Annotations

OpenSpecimen allows data capture by default for clinical annotations (e.g. environmental, follow-up, lab tests) and pathology for basic cancer types. Specimens can be annotated with College of American Pathologists (CAP) checklist-based data forms or by import, de-identification, and concept coding of pathology report text using caTIES-like functionality.

 

Pathology Information
This section outlines CAP-based (College of American Pathologists) pathology annotations. It involves a collection of information on a broad spectrum of tumors. It captures information about various features associated with tumors, such as TNM staging (tumor, node, and metastasis stage determination), histologic grading, histo-pathological examination, positive or negative margins, and other fundamental pathology details. The module consists of nine organ systems and data for these organ systems is independently captured.

The nine organ systems include the following:

  • Prostate
  • Pancreas
  • Kidney
  • Lung
  • Blood/Bone Marrow (labeled as Heme in OpenSpecimen Suite)
  • CNS
  • Colon and Rectum
  • Breast
  • Skin (labeled as Melanoma in OpenSpecimen Suite)

To accommodate pathology data for tumors that do not fall under the nine organ systems, there is a generic annotation to capture information specific to that organ system.
Clinical and Health Information

Clinical and health information comprises clinical information about the participant's:

  • Medical history
  • Follow-up
  • Medications administered (such as chemotherapy, radiation therapy, and so on
  • Social history (smoking and alcohol history)
  • Environmental exposure history (for example: exposure to asbestos)
  • Physical examinations
  • Laboratory test details
  • Family health history

The clinical annotations available in OpenSpecimen Suite can be found under the hook entities as outlined in the following table.

Participant

Specimen Collection Group

Specimen

  • Lab Annotation 
  • Family History Annotation 
  • Treatment Annotation 
  • Rad RX Annotation 
  • Chemo RX Annotation 
  • Treatment Regimen 
  • Environmental Exposure Health Annotation 
  • Alcohol Health Annotation 
  • Smoking Health Annotation 
  • Health Examination Annotation 
  • New Diagnosis Health Annotation 
  • No Evident Disease Health Annotation 
  • Recurrence Health Examination Annotation 
  • Local Recurrence Health Examination Annotation
  • Distant Recurrence Health Examination Annotation
  • Base Solid Tissue Pathology Annotation 
  • Base Hematology Pathology Annotation 
  • Radical Prostatectomy Pathology Annotation 
  • Needle Biopsy Prostate Pathology Annotation 
  • Retropubic Enucleation Pathology Annotation 
  • Transurethral Prostatic Resection Pathology Annotation 
  • Pancreas Pathology Annotation 
  • Lung Biopsy Pathology Annotation 
  • Lung Resection Based Pathology Annotation 
  • Kidney Biopsy Based Pathology Annotation 
  • Kidney Nephrectomy Pathology Annotation 
  • Melanoma Pathology Annotation 
  • CNS Pathology Annotation 
  • Breast Pathology Annotation 
  • Local Excision Based Colorectal Pathology Annotation 
  • Excisional Biopsy Based Colorectal Pathology Annotation 
  • Resection Based Colorectal Pathology Annotation
  • Specimen Based Solid Tissue Pathology Annotation 
  • Colorectal Specimen Pathology Annotation 
  • Pancreas Specimen Pathology Annotation 
  • Melanoma Specimen Pathology Annotation 
  • CNS Specimen Pathology Annotation 
  • Prostate Specimen Pathology Annotation 
  • Kidney Specimen Pathology Annotation 
  • Lung Specimen Pathology Annotation 
  • Breast Specimen Pathology Annotation