Monday, March 29, 2010

The Nonindigenous Aquatic Species Program Upgrades Web Site

The Nonindigenous Aquatic Species Database (NAS), an NBII partner, now offers species point distribution maps. These maps appear as separate links from any species search and from the top of any species page. The maps depict spatial accuracy of the point and species status at each location. Each one can be modified; for example, the background can be changed and various other spatial layers can be turned on or off. Additional environmental layers are planned for inclusion in the future.


Some examples of interactive nonindigenous species maps that are available from the NAS database:
Silver carp (Hypophthalmichthys molitrix)
Northern Snakehead fish (Channa argus)

(Photo: Silver carp (Hypophthalmichthys molitrix).

Regional Biodiversity Portal Toolkit

 The Pacific Basin Information Node (PBIN) technical staff is participating in the development of a Global Biodiversity Information Facility (GBIF) Nodes Portal Toolkit (NPT). The primary goal of the portal toolkit project is to develop an open-source platform for aggregation and dissemination of regional biodiversity-related content. Content will include but not be limited to species factsheets, observation records, publications, and spatial data.  In December 2009, GBIF Node Managers (including PBIN technical staff) met in Montreal to explore the development of the NPT. The group developed a draft action plan that will be carried out by        representatives from PBIN, the Canadian Biodiversity Information Facility, and the African Biodiversity consortium.  Initial tasks will be to conduct a user requirements document and implement a draft content management system based on the London Natural History Museum ScratchPads biodiversity portal project. A test interface will be demonstrated at the GBIF Nodes meeting in Seoul, Korea, in October 2010.

(Photo: Red-eyed Tree Frog (Agalychnis callidryas), Costa Rica.  Photo by Gregory Basco, 2003.  Courtesy of GBIF)

Friday, March 26, 2010

Pacific Biodiversity Information Forum (PBIF) Species Occurrence Database

When Pacific Biodiversity Information Forum (PBIF) was created in 2003, three of the four top information needs identified by regional representatives involved the creation of regional, sub-regional, and national taxonomic surveys. In support of these goals, PBIF has been working to bring together available species information from around the globe into a consolidated base of data for the Pacific region.  A database has been created that includes nearly 300,000 records.  PBIF staff have been working to digitize written species observations and assign geospatial coordinates to each record.  Click here for access to the database.


(Photo: A Large-billed tern (Phaetusa simplex) taken flight from a post emerging from the floating vegetation. © 2006 Arne J. Lesterhuis, Photo courtesy of life.nbii.gov.

Monday, March 22, 2010

Hawaii Early Detection Network Update

http://pbin.nbii.org/reportapest/pestlist/images/searchimages/wasaur2.jpgThe Hawaii Early Detection Network has conducted invasive species identification workshops with the Pacific Whale Foundation, Maui County road crews in Hana, and the nearly 100 U.S. Department of Agriculture-Animal Plant Health Inspection Service baggage inspectors. This partnership between the Pacific Basin Information Node (PBIN), the Island Invasive Species Committees (ISCs), and the state of Hawaii trains members of the public to become the “eyes and ears” on the watch for new invasive pests. All participants in the workshops learned how to conduct tests for little fire ant (Wasmannia auropunctata), one of the newest invaders of Maui County.  The little fire ant is considered one of the “world’s worst” invaders by the IUCN SSC Invasive Species Specialist Group and has major detrimental environmental and economic impacts on other Pacific islands.  Participants are encouraged to report all suspicious invasive plants and animals to the PBIN invasive species reporting system.

(Photo: Little fire ant (Wasmannia auropunctata); Image: SM Gallagher, AntWeb, hosted by California Academy of Sciences.

Friday, March 19, 2010

Vegetation Characterization Products Now Available for Hagerman Fossil Beds National Monument

USGS-National Park Service (NPS) Vegetation Characterization Program (VCP) documentation for Hagerman Fossil Beds National Monument has been completed and is available on the VCP Web site. Products include aerial photography - graphic of orthophoto mosaic, and spatial orthophoto data; project report - photointerpretation key, vegetation descriptions, vegetation key, photos of map class, and accuracy assessment, and classification of the plant communities report; field data - graphic of field plots, spatial field plots data, plots field database, physical descriptive for plots and species list for plots; geospatial vegetation information - graphics of vegetation communities, spatial vegetation data, spatial boundary data and plots and AA photos; accuracy assessment information - graphic of accuracy assessment points, spatial AA points data, AA field database, and contingency matrix; metadata, and a link to NPS information about Hagerman Fossil Beds National Monument. The goal of the VCP is to classify and map the vegetation communities of National Parks that have a natural resource component. Complete documentation is currently available for sixty-eight park units and two U.S. Fish and Wildlife refuge units. The VCP is managed by the USGS Center for Biological Informatics in cooperation with the NPS Inventory and Monitoring Program. The USGS Vegetation Characterization effort includes the management and upkeep of the VCP protocols, Web-based access to the standards, and the Web-based access to NPS Vegetation Characterization program finished products.

Thursday, March 18, 2010

The Hawaii Weed Risk Assessment Database

The NBII Pacific Basin Information Node (PBIN), under contract with the Hawaii Invasive Species Council (HISC), has completed the development of a database system for the Hawaii - Pacific Weed Risk Assessment (HPWRA).  The HPWRA is a methodology designed to identify high-risk species, facilitating informed decisions that will reduce the economic and ecological harm caused by invasive plants.  Historically, HPWRA data was stored in separate spreadsheets for each of the 800+ species assessed to date. In that form, it was cumbersome to track detailed information and data were difficult to extract for analysis and presentation.
 The new system is based in SQL Server with a Microsoft Access user interface. This model allows the application to be widely distributed in a desktop environment while aggregating data in one central server database. Next steps include the development of a Web site that provides access to HPWRA data to the public.

Photos: Melastoma sanguineum (fox-tongued melastoma) Flower at Keaukaha, Hawaii.; December 05, 2001. Photos by Forest & Kim Starr, HEAR.org

Tuesday, March 16, 2010

"The Very Handy Manual: How to Catch and Identify Bees and Manage a Collection" is Now Available

The latest edition (March, 2010) of "The Very Handy Manual: How to Catch and Identify Bees and Manage a Collection" is now available.

Compiled mainly by Sam Droege at the USGS Native Bee Inventory and Monitoring Lab with input from specialist researchers and taxonomists over several years from 2004-present, this guide provides detailed instructions on bee monitoring techniques including specimen collection, processing and management; bee identification; and more! The manual also provides guidance on the capture, monitoring, identification, and curation of native bees.

The NBII Pollinators Project coordinates and supports pollinator-related biological informatics projects carried out by the National Biological Information Infrastructure (NBII) and its partners, and provides in-kind support to ventures that benefit pollinators by improving pollinator data delivery and access, and developing decision support tools for resource managers.

You can also subscribe to Sam Droege's Youtube channel and learn How to Dry Bee Specimens, one of the handy techniques described in the manual.

Photo: Honeybee and Purple aster (Apis mellifera, Aster sp.) - A honeybee feeds on purple aster flowers.  Photo credit: Elizabeth A. Sellers.

DataONE 2010 Summer Internship Program

The Data Observation Network for Earth (DataONE) is a virtual organization dedicated to providing open, persistent, robust, and secure access to biodiversity, ecology, and environmental data.   DataONE is pleased to announce the availability of summer research internships.  The program is open to all undergraduate students, graduate students, and potsgraduates who have received their masters or doctorate within the past five years. 

Approximately six interns will be accepted this year.  As part of a larger virtual organization, interns will work in virtual groups of 2-3 with multiple mentors from DataONE.  Interns must be at least 18 years of age by May 23, 2010. Interns must be currently enrolled or employed at a university or other research institution and must currently reside in, and be eligible to work in, the United States.  Interns from previous years are eligible to participate. Given the broad range of projects, there are no restrictions on academic backgrounds or field of study.  Interns are expected to be available approximately 40 hours/week during the internship period (noted below) with significant availability during the normal business hours.


Projects

The project description page contains information about proposed projects and mentors.  These cover a range of topic areas including software development, library science, and sociotechnical aspects of scientific data.  These projects vary in the extent and type of technical expertise required.  The interests and expertise of the applicants will determine which projects will be selected for the program.  Please see the current list of projects and the full program announcement to learn more about the program, how to apply, and schedules.

For further information about DataONE, see the website (http://dataone.org).  The architecture documents and SubVersion repository are also publicly accessible.

Monday, March 15, 2010

The NBII Library of Images From the Environment (NBII LIFE) - Accessed by Users Worldwide

The NBII Library of Images From the Environment (NBII LIFE) is a collaborative platform for agencies, organizations, and individual partners to share high quality, authoritative images of our natural world. Subjects cover species, species interactions, landscapes, research, management, and environmental topics. The goal is to manage images as scientific records and ensure they are useful for future research and decision making.

Contributors and images must meet certain criteria, including that the images are available for nonprofit use and that detailed information (e.g., date, location, and context) is attached.

These standards and subject diversity make LIFE a valuable resource – as research and user feedback have confirmed. One type of user we get feedback from are those who contribute images to LIFE; examples include Finding Species, different groups within the U.S. Geological Survey (USGS), and the U.S. National Herbarium, Smithsonian Institution. But who in the broader community is accessing the site, and how do they use the images?

There are limits to what the U.S. government can record about users accessing government Web sites, but we know hundreds of thousands of people viewed millions of pages within the NBII LIFE in 2009, most from U.S. government computers. Globally, an average of 150 countries (out of 203 recorded) also had users entering the library each month. Leading countries include Canada, Great Britain, and India; but small countries such as Liechtenstein and Vatican City also accessed the NBII LIFE Web site.

Many organizations point to the NBII LIFE as a resource, including the U.S. Bureau of Land Management. Other federal sites include the USGS, the U.S. Fish and Wildlife Service (USFWS), and the Library of Congress. The Academy of Natural SciencesVireo Web site includes the LIFE under “Sites Worth Seeing” and Matcha College lists LIFE in an article, “100 Excellent Websites for Exploring the Ocean Online”.


LIFE is also finding that diverse organizations are using
photographs for exhibits, Web sites, publications, and research, including federal agencies such as the USGS (the biggest user), the USFWS, the U.S. Environmental Protection Agency (EPA), the National Institute of Health, the National Aeronautics and Space Administration, the U.S. Department of Agriculture (USDA), and the Smithsonian Institution. Local and state agencies (e.g., New York State’s Department of Environmental Conservation) and nonprofits (e.g., the Defenders of Wildlife) have also used LIFE's images. One research project incorporating LIFE images is the Tree of Life project.


News and information organizations also have used NBII LIFE images to illustrate online articles, including Public Radio International, Encyclopedia Britannica, Wikipedia, the Washington Post, and Science magazine. Also, hundreds of educational sites incorporate LIFE images into their lesson plans: students have used images for book reports and in computer modeling classes. Other users include libraries, museums, botanical gardens, film makers, artists, and bloggers. Users’ interests have been very diverse.

The NBII LIFE's images may soon be used in additional ways. The LIFE team is partnering with the Global Biodiversity Information Facility to make image metadata available to more researchers, especially modelers. Metadata about a photograph of a rare bird at a certain place and time could be fed into models predicting the effects of climate change on species distributions. Schema development is under way.

The LIFE team looks forward to increased use and further feedback, with the Web site’s latest tools online, continuing image uploads, and a new strategic plan to increase capabilities.

Photos from the NBII LIFE: (from top) Cactus (Sempervivum sp., Echeveria sp.) Cactus rosettes fill a garden bed. Photo by © 2008 Elizabeth A. Sellers; U.S. Geological Survey (USGS) hydrologist making a mini-piezometer measurement on the Yakima River to determine if ground-water discharge is occurring in this salmon rearing area. Photo by W. Simmonds; American bullfrog floats among lily pads (Rana catesbeiana). Photo by © 2008 Bruce Avera Hunter (Copyright held by Creator); Blue Ridge Parkway with fall foliage. Photo by Tanya Schoenhoff; Print and online publications using NBII LIFE images; A male scarlet tanager (Piranga olivacea) ready to be released after receiving a metal leg band applied by a wildlife biologist. Photo by © 2009 Elizabeth A. Sellers.

This is a revised version of the article published in the Winter 2010 (Vol. 13, No. 1) issue of the NBII Access Newsletter.

Thursday, March 4, 2010

FGDC Publishes a Fact Sheet on the WDIN Global Wildlife Disease News Map

In September 2009, Technical Manager, Megan Hines, and Node Manager, Jennifer Carlino, of the NBII Wildlife Disease Information Node (WDIN) were interviewed about the WDIN Global Wildlife Disease News Map application by the Federal Geographic Data Committee's (FGDC) Geospatial Line of Business group.

The Disease Map displays recently published media reports in a geographical context allowing users to see where news-worthy wildlife disease events are occurring around the globe. Before disease outbreaks become well-known, they often appear in informal sources, such as the news media. The Map visually organizes these news reports to show the global status of wildlife disease and to help government agencies and the general public stay abreast of ongoing developments. The Map also makes data freely available in compatible formats, which allows anyone to integrate this wildlife disease information with other applications, as seen in HealthMap.

The result of this interview generated a fact sheet on the project,
highlighting the impact the application has had on WDIN internal business, as well as what the application has provided for external users from the general public to other government agencies. The fact sheet was recently made available on the Geospatial Line of Business website.

Links that may be useful:

Vegetation Characterization Products Now Available for Petrified Forest National Park

USGS-National Park Service (NPS) Vegetation Characterization Program (VCP) documentation for Petrified Forest National Park has been completed and is available on the VCP Web site. Products include aerial photography - graphic of orthophoto mosaic, and spatial orthophoto data; project report - photointerpretation key, vegetation descriptions, vegetation key, photos of map class, and accuracy assessment; field data - graphic of field plots, spatial field plots data, field database, physical descriptive for plots and species list for plots; geospatial vegetation information - graphics of vegetation communities, spatial vegetation data, spatial boundary data and plots and AA photos; accuracy assessment information - graphic of accuracy assessment points, spatial AA points data, and contingency matrix; metadata, and a link to NPS information about Petrified Forest National Park. The goal of the VCP is to classify and map the vegetation communities of National Parks that have a natural resource component. Complete documentation is currently available for sixty-seven park units and two U.S. Fish and Wildlife refuge units. The VCP is managed by the USGS Center for Biological Informatics in cooperation with the NPS Inventory and Monitoring Program. The USGS Vegetation Characterization effort includes the management and upkeep of the VCP protocols, Web-based access to the standards, and the Web-based access to NPS Vegetation Characterization program finished products.

Tuesday, March 2, 2010

Critical Habitat: Threatened and Endangered Species of the Edwards Aquifer in the Central Southwest and Gulf Coast

The Edwards Aquifer is a hydrogeologically sensitive Karst aquifer in central Texas that is home to a variety of threatened and endangered species. Degradation of water quality can detrimentally impact species that rely on the aquifer for habitat. For example, the San Marcos Gambusia (Gambusia georgei) is documented to be extremely sensitive to habitat alteration, particularly changes in water turbidity or temperature. Managing changes in surface water and groundwater quantity and quality is critical to the stewardship of these threatened and endangered species. To facilitate management, aquifer managers and the public need information that shows changes through time and is spatially explicit. The newly developed Edwards Aquifer portal gives users information describing surface water quality, groundwater quality, groundwater quantity, surface water quantity, precipitation trends, species information, and critical habitat areas of the threatened and endangered species of the Edwards Aquifer. The portal also allows users to download spatial data for the region.



Image: The Major Aquifers in Texas; map created by the Houston Advanced Research Center.

Bird Monitoring Data Management Paper Published

A paper summarizing results from a bird monitoring data management session led by Bird Conservation Node Manager Elizabeth Martín at the 2008 Fourth International Partners in Flight Conference is now published and available online as part of the Partners in Flight Conference Proceedings. The paper titled “Gathering, Organizing, and Accessing Data for Use in Bird Conservation across the Americas” can be accessed here; it was authored by Ms. Martín and NBII partners’ staff Bruce Peterjohn (USGS Patuxent Wildlife Research Center) and Steve Kelling (Cornell Lab of Ornithology). This paper and session, which identified data management needs for bird monitoring data in North America and provided recommendations for addressing those needs, served as an initial step for some of the bird monitoring data management activities now being undertaken by the U.S. Monitoring Subcommittee of the North American Bird Conservation Initiative (NABCI).

Monday, March 1, 2010

NBII Wildlife Disease Information Node Presents Activities at USGS and NOAA Seminars

Dr. Joshua Dein, NBII Wildlife Disease Information Node (WDIN) Project Leader, and Megan Hines, WDIN Technical Manager, will make presentations on WDIN projects and products next week. On March 4, at 12 noon, at the USGS Headquarters in Reston, they will present, "Promoting Access to Wildlife Disease Data and Information." This presentation will also be available through WebEx. It will also be a seminar on March 3 at the NOAA National Marine Fisheries Service, Office of Protected Resources in Silver Spring, MD.

Vegetation Characterization Products Now Available for Indiana Dunes National Lakeshore

USGS-National Park Service (NPS) Vegetation Characterization Program (VCP) documentation for Indiana Dunes National Lakeshore has been completed and is available on the VCP Web site. Products include aerial photography - graphic of orthophoto mosaic, spatial orthophoto data, and flightline index; project report - photointerpretation key, vegetation descriptions, vegetation key, photos of map class, and accuracy assessment; field data - graphic of field plots, field database, physical descriptive for plots and species list for plots; geospatial vegetation information - graphic of vegetation communities and geodatabase; accuracy assessment information - graphic of accuracy assessment points, and contingency matrix; metadata, and a link to National Park Service Information about Indiana Dunes. The goal of the VCP is to classify and map the vegetation communities of National Parks that have a natural resource component. Complete documentation is currently available for sixty-six park units and two U.S. Fish and Wildlife refuge units. The VCP is managed by the USGS Center for Biological Informatics in cooperation with the NPS Inventory and Monitoring Program. The USGS Vegetation Characterization effort includes the management and upkeep of the VCP protocols, Web-based access to the standards, and the Web-based access to NPS Vegetation Characterization program finished products.

Vegetation Characterization Products Now Available for Craters of the Moon National Monument

USGS-National Park Service (NPS) Vegetation Characterization Program (VCP) documentation for Craters of the Moon National Monument has been completed and is available on the VCP Web site. Products include aerial photography - graphic of orthophoto mosaic, and spatial orthophoto data; project report - photointerpretation key, vegetation descriptions, vegetation key, photos of map class, and accuracy assessment; field data - graphic of field plots, spatial field plots data, field database, physical descriptive for plots and species list for plots; geospatial vegetation information - graphic of vegetation communities, and geodatabase; accuracy assessment information - graphic of accuracy assessment points, spatial AA points data, and contingency matrix; metadata, and a link to National Park Service about Craters of the Moon. The goal of the VCP is to classify and map the vegetation communities of National Parks that have a natural resource component. Complete documentation is currently available for sixty-five park units and two U.S. Fish and Wildlife refuge units. The VCP is managed by the USGS Center for Biological Informatics in cooperation with the NPS Inventory and Monitoring Program. The USGS Vegetation Characterization effort includes the management and upkeep of the VCP protocols, Web-based access to the standards, and the Web-based access to NPS Vegetation Characterization program finished products.