This was a presentation given at the workshop for small herbaria.

1. SILVERBIOLOGY
BIODIVERSIT Y INFORMATICS SERVICES
WWW.SILVERBIOLOGY.COM
MICHAEL GIDDENS
@SILVERBIOLOGY
MIKEGIDDENS@SILVERBIOLOGY.COM

2. SILVERBIOLOGY HISTORY
 Formed in 2008
 Provides consulting and software to advance digitization and
research in the scientific community
 Created SilverImage (rapid digitization workflow)
 Finalizing Biodiversity Image Server (management software
for scientific images)
 Developing HelpingScience.org (citizen science data transcription)
 Created SilverCollection (web research portal)
 Created Mobile Copy Station (designed for collection digitization )
 Provides Herbarium Barcode Labels

3. WHO WE HELP
 Cyberflora Louisiana Herbaria
 Mississippi Herbaria Project
 Georgia Herbaria Project
 Rio de Janeiro Jardim Botânico
 Denver Botanic Gardens
 California Academy of Sciences
 Angelo State Natural History Museum
 The Netherlands all collections
 Kansas State
 University of Queensland Australia
 And others…

4. SMALL HERBARIA OF MICHIGAN
 We will be providing:
 A mobile copy station to share among the collections.
 Remote technical support on how to image your collection.
 60k barcode labels
 A server running the Biodiversity Image Server software to house and
manage all 60k+ specimen images that will be captured.
 SilverCollection web portal through the MiCOB website to access
both images and occurrence data as that information becomes
available.
 Workflows and methods on how to transcribe label data using the
digital specimen images that are taken.
 Digital maps of georeferenced data.
 Consulting on how to make us of your images and occurrence data
for research, websites, and public projects.
 Helping to submit your occurrence data to Global Biodiversity
Information Facility (GBIF) Currently 388 million indexed records.

5. MOBILE COPY STATION
 Complete Kit
 115lbs but does have wheels
 Assembly & Instruction Guides
 <1hr to setup & breakdown
 Uses SilverImage to manage images
 Images automatically
upload to project
 Great for sharing
 Can fit in most cars
 Container can be
shipped as is

6. TECHNICAL SUPPORT
 We provide 9-6 MST technical support for mobile
copy stations and SilverImage
 Skype
 LogMeIn

7. BIODIVERSIT Y IMAGE SERVER
 Image management tools
 Grouping images by collection
 Metadata tagging (Darwin Core, Dublin Core, user defined)
 Associating images to geographical regions
 Events – great for use in expeditions, field trips, bioblitz, etc…
 Sets – used for image matrices
 Thumbnail generation
 OCR Analysis (Tesseract OCR)
 Taxonomic resolution services
 Barcode Detection
 RESTful web service
 SDK’s for software developers

8. BIS DESKTOP CLIENT
 Manage all local images before sending to BIS server
 Synchronization of all metadata and tags from BIS server
 Advanced tools for tagging images in bulk
 Uploads many images at once
 Great for:
 Microscopy stations
 Living plant photography
 Field station computer
 Home computer
 Office computer
 Lab computer
 BioBlitz event

9. SILVERCOLLECTION
 Web portal for all collection data
 Mobile version coming soon to Apple Store & Google Play
DEMO
 http://data.cyberfloralouisiana.com/lsu/

10. LABEL PROCESSING METHOD Developed by
HELPINGSCIENCE.ORG SilverBiology

11. GOAL (REPEAT 60+ MILLION TIMES)
From This To This
• StateProvince: Arkansas
• County: Bradley
• Genus: Botr ychium
• SpecificEpithet: biternatum
• Authorship: (Sav.) Under wood
• Collector: Sherri Leslie, Kaylon
Cornish
• CollectorNumber: 593
• DateCollected: 1984-09-23
• TRS: Sec. 3, T12S, R9W
Species Lookup: http://ecat-dev.gbif.org/usage/2650191

12. GOAL (REPEAT 60+ MILLION TIMES)
From This To This
• StateProvince: Arkansas
• County: Bradley
• Genus: Botr ychium
• SpecificEpithet: biternatum
• Authorship: (Sav.) Under wood
• Collector: Sherri Leslie, Kaylon
Cornish
• CollectorNumber: 593
• DateCollected: 1984-09-23
• TRS: Sec. 3, T12S, R9W
Species Lookup: http://ecat-dev.gbif.org/usage/2650191

13. WORKFLOW
Identify Enter Accept
Lexical
Identify OCR Primary Values Value Assemble
Grouping &
Labels Labels DwC for for Each Label Data
Verification
Fields Fields Field

14. IDENTIFYING LABELS
Step 1 To This
 Sign In
 Request Image
 Click & Drag
 Click & Drag
 <Enter>
 Repeat
 Average Time: 300/hr
per person

15. WORKFLOW
Identify Enter Accept
Lexical
Identify OCR Primary Values Value Assemble
Grouping &
Labels Labels DwC for for Each Label Data
Verification
Fields Fields Field

16. EVERNOTE OCR PROCESSING
Sample JPG label
$5/1GB per month JSON output
~ label cost: $0.001

17. AFTER EVERNOTE

18. WORKFLOW
Identify Enter Accept
Lexical
Identify OCR Primary Values Value Assemble
Grouping &
Labels Labels DwC for for Each Label Data
Verification
Fields Fields Field

19. STEP 2) IDENTIFYING LABELS
What we capture. What we leave on the label.
• Scientific Information • Habitat Information
( Fa m i l y, G e n u s , S p e c i e s , S u b s p e c i e s , A u t h o r )
• Locality Description
• Collection Information
( N a m e , N u m b e r, D a t e ) • Collector Notes
• Geographical Information • Other
( C o u n t r y, S t a t e , C o u n t y, L o c a l i t y,
Lat/Lon, TRS)
• Determination Information
( D e t e r m i n e r, S c i e n t i f i c N a m e , D a t e
Determined)
• Extra Information
( A c c e s s i o n N u m b e r, Ty p e S t a t u s )

20. WORKFLOW
Identify Enter Accept
Lexical
Identify OCR Primary Values Value Assemble
Grouping &
Labels Labels DwC for for Each Label Data
Verification
Fields Fields Field

21. LEXICAL GROUPING
Internal Step
 Compare words to
OCR value and if
it is distinct assign
to lexical set.
 Send image to
data entry.

22. BULK VALIDATION
Internal Step
 Look at the value
that will be assigned
to the list of images
if any are not the
correct value move to
manual data entry
blacklist.
 Repeat
 Based on Lexical Groups

23. WORKFLOW
Identify Enter Accept
Lexical
Identify OCR Primary Values Value Assemble
Grouping &
Labels Labels DwC for for Each Label Data
Verification
Fields Fields Field

24. DATA ENTRY
Public Step
 Multiple Interfaces
 Dates
 Lat/Lng
 Names
 Scientific Names
 User receive virtual
tokens to use in the
store for every correct
word

25. DATA ENTRY VARIATIONS

26. WORKFLOW
Identify Enter Accept
Lexical
Identify OCR Primary Values Value Assemble
Grouping &
Labels Labels DwC for for Each Label Data
Verification
Fields Fields Field

27. FIELD VERIFICATION
Computer: Asplenium Frequency
Volunteer 2: Asplenium Asplenium: 2
Volunteer 3: Asplenlum Asplenlum: 1
Volunteer 4: Asplenium Asplenium: 3
Asplenium: 1
Points Earned: Volunteer 2 & 4

28. WORKFLOW
Identify Enter Accept
Lexical
Identify OCR Primary Values Value Assemble
Grouping &
Labels Labels DwC for for Each Label Data
Verification
Fields Fields Field

29. OCCURRENCE DATA
 Export Formats
 CSV
 Darwin Core Archive
 Others on request
 Filters
 By any combination of Darwin Core Fields
 Restful web services

30. SUSTAINABILIT Y
 HelpingScience depends on a symbiotic relationship between
collections providing specimen sheets and volunteers to per form data
entr y.
 Volunteers are given HS Tokens to be used in the HS Store in
exchange for their time.
 The store is a percentage of the cost per label that is given back to
the community.
The Store
 Fundraisers
 Small micro loans given to botany undergraduate students for research
 Sponsorships for students to attend scientific conferences
 K12 equipment funding for science departments
 Charitable Organizations
 Fund Small Herbaria Digitization

31. SILVERBIOLOGY
BIODIVERSIT Y INFORMATICS SERVICES
WWW.SILVERBIOLOGY.COM
MICHAEL GIDDENS
@SILVERBIOLOGY
MIKEGIDDENS@SILVERBIOLOGY.COM