The New York Botanical Garden
The Macroalgae Digitization Project
Advancing online algal collections at the New York Botanical Garden and beyond
Stephen D. Gottschalk, Naveed Davoodian, Sarah N. Dutton, Juli A. Janis, Beryl C. M. Kahn, Theodore D. Kirkinis, Eli Min, Jonathan W. Toll, and Kenneth G. Karol
The New York Botanical Garden
The Macroalgal Consortium49 participating institutions, 25 states, 1 U.S. territory
Map courtesy of Christopher Neefus, 2014.
The New York Botanical Garden
Primary Digitization Centers
New York Botanical Garden
University of California
University of Michigan
University of New Hampshire
University of North Carolina
University of Washington
The New York Botanical Garden
Digitizing Institutions
Academy of Natural Sciences
Bishop Museum Brooklyn Botanic Garden
Duke University Field Museum of Natural History
Harvard University
Oregon State University University of Alaska SE University of Guam Marine Lab
University of Hawaii University of South Florida
University of Vermont
The New York Botanical Garden
Contributing InstitutionsBrown University Rutgers University
University of Connecticut
Butler University San Diego Nat. Hist. Museum University of Massachusetts
Florida Museum of Nat. History Shasta College
University of Rhode Island
Hopkins Marine Station Texas A&M University University of South Carolina
Humboldt State University Univ of North Carolina Wilmington
University of Texas Pan Am.
Louisiana State University Univ. of Alaska Museum University of Utah
Miami University Univ. of Texas Marine Science Institute TX
West Virginia University
Michigan State University University of Alabama Yale University
Mote Marine Laboratory University of California (Berkley)
Youngstown State University
Nat. Tropical Botanical Garden University of California (Davis)
New York State Museum University of California (Irvine)
The New York Botanical Garden
Scope
• More than 1.1 million specimens.
• Collections dating back 200 years.
• All major algal groups:
– Red Algae
– Green Algae
– Brown Algae
The New York Botanical Garden
Digitization will consist of . . .
A speciman image
The New York Botanical Garden
Digitization will consist of . . .
No. 60-11-21-1
In c. 4” of water, pool c. 100 ft. E of bridge,
Warrill River, c. 44.7 mi. N of Warwick,
Queensland, Australia.
Coll.: R. D. Wood
Nov. /21/1960
A label
transcription
The New York Botanical Garden
Digitization will consist of . . .
A taxon determination
Chara connivens P. Salzmann ex A. Braun
The New York Botanical Garden
Digitization will consist of . . .
A georeferenced point
The New York Botanical Garden
www.macroalgae.org
The New York Botanical Garden
Workflow Summary
Manual Data EntryIn-house or
crowd sourcing
Specimen Database
Skeletal recordsImages
Complete dataOCR
Specimen Curation
Specimen Imagingbarcode.jpg
OCR Textbarcode.txt
Skeletal Recordsbarcode
scientific name
GeoreferencingDuplicate Record Matching
(exsiccati)
The New York Botanical Garden
Workflow Summary
Manual Data EntryIn-house or
crowd sourcing
Specimen Database
Skeletal recordsImages
Complete dataOCR
Specimen Curation
Specimen Imagingbarcode.jpg
OCR Textbarcode.txt
Skeletal Recordsbarcode
scientific name
GeoreferencingDuplicate Record Matching
(exsiccati)
The New York Botanical Garden
Workflow Summary
Manual Data EntryIn-house or
crowd sourcing
Specimen Database
Skeletal recordsImages
Complete dataOCR
Specimen Curation
Specimen Imagingbarcode.jpg
OCR Textbarcode.txt
Skeletal Recordsbarcode
scientific name
GeoreferencingDuplicate Record Matching
(exsiccati)
The New York Botanical Garden
Workflow Summary
Manual Data EntryIn-house or
crowd sourcing
Specimen Database
Skeletal recordsImages
Complete dataOCR
Specimen Curation
Specimen Imagingbarcode.jpg
OCR Textbarcode.txt
Skeletal Recordsbarcode
scientific name
GeoreferencingDuplicate Record Matching
(exsiccati)
The New York Botanical Garden
Workflow Summary
Manual Data EntryIn-house or
crowd sourcing
Specimen Database
Skeletal recordsImages
Complete dataOCR
Specimen Curation
Specimen Imagingbarcode.jpg
OCR Textbarcode.txt
Skeletal Recordsbarcode
scientific name
GeoreferencingDuplicate Record MatchngDuplicate Record Matching
(exsiccati)
The New York Botanical Garden
Workflow Summary
Manual Data EntryIn-house or
crowd sourcing
Specimen Database
Skeletal recordsImages
Complete dataOCR
Duplicate Record Matching(exsiccati)
Specimen Curation
Specimen Imagingbarcode.jpg
OCR Textbarcode.txt
Skeletal Recordsbarcode
scientific name
Georeferencing
The New York Botanical Garden
Workflow Summary
Manual Data EntryIn-house or
crowd sourcing
Specimen Database
Skeletal recordsImages
Complete dataOCR
Specimen Curation
Specimen Imagingbarcode.jpg
OCR Textbarcode.txt
Skeletal Recordsbarcode
scientific name
GeoreferencingDuplicate Record Matching
(exsiccati)
The New York Botanical Garden
Specimen CurationPrevious curator Marshall A. Howe - died in 1936!
The New York Botanical Garden
Specimen CurationMany specimens mounted 50 – 100 years ago.
Paper frequently not acid free.
The New York Botanical Garden
Specimen CurationSpecimens poorly situated for digitization (information on the backs of specimens).
Multiple specimens and/or taxa per sheet.
The New York Botanical Garden
Rapid Data & Image Capture
Generate skeletal database records
• Barcode
• Scientific name (as filed)
Photograph every specimen
The New York Botanical Garden
Charophyc
eae
Coleochaetophyc
eae
Klebsorm
idiophyceae
Zygnematophyc
eae
Chlorophyc
eae
Prasin
ophyceae
Trebouxio
phyceae
Ulvophyc
eae
Cyanidiophyc
eae
Bangiophyceae
Compsopogonophyc
eae
Florid
eophyceae
Rhodellophyc
eae
Stylonematophyc
eae
Dinophyceae
Cryptomonadophyc
eae
Euglenida
Bacillario
phyceae
Chrysophyc
eae
Eustigmatophyc
eae
Phaeophyceae
Phaeothamniophyceae
Xanthophyceae
02000400060008000
1000012000140001600018000
NYBG Herbarium Snapshot
Algal class
Num
ber o
f dig
ital r
ecor
ds
= Barcoded groups
The New York Botanical Garden
Optical Character Recognition (OCR) and Cataloging
Records to be pre-sorted by OCR and cataloged in groups of similar label types.
The New York Botanical Garden
Optical Character Recognition (OCR) and Cataloging
Compiled from 3,000 lines of raw OCR from Charles Wright’s labels.
The New York Botanical Garden
Cataloging
The Macroalgae Portal using Symbiota.
The New York Botanical Garden
Cataloging
The Macroalgae Portal using Symbiota. www.macroalgae.org
The New York Botanical Garden
Cataloging
The Macroalgae Portal using Symbiota. www.macroalgae.org
The New York Botanical Garden
Cataloging
The Macroalgae Portal using Symbiota. www.macroalgae.org
The New York Botanical Garden
Georeferencing
Courtesy of Christopher Neefus, 2014.
The New York Botanical Garden
Algae Collections at the New York Botanical Gardens
An estimated 150,000 algal specimens.
Notable collectors:– Timothy F. Allen– Frank S. Collins –Marshall A. Howe– Nicolas Pike– Josephine Tilden– Richard D. Wood
Notable collections:– Charophytes– Coralline reds
The New York Botanical Garden
Impacts on the NYBG collections
• Improved state of the NYBG collection
• Better access to specimens.
• A more comprehensive type collection.
– Currently numbers more than 2,900.
–More than 150 types added since start of
project.
• Improved digitization workflows.
The New York Botanical Garden
NYBG Herbarium loans in the last 10 years
Algae Fungi Hepatics Lichens Mosses0
100
200
300
400
500
600
700
Specimen group
Num
ber o
f spe
cim
ens
loan
ed
The New York Botanical Garden
Broader Impacts
Facilitate further research in the following areas:– Bioinvasions
• Sleith, R. S. & K. G. Karol. The invasive macro alga Nitellopsis obtusa in New York State. Salve Regina University. Northeast Algal Society Symposium. Newport, RI. 25-27 April 2014.
– Climate Change• Bartsch, I. & R. Kuhlenkamp. 2000. The marine macroalgae of
Helgoland (North Sea): an annotated list of records between 1845 and 1999. Helgol Mar Res 54: 160-189.
– Human Impact• Littler, M. M. & S. N. Murray. 1975. Impact of sewage on the
distribution, abundance and community structure of rocky intertidal macro-organisms. Mar Biol 30: 277-291.
The New York Botanical Garden
Additional Information
• www.macroalgae.org• http://sciweb.nybg.org/science2/
VirtualHerbarium.asp
Thank you!