Small Herbaria Michigan - SilverCollection

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

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Small Herbaria Michigan - SilverCollection

  1. 1. SILVERBIOLOGYBIODIVERSIT Y INFORMATICS SERVICES WWW.SILVERBIOLOGY.COM MICHAEL GIDDENS @SILVERBIOLOGY MIKEGIDDENS@SILVERBIOLOGY.COM
  2. 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. 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. 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. 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. 6. TECHNICAL SUPPORT We provide 9-6 MST technical support for mobile copy stations and SilverImage Skype LogMeIn
  7. 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. 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. 9. SILVERCOLLECTION Web portal for all collection data Mobile version coming soon to Apple Store & Google PlayDEMO http://data.cyberfloralouisiana.com/lsu/
  10. 10. LABEL PROCESSING METHOD Developed byHELPINGSCIENCE.ORG SilverBiology
  11. 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. 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. 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. 14. IDENTIFYING LABELSStep 1 To This Sign In Request Image  Click & Drag  Click & Drag  <Enter>  Repeat Average Time: 300/hr per person
  15. 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. 16. EVERNOTE OCR PROCESSINGSample JPG label $5/1GB per month JSON output ~ label cost: $0.001
  17. 17. AFTER EVERNOTE
  18. 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. 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. 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. 21. LEXICAL GROUPINGInternal Step Compare words to OCR value and if it is distinct assign to lexical set. Send image to data entry.
  22. 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. 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. 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. 25. DATA ENTRY VARIATIONS
  26. 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. 27. FIELD VERIFICATIONComputer: Asplenium FrequencyVolunteer 2: Asplenium Asplenium: 2Volunteer 3: Asplenlum Asplenlum: 1Volunteer 4: Asplenium Asplenium: 3 Asplenium: 1Points Earned: Volunteer 2 & 4
  28. 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. 29. OCCURRENCE DATA Export Formats  CSV  Darwin Core Archive  Others on request Filters  By any combination of Darwin Core Fields Restful web services
  30. 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. 31. SILVERBIOLOGYBIODIVERSIT Y INFORMATICS SERVICES WWW.SILVERBIOLOGY.COM MICHAEL GIDDENS @SILVERBIOLOGY MIKEGIDDENS@SILVERBIOLOGY.COM

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