Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Uterine perforation as a complication of surgical abortion causing small bowel obstruction: a review

OBJECTIVE: Small bowel obstruction after unrecognized or conservatively treated uterine perforation is extremely rare. It is a surgical emergency and the delay in diagnosis and treatment has deleterious consequences for the mother. The purpose of this study is to critically review the available literature and ascertain the level of evidence for the mechanisms, diagnosis and management of small bowel obstruction after uterine perforation due to surgical abortion. ----- METHODS: Systematic literature search was conducted in Pubmed (1946 to 2012) and Pubmedcentral (1900 to 2012) including all available English and French language fulltext articles. Three evaluators reviewed and selected all available case reports and case series. Search terms included small bowel obstruction, bowel obstruction, bowel incarceration, bowel entrapment, vaginal evisceration, uterine perforation, uterine rupture, and abortion. The exclusion criteria were (1) complex injuries where small bowel incarceration was present but with bleeding and/or bowel perforation as the leading symptomatology; (2) articles only numbering the patients without details on the topic. Analyses of incidence, risk factors, mechanisms of the disease, time of clinical presentation, diagnostic modalities, treatment, and maternal outcome were included. ----- RESULTS: Of the 73 articles screened 30 cases of small bowel obstruction were included in the review forming incidence, risk factors, and mechanisms of the disease, diagnosis, therapy, and maternal outcome. ----- CONCLUSIONS: A systematic review defined four mechanisms of small bowel obstruction after transvaginal instrumental uterine perforation with significant variations in clinical presentation and time of presentation. Duration of symptoms depend on the mechanism of small bowel obstruction. Vaginal evisceration is surgical emergency and treatment is mandatory without diagnostic workup. Survival rate during last century is 93 %. Multicentric trials and publication of all such cases are needed to determine algorithms for diagnosis and management of small bowel obstruction caused by instrumental uterine perforation