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.
Topozone.com 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
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
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.
Usage is up considerably.
Discover Life's servers at the University of Georgia, www.discoverlife.org,
and Missouri Botanical Garden, usmo4.discoverlife.org,
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.
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.
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.
We build checklists and turn them into guides through the following steps detailed in our 2005 proposal
- create a checklist of valid scientific names;
- assemble species pages that include images, maps, text and links to other Websites;
- make a guide by scoring character-state attributes of each species;
- resolve the guide to make sure that it contains sufficient information to identify species;
- illustrate character-states, and
- 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
||740 + 20% unknown||751
||funded by USGS-BRD||619||104
||128 + unknown||134
||150 + unknown||118
||>900 freshwater||28,666 world
|Frogs & Toads
||165 + unknown||167
||177 + unknown||181
||common trees; important shrubs ('04)||1,275||0
Proposal for 2006
From: John Pickering <email@example.com>
To: Annie Simpson <firstname.lastname@example.org>
31 October, 2005
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: email@example.com ||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,
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:
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
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.
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.
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.
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.
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 Topozone.com, 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,
Topozone.com 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.|