Originally published at: http://contentmine.org/2015/09/daily-updates-on-iucn-red-list-species/
The ContentMine team have been working on user stories for our daily stream of facts. One such stand-out user story that we can easily cater-for with our tools is that of conservation biologists & practitioners looking to stay up-to-date with the very latest literature on IUCN Red List species.
Take for instance the journal PLOS ONE. It's open access but the high volume and broad subject scope mean that people sometimes struggle to keep-up with relevant content published there. Recently (May, 2015) an interesting article on an endangered species of frog was published in PLOS ONE; we shall use this as an example in this post henceforth: Roznik EA, Alford RA (2015) Seasonal Ecology and Behavior of an Endangered Rainforest Frog (Litoria rheocola) Threatened by Disease. PLoS ONE 10(5): e0127851. doi:10.1371/journal.pone.0127851
[caption id="attachment_1150" align="aligncenter" width="331"] Common Mist Frog (Litoria rheocola) of northern Australia. Credit: Damon Ramsey / Wikimedia / CC BY-SA[/caption]
This kind of peer-reviewed, published information is vitally important to conservation organisations. Typically, the Red List status of many groups is assessed and re-assessed by experts only every 5 years. It is extremely expensive, time-consuming, and tedious for humans to do these kinds of systematic literature reviews. We suggest that intelligent machines should do most of this screening work instead.
We think we could make the literature review process; cheaper, more rigorous, continuous and transparent by publishing a daily stream of facts related to all Red List species. For the above paper, our 26 summary snippet facts extracted from the full text, labelled by section, might look something like the below (bold emphasis is mine to highlight the entity we would match). Note this reduces the full text from over 6000 words to a more bite-size summary of just ~700. Multiply this effect across thousands of papers and searches for thousands of different species and you might begin to understand the usefulness of this:
* Note that because PLOS ONE is an openly-licensed journal we can re-post as much context around each entity as we wish.
Text as extracted by our ami-species plugin :
From the Introduction: section:
...One such species is the common mistfrog (Litoria rheocola), an IUCN Endangered species  that occurs near rocky, fast-flowing rainforest streams in northeastern Queensland, Australia ...
- ...Litoria rheocola is a small treefrog (average male body size: 2.0 g, 31 mm; average female body size: 3.1 g, 36 mm ) ...
- ...Habitat modification and fragmentation also threaten L.rheocola [23,27]...
- ...Very little is known of the ecology and behavior of L. rheocola. Individuals of this species call and breed year-round, although reproductive behavior decreases during the coolest weather [19,23]...
- ...We used harmonic direction finding [32,33] to track individual L. rheocola and study patterns of movement, microhabitat use, and body temperatures during winter and summer...
- ...The goal of our study was to understand the behavior of L. rheocola, and how it is affected by season and by sites that vary in elevation. ...
- ...The goal of our study was to understand the behavior of L. rheocola, and how it is affected by season and by sites that vary in elevation...
- ... We provide the first detailed information on the ecology and behavior of L. rheocola and suggest ecological mechanisms for observed patterns of infection dynamics...
and from other sections:
- Because L. rheocola are too small to carry radiotransmitters, we tracked frogs using harmonic direction finding [32,33].
- However, this was unlikely to cause a bias toward shorter movements in our study; L. rheocola has strong site fidelity and when a frog was not found on a particular survey (or surveys), it was almost always subsequently found less than 2 m from its most recent known location.
Litoria rheocola is a treefrog, and individuals move along and at right angles to the stream and also climb up and down vegetation; therefore, they use all three dimensions of space, with their directions of movement largely unconstrained in the horizontal plane but largely restricted to movements up and down individual plants in the vertical direction.
- These models lose and gain water at rates similar to frogs, and temperatures obtained from these permeable models are closely correlated with L. rheocola body temperatures .
- Fig 1. Distances moved by common mistfrogs (Litoria rheocola).
- Fig 2. Proximity of common mistfrogs (Litoria rheocola) to the stream.
- Fig 3. Distribution of estimated body temperatures of common mistfrogs (Litoria rheocola) within categories relevant to Batrachochytrium dendrobatidis growth in culture (<15°C, 15–25°C, >25°C).
- Fig 4. Mean estimated body temperatures of common mistfrogs (Litoria rheocola) over the 24-hr diel period.
- Table 1. Characteristics of microhabitats used by common mistfrogs (Litoria rheocola) during the day and night at two rainforest streams (Frenchman Creek and Windin Creek) during the winter (cool/dry season) and summer (warm/wet season).
- Table 2. Results of separate one-way ANOVAs comparing characteristics of nocturnal perch sites that were available to and used by common mistfrogs (Litoria rheocola) at two rainforest streams (Frenchman Creek and Windin Creek) during winter (cool/dry season).
- Our study provides the first detailed information on the ecology and behavior of the common mistfrog (Litoria rheocola), an IUCN Endangered species .
- Overall, we found that L.rheocola are relatively sedentary frogs that are restricted to the stream environment, and prefer sections of the stream with riffles, numerous rocks, and overhanging vegetation (Table 2).
- Our data confirm that L. rheocola are active year-round, but their behavior varies substantially between seasons.
- Retallick  also found that juvenile and adult L. rheocola in field enclosures altered their behavior by season in similar ways; frogs used elevated perches more often in summer, and aquatic microhabitats more often during winter.
- Additionally, Hodgkison and Hero  observed more L. rheocola at the stream during warmer months, suggesting that during that period frogs used perch sites that were more exposed and elevated than those used during cooler months, when frogs were seen less frequently.
- The sedentary behavior of L. rheocola also may increase the vulnerability of this species to chytridiomycosis, particularly during winter, when movements are reduced.
- Our results suggest that seasonal differences in environmental temperatures and L. rheocola body temperatures should cause this species to be more likely to develop B. dendrobatidis infections during cooler months and at higher elevations (Figs 3 and 4); this matches observed patterns of infection prevalence .
- Our study provides detailed information on the movements, microhabitat use, and body temperatures of uninfected L. rheocola, and reveals how these behaviors differ by season and between sites varying in elevation.
NOTE: We have shown all phrases in the PLoSONE paper about L. rheocola. However our ami software allows us to select particular sections for display, or to restrict our search and filtering (e.g. to the Methods section).
This approach provides far far more information than is indicated in the abstract for the paper. Yet it also condenses it down to useful & relevant facts. We think this could be very useful to many...