Literature Searches Benefit from Location Tagging

Via the ARS News Service.

By Rosalie Marion Bliss
October 29, 2014

Conducting literature searches for scientific papers just got more comprehensive, thanks to innovations by U.S. Department of Agriculture (USDA) scientists. Agricultural Research Service (ARS) ecologist Jason Karl and his collaborators have developed a search engine called “JournalMap,” which identifies scientific papers of interest by research locations and physical site variables. ARS is USDA’s chief intramural scientific research agency.

Articles in the JournalMap citation index are “geotagged” based on locations reported in the study and then plotted on a world map. This means that scientists can use JournalMap to search for environmental literature thematically and geographically by selecting a location on a map.

This new approach to combing through scientific literature can help researchers adapt published research and data for investigations in similar ecosystems where formal studies of environmental parameters are relatively sparse. The environmental factors tagged in JournalMap include a range of weather-related data, landform characteristics, soil characteristics and types of land cover.

Karl and his collaborators are also working with Taylor & Francis, a publisher of over 1,600 journals, to build literature geotagging into the publication process and to enable geographic literature searching across entire journal archives. Initially, this effort focused on geotagging the archives of three journals, including the Journal of Natural History, which has been published since 1838. The partnership now includes geotagging articles automatically when they are submitted for publication and standardizing how locations are reported.

The JournalMap citation index currently contains over 12,000 published papers from around 300 journals with more articles being added on a regular basis. Karl and his collaborators are continuing to refine JournalMap by expanding the content of available journals and papers. Authors and researchers are also able to upload their own geotagged articles to the JournalMap citation index and create their own georeferenced article collections at

Karl works at the ARS Range Management Research Unit in Las Cruces, New Mexico. The researchers published a report on the development of the citation database in BioScience in 2013.

Read more about this work in the October 2014 issue of Agricultural Research magazine.

Posted in INHS, ISAS, ISGS, ISTC, ISWS, Journals | Leave a comment

Just Released: The Butterflies of Illinois A Field Guide

INHS-man14.pngThe Illinois Natural History Survey’s Manual 14, Butterflies of Illinois: a Field Guide  has just been released.  The guide contains descriptions, field photos and life-size specimen photos of all Illinois’ butterfly species.   For more information about this Manual or to order click here.

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University of California Press Announces Plans to Roll Out Two Open Access Products

Read the full story from the University of California Press.

University of California Press is entering into the Open Access space with the launch of two new products: a mega journal focused on three core disciplines (life and biomedical sciences, ecology and environmental science, and social and behavioral sciences) and a monograph program designed to take advantage of rich, digital formats.

This move is part of University of California Press’s mission to bring progressive scholarship forward in ways that continue to meet the academic community’s needs for greater discoverability, accessibility, and audience reach. Rollout for both products is planned for 2015.

Posted in INHS, ISAS, ISGS, ISTC, ISWS, Open access | Leave a comment

Webinar: New Tools for Advancing our Understanding of Marine Mammal Behavioral Ecology

Thursday, November 6, 2014, 11:00 AM CT
Register at

For other webinars in the series, visit The topics are fairly wide-ranging.

Webinar Topics

The Relationship of Body Condition of Whales with Behavior and Reproductive Status by Dr. Patrick Miller

The risk of harm to cetaceans from underwater noise is an important environmental and regulatory issue faced by the Department of Defense, in particular the Navy. Noise may reduce foraging rates and thereby body condition, which is a good predictor of offspring survival and reproductive success. Current methods for estimating body condition in cetaceans, however, are descriptive or do not measure full-body fat (lipid) stores. This project is validating and using a novel, non-invasive method to measure total body lipid-stores of free-ranging cetaceans. The cornerstone of the approach is to measure body density of tagged animals, which corresponds to lipid content (fat stores) in mammals because lipids are less dense than other compartments (e.g., bone, skin). The two target species, Northern bottlenose and humpback whales, are being studied in established field sites in the North Atlantic Ocean. Results are validating an innovative technique to measure body condition in cetaceans and enable examining the interplay of body condition with foraging and anti-predator behaviors and the reproductive status of females.

Deep Mapping Squid-Feeding Whales and Their Prey Fields by Dr. Kelly Benoit-Bird

Deep-diving teuthivorous (squid-feeding) whales that have posed concerns related to sound exposure from Navy sonars. In the last decade great progress has been made in understanding the behavior and biology of whales such as sperm and beaked whales that feed primarily on squid. Studying their prey, however, has presented difficulties because of the squids’ rapid speed, relatively large size, and foraging depth. This project is developing an effective, easily deployed, adaptable remote sensing tool for measuring both the prey field and occupancy patterns of sperm and beaked whales to depths of at least 1200 m and utilizing this tool to understand how prey affects the behavior of deep-diving whales and how this behavior may affect sound exposure risk. The tool was developed by integrating an echosounder into an existing REMUS 600 UUV and developing onboard acoustical data processing capabilities within the integrated echosounder module. Results from a field expedition in and around the Navy’s Southern California Offshore Range (SCORE) are providing insights into how beaked whales use their habitat and into the prey that is critical for their survival.

Posted in INHS, Training opportunities | Leave a comment

Journal of Industrial Ecology publishes special issue on Industrial Ecology as a Source of Competitive Advantage

Read the full post from the Yale University School of Forestry & Environmental Studies.

Industrial ecology, a rapidly growing field focused on sustainable production and consumption, has contributed numerous important tools to modern environmental management — life cycle assessment; “industrial symbiosis,” or the by-product exchange between neighboring facilities; “design for environment”; and the use of material flow analysis to track resource use in supply chains, companies, and economies.

A new special feature of Yale’s Journal of Industrial Ecology, titled “Industrial Ecology as a Source of Competitive Advantage,” presents new research on how, when, and why the use of industrial ecology by business can lead to cost savings, higher profits, and other, more intangible, business benefits…

Some highlights from the issue include:

  • An examination of how the Dow Chemical Company uses replacement cost methodology and life cycle assessment (LCA) to systematically demonstrate the financial and environmental benefits of a constructed wetland at a plant in Texas.
  • An article about a tool that uses data mining and machine learning to rapidly generate product carbon footprints (PCFs) for PepsiCo and combine them with business key performance indicators for strategy and business planning.
  • A study of the relationship between industrial ecology and business model innovation at British Sugar, the UK’s largest sugar producer.
  • A description of the 20-year evolution of Interface’s use of LCA as a tool guiding the company toward more-sustainable practices in carpet manufacturing.
  • A profile of AU Optronics Corp., a global leader in thin-film-transistor liquid-crystal displays, that has differentiated itself from its peers and competitors by implementing carbon footprint management and dematerialization.
  • A case study showing economic and environmental benefits of an industrial symbiosis involving a municipal waste-to-energy incinerator and the Hyosung chemical company in South Korea.
  • An analysis of green consumers’ mind-set toward green product design and the environmental impacts of products throughout the entire life cycle.

Articles in the special feature will be freely available online for a limited time.

The Journal of Industrial Ecology is a bimonthly peer-reviewed scientific journal, owned by Yale University, published by Wiley-Blackwell and headquartered at the Yale University School of Forestry & Environmental Studies.

Posted in ISTC, ISWS, Publications | Leave a comment

Environmental Solutions for Communities Grant Program

The 2015 call for proposals is out for the Environmental Solutions for Communities Grant Program.

“Wells Fargo and the National Fish and Wildlife Foundation (NFWF) seek to promote sustainable communities through Environmental Solutions for Communities by supporting highly-visible projects that link economic development and community well-being to the stewardship and health of the environment. Approximately $2,500,000 is available nationwide for 2015 projects.”

Individual awards range from $25,000 to $100,000, and will go to “eligible entities working to help communities create a more sustainable future through responsible environmental stewardship”.  Eligible organizations are non-profit 501(c) organizations, state government agencies, local governments, municipal governments, Indian tribes, educational institutions.  U.S. Federal government agencies, businesses, unincorporated individuals and international organizations are ineligible.  Full proposals are due December 10, 2014.

The 2015 RFP gives preference to specific geographic areas. Illinois is unfortunately not on the list, but some neighboring states/communities are, including St. Louis, MO.

Posted in Funding opportunities, INHS, ISAS, ISGS, ISTC, ISWS, Prairie Research Institute | 1 Comment

Wilkin to speak on the future of the Illinois Library

If you are interested in the future of libraries in general and the future of the University Library in particular, you can hear the thoughts of the Dean of the University Library on the topic this Wednesday:

John WilkinJohn Wilkin, Dean of the University Library, University of Illinois at Urbana-Champaign
The Future of the Illinois Library, a Conversation
Wednesday, October 16, 2014, 4:30pm
Knight Auditorium, Spurlock Museum (600 S. Gregory St, Urbana)
Co-sponsored by the Illinois Program for Research in the Humanities and the Spurlock Museum.

The event is open to the public, and there will be a reception following the lecture.
For further info see the announcement on the IPRH website.

Posted in Events, INHS, ISAS, ISGS, ISTC, ISWS, Prairie Research Institute, The Library | Leave a comment

Future of Big Rivers Colloquium Series

The Future of Big Rivers: Form, Flux, Ecology and Management” is a colloquium series organized by Faculty Fellow Jim Best of the National Great Rivers Research and Education Center (NGRREC).  Five presentations are scheduled over the coming months, and the first takes place this week on the University of Illinois campus:

Professor Phil Ashworth
University of Brighton, United Kingdom,
“Why are the World’s Big Rivers so Different?”
Wednesday, October 8, 5pm
University of Illinois at Urbana Champaign,
Digital Computer Lab
(DCL), 1304 West Springfield Avenue
ROOM 1320

NGRREC is a partnership between the University of Illinois at Urbana-Champaign, the Illinois Natural History Survey and Lewis and Clark Community College, and is
“dedicated to the study of great river systems and the communities that use them.”

Posted in Events, INHS, ISAS, ISGS, ISTC, ISWS, Prairie Research Institute | Leave a comment

Preview the New Library Gateway

The University Library is updating its gateway page, and you are invited to preview it.    The new site is more compatible with mobile devices, and offers quick access to a wide range of library resources and services.  From the project team:

“Over the next week, we will be accepting comments and making final changes to the page.  If all goes according to plan, we will enable the page as a replacement for the current gateway on Monday, October 6.”

Posted in INHS, ISAS, ISGS, ISTC, ISWS, Prairie Research Institute, Web sites | 1 Comment

How you can use IDEALS and why you should

ideals-logo_339x70Illinois Digital Environment for Access to Learning and Scholarship (IDEALS) is our institutional repository, which “collects, disseminates, and provides persistent and reliable access to the research and scholarship of faculty, staff, and students at the University of Illinois at Urbana-Champaign.”  IDEALS was initiated in 2004, based upon recommendations from from CITES and the University Library.  The first file deposits were made in September 2005.  There are currently more than 50,000 works in IDEALS.  IDEALS is part of the University Library‘s holistic digital preservation program.

The Prairie Research Institute has a community in IDEALS which holds our in-house publications and reports.  There are currently more than 3,700 works in our growing community, which is one of the largest departmental communities in IDEALS.  There were more than 10,000 downloads of Prairie Research Institute content this month alone.  IDEALS is not just for departments, however.  IDEALS is available for all students, staff, and faculty to use as an archive of their work.  Guidelines for deposit into IDEALS are below, and are presented in detail on the IDEALS website:

  • Work to be deposited should be “wholly or in part produced or sponsored by University of Illinois at Urbana-Champaign faculty, researchers, staff, or students.”
  • Work should be “finished;” that is, you should not intend to edit files once deposited.
  • Work should comply with the IDEALS copyright and intellectual property policy.
  • Files of all types are accepted, but note that certain formats are more amenable to long-term preservation in IDEALS.

Services provided by IDEALS include persistent URLs (handles) for deposited works, long-term preservation of files, high visibility in web searches, full text searching, and download monitoring for deposited works.  Although open sharing of deposited content is recommended, it is permissible to restrict access completely, to specific user groups, or for a specified “embargo” period.

Here are some ways you can use IDEALS, and reasons to do so:

  • Archive your presentations.  You can share your presentation with colleagues immediately and in perpetuity by depositing slides and text into IDEALS.

Why do this?  Some conference or workshop proceedings are never published, or are published only partially or temporarily.  Archiving and sharing from IDEALS insures a permanent home and persistent link for your presentation files.

  • Archive your data.  IDEALS is not limited to text documents only.  You can archive research data as well.  While IDEALS cannot host complex relational databases and user interfaces, it is possible to archive preservation copies of data, along with descriptive and technical metadata to facilitate sharing and re-use.

Why do this?  Many funding agencies now require plans for sharing and long-term preservation of data for the projects they fund.  Depositing your data into IDEALS can satisfy both of these objectives.   Archiving data in IDEALS ensures it will be available to you and other researchers in perpetuity.  Even if your data are constantly updated and rely on a complex interface for user access from your website, IDEALS offers a home for preservation copies of your data as insurance against loss or corruption of locally maintained files.

  • Archive your manuscripts.  Most publishers do not allow authors to post the final published version of their own articles on their websites or networking tools such as ResearchGate (see Can you post your article on your profile?).   Many publishers do, however, allow authors to deposit accepted, post-review, corrected manuscripts into institutional or disciplinary repositories.  You can check publisher policies on institutional repository deposit and other author rights matters in the SHERPA/RoMEO directory, and by carefully reviewing publisher copyright transfer agreements, preferably before signing your rights away.

Why do this?  Depositing  is one way authors can legally provide open access to their work without paying additional fees to the publisher, where the publisher allows it.   The IDEALS record can include a link to the final published version of the article, but the manuscript in IDEALS allows any researcher at any institution to access your work, even if they do not have access to the journal.

  • Link to your work in IDEALS from your online vita or website.  Use IDEALS links to provide access to your work from your own web pages rather than storing files locally.

Why do this?  The IDEALS record has a persistent URL, so you will never need to update the link.   Using the IDEALS infrastructure, which is supported at the campus level, saves local server space and maintenance cost.

  • Request an IDEALS community for your research program. Related works can be gathered into communities and collections, and your librarian can help you with organization and deposit strategies.  Ask your librarian to create a community to gather the work from your research program into one place in IDEALS.

Why do this? Gathering your program output into one community provides a single place for users to access your research, and it allows you to track downloads of all program work in aggregate.

If you are a Prairie Research Institute researcher who would like assistance with IDEALS deposits and making the most of IDEALS, please contact us.

Further reading and resources:

Posted in Data Management, Digital Collections, INHS, ISAS, ISGS, ISTC, ISWS, Open access, Prairie Research Institute, Scholarly publishing, Tools, Uncategorized | Leave a comment