Strategic Plan for the

U.S. Geological Survey

Biological Informatics Program

2005-2009

U.S. Department of the Interior

U.S. Geological Survey

Strategic Plan for the U.S. Geological Survey

Biological Informatics Program: 2005-2009

By Michael Ruggiero, Marcia McNiff, Annette Olson, and Ben Wheeler

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

Gale A. Norton, Secretary

U.S. Geological Survey

P. Patrick Leahy, Acting Director

U.S. Geological Survey, Reston, VA: 2005

Suggested citation:

Ruggiero, Michael, Marcia McNiff, Annette Olson, and Ben Wheeler. 2005. Strategic

 Plan for the U.S. Geological Survey Biological Informatics Program: 2005-2009.

 U.S. Geological Survey, Biological Resources Discipline, 20 pp.

Photo on front and back covers by John J. Mosesso/NBII
EXECUTIVE SUMMARY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

BIOLOGICAL INFORMATICS: THE INTEGRATION OF INFORMATION FROM GENOMES 

TO BIOMES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3

The Call for Biological Informatics 

Challenges

BIOLOGICAL INFORMATICS IN THE ORGANIZATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4

Department of the Interior 

U.S. Geological Survey

Biological Informatics Program

 Added Value of Integration

 Partnerships

THE ROAD AHEAD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .12

Goal 1: Increase the availability and usefulness of biological resources data and 

 information (Content)

Goal 2: Implement technologies and tools to integrate, analyze, visualize, and apply 

 biological information to natural resource issues (Tools)

Goal 3: Develop, apply, and promote the adoption of standard practices, protocols, 

 and techniques to enhance knowledge discovery and retrieval from various 

 resources (Infrastructure)

Goal 4: Facilitate information science and technology research that supports the 

 advancement of biological informatics capabilities (Research)

Goal 5: Apply innovative technologies and best practices to improve the development,

 description, and dissemination of biological information to customers 

 (User Services)

IMPLEMENTATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13

Table 1: Strategies, Outcomes, and Measurements Necessary to Meet the Biological 

Informatics Program Mission, Goals, and Objectives

APPENDIX 1 Biological Informatics Program Subjects of Particular Interest . . . . . . . . . . . . . . . .19

APPENDIX 2 List of Abbreviations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20

CONTENTS
Acknowledgments

We want to thank all of those who have contributed to the production of this plan. We would especially 

like to thank the following people for their valuable comments and contributions: Gladys Cotter, 

Frank D’Erchia, Mike Frame, Tony Frank, Sharon Gross, Tom Gunther, John Hill, Lief Horwitz, Kate Kase, 

John Mosesso, Doug Muchoney, and Phaedra Ponds.

Finally, we acknowledge Ron Sepic and Michelle Davis of the NBII National Program Office who handled, 

respectively, the editing and design of this publication and who oversaw its production.
1

Biological resources, from the genetic information 

within organisms to the life-sustaining services 

provided by ecosystems, are vital to human well-being. 

In order for researchers, resource managers, decisionmakers, and interested citizens to understand these 

resources and assure their maintenance, it is important 

that the capacity exists for accessing, sharing, and 

utilizing pertinent data and information. The Biological 

Informatics Program is building this capacity in support 

of the Serving Communities mission area of the U.S. 

Department of the Interior (DOI) Strategic Plan. 

The mission of the U.S. Geological Survey (USGS) 

Biological Informatics Program is to create the 

informatics framework, provide the scientific content, 

and develop the public and private partnerships needed 

for the understanding and stewardship of our Nation’s 

biological resources. This mission is achieved through 

the following goals:

• Increase the availability and usefulness of 

biological resources data and information 

(Content),

• Implement technologies and tools to integrate, 

analyze, visualize, and apply biological 

information to natural resource issues (Tools),

• Develop, apply, and promote the adoption of 

standard practices, protocols, and techniques to 

enhance knowledge discovery and retrieval from 

various resources (Infrastructure),

• Facilitate information science and technology 

research that supports the advancement of 

biological informatics capabilities (Research), and

• Apply innovative technologies and best practices 

to improve the development, description, and 

dissemination of biological information to 

customers (User Services).

Governments and institutions are calling for the 

collection of and access to a wide variety of critical 

information about our biological resources. This spans 

information on species, habitats, and ecosystems, 

and also includes impacts of human activities, best 

practices for management, and more. The following 

core integrated components of the Biological 

Informatics Program have been created to design, 

develop, implement, and update the capabilities needed 

to accommodate its mission:

 Gap Analysis Program (GAP): provides State, 

regional, and national conservation assessments 

of native vertebrate species and natural land cover 

types.

 Vegetation Characterization Program (VEG): 

characterizes vegetation on public lands using a 

consistent methodology supported by national 

standards. 

 National Biological Information Infrastructure 

(NBII): implements a fully digital, interactive, 

distributed system that provides access to 

scientifically reliable natural science data and 

information.

 Integrated Taxonomic Information System (ITIS): 

provides an authoritative source of species names and 

their hierarchical classification.

 USGS Science Center-Based Informatics Projects: 

supports USGS Science Center-based knowledgesharing projects, planned for and executed at the 

Center level, that address Center priorities.

Strategic direction is set through consultation with 

Program stakeholders, partners, and customers 

throughout Federal, State, tribal, and local 

governments; non-governmental organizations; 

academic institutions; the private sector; and the 

global community. Progress toward these goals will be 

measured by means of a set of indicators that express 

the extent of the biological resources knowledge base 

made accessible through Program activities.

EXECUTIVE SUMMARY

1

Photo credit: John J. Mosesso/NBII
2

Information on swamp sparrows 

(Melospiza georgiana),

juvenile shown here, and 

many other North American 

birds is available through the 

NBII Bird Conservation Node 

<http://birdcon.nbii.gov/> and 

the Gap Analysis Program 

<http://gapanalysis.nbii.gov>.

Photo credit: John and Karen Hollingsworth/U.S. Fish and Wildlife Service
3

A diverse environment underpins human survival, health, 

and the economy. Similarly, changes caused by human 

and natural forces can have large ramifications. In order 

for researchers, resource managers, decision-makers, and 

interested citizens to further understand and maintain the 

environment and its multitude of biological resources, it 

is important that the capacity be improved for accessing, 

sharing, and utilizing the biological data and information 

resulting from research. Biological data and information, 

however, vary in format and content: they may pertain to 

genetics or other characteristics of a particular species, 

or they may pertain to an entire ecosystem. They 

can contain land-use characteristics, or geospatiallyreferenced information. Biological informatics, or 

bioinformatics, seeks to integrate these diverse data and 

information in order to enhance our knowledge of our 

environment, from genomes to biomes. 

The term bioinformatics includes the collecting and 

linking, storage, organization, integration, analysis 

and synthesis, delivery, and application of biological 

data and information. By applying information science 

and technology, as well as scientific principles, 

bioinformatics provides new gateways into vast, 

accessible warehouses of information. 

The Call for Biological Informatics

Biological informatics is rapidly growing in response 

to increasing needs by users and by the capabilities of 

technology. Researchers are asking both broader and 

more fine-tuned questions, examining the influence 

of numerous potential factors at multiple points along 

continuous temporal and spatial scales, often requiring 

access to diverse data from other sources. In response 

to ecological problems such as unsustainable resource 

use and invasive species, resource managers and 

decision-makers, from local to global, are calling for 

organizations to not only collect and organize as much 

biological information as possible, but to understand, 

model, and forecast environmental conditions. Finally, 

students and the general public are seeking increased 

access to both raw data and to compiled information 

and knowledge. For all users, it is crucial that the 

information is accurate and scientifically credible, 

relevant, timely, well-organized, easily accessible, 

and sufficiently documented. In addition, tools for 

visualization, synthesis, and analysis of raw data are 

needed to enhance understanding.

Biological informatics research and development 

has been identified as a critical national priority. 

The President’s Committee of Advisers on Science 

and Technology (PCAST) Panel on Biodiversity 

and Ecosystems1 and the President’s Information 

Technology Advisory Committee2 have recommended 

significantly increased activity in this area. The National 

Research Council’s Committee on Grand Challenges 

in Environmental Sciences has recently identified the 

need for fundamentally increased understanding of 

biodiversity and ecosystem functioning as one of the 

eight “Grand Challenges in Environmental Science” 

facing our Nation and the world today.3

BIOLOGICAL INFORMATICS:

THE INTEGRATION OF INFORMATION FROM GENOMES TO BIOMES

Biological informatics, or bioinformatics, 

seeks to integrate these diverse data 

and information in order to enhance our 

knowledge of our environment, from 

genomes to biomes. 

1 President’s Committee of Advisers on Science and Technology 

(PCAST) Panel on Biodiversity and Ecosystems, Teaming with Life: 

Investing in Science to Understand and Use America’s Living Capital

(Washington, DC: Executive Office of the President of the United 

States, 1998), xv.

2 President’s Information Technology Advisory Committee, Report 

to the President. Information Technology Research: Investing in Our 

Future (Arlington, VA: National Coordination Office for Information 

Technology Research and Development [NCO/IT R&D], 1999).

3

 National Research Council, Grand Challenges in Environmental 

Sciences. Committee on Grand Challenges in Environmental 

Sciences, Oversight Commission for the Committee on Grand 

Challenges in Environmental Sciences (Washington, DC: National 

Academy Press, 2001), 106 pp.

Photo credit: USGS Forest and Rangeland Ecosystem Science Center
4

Challenges

Critically important to the Nation’s ecosystems, economy, 

and security are significant biological issues, such as 

invasive species, emerging diseases, unsustainable 

resource use, and climate change. Although the Federal 

government invests more than $600 million per year 

in biological data collection, it is difficult to address 

these issues because of limited accessibility and lack of 

standards for data and information. 

There is still a lack of access to scientific data of known 

quality, despite the widespread availability of Internet 

connectivity. This deficit is primarily due to a lack of 

interoperability across hardware, software, and data 

systems; and a lack of applications and tools to meet user 

needs. Challenges relating to the integration of data and 

information reflect the complex nature of biodiversity 

and ecosystems data. Species can be studied at scales 

ranging from genomes to biomes, from microscopic 

to global, and from days to years. Variable quality, 

sources, methods, and formats (e.g., observations in the 

field, museum specimens, and satellite images) present 

additional challenges.

The biological informatics field must be able to adapt 

quickly to anticipate user needs and to incorporate 

rapidly emerging technologies that change the way 

data are collected, stored, managed, and disseminated. 

As technologies such as wireless communications 

proliferate, and computing platforms become smaller and 

more mobile, the ability to seamlessly extract, analyze, 

and process data in the field can be realized. Even though 

these technologies offer new solutions, they also create 

new informatics challenges. 

The USGS recognizes the value of information and its 

role in improving the quality of life and the environment. 

It established the Biological Informatics Program in 

1996 to focus on this role. The Program is a nationallevel capability within the USGS. The Biological 

Informatics Office (BIO) of the Biological Resources 

Discipline (BRD) administers the Biological Informatics 

Program and responds to the needs and requirements of 

both DOI and the USGS.

Department of the Interior

The DOI mission is to protect and manage the Nation’s 

natural resources and cultural heritage and provide 

scientific and other information about those resources. 

The DOI Strategic Plan further states that Department 

bureaus manage a wealth of accessible, online science 

BIOLOGICAL INFORMATICS IN THE ORGANIZATION

data and information systems and are committed to 

maintaining and improving these assets for the benefit of 

the public.

The Biological Informatics Program supports the DOI 

mission area of Serving Communities Goal 2 (Advance 

Knowledge Through Scientific Leadership and Inform 

Decisions Through the Applications of Science) and 

Serving Communities Goal 2, Strategy 1 (Improve 

Information Base, Information Management, and 

Technical Assistance).4

Close collaboration with a variety of partners is crucial 

to serving communities. The Program works with 

these partners to assemble the network that delivers the 

benefits of good science to planners, decision-makers, 

The biological informatics field must be able 

to adapt quickly to anticipate user needs and 

to incorporate rapidly emerging technologies 

that change the way data are collected, 

stored, managed, and disseminated.

4

 U.S. Department of the Interior, Strategic Plan, Fiscal Year 2003–

2008 (Washington, DC: U.S. Department of the Interior, 2003), 92 

pp. Available at <http://www.doi.gov/ppp/strat_plan_fy2003_2008.

pdf>.

Photo credit: USGS Vegetation Characterization Program 
5

researchers, educators, and the general public. Through 

activities at the local, regional, national, and global 

levels, the Biological Informatics Program works to 

make the biological resource knowledge of the United 

States available to the world and the world’s biological 

resource knowledge available to the United States. In 

addition, these activities support the U.S. Government’s 

international obligations relating to the sharing of 

biological information. Examples of these obligations 

include the Convention on Biological Diversity (CBD), 

Cartegena Biosafety Protocol, Summit of the Americas, 

and the Summit on Earth Observations.

U.S. Geological Survey

As the Department’s principal science bureau, the 

USGS “serves the Nation by providing reliable 

scientific information to describe and understand the 

Earth; minimize loss of life and property from natural 

disasters; manage water, biological, energy, and mineral 

resources; and enhance and protect our quality of life.”5

The USGS Strategic Plan has as one of its long-term 

goals to “ensure the continued availability of longterm environmental and natural resource information 

and systematic analysis and investigations needed by 

customers ... for informed decision-making about 

natural systems.”6 The long-term goal of Environmental 

Information Science, one of the USGS Future Science 

Directions, is: “To increase understanding of natural 

systems in terms of the information that is contained 

and processed through these systems. To be a leader 

in development and application of advanced scientific 

capabilities for the acquisition, analysis, understanding, 

and communication of environmental science 

information.”7 The Biological Informatics Program 

directly supports the Bureau mission and specifically 

addresses these long-term goals.

Biological Informatics Program 

The mission of the USGS Biological Informatics 

Program is to create the informatics framework, 

provide the scientific content, and develop the public 

and private partnerships needed for the understanding 

and stewardship of our Nation’s biological resources. 

The Biological Informatics Program provides credible, 

applicable, unbiased information for science-based 

decision-making, particularly as it pertains to the 

DOI STRATEGIC PLAN ELEMENTS

PERFORMED BY THE

BIOLOGICAL INFORMATICS PROGRAM

Mission Area: Serving Communities

End Outcome Goal 2. 

Advance knowledge through scientific leadership and inform decisions through the 

applications of science.

Strategy 2.1 

Improve information base, information management, and technical assistance.

Performance Measure 2.1.1

Inform Decisions through the Application of Science: Improved stakeholder access 

to needed science information and stakeholders reporting that information helped 

achieve goal.

Performance Measure 2.1.2

Content and Expanse of Knowledge Base: Percent of surface area with temporal 

and spatial monitoring, research, and assessment/data coverage to meet land-use 

planning and monitoring requirements.

5

 U.S. Geological Survey. “About USGS.” At U.S. Geological Survey 

Web site: <http://www.usgs.gov/aboutusgs>.

6

 U.S. Geological Survey, Strategic Plan: 2000–2005 (Reston, VA: 

U.S. Geological Survey, 2000), 25 pp. Available at <http://www.usgs.

gov/stratplan/stratplan_rev.pdf>.

7

 A. F. Frondorf, D. R. Boldt, D. R. Hutchinson, W. G. Miller, D. R. 

Posson, and S. A. Sipkin, U.S. Geological Survey Open-File Report 

2005-1180 (2005)—ONLINE ONLY. Available at <http://pubs.usgs.

gov/of/2005/1180/>.
6

conservation, management, and use of the Nation’s 

natural resources. The program is committed to making 

available the data and information that are critical to 

scientific discovery and application. Databases, maps, 

and publications are vital mechanisms for conveying 

this information to users. In addition, the Program is 

committed to the development and easy accessibility 

of tools, models, visualizations, and applications to 

aid policy and resource managers in the analysis and 

synthesis of scientific data to support 

decision-making. The Program works in cooperation 

with many organizations throughout the United States 

and the world to provide critical information to partners, 

stakeholders, customers, and the general public. Through 

electronic infrastructures, the Program delivers relevant 

data and information faster and in more interoperable 

formats than in the past, leading to better stewardship 

of the Nation’s natural 

resources.

Added Value of 

Integration

The core and 

interdependent 

components of BIO 

have been specifically 

designed to integrate 

information across 

geographic and political scales (local to global) and 

biological levels of organization (genomes to biomes). 

• Landscapes, Stewardship, and Species 

Distributions. GAP generates databases on 

native vertebrate species distributions and natural 

land cover types to provide State, regional, and 

national conservation assessments. It also serves 

as a standard geospatial and biological foundation 

upon which other biological information from the 

NBII can be analyzed.

• Vegetation Communities. The VEG component 

characterizes vegetation using a consistent 

methodology supported by national standards. 

The products are specifically intended to serve 

natural resource managers by providing them 

accurate, fine resolution vegetation land cover 

assessments that are then used by the land 

managers for managing biological resources 

under their stewardship. VEG supports the 

calibration of remote sensing methodologies and 

verification of land cover types used by GAP. 

• Genomes to Biomes. The NBII provides GAP, 

VEG, ITIS, and others with a fully digital, 

interactive, distributed system that provides 

scientifically reliable biological data and 

information. It also provides network-wide 

methods for organizing content to enhance the 

identification, retrieval, and use of information. 

These include the use of standard metadata 

and schema for documenting data sets and 

information products.

• Biosystematics and Nomenclature. ITIS provides 

an authoritative source of species names and their 

hierarchical classification. It serves as a taxonomic 

standard for other BIO components and the 

global community, enabling the comparison of 

biodiversity data sets at all biological levels.

The Program works collaboratively with others to ensure 

that it has high quality data and information that can 

be used to address issues of resources management. 

To that end, BIO engages USGS science centers, 

non-governmental 

organizations, 

museums, universities, 

international 

organizations, and other 

partners in the creation 

of data content and 

resources to address 

resource management 

needs.

Descriptions of the major activities of the Biological 

Informatics Program are provided below:

National Biological Information Infrastructure. The 

NBII is the premier partnership for making biological 

data, information, and associated tools and technologies 

more accessible for customers and partners to use in 

making cost-effective, informed decisions regarding 

resource management, environmental considerations, 

disease vectors, control of invasive species, and 

other issues. The NBII uses the capabilities of the 

World Wide Web and other advanced technologies to 

establish a distributed “federation” of biological data 

and information sources, through which users can find 

biological information, retrieve it, and apply it to resource 

management questions. Partners and customers who 

take part in this effort include government agencies at 

all levels, private sector organizations, natural history 

museums, libraries, academic institutions, international 

scientific organizations, and the public.

Gap Analysis. GAP provides broad geographic 

information on the status of species and their habitats. 

This involves identifying the degree to which native 

animal and plant species are represented in the presentday mix of conservation lands (those species not 

The core and interdependent 

components of BIO have been 

specifically designed to integrate 

information across geographic and 

political scales (local to global) 

and biological levels of 

organization (genomes to biomes).
7

adequately represented constitute conservation “gaps”). 

Currently, GAP products are available for most of the 

country, including digital databases describing Statewide 

land-cover assemblages, vertebrate distributions, and 

characterizations of land stewardship. The current 

emphasis of the program is on completing GAP 

projects in the few States where data are not available, 

developing regional data sets, updating selected 

regions of the country with state-of-the-art methods 

and technologies, organizing new aquatic projects, and 

developing partnerships with data users to facilitate the 

use of GAP information in land-management decisions.

Vegetation Characterization Program. VEG focuses 

on creating national vegetation standards, technologies, 

and products. It is a key component of the cooperative 

effort by the USGS and the National Park Service (NPS) 

to classify, describe, and map vegetation communities 

in more than 270 national park units across the Nation. 

This landmark program is both the first to provide 

national-scale descriptions of vegetation for a Federal 

agency and the first to create national vegetation 

standards for its data products. It is meeting specific 

information needs identified by NPS, with additional 

cooperative projects for the U.S. Fish and Wildlife 

Service (USFWS) and the Bureau of Land Management 

(BLM). Current efforts include dovetailing protocols 

for invasive species inventory and fire fuels related to 

vegetation to achieve efficient and integrated field data 

collection protocols. 

Integrated Taxonomic Information System. The 

USGS leads and works with other Federal agencies 

(including the Environmental Protection Agency [EPA], 

U.S. Department of Agriculture [USDA] Agricultural 

Research Service [ARS], USDA Natural Resources 

Conservation Service [NRCS], National Oceanic and 

Atmospheric Administration [NOAA], Smithsonian 

Institution [SI], National Science Foundation [NSF], 

and National Park Service [NPS]), organizations, 

institutions, and taxonomic specialists across the 

United States and internationally to operate the largest 

taxonomic thesaurus and database of its kind in the 

world. ITIS provides an accepted scientific name (with 

NBII

ITIS

NBII

INTEGRATION AND ACCESS

DATA

USER COMMUNITIES

Infrastructure

Standards

G

A

P

C

E

N

T

E

R

S

P

A

R

T

N

E

R

S

V

E

G

Figure 1. How Biological Informatics Program Components Are Integrated

Figure 1 illustrates how data and information are served to customers 

through a careful integration of BIO’s components. Data are generated 

through major programs such as GAP, VEG, Science Centers, and Partner 

initiatives. These data are passed through standards and protocols like 

ITIS and Federal Geographic Data Committee (FGDC) profiles to assure 

interoperability and quality. The NBII infrastructure provides the computing 

system foundation upon which these processes operate. Additional NBII 

functionalities serve the needs of the user community through data and 

information integration and dissemination.
8

a unique Taxonomic Serial Number) as the “common 

denominator” for accessing information on such topics 

as biodiversity, invasive species, declining amphibians, 

migratory birds, fishery stocks, pollinators, agricultural 

pests, and emerging diseases. ITIS is also the source 

of biological names for the NBII. ITIS supports the 

only comprehensive national taxonomic database that 

provides free access (directly over the Internet) to 

standard scientific names for all U.S. plant and animal 

species. Currently, ITIS is coordinating efforts with 

the NBII Invasive Species Information Node in the 

development of an early detection and rapid response 

system, building taxonomies for invasive species as a 

key component of that system.

USGS Science Centers. While the Biological 

Informatics Program is a national capability, the USGS 

Regions and Science Centers are important partners. 

A portion of the Program’s appropriated budget is 

distributed to the Centers to support informatics 

activities planned and executed at that level. 

Partnerships

Fundamental to the structure of the Program is its 

capacity to build and strengthen partnerships 

across Federal, State, local, international, academic, 

non-profit, and private sectors. In order for the Program 

to succeed in providing qualitative and quantitative 

natural resources data and information to decisionmakers, it must incorporate all of these interests to 

ensure a complete picture drawn from the best possible 

sources. Strategic partnerships are established to:

• Increase content,

• Develop and implement standards,

• Promote the development and implementation of 

advanced technology, and

• Leverage resources among partners.

The Program has built partnerships with organizations 

through which the major biological resource data and 

information management activities of the country are 

linked. Such partnerships include:

State agencies and organizations holding state data 

and information. States and associated organizations 

(such as the International Association of Fish and 

Wildlife Agencies) have key responsibilities for 

managing the Nation’s natural resources. In line with 

these responsibilities, they gather and maintain large 

quantities of natural resources data and information.

Global Biodiversity Information Facility (GBIF)

CBD Clearing-House Mechanism (CHM)

The Species 2000 and ITIS Catalog of Life

Inter-American Biodiversity Information Network (IABIN)

North American Biodiversity Information Network (NABIN)

Pacific Biodiversity Information Forum (PBIF)

National Biological Information Infrastructure (NBII)

Integrated Taxonomic Information System (ITIS)

State Natural Heritage Programs

Gap Analysis Program (GAP)

County/City Data

Vegetation Characterization (VEG)

GLOBAL

NATIONAL

LOCAL

HEMISPHERIC

Figure 2 illustrates biological informatics components that flow from local to national to 

hemispheric to global levels. This approach avoids duplicative investments in both technology 

and content and expands that content base available to the user community.

Figure 2. Biological Informatics – Local to Global
9

Biological and ecological research organizations. 

Numerous organizations across the Nation and around 

the world are engaged in scientific research in the 

biological/ecological realm. In order to access this 

vast source of data and information, partnerships are 

needed that facilitate unifying and synthesizing science 

information to address critical biological issues.

Federal and other land management organizations. 

The key objective of the Program is to provide 

information and tools to resource managers for 

decision-making. To do that, the Program develops 

national-level partnerships with agencies responsible 

for land and resource management to understand their 

information needs, to make their natural resources 

information accessible, and to leverage resources.

Leaders of biological networks and systems. The 

Program partners with other networks to facilitate 

complete content coverage, data access, standards 

development, and technology deployment.

Leaders of information science research and 

development (R&D) activities. The Program partners 

with organizations leading or conducting information 

science R&D that can be leveraged and applied to the 

biodiversity and ecosystems domain.

Stewards of natural science collections. Natural 

history museums, herbaria, botanical and zoological 

gardens, and other natural science collections are 

important contributors to the Program, providing both 

taxonomic expertise and specimen data.

International initiatives. Biological resource issues 

cross many political boundaries and, therefore, must 

be addressed at regional, hemispheric, and global 

levels. Organisms including disease vectors and 

invasive species can be transported anywhere in the 

world within 24 hours. Serious and costly issues such 

as invasive species and zoonotic diseases require 

the sharing of knowledge with other countries. 

Participation in continental, hemispheric, and global 

biodiversity networking initiatives provides the 

opportunity to make U.S. biological information and 

data resources available to the world and to make 

the world’s biological knowledge available to the 

United States.

Coordination for NBII efforts to develop an avian influenza detection system is 

centered at the USGS National Wildlife Health Center, which houses the NBII 

Wildlife Disease Information Node (WDIN). Today, WDIN is busy developing a 

Web-based system <wildlifedisease.nbii.gov/ai/> that may assist in projecting 

the spread of a highly pathogenic strain of avian flu (Asian H5N1). Injecting the 

virus into eggs (shown here) demonstrates the Center’s commitment to gain an 

understanding of the disease from a variety of perspectives.
10

Data and information about 

invasive species, such as 

multiflora rose (Rosa multiflora), are 

available through a variety of Biological 

Informatics Program components.

Photo credit: Elizabeth Sellers/NBII
11

Examples of Recent Accomplishments and Ongoing Work 

of the USGS Biological Informatics Program

National Biological Information Infrastructure

To date, over 250 agencies and organizations have partnered with the NBII, providing content, 

expertise, and in-kind contributions. Currently, the network has eight regional and four thematic 

nodes. The NBII, through the FGDC, developed the FGDC Biological Profile to support the 

creation of national metadata standards that are unique to biological data and information. The 

NBII supports the national Chronic Wasting Disease repository and is responsible for Web and 

digital map enabling of the Breeding Bird Survey, which is designed to track the status and 

trends of North American bird populations. The NBII is also helping to develop the DOI-wide 

Early Detection and Rapid Response capability.

Global issues such as emerging diseases and invasive species warrant the Program’s 

participation in leading international biological informatics initiatives. The Program, with 

direction from the Department, was instrumental in establishing IABIN, an effort to initiate the 

biodiversity information network for the Western Hemisphere. The Program also serves as the 

U.S. Focal Point(s) to IABIN and for the CHM of the CBD. It is also the U.S. Node of GBIF.

Gap Analysis Program

GAP has either finished or is completing its standard geospatial data layers for all states 

(approximately 83 percent coverage of the U.S. landmass), with the exception of Alaska. GAP’s 

statewide data products include: 1) land cover assemblages, 2) vertebrate species distributions, 

and 3) characterizations of land stewardship. ReGAP (Regional GAP) projects are currently 

updating state projects and combining them into multi-state regions. Current ReGAP projects 

include the Mid-Atlantic (three states), Southeast (ten states), and Southwest (five states) 

regions of the United States, with plans for additional regional updates to provide national 

coverage over the next five years. Aquatic GAP presently supports projects in both large and 

small watersheds, including the Great Lakes; and the Missouri, Upper Tennessee, and Lower 

Colorado rivers. The USGS also continues to emphasize GAP research and the development of 

applications to serve the needs of DOI’s land management agencies, including the USFWS and 

the BLM, as well as other Federal agencies such as the U.S. Forest Service.

Vegetation Characterization Program

VEG, in cooperation with the NPS, has developed vegetation products for more than 30 

national parks. This program is both the first to provide national-level descriptions of vegetation 

for a Federal agency and the first to create national vegetation standards for its data products. 

VEG results have provided input to fire fuel models at the national level. In cooperation with 

the USFWS, VEG products have also been generated for select National Wildlife Refuges.

Integrated Taxonomic Information System

ITIS is the comprehensive, standardized reference for the scientific names – as well as 

synonyms and common names – for all the plants and animals of North America and the 

surrounding oceans. The Biological Informatics Program took the lead in the creation and 

implementation of ITIS, a cooperative effort among many Federal agencies (e.g., EPA, USDA 

NRCS, NOAA, SI, and NSF). ITIS operates the largest taxonomic thesaurus and database of its 

kind in the world. It currently contains over 463,000 names for more than 213,000 species. In 

addition, ITIS and Species 2000 are also key partners in the creation and implementation of the 

Catalog of Life, the global taxonomy authority.
12

We will move forward to address the challenges with a 

broad federation of partners. Together, we will provide 

access to integrated data and information about the 

Nation’s biological resources. This will maximize the 

return on the sizable investment in data generation 

and collection by improving their access and usability. 

Overcoming the challenges will require a fully digital, 

Web-based, distributed system; scientifically reliable 

data and information; local to global data coverage; 

and new information technologies for science-based 

and effective decision-making. The following goals and 

objectives provide a pathway to success.

Goal 1. Increase the availability and usefulness of 

biological resources data and information (Content).

The scope of content of interest to the Program 

includes data, information, and knowledge of or about 

biological resources. Subject areas of interest include: 

biosystematics and nomenclature; landscape, ecosystems, 

and habitat; biodiversity and ecosystem assessment; 

species and populations; genes and ex-situ diversity; 

environmental drivers and ecological processes; and 

social and economic drivers. A complete list of the 

biological topics on which the Program focuses is 

included in Appendix 1. 

Objectives:

1A. Obtain the broadest possible participation of 

 both public and private sector stakeholders 

 and partners in identifying high priority data and 

 information needs.

1B. Increase access to data and information 

 for USGS Science Centers and partners, as 

 appropriate.

1C. Develop or select, implement, and promulgate 

 standards and protocols to promote 

 interoperability and information integration 

 capabilities.

1D. Increase the variety of data and information 

 available through the NBII.

Goal 2. Implement technologies and tools to 

integrate, analyze, visualize, and apply biological 

information to natural resource issues (Tools).

Tools developed, or acquired and adapted, by the 

Program include those necessary for the creation, 

discovery, retrieval, and management of appropriate 

content as well as those for manipulating and displaying 

selected content. Tools include catalogs and directories, 

decision support systems, visualization applications 

including mapping capabilities, models, standards, and 

protocols for the collection and reporting of data.

Objectives:

2A. Develop methods and techniques to improve 

 information organization and expand discovery 

 capabilities.

2B. Implement and enhance mechanisms to 

 develop and support the creation and 

 management of metadata for all types of data 

 and information.

Goal 3. Develop, apply, and promote the adoption 

of standard practices, protocols, and techniques to 

enhance knowledge discovery and retrieval from 

various resources (Infrastructure).

The Program’s infrastructure activities address the 

requirements of maintaining a distributed Internetbased network of resources. It includes the development 

or adoption of standards and protocols to increase 

data accessibility, integration, and usability. In some 

instances, it includes the installation, maintenance, and 

security of hardware and software resources to support 

specific requirements of the Program. 

Objectives:

3A. Develop the hardware and software systems 

 required to support the Program and all of its 

 components.

THE ROAD AHEAD

The Vision

The Biological Informatics Program will 

provide the premier enterprise system for 

accessing and disseminating integrated and 

reliable biological information.

Map credit: USGS Southwest Regional Gap Analysis Project
13

This program will be implemented through a series of 

steps, carefully coordinated among the major Program 

components and partners. Table 1 (next page) provides a 

description of the strategies, outcomes, and measurements 

necessary to meet Program mission, goals, and objectives.

The activities and progress of Biological Informatics 

Program components are reviewed through an ongoing 

dialog with groups of interested stakeholders. These 

3B. Support standards development to integrate core 

functionality of partner infrastructure.

3C. Support the computational capabilities required to 

apply models and other tools to available data.

Goal 4. Facilitate information science and technology 

research that supports the advancement of biological 

informatics capabilities (Research).

Research includes investigating new informatics 

techniques and technologies, as well as exploring 

how existing techniques and technologies might be 

applied in novel ways for possible application within 

the Program. Applied research areas of interest include 

data collection, mining and access, analysis, modeling, 

simulation, forecasting, interpretation, and visualization 

of biological and ecological data and information.

Objective: 

4A. Conduct research in bioinformatics to support 

 the discovery, management, visualization, and 

 application of biological data and information. 

Goal 5. Apply innovative technologies and best 

practices to improve the development, description, 

and dissemination of biological information to 

customers (User Services).

User services includes activities such as outreach, 

training, and technical assistance. These services target 

both users and contributors of the Program’s data and 

other information resources. This goal also includes 

Web site usability protocols and information diffusion 

assessments to understand customer needs.

Objectives:

5A. Increase user knowledge and application of 

 tools, techniques, and capabilities supported by 

 the Program.

5B. Implement feedback mechanisms, periodic 

 evaluations, and other techniques to improve 

 user capabilities.

groups – comprising individuals from both the public 

and private sector and representing various disciplines 

including biology, library and information science, and 

computer science – have included the Biodiversity and 

Ecosystems Informatics Work Group (BioEco), a working 

group under the Office of Science Technology and Policy; 

the NBII Science Committee; the BRD Watchers; the 

GAP review committee; and working groups coordinated 

by ITIS, among others. 

IMPLEMENTATION

This excerpt of a standard 

taxonomic report for the wood 

turtle (Glyptemys insculpta) is only 

a portion of the wealth of 

information available through ITIS. 

Photo credit: John J. Mosesso/NBII
14

Goal 1: Increase the availability and usefulness of biological resources data and information (Content).

Objective 1A: Obtain the broadest possible participation of both public and private sector stakeholders and partners in identifyinghigh priority data and information needs.

Strategy Outcome Measure1A1. Develop and implement a process to engage new and existing partners to identify high priority data and information needs.

Process is in place to identify, acquire, and distribute highest priority data and information, as defined by the global biological community.Highest priority needs of stakeholders are identified.

• Increase in number and variety of partners engaged 

in priority-setting process (2005-2009), and

• Number of workshops, consultations, and other 

mechanisms held in order to help set priorities (2005-2009).

Objective 1B: Increase access to data and information for USGS Science Centers and partners, as appropriate.

Strategy Outcome Measure1B1. Integrate USGS Science Center and other USGS Discipline activities into the development, implementation, and management of program priorities.

Close collaboration occurs between USGS Science Centers, other USGS Disciplines, and Biological Informatics Program components on biological information generation, management, and dissemination activities.

• Number of USGS Science Center and other USGS 

Discipline activities that collaborate in BIO prioritysetting (2005-2009),

• Number of USGS Science Center and other USGS 

Discipline activities that utilize and contribute to BIO products (2005-2009), and

• Percentage of Geography, Water, and Biology 

customers satisfied with the ease and timeliness of access to information products (GPRA/PART Measure; 2005-2009).

1B2. Integrate partner activities into the development, implementation, and management of program priorities.

Close collaboration occurs between partners and Biological Informatics Program components on biological information generation, management, and dissemination activities.

• Number of partner activities that utilize and contribute 

to BIO products (2005-2009).

1B3. Develop multilingual capabilities to discover, retrieve, and use biological resource data and information.

International and non-English-speaking users gain access to previously English-only biological data, tools, and applications.

• Multilingual versions of search software for InterAmerican Biodiversity Information Network and other 

program components (2005).

Table 1. Strategies, Outcomes, and Measurements Necessary to Meet the Biological Informatics Program Mission, Goals, and Objectives
15

Strategy Outcome Measure1B4. Increase content in NBII regional and thematic nodes in response to the priority biological issues of concern to our customers and stakeholders.

Content in NBII regional and thematic nodes is increased in response to the priority biological issues of concern to our customers and stakeholders; including expanded availability of GAP and VEG data and products.

• Increased content in regional and thematic nodes 

reflecting program and partner priorities (2005-2009),

• Regional updates to nationwide GAP data (2005-

2009),

• Aquatic GAP projects to update data on U.S. 

watersheds (2005-2009),

• Percentage of U.S. land with land characterization and 

species distribution information available for resource management decision-making updated in the last 5 years (PART Measure; 2005-2009),

• Percentage of North American migratory birds for 

which scientific information on their status (species distribution and number) and trends are available in a standardized and exchangeable format, to improve conservation plans of Federal and State agencies (PART Measure; 2005-2009), 

• Percentage of North American amphibians and 

reptiles for which scientific information on their status (species distribution) are available in a standardized and exchangeable format, to improve conservation plans of Federal and State agencies (PART Measure; 2005-2009),

• Percentage of North American mammals for which 

scientific information on their status (species distribution) are available in a standardized and exchangeable format, to improve conservation plans of Federal and State agencies (PART Measure; 2005-2009), and

• Percentage of surface area with temporal and spatial 

monitoring, research, and assessment/data coverage to meet land use planning and monitoring requirements (DOI One Plan Number of square miles assessed by GAP, GPRA/PART Measure; 2005-2009).
16

Objective 1C: Develop or select, implement, and promulgate standards and protocols to promote interoperability and informationintegration capabilities.

Strategy Outcome Measure1C1. Expand the Biocomplexity Thesaurus, ITIS, and other authorities required to promote biological and ecological information discovery, retrieval, and integration. 

Authorities are accepted and used by the biological informatics community.

• Number of terms added to authority files (2005-2009), 

and

• Increased use of authority files (2005-2009).

1C2. Develop and support the use of metadata standards and exchange protocols for all types of data and information.

There is widespread use of metadata standards and exchange protocols for all types of data and information.

• Number of NBII Clearinghouse metadata records 

(GPRA/PART Measure; 2005-2009), and

• Increase in number of people trained in use of metadata 

standards and exchange protocols (2005-2009).

Objective 1D: Increase the variety of data and information available through the NBII.

Strategy Outcome Measure1D1. Target information types and sources underrepresented among currently accessible resources.

Greater range and depth of data are served by Biological Informatics Program, components and tools.

• As U.S. node to GBIF, serve data from worldwide 

natural history museums, herbaria, zoological and botanical gardens, and aquaria (2005-2009),

• Percentage of Natural History Museum specimen 

data records available online via the NBII, to assist researchers in identifying and addressing threats to human and animal health (PART Measure; 2005-2009),

• Amount of invasive species data and information 

available online via the NBII, to assist in modeling and forecasting the spread of invasive species (PART Measure; 2005-2007),

• Amount of fire-related data and information available 

via the NBII, to assist land managers in fire management decision-making (PART Measure; 2005-2009),

• Percentage of U.S. Federally-listed threatened and 

endangered or indicator fish species for which scientific information on species status is available in a standardized and exchangeable format to improve conservation plans of Federal and State agencies (PART Measure; 2005-2009), and

• Number of cumulative gigabytes managed (GPRA/

PART Measure; 2005-2009).
17

Goal 2: Implement technologies and tools to integrate, analyze, visualize, and apply biological information to natural resource issues (Tools). 

Objective 2A: Develop methods and techniques to improve information organization and expand discovery capabilities.

Strategy Outcome Measure2A1. Identify and prioritize, in consultation with partners and users, various tools that will advance the functionality of biological information services.

Applications and tools are developed and implemented for a wide variety of geospatial, temporal, and trends-based biological data.

• Increased use of new tools and applications (2007-

2009).

2A2. Implement technologies to locate, access, and analyze large data sets and present data and information in forms appropriate to the user. 

Technologies are implemented to locate access, integrate, analyze, and present data and information in forms appropriate to the user and the application.

• Number of systematic analyses and investigations 

delivered to customers (GPRA/PART Measure; 2005-2009).

Objective 2B: Implement and enhance mechanisms to develop and support the creation and management of metadata for all types of data and information.

Strategy Outcome Measure2B1. Develop suites of integrated tools (i.e., “scientific desktops”) targeted to the information needs of selected user communities.

Tools are available for user communities that meet their specific needs.

• IABIN Biobot search utility refined for multilingual 

users in Latin America, Caribbean (2006),

• Portal communities created and managed for 

stakeholders (2005-2009), and

• IABIN Invasives Information Network (I3N) 

cataloging tool (2006).

2B2. Provide applications that increase the efficiency of content management. 

Content is managed efficiently. • Average cost per gigabyte of data available through 

servers under program control PART (Measure; 2005-2009).

Goal 3: Develop, apply, and promote the adoption of standard practices, protocols, and techniques to enhance knowledge discovery and retrieval from various resources (Infrastructure).

Objective 3A: Develop the hardware and software systems required to support the Program and all of its components.

Strategy Outcome Measure3A1. Develop innovative hardware and software systems required to support the Program and all of its components.

Program needs are met by new hardware and software. • Increased use of new hardware and software (2005-

2009).
18

Objective 3B: Support standards development to integrate core functionality of partner infrastructure.

Strategy Outcome Measure3B1. Provide standards, protocols, and techniques to support accessibility, integration of data, and usability among partners.

Partners use standards, protocols, and techniques provided. • Increased use of standards, protocols, and techniques 

by partners (2005-2009)

Objective 3C: Support the computational capabilities required to apply models and other tools to available data.

Strategy Outcome Measure3C1. Ensure adequate computational and storage capacity to apply models and other applications.

Program has adequate computational and storage capacity to apply models and other applications.

• Growth in storage and computational capacity devoted 

to modeling and applications (2005-2009).

Goal 4: Facilitate information science and technology research that supports the advancement of biological informatics capabilities (Research).

Objective 4A: Conduct research in bioinformatics to support the discovery, management, visualization, and application of biological data and information. 

Strategy Outcome Measure4A1. Support exploratory research workshops and symposia to identify new areas of research.

New areas of research are identified at workshops and symposia.

• Increased grant proposals on topics identified in 

workshops and symposia (2005-2009).

4A2. Work with the broader scientific community to conduct and leverage innovative research through collaborative plans and programs.

Innovative research is conducted through collaborative plans and programs.

• Increased funding or leveraging for collaborative 

research with the broader scientific community (2005-2009).

Goal 5: Apply innovative technologies and best practices to improve the development, description, and dissemination of biological information to customers (User Services).

Objective 5A: Increase user knowledge and application of tools, techniques, and capabilities supported by the Program. 

Strategy Outcome Measure5A1. Provide technical assistance and training to users.

New users are trained on new tools, applications, and metadata.

• Number of formal workshops or training provided 

to customers (instances/issues/events) (GPRA/PART Measure; 2005-2009).

5A2. Expand outreach and education activities. 

Outreach and education activities are expanded to a wider audience.

• Increased volume of updated materials such as teacher 

and student tool kits and online biological resources (2005-2009), and

• Increased presence at community events (2005-2009).

Objective 5B: Implement feedback mechanisms, periodic evaluations, and other techniques to improve user capabilities.

Strategy Outcome Measure5B1. Conduct periodic evaluations and solicit feedback to improve user satisfaction.

User feedback is effectively collected and integrated into program planning and activities.

• Increase in user feedback for planning process and 

activities (2005-2009).
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APPENDIX 1

Biological Informatics Program Subjects of Particular Interest

Landscape, Ecosystems, and Habitat

 Coastal

 Desert

 Ecoregions

 Forest

 Freshwater

 Habitats

 Land and water cover

 Marine

 Montane

 National map

 Prairie

 Protected Areas 

 Reef

 Riparian

Riverine

 Tundra

 Vegetation classification

 Wetlands 

Social and Economic Drivers

 Biocomplexity

 Human demographics

 Land use planning

Sustainable development

 Urban sprawl

Species and Populations

 Anadromous fish

 Culturally important species

 Endangered species

 Endemic species

 Harvested species

 Invasive species

 Marine mammals

 Migratory birds

 Wild relatives of crop species

Biodiversity and Ecosystem Assessment

Aquatic GAP

 Intensive monitoring

 Man and the Biosphere Program

 NSF Long Term Ecological Research Program

 Survey networks

Terrestrial GAP

Vegetation Characterization

Biosystematics and Nomenclature

Ecoregions 

Life zones and bioregions

 Taxonomic authorities (ITIS)

Collections and Reference Institutions

Bibliographic services

 Botanical gardens

Libraries

 Museums

 University collections

 Zoological gardens

Environmental Drivers and Ecological Processes

 Atmosphere

 Climate change

Contaminants

 Nutrient cycling

Soils

 Water

Genes and Ex-situ Diversity

 Plant and animal registries

Seed and germ plasm banks

 Tissue and gene banks
20

APPENDIX 2

List of Abbreviations

ARS Agricultural Research Service 

BIO Biological Informatics Office 

BLM Bureau of Land Management 

BRD Biological Resources Discipline 

CBD Convention on Biological Diversity 

CHM Clearing-House Mechanism 

DOI Department of the Interior

EPA Environmental Protection Agency 

FGDC Federal Geographic Data Committee 

GAP Gap Analysis Program 

GBIF Global Biodiversity Information Facility 

IABIN Inter-American Biodiversity

 Information Network 

ITIS Integrated Taxonomic Information 

 System 

NABIN North American Biodiversity 

 Information Network

NBII National Biological Information 

 Infrastructure 

NOAA National Oceanic and Atmospheric 

 Administration

NPS National Park Service 

NRCS Natural Resources Conservation 

 Service 

NSF National Science Foundation

PBIF Pacific Biodiversity Information Forum

PCAST President’s Committee of Advisers on 

 Science and Technology 

PITAC President’s Information Technology 

 Advisory Committee 

R&D Research & Development

ReGAP Regional GAP

SI Smithsonian Institution

USDA U.S. Department of Agriculture 

USFWS U.S. Fish and Wildlife Service 

USGS U.S. Geological Survey 

VEG Vegetation Characterization Program