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

Rediscovery of Five <i>Rinodina</i> Species Originally Described from Southwest China and One New Species

Rinodina is a lichenized fungal genus belonging to the Physciaceae, with c. 300 species worldwide. Nearly a century ago, Zahlbruckner described five species of the genus Rinodina from Southwest China. The type collections were the only records for these species. In the present study, new records for four of these species: Rinodina cornutula, R. globulans, R. handelii, and R. setschwana, and a recently described species, R. pluriloculata, are documented based on specimens collected from the holotype localities. Furthermore, one new species was discovered: Rinodina hengduanensis, characterized by areolate to subsquamulose thallus, jigsaw-like areoles, lecanorine apothecium, and Dirinaria-type ascospores. Rinodina setschwana is transferred to the genus Buellia based on its morphology, chemistry, and phylogeny and proposed as Buellia setschwana. We provide detailed morphological descriptions, pictures, and molecular phylogenetic analyses

Taxonomy of Buellia epigaea-group (Caliciales, Caliciaceae), revealing a new species and two new records from China

During the Second Tibetan Plateau Scientific Expedition and Research Program, we discovered that white terricolous lichenized fungal species of Buellia De Not. were widely distributed across the Tibetan Plateau. After examining their morphology, chemistry and phylogeny, we describe Buellia alpina Xin Y. Wang & Li S. Wang, sp. nov. as new to science. It is present in alpine meadows, and is characterized by its effigurate thallus, distinct linear marginal lobes, cover of thick white pruina and four-spored asci. This is also the first report of Buellia elegans Poelt and Buellia epigaea (Pers.) Tuck from China. The Buellia epigaea-group has previously been characterized by white and often effigurate thalli that occur mainly on soil. However, our results show that species in this group actually belong to two distinct clades. This conclusion is based on analyses of the nuITS region and the combined regions dataset (nuITS-nuLSU-mtSSU-β-tubulin). We discuss differences in morphology, anatomy, chemistry and ecology among the putative Buellia epigaea-group. Detailed descriptions and figures for the three species from China and a key for species of Buellia epigaea-group are provided

Squamarina (lichenised fungi) species described from China belong to at least three unrelated genera

Volume: 66Start Page: 135-15