Closed RuilingLiu closed 8 years ago
agbeltran
commented
8 years ago Hi @RuilingLiu, we are trying to interpret what you consider missing from your transformation file. Is it correct that you are saying that the DATS model is missing elements to: studyGroup.type studyGroup.description ? Are you saying we might need to move studyGroup.selectionCriteria to study.selectionCriteria? And we might need to add a relationship from studyGroup to Treatment?
RuilingLiu
commented
8 years ago Hi @agbeltran ,
I am not sure about the metadata. I think @jgrethe may know the answers.
agbeltran
commented
8 years ago @jgrethe following up on this, we have produced this example of ClinicalTrials.gov with DATS:
Maybe this help in identifying if everything is covered?
agbeltran
commented
8 years ago Closing this issue now, please let us know if the example we shared for clinicaltrials.gov is not enough.
/* Not in the metadata model */
/* Data monitoring committee */ transform column "$.'clinical_study'.'oversightinfo'.'authority'.'$'" to "clinicalStudy.oversight_info.authority";
transform column "$.'clinical_study'.'oversight_info'.'hasdmc'.'$'" to "clinicalStudy.oversight_info.has_dmc";
transform column "$.'clinical_study'.'overallstatus'.'$'" to "study.status"; transform column "$.'clinicalstudy'.'phase'.'$'" to "study.phase"; transform column "$.'clinical_study'.'armgroup'[].'arm_grouptype'.'$'" to "studyGroup.type[]"; transform column "$.'clinical_study'.'armgroup'[].'description'.'_$'" to "studyGroup.description[]";
transform column "$.'clinical_study'.'verificationdate'.'$'" to "dataset.verificationDate"; transform column "$.'clinical_study'.'is_fdaregulated'.'$'" to "dataset.is_fda_regulated"; transform column "$.'clinical_study'.'has_expandedaccess'.'$'" to "dataset.has_expanded_access";
/* In first iteration we can leave this - however, this should be added to the WG2 issue tracker as something to discuss with WG3 _/ transform column "$.'clinical_study'.'armgroup'[].'description'.'_$'" to "studyGroup.description[]";
transform column "$.'clinical_study'.'intervention'.'interventiontype'.'$'" to "treatment.title"; transform column "$.'clinical_study'.'intervention'.'interventionname'.'$'" to "treatment.agent"; transform column "$.'clinicalstudy'.'intervention'.'description'.'$'" to "treatment.description"; transform column "$.'clinicalstudy'.'eligibility'.'criteria'.'textblock'.'$'" to "study.recruits.criteria"; transform column "$.'clinicalstudy'.'eligibility'.'gender'.'$'" to "study.recruits.gender"; transform column "$.'clinical_study'.'eligibility'.'minimumage'.'$'" to "study.recruits.minimum_age"; transform column "$.'clinical_study'.'eligibility'.'maximumage'.'$'" to "study.recruits.maximum_age";
/* In first iteration we can leave this - however, this should be added to the WG3 issue tracker as something to discuss with WG3 / For other countries we need to turn that into a multi value array/ transform column "$.'clinicalstudy'.'location'.'facility'.'name'.'$'" to "study.location.name"; transform column "$.'clinicalstudy'.'location'.'facility'.'address'.'city'.'$'" to "study.location.city"; transform column "$.'clinicalstudy'.'location'.'facility'.'address'.'zip'.'$'" to "study.location.zip"; transform column "$.'clinicalstudy'.'location'.'facility'.'address'.'country'.'$'" to "study.location.country"; transform column "$.'clinical_study'.'locationcountries'.'country'.'$'" to "study.location.othercountries[0]";