Cooperative research on biodiversity informatics:
Creation of web-based tools for invasive species identification, reporting,
mapping and other biodiversity information.
Second year continuation of cooperative agreement G09AC00474.
Agreement's Principal Investigator:
Dr. John Pickering, Discover Life,
Agreement's Administrative Contact:
The Polistes Foundation
133 Washington Street
Belmont, MA 02478
Agreement's USGS Technical Representative
Annie Simpson, National Biological Information Infrastructure
The National Biological Information Infrastructure and Discover Life
are building a network of field sites across North America to study
natural history and track the impact of invasive species, climate change,
acid rain, pollinator declines, and other large-scale ecological factors.
This endeavor uses unique web tools that enable all participants to collect
high quality data. This is the second year of a new cooperative agreement to
develop databases, identification guides, and partnerships.
The USGS' National Biological Information Infrastructure is a Web-based system to provide better accessibility to our
nation's biological resources for land managers, decision-makers, and the general public; it has a broad partner base
from government, academia, and the private sector. The partner of this cooperative agreement is The Polistes Foundation,
the 501-c-3 non-profit umbrella organization of Discover Life, an online information system whose mission is to assemble
and share knowledge about nature in order to improve education, health, agriculture, economic development, and
conservation throughout the world.
This collaboration is part of a DOI-mandated project to create a national framework for invasive species early detection,
rapid assessment, and rapid response. Successful early detection of invasive species can only be accomplished through
the implementation of a series of components:
- A. Identification and Validation
- B. Reporting
- C. Expert Verification
- D. Occurrence Databases
- E. Rapid Assessment
- F. Planning
- G. Rapid Response
This year's continuation of the cooperative agreement will accomplish the following:
Improve interactive identification guides to North American plants and other groups.
Assemble data from life lists of species in participants' personal albums into field site inventories.
Further develop a smart phone interface for interactive species lists, guides, and maps.
Outreach to develop and test research protocols at field stations, schools, and other sites.
Database development, integration, training, and support for use at local through global levels.
At no charge to users, The Polistes Foundation will serve identification guides, images, maps, and databases
through existing Discover Life servers into the foreseeable future. If at some point Polistes is
unable to continue serving the information generated during this cooperative agreement, they will transfer the guides,
mapped information, and associated databases to a non-profit organization or government agency so that service
to users is not interrupted.
Since inception in 1998, Discover Life has had a total of over 649 million web hits.
In May, 2010, it served 25.4 million pages and images to 355,000 IP addresses.
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, albums, maps, and other services it provides.
During this collaboration, the investigators and partners will have no access to USGS
restricted information nor require access to government infrastructure. All work will
be performed at University or other non-federal locations.
4.0 PROJECTS -- PROGRESS AND EXPECTED DELIVERABLES
4.1 Identification Guides
We seek support from NBII to build showcase plant guides focused on the rich flora of the southeast.
We hope funding from other sources will enable us to extend this effort to species throughout North America.
4.1.1 FY09 Progress
4.1.2 Expected FY10 Deliverables
- 126.96.36.199 Improved Guide-building Methods -
Although we have been using our unique guide building technology for over a decade, we are still gaining sophistication in its use.
We have learned from experience and past mistakes how to put large guides together that resolve very quickly. Originally
we felt obligated to fill in the entire matrix of every state of every character for every species in a guide. We have
learned that not only is this time consuming, it does not work as well as a more
streamlined approach. We now only fill in characters that are obvious, distinctive, or have the power to quickly and
efficiently divide groups into smaller parts. For example, we do not need to describe the feet, beak, eye color,
and wing shape of a cardinal. We can get there in two quick strokes: Color red. Has crest. We simply do not score it
for the rest of the characters. They are unnecessary and confusing for the user. Having rebuilt the butterfly guide
this past year using this guide building philosophy, we have learned how to put together larger guides to thousands
of species much more rapidly.
- 188.8.131.52 Locality Filters Make Guides Easier to Use -
Because of existing information in the USDA PLANTS database that we integrated this year,
users can now customize our continental guides for plants to individual states/provinces.
For example, the wildflower guide that we developed six years ago is radically improved by filters for state/province,
major group (monocots, dicots, pteridophytes, gymnosperms), family, and genus. Thus, it is now much easier
to identify violet species, for example. They can be searched by state/province and the genus Viola, in addition to
their color and morphology. Users can quickly extract, for example, yellow violets in Georgia.
- 184.108.40.206 Integration of Online Tools -
In FY 2009, Discover Life made giant strides in integrating its online tools and plans to reap the benefits
this coming year. Specifically, we integrated the Global Mapper, IDnature guides, and albums contributed
by individuals. We use the albums to build maps, which in turn customize the
identification guides, which enable users to more rapidly identify the species in their albums and contribute to the maps.
This circular process enables us to provide services to identify, map, and rapidly detect novel invasive species.
- 220.127.116.11 Expansion of North American Plant Guides -
We now propose to expand and improve our guides to North American plants, focusing on
the eastern flora. The opportunity to accomplish this efficiently arises because digital cameras
are so much better and because our servers can now store millions of images.
This summer we will photograph large numbers of plant species using a protocol that enables identification during any season.
Students will take diagnostic photographs of between 1,000 and 2,000 species at the
Chattahoochee Nature Center, Atlanta Botanical Garden, Atlanta History Center, Georgia State Botanical Garden,
the University of Georgia's Horticulture greenhouses, and other sites in the southeast.
We will also incorporate photographs generously provided by regional contributors,
such as Les Mehrhoff of the Invasive Plant Atlas of New England.
Although we cannot commit to an exact number of species, our goal is to add images to over a thousand
species and resolve these species in the guides. By including photographs of native species and horticultural varieties
with invasive species, these guides will greatly advance the public's ability to detect and report invasives.
- 18.104.22.168 Integration of Other Natural History Websites into Plant Guides -
There are now good websites for wildflowers and other plants of Connecticut, Delaware,
Missouri, Texas, and elsewhere (see
While this information is accessible through Google and other search engines, it is not standardized across websites. Moreover, it is
not organized in a systematic way that allows user to search by characters such as opposite or alternate
leaves, flower color, season, and location. Using our mash-up technology, we propose to incorporate this information into our plant guides so
that users can more easily identify the species on these other resources. Our outreach coordinator will facilitate this process.
In return, she will help contributing websites embed our guides and maps on their sites.
4.2 Life Lists and Site Inventories
Our procedures greatly enhance the temporal and spatial components of data quality.
By following them, the general public can now collect data equal to or exceeding the quality of
most professional researchers.
4.2.1 FY09 Progress
- 22.214.171.124 Life Lists that Generate Site Inventories -
The new "List all" feature of our photograph albums generates a contributor's life list.
Additional new features build species checklists at different geographic levels from country, state,
and county, down to each site's name or exact latitude and longitude. By combining queries across
geographic locations and across contributors' albums and other databases, Discover Life can now generate
species lists for site inventories and monitoring.
We can compare such species lists across sites.
We also use this information to customize our identification guides
and help contributors identify species within their albums.
- 126.96.36.199 Incorporating Cell Phone and Digital Camera Technologies for Time and Place Data -
To improve data quality, we now take advantage of digital cameras' "EXIF" feature, which is a protocol that
embeds a device's date and time stamp into jpeg image. By comparing this value with
digital images of cell phones, we can ascertain the time and date of digital observations to the nearest minute.
Under the best conditions, when contributors also take photographs of a GPS unit,
we can accurately document observations to the nearest second.
Photographs of GPS units enable us to verify locations as well.
4.3 Smart Phones
For the purpose of photographing and reporting invasive species, smart phone technology is not quite ready,
largely because most current phone cameras are low resolution and cannot focus close-up.
They are not yet capable of reporting small
critters. They cannot provide sufficient diagnostic characters for small invasive species.
We hope that this coming year's generation of smart phones will overcome these inadequacies
and allow users to move beyond reporting escaped elephants from the zoo!
4.3.1 Expected FY10 Deliverables
We continue to develop a smart phone interface.
While the devices are not yet there as reporting devices, they are capable
of delivering customizable checklists and guides using the built in GPS units.
We are modifying our HTML code so that our guides, checklists, maps, and images can be delivered to hand-helds.
Our goal is to develop a network of study sites for monitoring large-scale ecological challenges such as
invasive species, climate change, and pollutants.
4.5 Mapping and Data Integration
4.4.1 FY09 Progress
4.4.2 Expected FY10 Deliverables
- 188.8.131.52 Outreach Projects -
We adapted "Goldenrod Challenge" to a more general project called "Bee Hunt" through which contributors can monitor pollinators at any site throughout the season.
Participants can use this project for a simple site survey or a comparison experiment of their own original design.
Progress on the "People's Online Plant Atlas (POPA)" continues with more specific protocols for recording vegetative characteristics
so that users can identify plants at any life stage.
We initiated a project to survey lichens and bryophytes called "Life on the Rocks" and have begun building an online guide to lichens.
We began a new moth survey called "Moth Party" which
encourages the social aspects of photography of noctural insects. Based on enthusiastic inital response, we anticipate this will entice greater participation.
- 184.108.40.206 Web Seminar, Webcast, and Data Collecting How-to Video -
On April 13, 2010, We participated in a web seminar that reached 60 science teachers in 23 states and the District of Columbia.
Our segment of the web seminar introduced teachers to our website and encouraged them to use our projects for teaching science in the classroom.
We scripted and participated in a 30 minute webcast from the Smithsonian National Zoo on May 12, 2010, reaching 1,200 schools and other sites.
For an archive of this webcast, please see
We also produced a video explaining our research protocol for collecting and reporting accurate what-where-when data,
which can be viewed at http://www.discoverlife.org/mp/20p?see=V_BEE1 .
- 220.127.116.11 Initiated Partnerships with Key Study Sites -
This year we have explored which groups of
contributors are likely to use our technology and contribute meaningful data
to Discover Life. Despite considerable effort, we have found that most K-12 teachers are too constrained by
teaching to standardized tests to participate in our research.
Although we are not giving up on formal education, we have found eager and skilled contributors
among nature centers, parks, field stations and other entities that in turn serve K-12 schools with
environmental education or serve undergraduates through REU programs and field courses.
After contacting many potential study sites, we have initiated partnerships with six field sites as pilot sites for a continental network:
Mountain Lake Biological Station, VA; Highlands Biological Station, NC; Balsam Mountain Preserve, NC; Wake Nature Preserve Partnership, NC; Chattahoochee River National Recreation Area, GA; and Stone Mountain Park, GA.
- 18.104.22.168 Provided Support for MP3 Sound Recordings
While we are focusing on high-resolution photographs to identify species, this past year we provided
support to New York City's "Cricket Crawl"
(see http://www.discoverlife.org/cricket ).
We added support for MP3 sound recording devices to
our repertoire of digital devices for documenting biodiversity. Similarly, we are testing and
developing methods for our contributors to use our site to store and manage videos.
- 22.214.171.124 Provide Guidance and Support to Pilot Sites -
In the coming year we propose to work with and provide technical support
to our pilot study sites. Our goals are to enhance both their
environmental education and their inventory and monitoring goals.
Specifically, we will customize our plant guides for each site, including ornamental and invasive species.
At some sites, we will teach photography protocols, set up Moth Party events, lead plant photography field trips, organize Bee Hunt events, or help conduct surveys of lichens and other target groups.
- 126.96.36.199 Build Partnerships with Biological Field Stations -
In September 2010, at the annual meeting of the Organization of Biological Field Stations (OBFS),
we will present Discover Life's technology to field station directors, planting seeds for future
partnerships across the continent. Ultimately we hope to provide infrastructure to many field
sites so that we can document and monitor changes in target taxa that are readily
identifiable from photographs or sound recordings.
4.5.1 FY09 Progress
Through our partnership with GBIF, we are in the process of integrating all their records into Discover Life.
We are also in the process of formatting data from Discover Life contributors into the Darwin Core schema so that they can
be served by GBIF.
4.5.2 Expected FY10 Deliverables
We continue to pull together and clean up data on species names. We now have over 1.3 million valid scientific
names link to family names in the system. In this regard,
our goal for the coming year is to solve the problem of homonyms, both across and within kingdoms.
For example, Stellaris montana is a homonym that is both a bee and an orchid. By this time next year,
we propose to have put the S. Montana bee on the bee pages and the S. montana orchid with their cousins.
We have yet to determine if S. montana pollinates S. montana, but anticipate having such important
information under control by next year!
|Dr. John Pickering||PI||$200||80||$16,000
|Nancy Lowe||Outreach Coordinator||$24||400||$9,600|
|Justin Long||System Support||$35||100||$3,500|
|Becka Walcott||Database Manager||$13||115||$1,495|
|Jill Talmadge||Lab Coordinator||$12||117||$1,405|
|The Polistes Foundation||Grant Management 5%||N/A||N/A||$1,905|
Discover Life employes undergraduates, high school students, and recent graduates
to help with photography, technical support, data entry, guide building, and manual error checking.
We pay these individuals between $9 and $15 per hour depending upon their skill level.