Transcript - Animal Diversity Web

A Biodiversity Content Management System for
Research, Education, and Outreach
Cynthia Sims Parr
University of Maryland, College Park
Co-authors Roger Espinosa, Tanya Dewey, George
Hammond, Phil Myers, of University of Michigan
University of Michigan
Museum of Zoology
Biodiversity is the extraordinary
variety of all life on Earth - from genes to
species to entire ecosystems.
Biodiversity
-- Smithsonian Institution Monitoring and Assessment of Biodiversity Program
Access
Access
Change
Change
Problems in Biodiversity Databases
Complex databases
 Organism names
 Habitats
 Conservation status
 Reproductive parameters
 Interactions, etc.
 Specimen-level and
aggregated
Diverse users
 Policy makers
 Land-use planners
 Educators, students
 Laypersons
 Biologists
Changes over time and in different locations
Changes in our view of what scale is important
Ecological dataset volume rapidly increasing
Changes in technology
Who will maintain these knowledgebases?
More general scientific data management questions
How to design a back-end so that contributors can easily enter
data, and end-users can easily retrieve what they want, data
managers can make big and small changes
How to use the same system for multiple constituent groups

research

education on different levels

outreach to the public
http://www.animaldiversity.org
Animal Diversity Web introduction
Geographically and taxonomically global
High traffic, 70,000 pages per day
From educational  outreach  science
Animal Diversity Web challenges
Data entry

Student contributors

Lack domain expertise, technical expertise

Few repeat contributors

Completeness, Structuring

Single template covering all animal phyla would have unnecessary
keywords and sections for most taxa
Data retrieval

To support inquiry education or science, must be able to get data out
via queries

Users diverse so may not have knowledge of controlled vocabulary
What happens when underlying data model changes?
ADW’s “loosely coupled” architecture
Nodes separately managed from
identifiers used to relate and display them
•Template
•Taxonomic names
•Stylesheets
Weinberger, 2002
Taxonomic MySQL database
Sources
ITIS
EMBL reptiles
SI mammals
Howard & Moore birds
CAS fishes
Walks
Common names
Creating content
Register for workspace
Identify subject
Receive customized template
(increasingly more structured)
Text, keywords, data fields
Attach references
Review, edit, publish
Taxon Filtering for customized templates
e.g. template section
customized for Aves
XML template
Taxon filter
Change template elements
Workflow, legacy content
If new content: receives
new template
Legacy objects remain
semantically tagged for
display and search
New template elements
available for ADW editors
Content display for different audiences
http://biokids.umich.edu
http://www.animaldiversity.org
A multi-use database supporting maximum
access and minimum barriers to change
Content all managed in the same system, with multiple displays
(loose coupling, taxon filtering, customized stylesheets)
Complex object templates can be created or modified,
but legacy data remains semantically marked up and thus
available for display and querying
New style sheets, updated taxon data
Where do we go next?
Vertical integration
ACCTTGAGATAG
ACCTTGAGATAG
ACCTTGAGACAG
Example: Biologist studying genetic
basis of a behavioral trait that varies
across Animalia.
Natural history ontology from Animal Diversity Web
+ SEEK ecological ontologies
+ Animal Behavior ontology
(for more information, see me)
+ Gene Ontology ….
Scaling, engagement, and interoperability

Contribution model scales well

User involvement fosters engagement

Accessible resource for science
Acknowledgements




ADW team: particularly Phil Myers, Roger Espinosa, Tricia Jones,
Tanya Dewey George Hammond
BioKIDS team: particularly Nancy Songer
Ontologies: Peter Midford and Jennifer Golbeck
NSF IERI (UMich) and ITR (UMd) grants
Ontologies, manuscript, and presentation can be found at
http://www.animaldiversity.org/site/about/technology/