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

The role of FDG-PET in the selection of patients with colorectal liver metastases.

Item does not contain fulltextBACKGROUND: Selection of patients for hepatic resection of colorectal liver metastases is still limited. After conventional work up by computed tomography (CT) scan, 60% of patients will develop recurrent disease in the early years after resection. The aim of the present study was to evaluate whether an additional fluorine-18-deoxyglucose positron emission tomography (FDG-PET) improves patient selection and therefore adds value to select patients for curative liver resection. METHODS: Data from 203 patients selected for surgical treatment of colorectal liver metastases between 1995 and 2003 were collected in a prospective database. Group A consisted of 100 consecutive patients selected for hepatic surgery by conventional diagnostic imaging (CT chest and abdomen) only. Group B consisted of 103 consecutive patients selected for hepatic surgery by conventional diagnostic methods plus an additional FDG-PET. RESULTS: The number of patients with futile surgery, in which further treatment was considered inappropriate at laparotomy, was 28.0% in group A and 19.4% in group B. The reason for unresectable disease differed between groups. In group A, 10/100 (10.0%) patients showed extrahepatic abdominal disease versus 2/103 patients (1.9%) in group B (P = .017). In all other cases, resection was not performed because liver disease proved too extensive at laparotomy. For patients ultimately undergoing surgical treatment of the metastases, survival was comparable between groups. Overall survival at 3 years was 57.1% in group A versus 60.1% in group B. Disease-free survival at 3 years was 23.0% in group A and 31.4% in group B. CONCLUSIONS: In patients with colorectal liver metastases, FDG-PET may reduce the number of negative laparotomies. However, the effect size on the selection of these patients seems not sufficient enough to affect the overall and disease-free survival after treatment