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