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

Taxonomy, phylogeny, and diversity of the extinct Lesser Antillean rice rats (Sigmodontinae: Oryzomyini), with description of a new genus and species

Rice rats (Sigmodontinae: Oryzomyini) are abundant in the Late Quaternary fossil record and in Holocene pre-Columbian archaeological middens across the Lesser Antilles. All of these rice rats are now extinct, and their regional diversity and systematics remain extremely poorly understood. We redescribe all of the region's rice rat taxa known from adequate diagnostic material (Megalomys desmarestii, Megalomys luciae, and Oligoryzomys victus), and describe a new genus and species, Pennatomys nivalis gen. et sp. nov., from archaeological sites on St. Eustatius, St. Kitts, and Nevis, which formed a single larger island during Quaternary low sea-level stands. Cladistic analysis supports the inclusion of O. victus within Oligoryzomys, and identifies Megalomys as a sister group of the large-bodied genera Sigmodontomys or Sigmodontomys + Nectomys, suggesting that large body size in Megalomys represents phyletic gigantism rather than ‘island gigantism’. Megalomys and Pennatomys belong to an oryzomyine clade that has undergone remarkable radiation throughout the oceanic and continental-shelf islands of the Neotropical region, but these genera do not represent a monophyletic group within the Nectomys subclade, indicating multiple over-water colonization events of the Lesser Antillean island chain. Although Lesser Antillean rice rats were heavily exploited by prehistoric Amerindians, it is likely that most or all of these taxa survived until European arrival in the region.<br/