Clinical data is meant for all kinds of measurements not falling into other categories. It can be data from questionnaires, physical body measurements or socio-economic info about the patients.
The bare minimum that is needed to upload clinical data is a data file and a column mapping file.
The parameters file should be named clinical.params and may contain:
COLUMN_MAP_FILE(Mandatory) Points to the column mapping file.WORD_MAP_FILEPoints to the word mapping file.XTRIAL_FILEPoints to the cross study concepts file.TAGS_FILEPoints to the concepts tags file. Alternatively this may be specified in your tags parameter file.ONTOLOGY_MAP_FILEPoints to the ontology mapping file.TRIAL_VISIT_MAP_FILE(Not yet implemented) Points to the trial visit mapping file.PATIENT_VISIT_MAP_FILE(Not yet implemented) Points to the patient visit mapping file.
Uploading the clinical data is usually the first procedure when uploading a study to tranSMART:
- Place the
clinical.paramsfile into theclinicalfolder of your study, alongside all other low-dimensional files that should be part of this upload, as specified in your clinical parameters (see above). - Run the upload pipeline from your transmart-batch folder:
./transmart-batch.sh -p ./studies/GSE8581/clinical/clinical.params
Clinical data observations can be deleted by running the backout.params.