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structured-reporting

This is an early prototype of a structured reporting tool for radiology and pathology of prostate cancer. It runs in modern web browsers such as Chrome. The main technoloies used are Clojure, ClojureScript, and Om.

Usage

Make sure you have Leiningen installed, then:

  1. Check out this repository:

     git clone https://github.com/jamesaoverton/structured-reporting.git
 cd structure-reporting

  2. Convert the tables in data to the file src/cljs/structured_reporting/data.cljs (using the code in src/clj/structured_reporting/convert.clj):

     lein run

  3. Compile all the ClojureScript code in src/cljs to a single JavaScript file (dev-sources/public/js/structured_reporting.js):

     lein cljsbuild once

  4. Open the dev-resources/public/index.html file in your browser.

Data

Our current data model has four tables and is limited to MRI imaging. A patient can have zero or more reports; a report can have zero or more lesions; a lesion will have a fixed number of observations, depending on the modality of the imaging.

  • patients
    • ID: unique identifier for this patient
    • Name: patient's full name or identifier
    • Date of Birth -- YYYY-MM-DD
    • History: a summary of the patient's medical history -- free text
  • reports
    • ID: unique identfier for this report
    • Patient: the ID of the patient
    • Exam Date -- YYYY-MM-DD
    • Report Date: some time after the exam date -- YYYY-MM-DD
    • Modality: currently only MRI
    • Prostate Size [Axis]: in millimeters along this axis
    • Measured PSA: the measured Prostate Specific Antigen level previous to this report
    • BPH Change: Benign Prostatic Hyperplasia -- mild, mild to moderate, moderate, moderate to severe, severe (NOTE: may be changed to an numeric value)
    • Peripheral Zone Diffuse Anomaly -- none, hyperintense, hypointense, heterogeneous
    • Transition Zone Diffuse Anomaly -- none, hyperintense, hypointense, heterogeneous
    • Seminal Vesicles: normal, hypertrophic, hypotrophic
    • Technique: how the exam was performed -- free text
    • Concluions -- free text
  • lesions: a region of interest within the prostate
    • ID: unique identifier for this lesion (in this report -- we don't yet link lesions between reports)
    • Report: the ID of the report for this lesion
    • Location [Axis]: in millimeters from the centre of the prostate along this axis
    • Size [Axis]: in millimetres along this axis
    • Zone: qualitiative location in the prostate -- peripheral zone, transition zone, both zones
    • Capsule: location relative to the capsule of the prostate -- inside, abutting, beyond
  • mri-observations: characteristics of a lesion in a given MRI sequence
    • ID: unique identifier for this mri-observation
    • Lesion: the ID of the lesion that this mri-observation entry is about
    • Type: the MRI sequence type -- T1, T2, diffusion, ADC, early phase contrast, late phase contrast
    • Observed: is the lesion observed in this sequence? -- true or false
    • Hyperintense: is the lesion more intense than the surrounding tissue? -- true or false
    • Isointense: is the lesion as intense as the surrounding tissue? -- true or false
    • Hypointense: is the lesion less intense than the surrounding tissue? -- true or false
    • Rim: is there a rim around the lesion? -- none, continous, discontinuous

Development

This tool is based on the om-start-template. See those instructions for enabling interactive development with a browser-based REPL.

TODO: unit testing, integration testing

License

Copyright © 2014 James A. Overton