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

Taxa, petitioning agency, and lawsuits affect time spent awaiting listing under the US Endangered Species Act

The United States\u27 Endangered Species Act (ESA) is the world\u27s foremost law for protecting species at risk of extinction; however, species must first be listed as threatened or endangered before receiving protection under the Act. We used an information theoretic approach to assess whether listing budget, policy phase (which was correlated with presidential administration), or both factors were associated with the number of species listed annually between 1983 and 2014. Annual listing rates were positively affected by larger listing budgets; policy phase also had a significant impact on annual listing rates after accounting for the effects of budget. However, the listing process for any one species spans multiple years, thus we also evaluated how taxonomic affiliation, the initiating organization, and lawsuits affected the amount of time 1338 listed species spent in review between 1973 and 2014. Species waited a median of 12.1 years to receive protection, with plants and invertebrates experiencing longer wait times than vertebrates. These process times exceed ESA deadlines, which are two years when initiated from a third party; this may perpetuate population declines and hinder recovery efforts. We observed that at the time of a lawsuit filling for either a proposed or final rule, species had waited, respectively, 4.19 and 0.70 years longer than species for which no lawsuits were filed, indicating lawsuits targeted species that experienced longer delays. We discuss how changes in ESA implementation over time interacted to produce high variability and often long wait times in the listing process. Our results indicated a positive role for both citizen petitions and budget increases to advance the listing process, thus hastening biodiversity protection

yahoo_lake_data

Microsoft Excel file contains the data contained in each figure

Data from: Postglacial climate and fire-mediated vegetation change on the western Olympic Peninsula, Washington

The mode and tempo of forest compositional change during periods of rapid climate change, including the potential for the fire regime to produce non-linear relationships between climate and vegetation, is a long-standing theme of forest ecological research. In the old conifer forests of the coastal Pacific Northwest, fire disturbances are sufficiently rare that their relation to climate and their ecological effects are poorly understood. We used a 14,700-year high-resolution sediment record from Yahoo Lake on the Olympic Peninsula to examine vegetation (landscape vegetation from pollen and local vegetation from macrofossils) and fire (landscape fire from total charcoal and local fire from charcoal peaks) in conjunction with independent records of climate. We hypothesized that the successional stage of the local forest will exhibit alternate stable states over a range of fire activity, that species turnover will increase abruptly above a certain level of fire activity and that both responses would be more gradual at the landscape scale than the local scale. Supporting these hypotheses, at the local scale we found strong evidence for alternate stable states of late vs. early successional communities and inertia of species turnover to changing fire activity. At the landscape scale, vegetation responded more gradually to changing fire activity. From 14,700 to 7000 years ago, high landscape vegetation turnover occurred along with high landscape fire activity, especially during the warm summers of the early Holocene. In several instances local species turned over completely following fire events but several centuries after climate change. In contrast, during the last 7000 years the local forest composition was dominated by late-successional species with little species turnover despite periods of moderate fire activity. We suggest that the relatively minor climate fluctuations of the past 7000 years were not sufficient to cause large-scale species turnover after fire. The Yahoo Lake fire and vegetation record of the early Holocene provides a model for dramatic ecosystem change following an anticipated shift to warmer summer temperatures

Forum 686 BioScience

With few exceptions, the US Endangered Specie

Puckett_etal_BioCon2016-ListSuit

Data file for length of time for species where lawsuits were filed within the proposal to final rule phase of listing. Columns include: SppCode (US FWS TESS database species code), Prop_Suit (number of days between proposed rule and lawsuit), Suit_List (number of days between lawsuit and final listing rule)

Puckett_etal_BioCon2016-Annual_List

Data set for the Annualized Listing Rate analysis. Data columns include: Year and Year_C, Init (number of species initiated in that year), Lst (number of species listed in that year), AdminList (number of species listed, shifted from a yearly start date of Jan 1 to Jan 20 due to presidential administrative cycles), L_Budget (US Fish & Wildlife annual listing budget in millions of $ adjusted for inflation to the value in 2014), Candidates (the number of candidate species for that year), Admin (the presidential administration including: RR: Ronald Reagan; GHB: George H W Bush; BC: William (Bill) Clinton; GWB: George W Bush; BO: Barack Obama); Phase (the policy phase as described in the text)

Puckett_etal_BioCon2016-Rcode

R code for the annualized listing rates, and process time analyses (initiation to proposed, proposed to listing, initiation to listing