USGS Center for Biological Informatics Monthly Report
March 1999

This summary provides, both graphically and narratively, selected highlights and accomplishments of the USGS Center for Biological Informatics (CBI) during March 1999. Accomplishments are categorized according to the CBI Strategic Plan goals and objectives (under review) they support. More detailed information appears in the CBI Weekly Highlights (http://biology.usgs.gov/cbi/about/hi-lights/) and in the attachments to this report.

Goal 1: Applying science information to conservation and management

Major Accomplishments

• CBI scientist Tom Owens was invited to a March 4 meeting sponsored by the U.S. Army Corps of Engineers (USACE) to demonstrate a Web-based tool that facilitates classification of vegetation communities. The system will be implemented at Fort Hood, Texas, and will also serve as a prototype for vegetation classification at other military bases. Owens, with other Federal and NGO scientists, provided comments and feedback on the design and implementation of the Web tool and classification of Fort Hood's vegetation communities. The USACE is planning to use the U.S. National Vegetation Classification Standard (NVCS) for vegetation community classification on military bases. The NVCS is the Federal Geographic Data Committee standard for classifying vegetation communities; CBI is implementing the NVCS in the USGS-NPS Vegetation Mapping Program.
  
• On March 10-12, CBI sponsored a scoping meeting in Flagstaff, Arizona, to plan for the vegetation mapping and classification of Sunset Crater, Wupatki, and Walnut Canyon National Monuments. Participants from the USGS Biological Resources Division (BRD), the National Park Service (NPS), The Nature Conservancy, and the Bureau of Reclamation discussed issues relating to the assessment of specific park needs and the organization and implementation of the USGS-NPS Vegetation Mapping Program at these three monuments. Possible applications of data developed by the Program include fire management, monitoring of rare plants and communities, and creation of an invasive plant inventory. CBI provides management oversight and scientific guidance to the program.
  
• On March 10-17, representatives from the Office of Biological Informatics and Outreach, CBI, and the University of Kansas Natural History Museum and Biodiversity Research Center met to discuss possible cooperative ventures related to the Gap Analysis Program (GAP)and the National Biological Information Infrastructure (NBII). Attendees agreed to cooperate on developing information tools, expertise, and support and sharing of data to test data analysis applications and compare species distribution models.
  
• On March 16-18, the BRD Geospatial Technology Coordinating Group (GTCG) held their semi-annual meeting at the USGS Florida Caribbean Science Center in Gainesville. GTCG members represent BRD science centers and CBI. Ralph Root, Maury Nyquist, and Jim Getter attended for CBI. Root provided information on decision support systems and Nyquist presented an overview of the Aurora Partnership. BRD Geospatial Technology Program manager Getter led discussions on the Global Fiducial Program, the National Technical Means program, and security clearance issues. In addition to discussing other topics, the GTCG planned for the upcoming BioGeo 99 symposium to be held at the USGS National Wetlands Research Center in November. To find out who the GTCG representatives are, and more about the Geospatial Technology Program, visit the Web pages at <http://biology.usgs.gov/geotech/>.
  
• CBI scientist Ralph Root continued work with a team of scientists exploring the potential for detecting and mapping leafy spurge at Theodore Roosevelt National Park. Root was asked by NASA to help evaluate the use of a low altitude platform for NASA's Airborne Visible and Infrared Imaging Spectrometer (AVIRIS). Airborne spectrometer data collected from this low altitude (Twin Otter at 12,500 feet) version of AVIRIS are of much higher spatial resolution (3-m pixel size) than the nominal AVIRIS data collected from its usual U-2 high altitude aircraft, which flies above 60,000 feet (20-m pixel size). Early indications from a low altitude test flight over the park show that data are spectrally comparable to those collected at higher altitudes but have spatial resolution nearly two orders of magnitude greater. More information and "quicklook" images from low altitude AVIRIS can be viewed on NASA's AVIRIS Web site at <http://makalu.jpl.nasa.gov/>.
  
• On March 17-19 the initial workshop for new GAP state projects and their cooperators was presented in Honolulu. Hawaii is the 49^th state to initiate a statewide GAP project. The project will be conducted by the Hawaii Ecosystem Data Group, a partnership of conservation organizations that includes the U.S. Fish and Wildlife Service, The Nature Conservancy of Hawaii, the USGS Biological Resources Division, the University of Hawaii's Center for Conservation Research and Training, the State of Hawaii's Department of Land and Natural Resources, and the Hawaii Ecosystems at Risk program. Other cooperators include the National Park Service, the National Resources Conservation Service, the Office of Hawaiian Affairs, and the Bishop Museum. GAP is coordinated by the USGS and is managed by CBI.
  
• The long-awaited 1998 issue of the GAP Bulletin was mailed out the week of March 22. The Bulletin features 17 articles and 9 notes on various aspects of GAP methods and results. Topics include decision support systems, vegetation mapping, aquatic GAP, analysis for plant and ant species, application to land use planning, vertebrate species distributions, establishing partnerships, and GAP in Mexico. Updates on the status of each GAP state project are also included. The Bulletin is also posted on the GAP home page (www.gap.uidaho.edu/).
  

Goal 2: Managing and distributing biological resource data and information

Major Accomplishments

• BRD Web pages <biology.usgs.gov> received 1,057,138 accesses (includes image and audio files). See Report for Selected BRD Web Sites <http://biology.usgs.gov/cbi/about/monthly/1999/stats/Mar_1999.html>.
  
• Fifty-nine queries were received through <biologywebteam@usgs.gov>, which were answered directly or through expert sources (see attached Outreach Report).
  
• CBI staff provided 112 instances of technical assistance to other divisions, science centers, co-ops, DOI bureaus, and others (see attached Technical Assistance Report).
  
• The number of messages processed through the Biological Resources Division (BRD) cc:Mail hub in March was 280,647, which is 11% more than one year ago. The number of megabytes processed through the BRD cc:Mail hub in March was 5,865, which is 75% more than one year ago.
  
• On March 2, Peter Strong of CBI represented the BRD at a meeting of the Remote Access Team in Reston. The team is developing a plan to provide dial-up access to USGS computer resources for all USGS employees.
  
• On March 1-5, John Clark of CBI represented the BRD on the Lotus Implementation Group. The team met with Notes design engineers to begin the process of designing the next USGS messaging and collaborative system. The first priority is designing a common Division-wide electronic mail system.
  
• On March 2-4, Sharon Shin of CBI and Jennifer Gaines of the Office of Biological Informatics and Outreach presented an NBII Metadata Workshop in Sacramento, California, hosted by William Perry of the USGS Western Fisheries Research Center. On March 16-17, they conducted another NBII Metadata Workshop in Fort Collins, Colorado, hosted by the USGS Midcontinent Ecological Science Center.
  

Goal 3: Applying information science to biological resources

Major Accomplishments
 

• On March 3, in follow-on to two visits made to the University of Colorado by CBI staff, University of Colorado-Boulder Associate Professor Barbara Buttenfield and one of her graduate students visited CBI. Discussions centered on USGS-NPS Vegetation Mapping Program and USGS Gap Analysis Program datasets, and the possibility of analyzing them as part of a master's thesis. Datasets for Voyageurs National Park were proposed as a good first candidate for the project.
  
• On March 16-17, Anne Frondorf (NBII, Reston) and Gary Waggoner (NBII, Denver) hosted a workshop at CBI in Denver for 11 scientists conducting research in biodiversity and biological informatics. The attendees were recipients of three-year grants funded by the NBII and the National Science Foundation. The purpose of the workshop was to familiarize these university scientists with the NBII and selected activities that directly relate to their individual research interests. Waggoner provided a presentation on the Integrated Taxonomic Information System--ITIS--and the Taxonomic Resources and Expertise Directory--TRED. CBI's Susan Stitt spoke on NBII metadata and Clearinghouse activities and Mike Frame presented an overview and demonstration of selected NBII biological data discovery tools and approaches being developed at CBI. Each of the scientists also made presentations on their particular research projects and expressed interest in helping to further the development of the NBII.
  
• With support from the USGS Patuxent Wildlife Research Center (PWRC) and the USGS Northern Prairie Wildlife Research Center (NPWRC), a prototype species locator system is being created by CBI staff. The system will allow NBII users to seamlessly access species information through a "single" portal or access method, eliminating the need for the user to know the specific site where the information may exist. The effort to date has focused on use of existing metadata at the various sites. CBI has established a partnership agreement with Hiawatha Island Software to use their TagGen Metadata Solutions product to facilitate this effort. CBI and PWRC staff worked together to generate the required metatags to improve Internet access to their information and also to improve NBII search and retrieval of this information. A similar effort is currently under way with NPWRC. After the necessary meta information is complete at all of the various locations, a working model or prototype will be developed for demonstration purposes.
  

USGS Center for Biological Informatics
March 1999

Outreach

The following table summarizes responses to outreach queries primarily made through the BRD Home Page <biologywebteam@usgs.gov>. Responses have been provided directly or through expert sources.

Total = 59

• We received 8 complimentary or thank-you notes.
• Assistance in responding was provided by expert sources in NMD, WRD; ABSC, CERC, FCSC, FRESC, MESC, NPWRC, NWRC, UMESC.
  

Technical Assistance

The following table summarizes technical assistance provided by CBI staff. Includes metadata, NBII, Internet, SIS, E-mail, system/network administration, and publications help.

Total = 251

Includes assistance provided to:

• All BRD science centers and several field stations, all USGS divisions
• USFWS, BOR, MMS, NPS, IOS, BIA
• Wisconsin State DNR, Nebraska Natural Resources Commission, State of Montana, Connecticut River Museum, EDAC in New Mexico
• The Nature Conservancy
• University of Washington, Dartmouth
• NOAA, COMSEC, Coast Guard, NASA, GAO, FGDC