Showing posts with label Biodiversity. Show all posts
Showing posts with label Biodiversity. Show all posts

Monday, January 31, 2011

Using Interactive Biodiversity Information System (IBIS) Data in Decision Making

The Northwest Habitat Institute used their Habitat Value System called Combined Habitat Assessment Protocols (CHAP) to resolve a 25-year old issue regarding the loss of wildlife-habitat caused by the construction and operation of Willamette River basin dams.  CHAP works in conjunction with the IBIS data sets, which are supported by the USGS National Biological Information Infrastructure Program (NBII). The mitigation for these losses is called for in the Northwest Power Act of 1980. An initial Settlement Agreement for $103 million was reached by the Bonneville Power Administration with the State of Oregon. These impoundments inundated 17,791 acres and using CHAP findings the Settlement Agreement calls for 26,537 acres. The CHAP approach gives Bonneville Power Administration and the State of Oregon a scientific rationale that is being explained to the public to justify the acreage amounts.

(Photo: Logo from the Northwest Habitat Institute web site)

Wednesday, October 20, 2010

The Inter-American Biodiversity Information Network and Nature Conservancy Debut New Online Ecosystem Assessment Tool

The Nature Conservancy (TNC) and the Inter-American Biodiversity Information Network (IABIN) recently launched the Ecosystem Analysis and Reporting (EAR) tool to visualize ecosystem status and threats in the Americas. The tool is available in both browser-based and ARC desktop-based formats (with English and Spanish user manuals).    The design and development of the tool was executed by TNC’s Caribbean Science Program, working closely with the Department of Geography and Geology at the University of Southern Mississippi.

This tool builds on the information made available through IABIN’s Ecosystems and Protected Areas Thematic Networks by providing conservation decision makers with products for assessing the extent of ecosystems under effective conservation, and offering direction on where to work and what actions may be needed to improve biodiversity conservation.

The tool currently includes data from two pilot regions: the Mesoamerican Reef (in Belize and the Yucatan Peninsula) and the Northern Andes of Colombia, Peru, and Ecuador. TNC led a presentation and workshop utilizing the tool at the Society for Conservation GIS meeting in Monterey, CA, in July and will also present the tool at upcoming IABIN meetings.

This tool is the first in a series of five planned “value-added products for decision makers” that IABIN is developing with funds from the Global Environment Facility (GEF). Future tools will integrate additional types of data IABIN has digitized and made available through its GEF project and related activities. The tools will make this data available in more user-friendly and interactive formats, and will also allow select conservation-focused analyses to be performed utilizing this data. For further information, please contact Ben Wheeler at .

Photo: Tripod Fire, Washington State. Photograph by Philip Higuera, National Parks Ecological Research.)

Tuesday, July 6, 2010

NBII Presents Resources of a Botanical Nature at Botanical Society of America Annual Meeting

 to view larger: American skunkcabbage (Lysichiton americanus) The NBII will be well-represented at this year’s Botanical Society of America Annual Meeting, and United States Virtual Herbarium Workshop, August 1-4, 2010 in Providence, Rhode Island. Ms. Elizabeth Sellers (Manager, NBII Botany Project) and Mr. Giri Palanisamy (Oak Ridge National Laboratory, an NBII partner) will represent the NBII at these meetings as members of the USVH Steering Committee and USVH Communications Infrastructure Task Force. In addition to staffing the NBII Exhibit, Ms. Sellers will present a Task Force report at the USVH Annual Meeting, including an overview of the new USVH Web site, hosted by the University of Tennessee SunSITE and developed with help from Mr. Palanisamy and other Task Force members. Mr. Palanisamy will also represent the NBII’s role as the U.S. Node to the Global Biodiversity Information Facility (GBIF) by providing his expertise on the Integrated Publishing Toolkit developed by GBIF.

Ms. Jennifer Carlino (Manager, NBII California, Pacific Northwest, and Mountain Prairie Information Nodes) and Ms. Marcia NcNiff (Manager, NBII Northeast Information Node) will also attend the meetings, representing the NBII’s contributions and participation in several of the regional herbarium and collection networks associated with the USVH project. And Dr. Gerald Guala will represent the NBII-hosted Integrated Taxonomic Information System (ITIS) at the meetings, the standard for taxonomy for NBII and numerous other Federal and non-Federal data systems. Plant specimens represent a valuable scientific resource that can help provide key information for addressing national issues such as climate change, land use effects, and invasive species. But access to these collections varies dramatically. The USVH project is the primary project of an alliance of U.S. herbaria, regional herbarium networks, universities, and other organizations and individuals to digitize and increase access to all botanical specimens held in U.S. herbaria. As a nationally recognized authority on bioinformatics, the NBII will provide expertise on biological data hosting, publishing and standards, and help guide the continued progress of the USVH project.

(Photo: Yellow flower of the American skunkcabbage (Lysichiton americanus).  Photo by © 2007 Ted Niehaus/NBII LIFE. Note: The Creator has granted the Source the authority to distribute the images: images may be used for any nonprofit purposes. Contact the Source to request a copy of the archival master, or for any commercial uses).

Southern Appalachian Information Node (SAIN) Assessment

Click to view larger: Wild crane's-bill (Geranium maculatum)Dr. Miriam Davis and Ms. Amber Conger were lead authors for two posters featuring SAIN that were presented at the University of Tennessee's (UT) 2010 College of Communication and Information Research Symposium, "Communication and Information in a Digital Age." The posters were co-authored by UT School of Information Science faculty, including Dr. Carol Tenopir, Dr. Vandana Singh, Dr. Suzie Allard, and Dr. Lorraine Normore. "Increasing Biodiversity Information Sources for the Southern Appalachian Information Node: Developing a Matrix for Environmental Decision-Making" presented a matrix identifying environmental decision makers in the Southeast, a key audience for SAIN information, which can be used at multiple levels of granularity. "Evaluating Usage of the Southern Appalachian Information Node: A Baseline Assessment" found that the NBII and SAIN staff are actively promoting SAIN to relevant scientific communities, and other scientists and unaffiliated organizations frequently point to SAIN as a resource of value.

(Photo: Purple Wild crane's-bill (Geranium maculatum) flowers beside a hiking trail in an eastern Appalachian forest.© 2009 Elizabeth A. Sellers, Courtesy of

Wednesday, June 30, 2010

NBII Participates in 2010 Jamaica Bay BioBlitz

The 2010 Jamaica Bay BioBlitz, which was held on June 11th and 12th at the Floyd Bennett Field and adjacent areas including Plumb Beach and Dead Horse Bay, attracted hundreds of scientists and amateur naturalists. NBII’s Ricardo McClees-Funinan took part in the 24-hour marathon to catalog the biodiversity of the area and shared some of his photos with us.  Visit the NBII Facebook Fan page for images from the Jamaica Bay 2010 BioBlitz.

The Jamaica Bay Research and Management Information Network (JBRMIN), hosted by the National Biological Information Infrastructure (NBII)'s Northeast Information Node (NIN) at the Center for International Earth Science Information Network (CIESIN), is the official Web site of the 2010 BioBlitz.  You can also follow the National Park Service (NPS) on Twitter at

(Photo: milkweed (Asclepias sp.) along trail leading towards Dead Horse bay.  Photo by Ricardo McClees-Funinan)

Monday, May 24, 2010

NBII to Help Fund Vertnet Project

The February 2010 edition of PLoS Biology featured an article on "Vertnet: A New Model for Biodiversity Data Sharing."  The VertNet project is being developed as a result of the work by many in the scientific community to increase our understanding of the Earth’s biodiversity and the ongoing threats to its survival. Meeting this challenge has emerged as a global priority. The community of vertebrate natural history collections has begun to play its role in solving this challenge by establishing social and technological infrastructures that provide open access to species occurrence data. The PLoS article mentions that the NBII is helping to fund this work through establishing a programmer position to offer network support to meet the growing demands on the systems under development.

This is a revised version of the article published in the Spring 2010 (Vol. 13, No. 2) issue of the NBII Access Newsletter.

Wednesday, April 21, 2010

WDIN Attends Biodiversity Information Standards (TDWG) Annual Conference

Dr. Joshua Dein, Project Leader for the NBII Wildlife Disease Information Node (WDIN), attended the TDWG Annual Conference in Montpellier, France, November 9-13, 2009.   Dr. Dein worked with the NBII Program Office to develop presentation and discussion sessions to explore the potential overlap between biodiversity and health informatics and how they can be used to ensure that environmental and species data can be easily integrated into emerging disease surveillance systems.

(Photo: Sandpiper (Actitis hypoleucos), by Robert E. Gill, Jr., USGS.  Photo from the Wildlife Disease Information Node's HEDDS page)

Monday, March 29, 2010

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

Thursday, January 28, 2010

New One-Stop Source for Scientific Information about U.S. Oceans and Waters

A one-stop source for biogeographic information collected from U.S. waters and oceanic regions is now available from the National Biological Information Infrastructure (NBII) Program OBIS-USA website offers a unique combination of tools, resources, and biodiversity information to aide scientists, resource managers and decision makers in the research and analyses critical to sustaining the nation’s valued marine ecosystems.
OBIS-USA was established in 2006 in cooperation with the U.S. National Committee for the Census of Marine Life a committee composed of renowned marine community leaders. OBIS-USA – a partnership of state, federal and scientific organizations -- is the United States’ contribution to the International Ocean Biogeographic Information System, an effort led by the Census of Marine Life to provide “open access” to global biodiversity data on the myriad of marine life that inhabits the ocean.
“The world’s ocean is critically important, not only because of how it influences the climate, but also because it provides the resources for commercial, recreational, cultural, scientific, conservation, and national security activities,” said John Mosesso, OBIS-USA co-lead. “At the same time, the ocean is threatened by a variety of changes, including warming temperatures, increasing ocean acidity, invasion by non-native species, overharvesting, and loss of habitat for species of concern.”
OBIS-USA provides data and functional tools to address key questions and information needs related to scientific understanding of sustainable and resilient ecosystems, marine spatial planning, climate change, ocean acidification, invasive species, and managing the nation’s fisheries. To address these ocean threats requires access to critical information on marine biodiversity, Mosesso noted.
OBIS-USA data holdings comprise millions of individual records supplied by marine data sponsors from across the nation. The site provides a work space for visitors to search and manipulate that data. This is accomplished in collaboration with data providers to produce a compilation of data in a common format. Data are interoperable and can be consistently viewed and applied by researchers, decision makers and resource managers.
Users can search and download data and metadata describing when and where species were observed or collected. The site’s offerings are available through an atlas (where users can review and select specific data sets). Individual or composite data sets (user-created selections from the entire holdings) may be viewed through several functions, including:

  • data dashboard - provides a pictorial view of data attributes that lets users assess their utility;
  • data richness - assesses how well the data are populated for selected elements;
  • data quality - provides key data collection information;
  • duplication status - indicates if a data set may contain duplicate records;
  • general metadata – displays the Federal Geographic Data Committee data record;
  • geographic coverage – displays data collection sites spatially;
  • participants - names OBIS-USA participants, with the option to connect back to the atlas, dashboard, and metadata functions; and
  • taxonomic depth - table shows the levels of taxonomic hierarchy for each organism.
OBIS-USA goals this year include an increase to over 10 million total data records and expanded functionality to address needs such as integration with non-biological data and further capability regarding species distributions.
To learn more about OBIS-USA, including growing its list of data and exploring partnerships, contact the NBII’s Mark Fornwall or John Mosesso.
Coordinated by the U.S. Geological Survey, the NBII is a broad, collaborative program to provide increased access to data and information on the nation's biological resources.

(Photos: Sea angel (Clione limacina), the most common shell-less pteropod of arctic waters. Courtesy of the census of Marine Life Arctic Ocean Diversity project, © Kevin Raskoff. (Full size image)
Nardoa rosea sea star as seen from the underside. Photographed during Census of Coral Reef Ecosystems (CReefs) research, Heron Island, Australia. Gary Cranitch © 2008. (Full size image)

Tuesday, December 15, 2009

NBII's Regional Partnerships in Support of Biodiversity Inventory in the Great Smoky Mountains

On December 10-12, 2009 the All Taxa Biodiversity Inventory (ATBI) held its annual meeting in Gatlinburg, Tennessee. This regular end of the year event brings together “scientists, volunteers, and general public to hear about year's field work results, and to celebrate our living natural resources in the Great Smoky Mountains National Park”.

Scientists and staff of the Great Smoky Mountains National Park (GSMNP) have teamed with the not-for-profit group Discover Life in America (DLIA) to coordinate the inventory of an estimated 100,000 species living in the park. The NBII's Southern Appalachian Information Node (SAIN) is working with the GSMNP and DLIA to help define and implement ways to disseminate the many types of data being collected, analyzed, and summarized. SAIN is providing web page hosting, development and design, as well as database assistance and coordination with other inventory & monitoring projects to ensure that users are able to interact effectively with the data and information provided.

ATBI started at the Big Thicket National Preserve, an area of rich biodiversity and the first preserve in the National Park System. The Natural Resources Department of the Big Thicket National Preserve has a wealth of biological data. Most of the data have geographic identifiers but are decentralized or are not in their correct geographic projection. Staff of the NBII Central Southwest Gulf Coast Information Node (CSWGCIN) worked with the Big Thicket to gather the various data sets describing the preserve and to organize the data into a logical structure, filling data gaps where applicable.

(Photo: Winter - Snowy Stream at the Great Smokey Mountains National Park. Photo courtesy

Friday, December 11, 2009

GBIF Integrated Publishing Toolkit for Helpdesk Experts

The United States National Biological Information Infrastructure (NBII) program, in collaboration with the Global Biodiversity Information Facility (GBIF), has developed and is supporting an Integrated Publishing Toolkit (IPT) to facilitate access, discovery, and use of collections and observational data. A new training CD on the GBIF IPT has recently been published. This CD, based on materials from the Helpdesk Experts Workshop on the GBIF IPT , is a compilation of presentations, promotional materials, technical documents, videos, and online resources. The Helpdesk Experts Workshop was designed to:
"provide a selected group of technically capable people with extensive knowledge on the GBIF IPT so they can get more involved in the development and deployment of the tool, acting as a distributed helpdesk network for the benefit of their communities and regions."
The CD may be obtained by visiting the GBIF Training CDs page and clicking the link. The CDs are available in .ISO format and it is suggested on the Web site to use the image burning feature of your CD burning software to convert them into actual CDs.

About the GBIF IPT (from the IPT Web site):

"The GBIF Integrated Publishing Toolkit (IPT) is an open source, Java (TM) based web application that connects and serves three types of biodiversity data: taxon primary occurrence data, taxon checklists, and general resource metadata. The data registered in a GBIF IPT instance is connected to the GBIF distributed network and made available for public consultation and use. This tool is made freely available for both those who wish to use it to publish their data and those who wish to participate in its development, documentation, and helpdesk."

To learn more about GBIF and NBII collaborations, please visit the NBII GBIF network Web site.

Thursday, November 19, 2009

Pacific Biodiversity Information Forum (PBIF) Highlights Updates to the Pacific Protected Areas Database

Created in 2003, the Pacific Protected Areas Database (PPAD) is a work in progress to document protected areas in the Pacific islands region of Oceania (Micronesia, Melanesia, and Polynesia). Final data for the Federated States of Micronesia (FSM) and Kiribati are being added. FSM and Kiribati complete the Micronesian section of the database. Additionally, a new online interface has been developed and is now live. Visit the website at at

(Photo: from the PBIF website. PBIF's geographic scope includes the countries of Polynesia, Micronesia and Melanesia, as well as the Australasian countries bordering these regions.)

Tuesday, September 22, 2009

California Partners in Flight Study Areas Database Now Hosted by Point Reyes Bird Observatory (PRBO)

In collaboration with the University of California (UC)-Davis through the California Information Node (CAIN), the California Partners in Flight (CalPIF) Study Areas Database provides bird monitoring sites and serves as a repository for species breeding status information for the entire state. The database provides an interactive map that shows all CalPIF collaborators’ study areas contributed to date, an interactive focal species breeding status map that show all study areas and detailed information for each focal species, and habitat maps for California. Originally launched in 2005 in collaboration with UC-Davis and Point Reyes Bird Observatory (PRBO) as part of CAIN, the database has moved to PRBO for long-term maintenance and hosting.

(Image: screen shot of the California Partners in Flight Study Areas Database)