The Macroalgae Digitization Project

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 Macroalgal Consortium49 participating institutions, 25 states, 1 U.S. territory

Map courtesy of Christopher Neefus, 2014.


Primary Digitization Centers

New York Botanical Garden

University of California

University of Michigan

University of New Hampshire

University of North Carolina

University of Washington


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


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)


Scope

• More than 1.1 million specimens.

• Collections dating back 200 years.

• All major algal groups:

– Red Algae

– Green Algae

– Brown Algae


Digitization will consist of . . .

A speciman image



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



A taxon determination

Chara connivens P. Salzmann ex A. Braun



A georeferenced point


www.macroalgae.org


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)


Workflow Summary


crowd sourcing

Specimen Database


Complete dataOCR

Specimen Curation


OCR Textbarcode.txt


scientific name


(exsiccati)


Workflow Summary


crowd sourcing

Specimen Database


Complete dataOCR

Specimen Curation


OCR Textbarcode.txt


scientific name


(exsiccati)


Workflow Summary


crowd sourcing

Specimen Database


Complete dataOCR

Specimen Curation


OCR Textbarcode.txt


scientific name


(exsiccati)


Workflow Summary


crowd sourcing

Specimen Database


Complete dataOCR

Specimen Curation


OCR Textbarcode.txt


scientific name

GeoreferencingDuplicate Record MatchngDuplicate Record Matching

(exsiccati)


Workflow Summary


crowd sourcing

Specimen Database


Complete dataOCR

Duplicate Record Matching(exsiccati)

Specimen Curation


OCR Textbarcode.txt


scientific name

Georeferencing


Workflow Summary


crowd sourcing

Specimen Database


Complete dataOCR

Specimen Curation


OCR Textbarcode.txt


scientific name


(exsiccati)


Specimen CurationPrevious curator Marshall A. Howe - died in 1936!


Specimen CurationMany specimens mounted 50 – 100 years ago.

Paper frequently not acid free.


Specimen CurationSpecimens poorly situated for digitization (information on the backs of specimens).

Multiple specimens and/or taxa per sheet.


Rapid Data & Image Capture

Generate skeletal database records

• Barcode

• Scientific name (as filed)

Photograph every specimen


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


Optical Character Recognition (OCR) and Cataloging

Records to be pre-sorted by OCR and cataloged in groups of similar label types.


Optical Character Recognition (OCR) and Cataloging

Compiled from 3,000 lines of raw OCR from Charles Wright’s labels.


Cataloging

The Macroalgae Portal using Symbiota.


Cataloging

The Macroalgae Portal using Symbiota. www.macroalgae.org


Cataloging



Cataloging



Georeferencing

Courtesy of Christopher Neefus, 2014.


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


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.


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


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.


Additional Information

• www.macroalgae.org• http://sciweb.nybg.org/science2/

VirtualHerbarium.asp

Thank you!

Documents

The Macroalgae Digitization Project