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

The potential of non-pathogenic Gaeumannomyces spp., occurring naturally or introduced into wheat crops or preceding crops, for controlling take-all in wheat

Take-all disease (Gaeumannomyces graminis var. tritici) in wheat crops is known to be suppressed by naturally occurring antagonistic fungi, closely related to the pathogen, that infect grasses and cereals. This form of suppression was re-investigated because of the changing importance and role of grass weeds and grass covers in arable farming. Natural populations of the competitive fungus Gaeumannomyces cylindrosporus, allowed to develop under rye-grass, were more effective than artificially introduced populations in suppressing the development of take-all in following wheat crops. To be effective, the antagonist needs to be present before the start of wheat cropping. Introducing G. cylindrosporus, but not G. graminis var. graminis (a potential antagonist that is faster growing), into a previous crop, or just after the previous crop, sometimes suppressed take-all, but the effect was small. It is concluded that, for any future attempts at biocontrol by these fungi, they should be introduced into a preceding crop not susceptible to take-all. Take-all inoculum in the soil should be at a minimum and effective hosts of the take-all pathogen must not be present as weeds or volunteers