Collection of FHIR JSON objects representing fictious patient vignettes for use in our hackathon environment.
The Society for Imaging Informatics in Medicine (SIIM) is supporting the new DICOMWEB and FHIR standards by creating opportunities for it's members to interact with these systems at the annual meeting, and throughout the year through it's Hackathon/HackPack projects.
We're using images from The Cancer Imaging Archive (TCIA) and creating fictious but believable narratives that illustrate concepts common in imaging.
This project will contain FHIR JSON objects surrounding these patient narratives.
During our first hackathon, we realized that in order to have a successful hackathon across multiple platforms, we need to have a cohesive, rich dataset that will allow people to build interesting applications.
In the top level directory there are directories for resources that cross patients (Medications, Practitioner, Organizations)
Also within the top level directory are a set of sub-folders for each patient. This skeleton contains a set of top-level directories that correspond with the FHIR Resources: http://www.hl7.org/implement/standards/fhir/resourcelist.html. Within these sub-folders are json FHIR documents.
Each FHIR document should have a commented header that looks like this: // filename // id: random
If set to something other than random, this will be used to create the FHIR resource.
This is not meant to be an exhaustive collection, the types are chosen based on relevance to imaging patients.
cp fhir_server.yml.dist fhir_server.yml
Edit fhir_server.yml to fit your needs.
Install dependencies: ruby, bundler
Run Bundler to install needed gems bundle install
Run the script to upload all of the resources in the folders ruby update.rb
- Fork this repo
- Make your changes/improvements
- Send a pull request
###Sally SIIM (mrn: BreastDx-01-0003) 58 yo female DOB: 04/12/1950
HPI: Had a palpable left breast mass discovered on self-breast exam. Patient was initially seen for diagnostic mammogram on 4/12/2008. Patient had a lumpectomy on 5/24/2008.
PMHx: Hypothyroidism
Allergies: NKDA
Medications: levothyroxine sodium 50mcg once daily
Lab/Radiology
DIAGNOSTIC BILATERAL 4/12/2008
Clinical History: 59 year-old female with history of left invasive ductal carcinoma (age 55) status post lumpectomy.
Technique: Bilateral CC and MLO, Left spot compression LMLO views were obtained
Findings:
LEFT BREAST: There are scattered fibroglandular densities. There are expected lumpectomy changes in the upper outer quadrant with surgical clips in place. Skin thickening is consistent with post radiation changes. No concerning masses, architectural distortions, or suspicious calcifications are identified.
RIGHT BREAST: There are scattered fibroglandular densities. No concerning masses, architectural distortions, or suspicious calcifications are identified.
Impression:
LEFT BREAST: Expected lumpectomy changes. Benign. BI-RADS 2 - Recommend routine screening in 1 year.
RIGHT BREAST: Negative. BI-RADS 1 - Recommend routine screening in 1 year.
OVERALL BI-RADS 2 (Benign)
Bilateral Breast MRI 04/19/2008
Clinical History: 59 year-old female with history of left invasive ductal carcinoma (age 55) status post lumpectomy. High-risk screening MRI exam.
Technique: Bilateral axial imaging of the breasts was obtained including T1, STIR, T1FS, and sequential T1FS+C. Digital subtraction and dynamic contrast curve analysis was performed on a separate workstation.
Findings:
LEFT BREAST: There is minimal benign background enhancement. There are expected post surgical changes in the upper outer breast. Multiple signal voids represent surgical clips in place. Skin thickening is consistent with post radiation change. There is no abnormal enhancement to indicate residual or recurrent disease. There are no morphologically abnormal axillary lymph nodes.
RIGHT BREAST: There is minimal benign background enhancement. There is no abnormal enhancement or lymphadenopathy.
Impression:
LEFT BREAST: Expected post treatment changes. Benign. BI-RADS 2. Recommend routine screening mammography in 1 year.
RIGHT BREAST: Negative. BI-RADS 1. Recommend routine screening mammography in 1 year.
OVERALL BI-RADS 2 (Benign)
Full Field Digital Left Diagnostic Mammogram 4/22/2008
Clinical History: 59 year-old female with history of left invasive ductal carcinoma (age 55) status post lumpectomy.
Technique: LML, L XCCL
Findings:
LEFT BREAST: There are scattered fibroglandular densities. There are expected lumpectomy changes in the upper outer quadrant with surgical clips in place. Skin thickening is consistent with post radiation changes. No concerning masses, architectural distortions, or suspicious calcifications are identified.
Impression:
LEFT BREAST: Expected changes status post lumpectomy and radiation. Benign. BI-RADS 2 - Recommend routine screening in 1 year.
05/24/2008 Surgical Specimen Radiograph
Clinical History: Unknown
Technique: Single surgical specimen radiograph
Findings: The surgical specimen contains an intact wire and surgical clip. No masses or calcifications are identified.
Impression:
Specimen radiograph with intact wire and surgical clip.
###Ravi SIIM (mrn: LIDC-IDRI-0132)
###Joe SIIM (mrn: TCGA-17-Z058) HPI: 60 yo male with history of lung adenocarcinoma.
####Imaging Exams
#####CT Chest 3/30/1986 (ct-0433)
CT Onco Lung Mass 3/30/1986
Clinical information 60 yo male with left hilar mass.
Comparison None.
Findings Lung mass Size: 5.3 x 4.0 x 4.0 cm
Location: left hilar region
Shape: Smoothly marginated
Internal consistency: homogenous, hypodense to surrounding muscle.
Local extent Pleural surface: Left lower lobe metastasis
Chest wall: No involvement.
Airway: Compression of the lingula
Vessels: Mass surrounds and nearly occludes the left inferior pulmonary artery.
Nerves: No involvement.
Regional extent Lymph nodes: AP window, and right hilar adenopathy.
Distant metastases (chest and upper abdomen): None.
Other findings Other findings: None.
Impression: Left hilar mass concerning for malignancy.
#####PET Oncologic Study 4/22/1986 (pet-5759, pet-7180, ct-3115)
Duration of fast prior to injection: 6 hours
Blood glucose prior to injection: 85 mg/dl
Scan region: Brain, Neck, Chest, Abdomen
Radiopharmaceutical: F-18 FDG 10 mCi IV
Calibration time: 4/22/1986 10:30 AM
Administration time: 4/22/1986 10:32 AM
Injection site: left antecubital fossa
Post-injection imaging delay: 60 minutes
Attenuation correction: Rod source transmission scan.
Clinical information 60 yo male with left hilar mass, evaluate for metastatic disease
Comparison Chest CT scan 3/30/1986
Findings Hypermetabolic foci: 5.0 cm hypermetabolic left hilar mass on image 162 with a maximum SUV of 3.2. 1.8 x 1.2 cm hypermetabolic AP window lymph node on image 132 maximum SUV of 2.7 There is spurious activity in the neck musculature. No contralateral hypermetabolic lesions are appreciated.
The right hilar adenopathy suspected on the prior CT scan is not seen.
Other findings: The visualized brain parenchyma is unremarkable. The soft tissues of the neck are unremarkable. The thyroid gland is unremarkable. No axillary adenopathy. No focal infiltrate. No pneumothorax. There a tiny left pleural effusion vs. pleural thickening. This is not FDG avid. The heart size is normal. No pericardial effusion.
Lack of IV contrast mildly limits evaluation of the organs in the abdomen and pelvis. The liver is unremarkable without focal lesion. The adrenals are normal. The pancreas, spleen, and kidneys are unreamarkable.
Atherosclerotic calcification is seen throughout the aorta. No abnormally dilated bowel. No suspicious retroperitoneal or mesenteric adenopathy.
There are no suspicious bony lesions.
Impression
- Findings again compatible with left hilar malignancy with a left AP window lymph node. There is no evidence of contralateral disease.
EORTC Response Criteria: N/A - Baseline
SIIM Diagnostic Lab Leesburg, VA Tel: (555) 555-5555 Fax: (812) 353-5445
Surgical Pathology Report
Patient Name: TCGA-17-Z058. Accession #: XXX66-4444 Med. Rec. #: TCGA-17-Z058 Taken: 4/25/1986 Encounter #: 000111111111 Received: 4/25/1986 Gender: M Reported: 4/26/1986 16:50 DOB: (Age: 60) Submitting Physician: REFERRING, MD Additional Physician(s): Location: ENDOSCOPY BL
Pre-Operative Diagnosis: Lingular lung mass
Post-Operative Diagnosis: Same
Specimen Received: Lingular lung bxs
Final Pathologic Diagnosis: Lingula, lung, transbronchial biopsies: Adenocarcinoma (see note)
The examination of this case material and the preparation of this report were performed by the staff pathologist. Electronically Signed by Joe Pathologist, M.D.
Signing Location: SIIM Laboratory Services, Leesburg, VA
Gross Description: Submitted in formalin as "left upper lobe-lung biopsies" are multiple fragments of light tan tissue each measuring up to 0.5 cm in greatest dimension. The entire specimen is submitted in a single cassette.
Microscopic Description: Sections of bronchial mucosa demonstrate infiltration by poorly differentiated malignant cells which form cords and some, and somewhat pale cytoplasm. Some cells have a suggestion of signet ring cell morphology. No keratinization is evident.
NOTE: This is a fictious report that was created to match the TCIA images. This is NOT the actual report for this patient.
END OF REPORT
Clinical Indication: Acute shortness of breath, elevated D-dimer. History of lung cancer. Concern for PE.
Comparison: PET/CT from 4/22/1986
Technique: Multidetector axial CT of the chest was performed after the administration of intravenous contrast in the arterial phase using a pulmonary embolus protocol.
Findings: Enteric drainage catheter courses into the stomach. Endotracheal tube terminates in the mid-thoracic trachea.
There is adequate opacification of the pulmonary vasculature to the subsegmental level without significant motion artifact. No evidence of pulmonary embolism. The main pulmonary artery and right heart are normal in size. A small pericardial effusion is present.
The thyroid and thoracic inlet are normal. No axillary lymphadenopathy. There is stable right hilar lymphadenopathy, slightly enlarged compared to the prior exam.
Emphysema again noted. Post surgical changes from interval left lower lobectomy. A large left hydropneumothorax is noted. There is diffuse bilateral septal thickening compatible with pulmonary edema. The major airways are patent.
Stable indeterminate subcentimeter enhancing lesion in the hepatic dome. Stable mildly enlarged gastrosplenic lymph node. Upper abdomen otherwise unremarkable.
Surgical defect noted in the posterior 6th rib. Osseous structures otherwise unremarkable.
Impression:
- No evidence of pulmonary embolism.
- Interval left lower lobectomy with large left hydropneumothorax.
- Development of severe pulmonary edema.
- Slight interval enlargement of right hilar lymph node and stable mild enlargement of a gastrosplenic node.
Clinical indication: Followup lung mass.
Comparison: Chest CTA from 5/5/1986
Technique: Multidetector axial CT of the chest was performed without the administration of intravenous contrast.
Findings:
Interval placement of a tracheostomy tube.
The thyroid and thoracic inlet are normal. There are no grossly enlarged axillary or mediastinal lymph nodes, however the hila are difficult to assess without the use of contrast. There is relative hyperdensity of the intraventricular septum suggestive of anemia. The heart is normal in size without significant pericardial effusion. A small hiatal hernia is present.
Stable emphysema. Post-surgical changes from left lower lobectomy again seen with persistent moderate to large subpulmonic loculated hydropneumothorax. Interval decrease in septal thickening with mild persistent septal prominence within the right lung.
Upper abdomen unremarkable given lack of IV contrast.
Stable surgical defect in the posterior left 6th rib. No suspicious osseous lesions.
Impression:
- Stable findings of left lower lobectomy with persistent subpulmonic hydropneumothorax.
- Interval decrease in pulmonary edema with mild residual right sided septal prominence.
Clinical indication: History of lung adenocarcinoma, followup.
Comparison: Multiple prior CTs, the most recent from 5/31/1986
Technique: Multidetector axial CT of the chest, abdomen and pelvis was performed after the administration of intravenous contrast in the portal venous phase.
Findings:
Thorax: The thyroid and thoracic inlet are normal. There are no enlarged axillary lymph nodes. There has been interval development of an enlarged lymph node conglomerate mass within the posterior mediastinum just anterior to the descending aorta, measuring 2.8 x 4.2 cm in axial dimension (series 5, image 36). This mass anteriorly displaces and mildly narrows the left main pulmonary artery. There is no clear evidence of vascular invasion. There is stable right hilar adenopathy. A new markedly enlarged precardial lymph node is also now seen, measuring 3.3 x 1.7 cm (series 5, image 42).
There is stable severe emphysema. A 4 mm left apical nodule (series 5, image 6) appears stable. Surgical changes from prior left lower lobectomy are evident with associated pleural thickening. Interval resolution of the previously noted left hydropneumothorax. A small left lateral rim enhancing pleural collection is suspicious for infection.
No suspicious osseous lesions. The visualized soft tissues are unremarkable.
Abdomen: Punctate calcifications noted in the right hepatic lobe. Liver otherwise unremarkable. Gallbladder, pancrease, speen, and adrenal glands are normal. Bilateral renal cysts are noted. The kidneys are otherwise unremarkable with normal enhancement.
An enlarged gastrosplenic node is noted, measuring 1.3 cm in short axis dimension (series 6, image 13). The visualized bowel is within normal limits.
Impression:
-
Post surgical changes from left lower lobectomy.
-
Development of posterior mediastinal and precardial lymphadenopathy concerning for disease progression. An enlarged gastrosplenic node is nonspecific and appears grossly stable compared to CT from 4/22/1986 given differences in technique.
-
Small rim enhancing left pleural fluid collection concerning for infection.
###Andy SIIM (mrn: TCGA-50-5072)
###Neela SIIM (mrn: TCGA-BA-4077)