What is this?

ehr-to-rd is an algorithm of two files written in Python 3, technician.py and screening.py. If you paste ophthalmology notes from MiChart, for the MI-SIGHT program, into .txt files, then you can use this algorithm to extract the data and output as an Excel file that needs some manual editing before being converted to a .csv and uploaded to REDCap.

How do I use this?

If you do not already have Python 3 installed on your device, you will need to use that first. Additionally, you will need .txt files, one for each participant's full note, copy-pasted from MiChart. Additionally, you will need some time, as much manual editing still needs to be done even after the output .xlsx files are produced.

You can download the algorithm by clicking the green CODE ▼ button, then extracting into a folder of your choosing.

Within that folder, produce a directory named files. This is where you will place the .txt files.

Then, read the following instructions, and run technician.py and screening.py. You may need to install some dependencies, which are listed and commented at the start of the .py files.

Instructions for Technician Eye Exam

For person who produces text files:

Ensure that newlines are in the correct places after the following questions. Generally, these newlines are present after the first time copy/pasting from MiChart. Each of the following questions should have two newlines between the question and the answer:

• Presenting visual acuity (Right/OD) DISTANCE
• Presenting visual acuity (Left/OS) DISTANCE
• Post-refraction Best corrected visual acuity (Right/OD) DISTANCE
• Post-refraction Best corrected visual acuity (Right/OD) NEAR
• Post-refraction Best corrected visual acuity (Left/OS) DISTANCE:
• Post-refraction Best corrected visual acuity (Left/OS) NEAR:
• Contrast sensitivity (Right/OD):
• Contrast sensitivity (Left/OS):
• Autorefraction (Right/OD) Sphere:
• Autorefraction (Right/OD) Cylinder:
• Autorefraction (Right/OD) Axis:
• Autorefraction (Left/OS) Sphere:
• Autorefraction (Left/OS) Cylinder:
• Autorefraction (Left/OS) Axis:
• Manifest refraction (Right/OD) Sphere:
• Manifest refraction (Right/OD) Cylinder:
• Manifest refraction (Right/OD) Axis:
• Manifest refraction (Right/OD) Add
• Manifest refraction (Left/OS) Sphere:
• Manifest refraction (Left/OS) Cylinder:
• Manifest refraction (Left/OS) Axis:
• Manifest refraction (Left/OS) Add:
• Afferent pupillary defect (Right/OD):
• Afferent pupillary defect (Left/OS):
• Pachymetry (Right/OD) NOT DONE: Pachymetry (Right/OD):
• Pachymetry (Left/OS) NOT DONE: Pachymetry (Left/OS):
• Which eye did you dilate
• Inter-pupillary distance:

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For person who runs the code: Make sure the variable newlines below is set to the right variable

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For person who produces output file:

Produce the following new columns:

• Produce a column named redcap_event_name

  • The value is screening_arm_1 for first-time visits or m12m24_arm_1 for follow-up visits

• Produce a column named technician_eye_exam_complete

  • The values in this column should all be 1 which corresponds to a form status of Unverified in REDCap

• Fill in the column titled thrdipmreq based on whether thrdipmrod or thrdipmlos has a value

Visually check the following columns:

• All columns for “unable” – ensure this is coded correctly per column

• bcvasdislos. If this is in text rather than number, put an 88 here, and in the next column (bcvasdislostx), put that text

• bcvasdisrod. Same as above

• bcvasnearlos. Same as above

• bcvasnearrod. Same as above

• pvasdislos. Same as above

• pvasdisros. Same as above

• cslos. Same as above

• csrod. Same as above

• eyedrops. If the patient is taking eyedrops, it will say which one here – put this information in eyedropstx. And in eyedrops, put a 1

• examstrttime. Look for missing times. Go to the original text file and grab that information

• phmerylos_hand. If there is text here, code it correctly and make sure phmerylos__87 is coded correctly.

• phmeryrod_hand. Same as above

• thrdipmreq. If there is a number in thrdipmrod and thrdipmlos, then thrdipmreq should be 1. Else, it should be 0

• trialframe. If there is a 0 here, go to the original text file, figure out why the patient did not receive trial frames, and then put that in trialframetx\n"

• Apply the following logic in Excel to the columns arodcylin, arloscylin, mrrodcylin, mrloscylin, etc.:

• If sphere has a value, then any missing values in cylinder/axis/add must be changed to 0.

  • If the axis is missing, but the cylinder is zero, then we can fill in the axis as zero
  • If any of the sphere/cylinder/axis values are non-missing, but the ADD variable is missing, then the missing for ADD can be replaced with a zero.
  • If the patient is CF, HM, LP, or NLP for VA then the sphere/cylinder/axis/add should remain missing and not be replaced by zero
  • If cylinder is missing specifically, need to MANUALLY check whether it wasn’t measured versus should be a zero
  • Produce a list of patients who were unable to perform anything

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Instructions for Screening Results

For person who produces text files: Just copy the whole note, including the physician's name at the top, and the section at the bottom that says "Letter sent to" at the bottom. Just do control-A (Windows) or command-A (Mac) from the MiChart entry, and then copy and paste it straight into a plaintext editor (NOT Microsoft Word) such as Notepad++ or Sublime Text 3. Then save the file, with the filename being the participant ID. Thank you!

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For person who produces output file:

For all participants, manually create the following columns:

• Produce a column named redcap_event_name
  • The value is screening_arm_1 for first-time visits or m12m24_arm_1 for follow-up visits
• Produce a column named screening_results_complete
  • The values in this column should all be 1 which corresponds to a form status of Unverified in REDCap
• In the columns for refractfurod, only keep the data in a cell if any of refractperyod__2 OR __3 OR __6 is equal to 1. Same for these variables but *los

For any participants who have "Index Errors" at the bottom of this code file:

• Go to their text files and edit them. The issue is often that some lines are missing. Typically, this is because the OCT photos were missing, so the provider removed the relevant lines. Add these lines back after the question Were OCT images of sufficient quality for interpretation?:
• OCT Results OD: overall thickness OD checklist · OS: overall thickness OS checklist ·

For all participants, visually check the following columns for MANUAL:

• extnlpdat

  • Here, you have to remove "T00:00:00" from every entry. Use the Excel SUBSTITUTE function

• extnlpsrttm

• refractrecpresc

• extnlpnorm thru extnabnrmothtx

• rodoctpqlty, rodoctpqltytx

• losoctpqlty, losoctpqltytx

• rodsupr, rodinferior, rodnasal, rodtemprl

• lossupr, losinferior, losnasal, lostemprl

• fundusreslts__88; addretinadiag__1 thru retinatxeye

• spcserviceyn thru spcservicetx

• extnlpstptm

• ctdrrod and ctdrlos. This is bolded because if there is text here, it will often be a glaucoma sign (e.g. notching), so you also have to go to the glaucsignrod and glaucsignlos variables and make sure that comments in ctdrrod and ctdrlos are added to glaucsignrod and glaucsignlos respectively.

• Apply this logic in Excel to edit fields of csv after exporting:

• If fundusreslts == “”, amd == “” OR “0”, addretinadiag == “99”, and nerveabnrm == “” OR “0”, then fundusabnrm = “0” (see YP0680) – you can use the following Excel logic in a column to the right of fundusabnrm, granted that you've added the redcap_event_name and screening_results_complete columns: =IF(AND(NUMBERVALUE(ER10)=0,NUMBERVALUE(ES10)=0,NUMBERVALUE(ET10)=0,NUMBERVALUE(EY10)=0,NUMBERVALUE(FB10)=0,NUMBERVALUE(FC10)=0,NUMBERVALUE(FD10)=0,NUMBERVALUE(FE10)=0,NUMBERVALUE(FF10)=0,NUMBERVALUE(FG10)=0,NUMBERVALUE(FH10)=0,NUMBERVALUE(FI10)=1,NUMBERVALUE(FT10)=0),0,""). (Make sure you verify these Excel column letters)

• If there is a diagnosis in addretinadiag, then fundusreslts__88 = “1”

• If refractyperod__2 == 1 OR refractyperod__3 == 1 OR refractyperod__6 == 1, then refractfurod__1,__2,__3,... should have values. Else, refractfurod__* == “”. Same for refractfulos__*

• If thrdipmrod and thrdipmlos are present, then thrdipmreq = “1”"

• Produce a list of patients who were unable to perform anything