NED Redcap Database Overview

 
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The database is designed to manage clinical and research data for our epilepsy patients.

The only people who can access it are approved by the hospital to be involved in epilepsy patients’ care, and have ethics (IRB/HRPP) approved involvement in the research studies included here. The database is housed on a HIPAA-compliant server within the hospital.

Neuropsychology in Epilepsy Database (NED). Inputs represent situations or contexts in which data may be entered.

Neuropsychology in Epilepsy Database (NED). Inputs represent situations or contexts in which data may be entered.

Data is entered in the following contexts.

  1. Neuropsychological test data. This allows data to be accessed when patients are seen in later appointments or if for a study.

  2. Epilepsy conference data. Summaries of a patient’s findings focused on the cause of their seizures and the best treatment.

  3. Stimulation mapping. Summaries of a patient’s findings are focused on identifying and preserving critical language areas.

  4. Surgeries. Surgery scheduling and procedures are tracked. This allows us to ensure patients receive the required preoperative and postoperative neuropsych assessments.

  5. Functional MRI (fMRI). Referrals, scheduling, and results are tracked and stored. This ensures data is available for research and the team.

For each of these contexts, data can be entered multiple times. For example, patients can have multiple neuropsych assessments, multiple conference presentations (or summaries). In redcap terms, the data entry forms can repeat.

Case IDs

Each case (redcap ‘record’) needs to have an identifier that can be calculated easily when a patient’s name is given. This allows (e.g.) record IDs to be generated when neuropsych test data is prepared for upload completely independent of NED.

Record ids therefore have the format

lastname_firstname_dob

Where last and first name are all lower case, and the date of birth (dob) is in format YYYYMMDD

It is also necessary sometimes to identify all data from a single case session; such as the multiple tasks (redcap forms) from a single neuropsych assessment or a single research study encounter (paired neuropsych assessment and fMRI). To simplify things in redcap each form therefore also has a session ID

lastname_firstname_dob_doe

Where last and first name are all lower case; and both the date of birth (dob) and date of encounter (doe) are in format YYYYMMDD.

Data entry

The flow chart for data entry into NED is as follows.

Neuropsychology in Epilepsy Database (NED): Data entry (and output) in greater detail.

Neuropsychology in Epilepsy Database (NED): Data entry (and output) in greater detail.

Data entry: Neuropsychological data

  • Forms used: (1-10+) Neuropsych test forms

  • Data entry mode: use data import to upload data files (.csv files)

Neuropsychological tests are typically administered by pen and paper, or on computer. At the end of a test session the neuropsychologist enters these scores into (1) scoring software, which can produce a table of scores (.csv) and (2) a manually compiled summary for review, interpretation, and report writing in patient care (.xlsx).

When data is to be entered, a bash shell script is run to convert data from the scoring software format to NED’s redcap format. This takes as input a .csv file holding one or more patients’ data and formats it for NED. In reality, there is little manipulation of this data. The data largely in the same format and location used by the scoring software, but headings (redcap columns – e.g., the record and session IDs) are added for each patient (each row in the .csv).

To convert data from the summary .xlsx file, a bash shell script is also run. This converts the file to a .csv file (using Gnumeric’s ssconvert). It then extracts the data for key tests of interest to us.

The resulting files are then uploaded into NED using redcap’s data import function.

Data entry: fMRI

  • Forms used: (1) fMRI, (2) demographics.

  • Data entry mode: web interface.

  • Person entering data: team member, Dr. Benjamin

Functional MRI referrals are forwarded by the team. These need to be recorded, patients awaiting scheduling and scanning to be tracked, and then the analysis of the data summarized. The data is stored (of course) outside NED in a folder following (anonymous) BIDS conventions, on a separate HIPAA-compliant server share to NED.

  • When patients are referred, NED is accessed via the web interface by a team member and the patient’s record_id is entered. The details of the referral are entered into the fMRI form. The demographics are entered in the demographics form.

  • When a patient is contacted for scheduling progress is tracked with each contact in the fMRI form (web interface–team member).

  • On the day of scanning, key information about how the scan went is entered into the fMRI form (web interface–team member).

  • After fMRI analysis, a copy of the result and the key images is uploaded to the database (web interface–Dr. Benjamin).

Data entry: Surgical conference/summary

  • Forms used: (1) summary

  • Data entry mode: web interface

  • Person entering data: Dr. Benjamin, potentially team member

All key clinical data are stored in the data summary form. The focus is on key information required for decision making: the laterality and the localization of the seizure onset, and the laterality or hemispheric dominance of language and memory.

  • When a patient is discussed at conference, the data are entered directly via the web interface.

  • Data are also entered separately via the web interface when a case is summarized, e.g. in clinic.

There are also fields to upload key relevant data to the summary sheet including the Wada test results and the case overview powerpoint.

Data entry: Language mapping

  • Forms used: (1) summary

  • Data entry mode: web interface

  • Person entering data: Dr. Benjamin

When intracranial language mapping is completed, the resulting data include images (jpgs or pptx) of the electrode placement; of the mapping results (jpgs or pptx); and a summary of the results of contacts being stimulated (xlsx).

  • Here data are uploaded directly via the web interface subsequent to mapping.

Data entry: Surgery scheduled

  • Forms used: (1) surgery

  • Date entry mode: web interface

  • Person entering data: Team member, Dr. Benjamin

Patients are scheduled for surgery and the team is alerted.

If the patient is undergoing resective surgery, Dr. Benjamin needs to be notified so that we can schedule (A) final pre-operative neuropsych to ensure all required clinical tasks are up to date and (B) one year post-operative evaluation for ongoing care.

  • When patients are referred, the patient’s record ID is entered into the web interface along with key details on the planned surgery by a team member.

  • When patients have completed surgery, the surgery details are updated in the web interface (team member).

*The following section is still being written*

Data exporting/reporting

  • To be determined.

Questions/reports required (examples):

  • Clinical: Who completed surgery in the last three months? This list will be used to update the surgical sheet with the exact details of the surgery.

  • Clinical: Who completed surgery 10-14 months ago? We need to make sure they have their 12 month follow up.

  • Research: Who had their research fMRI and also language neuropsych assessment?

  • Research: Who had research fMRI and intracranial mapping?

  • Research: Who had both neuropsych measures 1 and 2 at their neuropsych assessment?

Quality checking:

  • All forms include a set of quality checking variables at the end. These are hidden on the web interface.

Also to be added

  • Overview of import scripts (bash)

  • Overview of how to create new forms for redcap