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Small Herbaria Michigan - SilverCollection
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Small Herbaria Michigan - SilverCollection

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

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

Published in: Technology

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  • 1. SILVERBIOLOGYBIODIVERSIT 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 byHELPINGSCIENCE.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, R9WSpecies 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, R9WSpecies Lookup: http://ecat-dev.gbif.org/usage/2650191
  • 13. WORKFLOW Identify Enter Accept LexicalIdentify OCR Primary Values Value Assemble Grouping & Labels Labels DwC for for Each Label Data Verification Fields Fields Field
  • 14. IDENTIFYING LABELSStep 1 To This Sign In Request Image  Click & Drag  Click & Drag  <Enter>  Repeat Average Time: 300/hr per person
  • 15. WORKFLOW Identify Enter Accept LexicalIdentify OCR Primary Values Value Assemble Grouping & Labels Labels DwC for for Each Label Data Verification Fields Fields Field
  • 16. EVERNOTE OCR PROCESSINGSample JPG label $5/1GB per month JSON output ~ label cost: $0.001
  • 17. AFTER EVERNOTE
  • 18. WORKFLOW Identify Enter Accept LexicalIdentify OCR Primary Values Value Assemble Grouping & Labels Labels DwC for for Each Label Data Verification Fields Fields Field
  • 19. STEP 2) IDENTIFYING LABELSWhat 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 LexicalIdentify OCR Primary Values Value Assemble Grouping & Labels Labels DwC for for Each Label Data Verification Fields Fields Field
  • 21. LEXICAL GROUPINGInternal Step Compare words to OCR value and if it is distinct assign to lexical set. Send image to data entry.
  • 22. BULK VALIDATIONInternal 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 LexicalIdentify OCR Primary Values Value Assemble Grouping & Labels Labels DwC for for Each Label Data Verification Fields Fields Field
  • 24. DATA ENTRYPublic 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 LexicalIdentify OCR Primary Values Value Assemble Grouping & Labels Labels DwC for for Each Label Data Verification Fields Fields Field
  • 27. FIELD VERIFICATIONComputer: Asplenium FrequencyVolunteer 2: Asplenium Asplenium: 2Volunteer 3: Asplenlum Asplenlum: 1Volunteer 4: Asplenium Asplenium: 3 Asplenium: 1Points Earned: Volunteer 2 & 4
  • 28. WORKFLOW Identify Enter Accept LexicalIdentify 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. SILVERBIOLOGYBIODIVERSIT Y INFORMATICS SERVICES WWW.SILVERBIOLOGY.COM MICHAEL GIDDENS @SILVERBIOLOGY MIKEGIDDENS@SILVERBIOLOGY.COM