A sustainable visual representation of available histopathological digital knowledge for breast cancer grading
Creators: name: Traore, Lamine
name: Daniel, Christel
name: Jaulent, Marie-Christine
name: Schrader, Thomas
name: Racoceanu, Daniel
name: Kergosien, Yannick
Publisher: name: Diagnostic Pathology
Year: 2016
Subjects: Breast cancer grading, semantic annotation, knowledge formalization and modeling, standardization, computer aided diagnosis, high-content image exploration, digital pathology

description: Background

Recently, anatomic pathology (AP) has seen the introduction of several tools such as slide scanners and virtual slide technologies, creating the conditions for broader adoption of computer aided diagnosis based on whole slide images (WSI). This change brings up a number of new scientific challenges such as the sustainable management of the explicit and unambiguous semantics associated to the diagnostic interpretation of AP images by both humans (pathologists) and computers (image analysis algorithms) . In order to reduce inter-observer variability between AP reports of malignant tumors, the College of American Pathologists edited more than 60 organ-specific Cancer Checklists and associated Protocols (CAP-CC&amp;P). Each checklist includes a set of AP observations that are expected to be reported by pathologists in organ-specific AP cancer reports. Our objective was to i) identify the available histopathological formalized knowledge from NCBO Bioportal and UMLS metathesaurus in the scope of the CAP CC&amp;P for breast cancer grading and ii) to build a sustainable visual representation of this knowledge using UMLS semantic types.

Methods 

Our methodology was applied on the two breast cancer CAP-CC&amp;Ps dedicated to invasive carcinoma (IC) and ductal carcinoma in situ (DCIS). We focused on a subset of quantifiable AP observations of the CAP-CCs - i.e. observable entities that could be computed by image analysis tools and on the corresponding notes in the protocols that unambiguously describe how pathologists should derive a high-level observation (e.g. Nottingham score) from low-level morphological characteristics observed in images (e.g. mitotic count or glandular/tubular differentiation).The notes were annotated manually by two AP experts (gold standard) and automatically by NCBO Annotator using the 508 ontologies available on the NCBO platform. A sub-set of reference ontologies was selected based on their capacities to automatically identify concepts in the notes and compared to the subset of ontologies selected based on their capacity to identify the concepts identified by experts (gold standard). Once automatically extracted from the notes, the concepts belonging to different ontologies, were integrated into a unique graph and organized according to UMLS semantic types.

Results 

The most relevant biomedical ontologies to be used for the annotation of the notes describing quantifiable observable entities of breast cancer CAP-CC&amp;Ps are SNOMED-CT, LOINC, NCIT, NCI CaDSR Value Sets and PathLex. A visual representation integrating 25 concepts from the 5 different ontologies organized according to 11 UMLS semantic types was built to support AP experts for building a formal representation of the low-level quantifiable entities automatically extracted from the CAP-CC&amp;Ps notes.

Conclusion 

The proposed approach and tools, based on the CAP-CC&amp;Ps, aim at supporting AP experts in building a standard-based representation of low-level morphological abnormalities observed in cancer that can be quantified using image analysis tools. This effort is complementary to the Integrating the Healthcare Enterprise (IHE) initiative building a standard-based representation of high-level AP observations required in cancer AP reports. Additional efforts are needed to achieve a workable standard-based formal representation of histopathological knowledge integrating both observable entities reported by humans (pathologists) and quantifiable entities automatically computed by machines. Providing such unique formal representation paves the way for more efficient use of computer aided diagnosis in AP as well as for the development of new biomarkers based on automatic analysis of whole slide images (WSI).
description: Diagnostic Pathology, Vol 2 No 1 (2016): 2016