Merge branch 'release/0.2.0'

CHANGELOG.md

@@ -2,6 +2,20 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.2.0][2015-09-11]
+### Added
+- Add MEDDRA LLT lookup to ae_suppae_aesosp (Philip Chase)
+- Add field annotations to ae_aesdth field (Philip Chase)
+- Restore HCVTarget-like conmeds fields with a pick list and auto-completed 'other' field (Philip Chase)
+
+### Changed
+- Update README and README-developer with more details on contributing, contributors, development workflows, and typographical fixes. (Philip Chase)
+- Revise 'make clean' to remove zip files (Philip Chase)
+- Repair form list in package-instrument.sh (Philip Chase)
+
+### Removed
+- Remove transfusion fields from cm_coding form (Philip Chase)
+
 ## [0.1.0][2015-09-11]
 ### Added
 - Initial release of Adverse Events and Concomitant Medication instruments

Makefile

@@ -17,4 +17,4 @@ build:
 	bash package-instrument.sh
 
 clean:
-	rm instrument.csv
+	rm instrument.csv *.zip

README-developer.md

@@ -12,5 +12,16 @@ To export these dictionaries from a project, use the redcap_metadata command to
 
     redcap_metadata --token [your_token] --url https://yourhost.domain.org/redcap/api/ > all.csv
 
-If these dictionaries are mixed with other forms you want to exclude, these command can extract them nicely witht he script `export-all.sh`
+If these dictionaries are mixed with other forms you want to exclude, these command can extract them nicely with the script `export-all.sh`
 
+
+## Contributions
+
+To make your own contribution to this instrument, please fork repo at Github, modify files as needed and submit a pull request. Please submit pull requests to the develop branch if it exists.
+
+
+## Releases
+
+The project is managed with Gitflow to create releases. We use GitFlow defaults for branch naming. The ChangeLog is managed according to the [Keep a CHANGELOG](http://keepachangelog.com/). Version numbers adhere to [Semantic Versioning 2.0.0](http://semver.org/)
+
+TODO: Consider using https://github.com/aktau/github-release to add packaged instruments to the Github release.

README.md

@@ -1,22 +1,24 @@
 # Adverse Events and Concommitant Medications Forms
 
-These forms provide a standards-based method of reporting Adverse Event and Concommitant Medications on a clinical trial. They use REDCap's text auto-completion and the MEDDRA, ATC, and RxNorm ontologies to provided assisted text entry and validation of data entry.  These features simplify the aggregation and sharing of medication and adverse event data in clinical trials.
+These forms provide a standards-based method of reporting Adverse Event and Concommitant Medications on a clinical trial. They use REDCap's text auto-completion and the MEDDRA, ATC, and RxNorm ontologies to provided assisted text entry and validation of data entry. These features simplify the aggregation and sharing of medication and adverse event data in clinical trials.
+
+TODO: Add a field description to the field annotation to describe the field in a machine-parsable way.
 
 ## Requirements
 
-These forms require features first release in REDCap 6.7.0 and were developed using in REDCap 6.8.1.  These forms use reference ontologies served by http://data.bioontology.org  Access to that service requires an API key from http://bioportal.bioontology.org/  No special REDCap extensions are required.
+These forms require features first release in REDCap 6.7.0.  The forms were developed using REDCap 6.8.1.  Each of the forms references ontologies served by http://data.bioontology.org  Access to that service requires an API key from http://bioportal.bioontology.org/  No special REDCap extensions are required.
 
 ## Installation
 
-These forms are distributed as a REDCap instrument
+These forms are distributed as REDCap instruments. Each zip file has to be imported separately to get the full functionality of the forms.
 
 ## Contributors
 
-These forms are based on work by Ken Bergquist done for the [HCV Target](http://www.hcvtarget.org/) project.  These forms were adapted for use at the University of Florida by Philip Chase <pbc@ufl.edu> and Ruchi V. Desai <ruchivdesai@gmail.com>.  Many thanks to David Nelson, MD, Director of UF's Clinical Translational Science Institute and Principal Investigator on the HCV Target project for his support of this work.
+These forms are based on work by Ken Bergquist done for the [HCV Target](http://www.hcvtarget.org/) project.  The forms were adapted for use at the University of Florida by Philip Chase <pbc@ufl.edu>, Ruchi V. Desai <ruchivdesai@gmail.com> and Christopher P. Barnes <senrabc@gmail.com>.  Many thanks to David Nelson, MD, Director of UF's Clinical Translational Science Institute and Principal Investigator on the HCV Target project for his support of this work.
 
 ## Contributions
 
-To make your own contribution to this instrument, please fork the repo at Github, modify files as needed and submit a pull request.
+We welcome contributions to these instruments.  The authoritative copy is on Github at https://github.com/ctsit/ae_and_conmeds.  Please fork the repo at Github, modify files as needed and submit a pull request.  For more details on making contributions, please see the [Developers Notes](README-developer.md)
 
 ## License
 

adverse_events.csv

@@ -5,12 +5,12 @@ ae_aeterm,adverse_events,,text,"Adverse Event",BIOPORTAL:MEDDRA,"Enter MEDDRA Lo
 ae_aecontrt,adverse_events,,radio,"ConMeds given to treat this Adverse Event?","N, NO | Y, YES","(Please update the ConMeds page as applicable)",,,,,"[ae_aeoccur] = 'Y'",y,,,,,
 ae_suppae_aexacerb,adverse_events,,radio,"Exacerbation of previous condition?","N, NO | Y, YES",,,,,,"[ae_aeoccur] = 'Y'",y,,,,,
 ae_aeser,adverse_events,,radio,"SAE (Serious Adverse Event)?","N, NO | Y, YES",,,,,,"[ae_aeoccur] = 'Y' ",y,,,,,
-ae_aesdth,adverse_events,"Outcomes attributed to SAE",radio,Death,"N, NO | Y, YES",,,,,,"[ae_aeser] = 'Y'",y,,,,,
+ae_aesdth,adverse_events,"Outcomes attributed to SAE",radio,Death,"N, NO | Y, YES",,,,,,"[ae_aeser] = 'Y'",y,,,,,"{'field_description':{'ontology':'SNOMEDCT','revision':'2015-03-19 00:00:00.000000000','code':'C1705232','concept':'Death Related to Adverse Event'}}"
 ae_aeslife,adverse_events,,radio,Life-threatening,"N, NO | Y, YES",,,,,,"[ae_aeser] = 'Y'",y,,,,,
 ae_aeshosp,adverse_events,,radio,"Hospitalization - initial or prolonged","N, NO | Y, YES",,,,,,"[ae_aeser] = 'Y'",y,,,,,
 ae_aesdisab,adverse_events,,radio,"Disability or Permanent Damage","N, NO | Y, YES",,,,,,"[ae_aeser] = 'Y'",y,,,,,
 ae_aescong,adverse_events,,radio,"Congenital Anomaly or Birth Defect","N, NO | Y, YES",,,,,,"[ae_aeser] = 'Y'",y,,,,,
 ae_aesmie,adverse_events,,radio,"Other Serious (Important Medical Events)","N, NO | Y, YES",,,,,,"[ae_aeser] = 'Y'",y,,,,,
-ae_suppae_aesosp,adverse_events,,text,"Other Serious (Important Medical Events): Specify",,,,,,,"[ae_aesmie] = 'Y'",y,,,,,
+ae_suppae_aesosp,adverse_events,,text,"Other Serious (Important Medical Events): Specify",BIOPORTAL:MEDDRA,"Enter MEDDRA Low Level Term",,,,,"[ae_aesmie] = 'Y'",y,,,,,
 ae_aeout,adverse_events,Outcome,radio,"Outcome of Adverse Event","FATAL, Fatal | NOT_RECOVERED_NOT_RESOLVED, Not recovered/not resolved | RECOVERED_RESOLVED, Recovered/resolved | RECOVERED_RESOLVED_WITH_SEQUELAE, Recovered/resolved with sequelae | RECOVERING_RESOLVING, Recovering/resolving | UNKNOWN, Unknown",,,,,,"[ae_aeoccur] = 'Y' AND [ae_aeser] = 'Y'",y,,,,,
 ae_aeendtc,adverse_events,,text,"Date of Resolution or Death",,"YYYY-MM-DD ",date_ymd,,,,"[ae_aeout] = 'RECOVERED_RESOLVED' OR [ae_aeout] = 'RECOVERED_RESOLVED_WITH_SEQUELAE' OR [ae_aeout] = 'FATAL'",y,,,,,

cm_coding.csv

@@ -7,8 +7,3 @@ cm_suppcm_atc2name,cm_coding,,text,"Level 2 ATC name for ConMed Medication: [cm_
 cm_suppcm_indcmodf,cm_coding,,text,"Modified reported term for ConMed Indication: [cm_cmindc]/[cm_oth_cmindc]",BIOPORTAL:MEDDRA,"Enter MEDDRA Low Level Term",,,,,,,,,,,
 cm_suppcm_indcod,cm_coding,,text,"Dictionary derived term for ConMed Indication: [cm_cmindc]/[cm_oth_cmindc]",BIOPORTAL:MEDDRA,"Enter MEDDRA Preferred Term",,,,,,,,,,,
 cm_suppcm_indcsys,cm_coding,,text,"Body system or organ class for ConMed Indication: [cm_cmindc]/[cm_oth_cmindc]",BIOPORTAL:MEDDRA,"Enter MEDDRA System Organ Class",,,,,,,,,,,
-xfsn_cmdecod,cm_coding,Transfusions,text,"Dictionary derived term for transfused blood product: [xfsn_cmtrt]",BIOPORTAL:RXNORM,"Enter RXNORM description or code",,,,,,,,,,,
-xfsn_suppcm_atcname,cm_coding,,text,"Level 1 ATC name for transfused blood product: [xfsn_cmtrt]",BIOPORTAL:ATC,"Enter Level 1 ATC name",,,,,,,,,,,
-xfsn_suppcm_atc2name,cm_coding,,text,"Level 2 ATC name for transfused blood product: [xfsn_cmtrt]",BIOPORTAL:ATC,"Enter Level 2 ATC name",,,,,,,,,,,
-xfsn_suppcm_indcod,cm_coding,,text,"Dictionary derived term for Transfusion indication: [xfsn_cmindc]",BIOPORTAL:MEDDRA,"Enter MEDDRA Low Level Term",,,,,,,,,,,
-xfsn_suppcm_indcsys,cm_coding,,text,"Body system or organ class for Transfusion indication: [xfsn_cmindc]",BIOPORTAL:MEDDRA,"Enter MEDDRA System Organ Class",,,,,,,,,,,

conmeds.csv

@@ -3,6 +3,7 @@ cm_cmoccur,conmeds,,radio,"Did the subject take any concomitant medications duri
 cm_suppcm_cmprtrt,conmeds,,radio,"Was this subject taking this medication at OR prior to baseline?","N, NO | Y, YES",,,,,,"[cm_cmoccur] = 'Y'",y,,,,,
 cm_cmstdtc,conmeds,,text,"ConMed start date",,"YYYY-MM-DD ",date_ymd,,,,"[cm_cmoccur] = 'Y' and [cm_suppcm_cmprtrt] = 'N'",y,,,,,
 cm_cmtrt,conmeds,,text,Medication,BIOPORTAL:RXNORM,"Enter RXNORM description or code",,,,,"[cm_cmoccur] = 'Y'",y,,,,,
-cm_cmindc,conmeds,,text,Indication,BIOPORTAL:MEDDRA,"Enter MEDDRA Low Level Term",,,,,"[cm_cmoccur] = 'Y'",y,,,,,
+cm_cmindc,conmeds,,radio,Indication,"NAUSEA, Nausea | VOMITING, Vomiting | DIARRHEA, Diarrhea | HEADACHE, Headache| FATIGUE, Fatigue | INSOMNIA, Insomnia | FLU_LIKE_SYMPTOMS, Flu-Like Symptoms | DYSPNEA, Dyspnea | RASH, Rash | PRURITUS, Pruritus | PHOTOSENSITIVITY, Photosensitivity | ANAEMIA, Anemia | THROMBOCYTOPAENIA, Thrombocytopenia | NEUTROPENIA, Neutropenia | HYPERBILIRUBINAEMIA, Hyperbilirubinemia | ASCITES, Ascites | HEPATIC_ENCEPHALOPATHY, Hepatic Encephalopathy | ESOPHAGEAL_VARICES_WITH_BLEEDING, Esophageal Variceal Bleed | PORPHYRIA, Porphyria | HYPERTENSION, Hypertension | DEPRESSION, Depression | ANXIETY, Anxiety | DIABETES, Diabetes | NUTRITIONAL_SUPPLEMENT, Nutritional Supplement | NOT_SPECIFIED, Not Specified | OTHER, Other","","","","","","[cm_cmoccur] = 'Y'","Y","","",""
+cm_oth_cmindc,conmeds,,text,"Indication other",BIOPORTAL:MEDDRA,"Enter MEDDRA Low Level Term","","","","","[cm_cmindc] = 'OTHER'","Y","","",""
 cm_suppcm_exacindc,conmeds,,radio,"Exacerbation of previous indication?","N, NO | Y, YES",,,,,,"[cm_cmoccur] = 'Y'",y,,,,,
 cm_suppcm_prphindc,conmeds,,radio,"Prophylaxis for this indication?","N, NO | Y, YES",,,,,,"[cm_cmoccur] = 'Y'",y,,,,,

package-instrument.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-forms=( ae_coding advere_events cm_coding conmeds )
+forms=( ae_coding adverse_events cm_coding conmeds )
 
 echo "Packaging forms into REDCap instruments"
 for form in "${forms[@]}"