Using SNOMED-CT to encode summary level data - a corpus analysis.

Extracting and encoding clinical information captured in free text with standard medical terminologies is vital to enable secondary use of electronic medical records (EMRs) for clinical decision support, improved patient safety, and clinical/translational research. A critical portion of free text is comprised of 'summary level' information in the form of problem lists, diagnoses and reasons of visit. We conducted a systematic analysis of SNOMED-CT in representing the summary level information utilizing a large collection of summary level data in the form of itemized entries. Results indicate that about 80% of the entries can be encoded with SNOMED-CT normalized phrases. When tolerating one unmapped token, 96% of the itemized entries can be encoded with SNOMED-CT concepts. The study provides a solid foundation for developing an automated system to encode summary level data using SNOMED-CT.

Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules.

OBJECTIVE: This paper describes the coreference resolution system submitted by Mayo Clinic for the 2011 i2b2/VA/Cincinnati shared task Track 1C. The goal of the task was to construct a system that links the markables corresponding to the same entity. MATERIALS AND METHODS: The task organizers provided progress notes and discharge summaries that were annotated with the markables of treatment, problem, test, person, and pronoun. We used a multi-pass sieve algorithm that applies deterministic rules in the order of preciseness and simultaneously gathers information about the entities in the documents. Our system, MedCoref, also uses a state-of-the-art machine learning framework as an alternative to the final, rule-based pronoun resolution sieve. RESULTS: The best system that uses a multi-pass sieve has an overall score of 0.836 (average of B(3), MUC, Blanc, and CEAF F score) for the training set and 0.843 for the test set. DISCUSSION: A supervised machine learning system that typically uses a single function to find coreferents cannot accommodate irregularities encountered in data especially given the insufficient number of examples. On the other hand, a completely deterministic system could lead to a decrease in recall (sensitivity) when the rules are not exhaustive. The sieve-based framework allows one to combine reliable machine learning components with rules designed by experts. CONCLUSION: Using relatively simple rules, part-of-speech information, and semantic type properties, an effective coreference resolution system could be designed. The source code of the system described is available at https://sourceforge.net/projects/ohnlp/files/MedCoref.