Progress report & proposal to NBII, October, 2005

Web tools to identify, report,
and map invasive species

Cooperative Agreement
The Polistes Foundation

John Pickering
University of Georgia, Athens

31 October, 2005

Ailanthus altissima, Tree-of-heaven
Ailanthus altissima fruit
Tree-of-heaven or Chinese Sumac
an invasive species of New England
Illustration by Cheryl Reese, 2004
Last updated: 1 November, 2005

Invasive species threaten our health, food supply, economy, environment, and general well-being. The USGS-NBII and Polistes Foundation entered a 5-year cooperative agreement in 2004 to develop, test, and implement the human and technical infrastructure needed to improve vastly our quarantine, rapid detection, monitoring, and response to noxious species. The following sections describe our technology, partnership, progress in 2005, and proposal for 2006.

Discover Life uses server-side technology to gather and share information over the Web. Its software is licensed from The Polistes Corporation at no cost and provides the power behind the IDnature guides, Global Mapper, and other databasing tools that we share via the Web. kindly gives us maps and aerial photographs for displaying the distribution of species. Other partners, most notably the Missouri Botanical Garden, Smithsonian Tropical Research Institute and ASEANET, provide taxonomic expertise, images, data, and Web services that we integrate into guides, maps, species pages, and navigation tools. For technical details and a prospectus outlining our plan to build an international network of technical training and support centers please see

Since 2002, the U. S. Geological Survey's National Biological Information Structure (NBII) has been the major financial supporter of The Polistes Foundation and its partners to build Web-based identification guides to North America's flora and fauna. As described in our 2002 and 2003 proposals, the NBII-Polistes partnership started by developing guides to common North American butterflies, caterpillars, wildflowers, and invasive species. In May, 2004, the NBII and Polistes Foundation signed a 5-year cooperative agreement to use Web tools to identify, report, and map invasive species in North America. NBII funded the 2004 and 2005 proposals to build guides to various additional North American taxa.

By any metric, the past year has been a very successful one for our cooperative agreement. Discover Life is most grateful and thanks NBII for their support. It has enabled us to grow and serve the Web community in many ways.

Increased usage
Usage is up considerably. Discover Life's servers at the University of Georgia,, and Missouri Botanical Garden,, served over 2,530,000 pages and images to over 67,900 IP addresses in October, 2005. This compares with 1,045,000 pages and images served to nearly 40,000 users in October, 2004.

Database growth
Because of advances in technology that allow us to rapidly incorporate information from contributors, our databases are growing rapidly in both size and number. In April, 2005, when we added a new search box to Discover Life, we had information on 97,000 species. Six months later, our databases now have information on nearly 224,000 species. Highlights in database growth include our success in working with Bob Magill at Missouri Botanical Garden to mirror their Tropicos database into Discover Life's tools. Currently our servers automatically update over 2.5 million records per night from Missouri. In addition to Mobot's Tropicos database, we are on track for integrating a total of 50 spatial databases into the Global Mapper by the time we finish the work specified in our 2005 proposal. These range is size from a few hundred snake records provided by Andrew Durso, a Freshman at the University of Georgia, to over 600,000 records maintained by Steve Ashe at the Snow Entomology Collection at the University of Kansas.

Regional centers
This summer Ed Wilson at Harvard University offered to help us find support for 8 regional technical support and training centers to speed collecting and sharing information around the world. By expanding our network of partners worldwide, we intend to complete IDnature guides and build an on-line encyclopedia of life to a million species by 2012 (see Part of our plan is to build online guides to all the described species in North America and potential invasive ones from elsewhere, thus supporting the goals of our cooperative agreement. Recently we partnered with ASEANET and the Smithsonian Tropical Research Institute to establish support centers in Malaysia and Panama, respectively. STRI has committed 50% time of one of their senior database staff, Steve Paton, to oversee the center in Panama. In addition to the proposed international centers, we are working with Mammoth Cave National Park and Western Kentucky University to build another North American center to help support our efforts here.

Guide development
We build checklists and turn them into guides through the following steps detailed in our 2005 proposal (

  1. create a checklist of valid scientific names;
  2. assemble species pages that include images, maps, text and links to other Websites;
  3. make a guide by scoring character-state attributes of each species;
  4. resolve the guide to make sure that it contains sufficient information to identify species;
  5. illustrate character-states, and
  6. include feedback from users.

We are first targeting the groups listed in the first column of the following table. For each group our goal is to build a checklist and guide for all North American species. Clicking on the blue links in this column takes you to either a checklist or guide, depending on how far we have progressed with the group. Please see our 2005 proposal, for a detailed explanation of each column ( As work continues this year, we will update the numbers in the table. Please see individual guides and checklists to get the most up-to-date figures on our progress. Highlights of recent progress include the guides to North American Trees & shrubs and Opuntia cacti. We have not started work on some groups, such as the spiders and moths, and will not have them up until January.

IDnature guides for North America
Group Species Kinds Illustrations
North America

(for year)
Drawn Photo None
Ants 740 + 20% unknown751 ('05)834> 700 475679
Bees 4,500360 funded by USGS-BRD619104 70121958
Beetles >20,00023
448 0645
Birds 9951,079 1,200 ('04)1,75217 810198
Butterflies 7721,001 >600 ('02)1,2101034 94050
Caterpillars 15,000165 150 ('02)154129 0230
Damselflies 128 + unknown134

checklist only

Dragonflies 311319
316203 2006
Earthworms 150 + unknown118 ('05)118118 0
Ferns 1,100471
150checklist only

Fish >900 freshwater28,666 world ('05)
by family 0
Fungi 5,000221
23466 0072
Frogs & Toads 98107 102 ('04)1040 380107
Grasses 3,100615
616checklist only

Invasives species >1,0611,364 >350 ('02,'06)1,103200 5030133
Liverworts 500614
613193 06254
Lizards 150 +165
Mammals 455499
468201 100402
Millipedes >90091

checklist only

Mosquitoes 165 + unknown167
16744 82048
Moths >14,0000 ('05)

Opuntia Cacti 30179 ('05)1900 140
Salamanders 154164 70 ('04)17051 29074
Sawflies 1,0001,744 ('05)
checklist only

Snakes 137147 300 ('04)16446 420107
Spiders 550 genera23 ('05)25
Ticks 177 + unknown181
712193 60034
Turtles 5764 50 ('04)718 40093
Trees 6,2001,417 common trees; important shrubs ('04)1,2750 1036118
Wildflowers 17,8002,935 >600 ('02,'06)2,786>1,000 4511186

Proposal for 2006

From: John Pickering <>
To: Annie Simpson <>

31 October, 2005

Annie Simpson
National Biological Information Infrastructure


Here is our proposal for FY2005-6 totaling $50,000. The first part is to continue building IDnature guides for North American invasives, their look-alikes, and other species. In the second part, we propose to mirror upto 80 new databases into Discover Life tools to help NBII build an early detection and rapid response system targeting invasive species. In the final part, we propose to integrate upto 5 databases of your choosing into Discover Life's tools and manage information on human experts knowledgeable about the identification and control of invasives.

If the proposal meets your approval, please relay it to Gladys. If not, send me your recommendations, and I'll change it.

John Pickering Office: 706-542-1115
517 Biological Sciences Building FAX: 706-542-3344
University of Georgia Denise Lim: 706-542-6676
Athens, GA 30602-2602 Department: 706-542-3379
e-mail: Home: 706-353-7076

Title: Web tools to identify, report, and map invasive species in North America -- 3rd year continuation.

Principal Investigator: John Pickering, University of Georgia, Athens

Administrative Contact: Kevin Weick, The Polistes Foundation,,_Kevin.html

Our ultimate goal is to provide everyone with the technology they need to identify, report, and help monitor the distribution and movement of species worldwide. Our first objective is to build identification guides to the flora and fauna of North America so that the general public can help find and accurately identify target species. Our second objective is to assemble, manage, and distribute data and Web tools that will help scientists, land managers, and other citizens rapidly detect and respond to invasive species.

We are developing technology to overcome the two major hurdles that greatly impeded citizens from contributing to the study and management of biological diversity. Many schools and volunteer organizations could help detect and manage invasive species, for example, simply by studying nature in their local communities and reporting what they find. However, most cannot contribute valuable data. They lack the ability to identify target species reliably and cannot easily share their findings with others in a timely manner. We need identification guides that can be successfully used by non-experts. We also need database tools that empower everyone to contribute information and view maps that filter data by source and reliability.

We propose to do the following:

  1. IDnature guides
    Using the methods described in our 2005 proposal (, we propose to continue to improve and illustrate on-line identification guides to distinguish invasive species from each other and their look-alikes. We will focus on helping users answer the following two questions:
    • Is it a known invader?
      As our primary goal for 2006, we propose to incorporate all the character-state information that has been recently added to the Global Invasive Species Database database to tell invasive species from look-alikes. We propose to add all the look-alike species in the Global Invasive Species Database to a new guide called North_American_Invasive_lookalikes. By combining and resolving this guide with our existing North_American_Invasive guide into a new North_American_Invasives_AND_lookalikes guide, we will help users determine whether they have an known invader or not.
    • What is it?
      Unless users are specifically interested in whether a species is invasive or not, they are more likely to seek an identification tool that will help them determine what it is. Once they have an identification, they can then link to information that will tell them the status of whether what they have is invasive to a particular location. While it is more work to build a guide to say all trees, rather than just invasive ones, in the long run we feel that more people will use guides that include all members of a group, not just the invasive species and their look-alikes. Hence, we propose to continue building general guides to the flora and fauna of North America. In 2006, we propose to devote as much effort as possible to help in the indentification of small plants, i. e., wildflowers or weeds, depending on ones perspective.

    Whenever possible, as we have done for trees and shrubs, we will link each species in the guides to high-quality photographs, a distribution map, and textual information provided by our partners' databases and other Websites.

  2. Importing databases to share biodiversity information
    In partnership with NBII, we propose to help build the national framework for invasive species early detection and rapid response. Discover Life's new software tools can rapidly integrate time-sensitive, geo-spatial data from numerous sources into on-line maps, guides, species pages, image manager, and search tools. With these tools we can share vast quantities of quality controlled information via the Web to help monitor and manage alien invasives. Furthermore, because our import tools do not require data providers to put their information into a standard schema, we can rapidly import data using our translators from any small or large databases that can export an ASCII text table.

    To aid NBII in integrating information from international, federal, state, and local databases into an integrated, Web-based data management system to help folks identify, detect, map, and respond to invasive species, we propose to integrate up to 1 terabyte of information from up to 80 additional databases of NBII's choosing into Discover Life's tools and serve them on the Web.

    After giving suitable training and support to data sources, we will expect them to provide us with ASCII tables or jpegs that they can either send to us as attachments, upload to secure accounts that we will set up for them, or put their files on the Web so that our robots can access them. We will index and process a wide range of information (geospatial records, images, text, taxonomic lists, character-states, etc.) into our integrated mapper, guides, image manager, species pages, and search tools as described in our prospectus ( Because of the flexibility of our translators, we will enable data providers to upload fields of their choosing, in any order, in either flat tables or relational ones. We will expect geo-coordinates to be in either latitude-longitude or UTM, ideally using the NAD83/WGS84 datum. Where feasible, we propose to set up automatic nightly jobs to update data from providers, as we have done for Mobot's Tropicos database.

  3. Assembling and managing database of experts
    We propose to build a Web-enabled database on Discover Life that integrates up to five personnel databases of NBII's choosing to manage information about experts on invasive species or general biodiversity. We anticipate working with TRED, an Ecological Society of America's database, Pam Fuller's database on aquatic experts, and possibly information provided by the U.S. Department of Agriculture. As above, we will expect data sources to provide us with data in ASCII tables, such as exported from Excel or Access with tab delimited fields. We will set up a Web front-end using our tools to allow data providers to change records via their browsers. We will also set up search tools so that Web users can make sophisticated searches by taxon, geographic location, terrestrial versus aquatic, and other useful criteria.

  4. Servers
    At no charge to users, we will serve the proposed guides, images, maps, and databases through existing Discover Life servers into the foreseeable future.
    • Currently we have 11 Sun servers at the University of Georgia, Athens; 6 Sun servers, donated by Sun Microsystems Inc., at Missouri Botanical Garden, and one Linux server at the Agricultural Research Council, South Africa. Together they served over two million pages and images in October, 2005, and are capable of handling Discover Life's anticipated growth in load through 2006.
    • If at some point we are unable to continue this service, we will transfer the guides and associated databases to a non-profit organization or government agency so that service to users is not interrupted.

  5. Copyright
    The PI and other contributors will retain ownership and exclusive copyright, with all rights reserved, to any illustrations, photographs, maps, text, or databases that they place in the guides or elsewhere on the Discover Life or associated Websites. The Polistes Corporation does the same for the 20q software that serves the guides, and, for the mapping software and services it provides.

Budget requested from NBII:
$32,041 Technical support & scientific illustration ($7.00 - $20.00/hour)
$13,678 PI Salary (17% time)
$1,900 Travel, including NBII All Node Meeting
$2,381 5% indirect costs for The Polistes Foundation to manage the grant

Other in kind services:
As part of the partnership to develop the Global Mapper, donates over $35,000 per year in maps and aerial photographs to Discover Life.

Anticipated completion date:
9 months from completion of paper work between USGS-NBII and The Polistes Foundation.

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