Web-based Specimen Databasing:Lessons from the Plant Bug
Planetary Biodiversity Inventory Project
presented by
Randall T. SchuhCurator and Chair
Division of Invertebrate ZoologyAmerican Museum of Natural History, New York
http://research.amnh.org/pbi
•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
keyor mouse•Multiple modes
–Museum Mode–Edit Mode–Report Mode
•Unique specimen identifiers, batch loading
PBI Specimen Database Approach
Justification•Facilitate specimen tracking
Necessary Attributes•Machine readability– Bar codes– Matrix codes
•Human readability•Small size of code-bearing
labels•Ease of integration intoexisting collection practices
Unique Specimen Identification
•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
Museum Mode
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
Output publication-ready specimens-examined data for:
• New species• Previously described species
Generate downloadable reports for:
• Host lists• Specimen lat/lon data for mapping
Report Mode
•Create usernames and passwords
•Allocate access privileges
•Create database interfaces and specify settings
Admin Mode
Performed on a centralized basis or by theuser 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
Georeferencing
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 on-line systematic catalog
•GBIF data provider
Database Outputs & Extensions
• 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
Interface/Web 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 Strengths
•Requires broadband connection
•Requires high resolution monitor
Database/Interface Requirements
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
Lessons Learned
Special thanks to:Nina GregorevSheridan Hewson-Smith
Additional thanks to:James AsheMark BreedloveGerry CassisDavid FurthLorenzo PrendiniMichael SchwartzTom TromboneChristiane WeirauchDenise WynigerNational Science FoundationAmerican Museum of Natural HistoryAustralian Museum
http://research.amnh.org/pbi
Acknowledgments
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