1. Getting collection data, maps, and
images online via open source and
commercial solutions
Michael Giddens

2. Software developer with a focus in
biodiversity informatics.
Follow me @silverbiology

3. What we do
• Design workflows and software to optimize
image capture
• Analyze & Process label images
• Create portals for entomological and scientific
collections
• Develop interactive maps to tell stories about
data
• Provide support and technical advice for NSF
projects

4. Digitization & Data Capture
•
•
•
•
•
•
•
Seconds count
28,800 seconds in an 8 work day
100k @ 30 seconds = 34.7 days
100k @ 29 seconds = 33.5 days
…
100k @ 15 seconds = 17.3 days
Humans are not robots

5. Solutions
•
•
•
•
•
•
Look at every action as a micro task
Find tasks to fill any wait time
Stick to a single workflow
Filename conventions are important
Stick with image sizes and formats needed
Renaming filenames using scanners or data
entry
e.g. SilverImage
• Backup Images!!!

6. Things we learned
• Make sure your lighting environment does not
change
• Dragon dictation is not accurate enough for
number or scientific words
• Manually renaming files is slow
• Some student workers do not care as much as
you do about your collection
• People get burned out

7. Data Processing
•
•
•
•
Optical Character Recognition Engines
Machine Learning
Crowd Sourcing
Human in the Middle

8. Optical Character Recognition Engines
• Free
– Tesseract
• Commercial
– OmniPage
– Abbyy
• Services
– www.silverbiology.com
• Font Training
• No handwriting solution on market

9. Machine Learning
•
•
•
•
•
Data Dictionaries
Conditional logic / Decision Trees
Past data to predict future data
Label / Word Boundaries
Orientation

10. Crowd Sourcing
Notes From Nature
• http://www.notesfromnature.org
Ornithological
from Natural History Museum
Calbug – Essig Museum Collections

11. ALA Volunteer Program
• http://volunteer.ala.org.au

12. Human In The Middle
•
•
•
•
•
•
Rotating Images
Tagging Areas
Metadata tagging
Identifying False Positives
Verification Steps
Bulk Validation

13. Web Portals
•
•
•
•
In-House
Specify 6 Portal
Symbiota
SilverCollection
– California Academy of Sciences
– Angelo State Natural History Museum
– Louisiana State Arthropod Museum
– Kansas State University Entomology Dept.
– Mississippi Entomological Museum
– NLBIF

14. Explore / Browse
•
•
•
•
•
•
•
•
Taxonomy
Taxonomy (Filtered)
Family
Genus
Type Status
Regions
Collectors
Custom

15. Custom Checklists

16. Spreadsheet Format

17. Collecting Events

18. Images

19. Specimen Details

20. Reports

21. Interactive Maps

22. • Online service to Map, Analyze and Build
applications with your data
• Simple to use
• Easily create distribution maps, heat maps,
and category maps
• Access to full geospatial query engine
• Visualizing ecological models
• Works well with lots of data

23. GBIF - 350 Million Records
http://www.gbif.org/occurrence

24. Visualizing two months
in the life of seagull Eric
Blog on Lifewatch by Peter Desmet

25. Interactive Occurrence Data

26. Interactive Map Modes
Density Maps
Polygons
Grids

27. Useful Tools Provided By the
Global Biodiversity Information Facility
http://tools.gbif.org
•
•
•
•
•
•
•
Darwin Core Archive Assistant
Darwin Core Archive Validator
Higher Taxonomy Services
Name Finder
Name Parser
GBIF API Services
Integrated Publishing Toolkit (IPT)

28. Global Names Architecture
http://www.gloablnames.org
• Global Names Recognition and Discovery
• Global Names Index

29. Questions?
Michael Giddens
www.silverbiology.com