Download View slideshow here - American Museum of Natural History

Web-based Specimen Databasing:
Lessons from the Plant Bug
Planetary Biodiversity Inventory
Project
presented by
Randall T. Schuh
Curator and Chair
Division of Invertebrate Zoology
American Museum of Natural History, New York
http://research.amnh.org/pbi
PBI Specimen Database Approach
•
•
•
•
•
•
Tailored to entomological/invertebrate
collections
Browser based
Data entry over Internet to central server
Open source software – MySQL database
Efficient data entry navigation using TAB key
or mouse
Multiple modes
–
–
–
•
Museum Mode
Edit Mode
Report Mode
Unique specimen identifiers, batch loading
Unique Specimen Identification
Justification
• Facilitate specimen tracking
Necessary Attributes
• Machine readability
– Bar codes
– Matrix codes
• Human readability
• Small size of code-bearing labels
• Ease of integration into
existing collection practices
Museum Mode
•
Main data entry mode
•
Most effective using Mozilla Firefox browser
– Allows for multiple keystroke searching in
–
drop-down menus
Retains and displays prior entries in memory
Edit Mode
Allows the user to:
•
•
•
•
Check and emend data entered
through Museum Mode
Add higher taxon names, institutions,
and larger scale locality information,
which cannot be added through
Museum Mode
Correct taxon names, institutions,
collectors, and locality information
Query, select, and batch-modify
specimen and host information
Report Mode
Output publication-ready specimensexamined data for:
• New species
• Previously described species
Generate downloadable reports for:
•
•
Host lists
Specimen lat/lon data for mapping
Admin Mode
•
Create usernames and passwords
•
Allocate access privileges
•
Create database interfaces and
specify settings
Georeferencing
Performed on a centralized basis or by the
user at the time of locality data entry
GEOLocate
Desirable Features
• Easy to use
• Individual & batch processing
• Manual correction capability
Limitations
• erroneous parsing of some locality names
• still under development
http://www.museum.tulane.edu/geolocate/default.aspx
Database Outputs & Extensions
Current
•
•
Reports for specimen data, coordinates,
and hosts
Mapping in real time via link to on-line
systematic catalog
Future
•
•
•
Support for specimen, host, habitat images
HTML species pages produced via online systematic catalog
GBIF data provider
Interface/Web Strengths
•
Easy to use
•
Intuitive
•
Incorporates look-up functions to facilitate
rapid and accurate data entry
•
Allows multiple simultaneous users at diverse
locations around the world
•
Allows simultaneous use of multiple modes
•
Allows for centralized georeferencing
•
Allows data entry from locations other than
home institutions
Database Strengths
•
Relational and highly normalized
•
MySQL enterprise-level multithread backend
•
SQL compliant, facilitating data retrieval
•
Highly scaleable with no restrictions on
database size or numbers of users
•
Rapid response time
•
GBIF compliant
•
Allows for both unique specimen identification
and lot-based approaches
Database/Interface Requirements
•
Requires broadband connection
•
Requires high resolution monitor
Lessons Learned
Positive
•
•
•
Web-based approach well-adapted to
geographically distributed team
Web-based research tools improve productivity
through user feedback network
Common problems resolved through singular
solutions
Negative (applying to all software usage)
•
•
Data model allows for duplications due to lack
of familiarity and training
Effective use requires some adaptation on part
of users
Acknowledgments
Special thanks to:
Nina Gregorev
Sheridan Hewson-Smith
Additional thanks to:
James Ashe
Mark Breedlove
Gerry Cassis
David Furth
Lorenzo Prendini
Michael Schwartz
Tom Trombone
Christiane Weirauch
Denise Wyniger
National Science Foundation
American Museum of Natural History
Australian Museum
http://research.amnh.org/pbi