RxCUI]
- -c med-codes i2B2 export
- -p problem-codes codes that have identified problems and don't appear in i2B2 observation data for analysis [config/problem-codes.txt]
OUTPUTS:
map.mdctn-dose-units-drug
Tab-delimited file
Columns:
| Col | Name | Description |
| --- |:--------:| ---------------------------------------------------------------------------------------------------:|
| 1 | MDCTN | Medication code, every code represented from CONCEPT_DIMENSION.csv, |
| | | e.g., MDCTN:00005306231 |
| 2 | dose | Integer amount of dose |
| | | e.g., 200 |
| 3 | units | Units of dose |
| | | e.g., mg |
| 4 | drug | Drug name, from config/map.medTarget-RxCUI |
| | | e.g., prednisone |
map.MDCTN-genRxCUIs-genNames-subRxCUIs-subNames
Tab-delimited file
Columns:
| Col | Name | Description |
| --- |:--------:| ---------------------------------------------------------------------------------------------------:|
| 1 | MDCTN | Medication code, every code represented from CONCEPT_DIMENSION.csv |
| | | e.g., MDCTN:00005306231 |
| 2 | genCUI | semi-colon delimited list of general medication names, without dosing or compound drug information |
| | | e.g., 25255;108118; formoterol;Mometasone; |
| 3 | labels | semi-colon delimited list of drug labels (most general, not including dose or other compounds) |
| | | e.g., prednisone |
| 4 | broadCUI |semi-colon delimited list of CUIs, not including anything from genCUI |
| | | e.g., 245314;745679; |
| 5 | names |semi-colon delimited list of the names of each MDCTN as found in the CONCEPT_DIMENSION.csv |
Inputs:
- -c med-codes
i2B2 export
e.g.,CONCEPT_DIMENSION.csv
Tab-delimited file
Columns:
| Col | Name | Description |
| --- |:---------------:| ---------------------------------------------------------------------------------------------------:|
| 1 | CONCEPT_PATH | path may contain the rxCUI code |
| | | e.g., "\i2b2\MEDS\N0000010574\N0000029154\N0000029160\RX:313847\MDCTN:24730\" |
| 2 | CONCEPT_CD | the MDCTN code |
| | | e.g., "MDCTN:24730" |
| 3 | NAME_CHAR | free text string describing drug, dose and units |
| | | e.g., "alitretinoin 0.001 MG/MG Topical Gel" |
| 4 | CONCEPT_BLOB | ignored |
| 5 | UPDATE_DATE | ignored |
| 6 | DOWNLOAD_DATE | ignored |
| 7 | IMPORT_DATE | ignored |
| 8 | SOURCESYSTEM_CD | ignored |
| 9 | UPLOAD_ID | ignored |
- -t med-targets
Tab-delimited, manually curated list of interesting drugs, paired to their most generic RxCUI
e.g.,config/map.medTarget-RxCUI
Tab-delimited file
Columns:
| Col | Name | Description |
| --- |:-----:| ---------------------------------------------------------------------------------------------------:|
| 1 | label | path may contain the rxCUI code |
| | | e.g., prednisone |
| 2 | rxCUI | standardized rxnorm ID from https://rxnav.nlm.nih.gov |
| | | e.g., 8640 |
- -p problem-codes
ASCII list of codes that have identified problems and that don't appear in i2B2 observation data for analysis
e.g.,config/problem-codes.txt
src : all programs, incidental scripts, test cases and teset data
config : configuration files here
Use sudo cpan install <dependency> to ensure each of the following are installed:
- Data:Dumper
- File::Basename
- Cwd
- Getopt::Long
- Switch
- JSON
- MIME::Base64
- REST::Client