small herbaria michigan - silvercollection
DESCRIPTION
This was a presentation given at the workshop for small herbaria.TRANSCRIPT
SILVERBIOLOGY BIODIVERSITY INFORMATICS SERVICES
WWW.SILVERBIOLOGY.COM
MICHAEL GIDDENS @SILVERBIOLOGY
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 (cit izen science data transcription)
Created SilverCollection (web research portal)
Created Mobile Copy Station (designed for col lection digit ization )
Provides Herbarium Barcode Labels
SILVERBIOLOGY HISTORY
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…
WHO WE HELP
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.
SMALL HERBARIA OF MICHIGAN
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
MOBILE COPY STATION
We provide 9-6 MST technical support for mobile
copy stations and SilverImage
Skype
LogMeIn
TECHNICAL SUPPORT
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
BIODIVERSITY IMAGE SERVER
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
BIS DESKTOP CLIENT
Web portal for all collection data
Mobile version coming soon to Apple Store & Google Play
DEMO http://data.cyberfloralouisiana.com/lsu/
SILVERCOLLECTION
Developed by
SilverBiology
LABEL PROCESSING METHOD
HELPINGSCIENCE.ORG
From This To This
• StateProvince: Arkansas
• County: Bradley
• Genus: Botrychium
• SpecificEpithet: biternatum
• Authorship: (Sav.) Underwood
• Collector: Sherri Leslie, Kaylon
Cornish
• CollectorNumber: 593
• DateCollected: 1984-09-23
• TRS: Sec. 3, T12S, R9W
GOAL (REPEAT 60+ MILLION TIMES)
Species Lookup: http://ecat-dev.gbif.org/usage/2650191
From This To This
• StateProvince: Arkansas
• County: Bradley
• Genus: Botrychium
• SpecificEpithet: biternatum
• Authorship: (Sav.) Underwood
• Collector: Sherri Leslie, Kaylon
Cornish
• CollectorNumber: 593
• DateCollected: 1984-09-23
• TRS: Sec. 3, T12S, R9W
GOAL (REPEAT 60+ MILLION TIMES)
Species Lookup: http://ecat-dev.gbif.org/usage/2650191
Identify Labels
OCR Labels
Identify
Primary DwC
Fields
Lexical Grouping & Verification
Enter Values
for Fields
Accept Value
for Each Field
Assemble Label Data
WORKFLOW
Step 1 To This
IDENTIFYING LABELS
Sign In
Request Image
Click & Drag
Click & Drag
<Enter>
Repeat
Average Time: 300/hr
per person
Identify Labels
OCR Labels
Identify
Primary DwC
Fields
Lexical Grouping & Verification
Enter Values
for Fields
Accept Value
for Each Field
Assemble Label Data
WORKFLOW
Sample JPG label
JSON output $5/1GB per month
~ label cost: $0.001
EVERNOTE OCR PROCESSING
AFTER EVERNOTE
Identify Labels
OCR Labels
Identify
Primary DwC
Fields
Lexical Grouping & Verification
Enter Values
for Fields
Accept Value
for Each Field
Assemble Label Data
WORKFLOW
What we capture.
• Scientific Information (Fami ly, Genus , Spec ies , Subspec ies , Author )
• Collection Information (Name, Number, Date )
• Geographical Information (Count r y, S tate , County, Loca l i ty,
Lat/Lon , TRS)
• Determination Information (Determiner, Sc ient i f i c Name, Date
Determined)
• Extra Information (Access ion Number, Type S tatus )
What we leave on the label.
• Habitat Information
• Locality Description
• Collector Notes
• Other
STEP 2) IDENTIFYING LABELS
Identify Labels
OCR Labels
Identify
Primary DwC
Fields
Lexical Grouping & Verification
Enter Values
for Fields
Accept Value
for Each Field
Assemble Label Data
WORKFLOW
Internal Step
Compare words to
OCR value and if
it is distinct assign
to lexical set.
Send image to
data entry.
LEXICAL GROUPING
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
BULK VALIDATION
Identify Labels
OCR Labels
Identify
Primary DwC
Fields
Lexical Grouping & Verification
Enter Values
for Fields
Accept Value
for Each Field
Assemble Label Data
WORKFLOW
Public Step
Multiple Interfaces
Dates
Lat/Lng
Names
Scientific Names
User receive vir tual
tokens to use in the
store for every correct
word
DATA ENTRY
DATA ENTRY VARIATIONS
Identify Labels
OCR Labels
Identify
Primary DwC
Fields
Lexical Grouping & Verification
Enter Values
for Fields
Accept Value
for Each Field
Assemble Label Data
WORKFLOW
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
FIELD VERIFICATION
Identify Labels
OCR Labels
Identify
Primary DwC
Fields
Lexical Grouping & Verification
Enter Values
for Fields
Accept Value
for Each Field
Assemble Label Data
WORKFLOW
Export Formats
CSV
Darwin Core Archive
Others on request
Filters
By any combination of Darwin Core Fields
Restful web services
OCCURRENCE DATA
HelpingScience depends on a symbiotic relationship between collections providing specimen sheets and volunteers to perform data entry.
Volunteers are given HS Tokens to be used in the HS Store in exchange for their t ime.
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
SUSTAINABILITY
SILVERBIOLOGY BIODIVERSITY INFORMATICS SERVICES
WWW.SILVERBIOLOGY.COM
MICHAEL GIDDENS @SILVERBIOLOGY