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.
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:
- Blood/Bone Marrow (labeled as Heme in OpenSpecimen Suite)
- Colon and Rectum
- 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
- 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.
Specimen Collection Group