A manual corpus of annotated main findings of clinical case reports.

Neil R Smalheiser,Mengqi Luo,Xiaokai Cui,Sidharth Addepalli

doi:10.1093/database/bay143

Abstract

Clinical case reports are the `eyewitness reports’ of medicine and provide a valuable, unique, albeit noisy and underutilized type of evidence. Generally a case report has a single main finding that represents the reason for writing up the report in the first place. In the present study, we present the results of manual annotation carried out by two individuals on 500 randomly sampled case reports. This corpus contains main finding sentences extracted from title, abstract and full-text of the same article that can be regarded as semantically related and are often paraphrases. The final reconciled corpus of 416 articles comprises an open resource for further study. This is the first step in establishing text mining models and tools that can identify main finding sentences in an automated fashion, and in measuring quantitatively how similar any two main findings are. We envision that case reports in PubMed may be automatically indexed by main finding, so that users can carry out information queries for specific main findings (rather than general topics)—and given one case report, a user can retrieve those having the most similar main findings. The metric of main finding similarity may also potentially be relevant to the modeling of paraphrasing, summarization and entailment within the biomedical literature.

Highlights

Clinical case reports are the ‘eyewitness reports’ of medicine, in which novel or interesting observations are made of one or a few patients
We present the results of manual annotation carried out by two individuals on 500 randomly sampled case reports, which comprises an open resource for further study
Supplemental File 1 displays the annotations resulting from discussion and corrections between the two annotators. (Of the 500 articles initially annotated, one article was excluded because the PubMed Central Identifier (PMC ID) was incorrectly cross-listed in PubMed.) There were a total of 416 articles in which both annotators agreed upon: (i) the article was a typical case report, (ii) the title either directly expressed or alluded to the main finding, (iii) the abstract expressed a main finding and (iv) both agreed which sentence(s) expressed the main finding within the abstract

Summary

Introduction

Clinical case reports are the ‘eyewitness reports’ of medicine, in which novel or interesting observations are made of one or a few patients. The major biomedical search engine, PubMed, indexes almost two million articles as having the Publication Type ‘case reports’, ∼7% of all biomedical articles There is considerable value in identifying findings that have been independently published in multiple case reports, since that would alert readers to evidence that has high reliability and potential impact [2]. This might encourage wider judicious use of case reports in evidencebased medicine and other tasks such as surveillance of drug side-effects

Methods

Results

Conclusion