Natural science collections have a long history of engaging volunteers in onsite projects. However, as I recently reviewed with collaborators in this cover story for BioScience, new web resources provide scientists with opportunities to engage the public in ways and at scales not previously possible.
I&apos;ll demonstrate this by focusing on one such resource, Notes from Nature, and one such activity, transcription. Notes from Nature will be 3 years old in April. &gt;1.2 million transcriptions of specimen labels and ledgers have been contributed, demonstrating strong public interest in volunteering in this area.
A month ago, we hosted the first of what is planned to be an annual WeDigBio event. Over four days hundreds of volunteers around the world transcribed more than 30,000 specimen labels. Volunteers participated both at 25 onsite events and from offsite elsewhere—ip addresses mapped to at least 54 countries. Events spanned middle school and undergraduate science classrooms, as illustrated here,
Contributors fill out 9 fields that provide the what, when, who, etc., from the collection label as shown in the specimen image. Because anyone, anywhere, can contribute we show each image to four contributors and reconcile the replicate transcriptions. You might&apos;ve noticed the script on the label—it is hard for a computer to interpret that correctly, but humans can do it with relative ease.
Notes From Nature, GEOLocate
Big Data for Virginia Plant Taxonomy
Andrea Weeks, Ph.D.
Associate Professor, Plant Systematics
Director, Ted R. Bradley Herbarium
George Mason University
Virginia Native Plant Society Potowmack Chapter, February 11, 2016
• Big data defined for botany
• Biodiversity informatics: why bother?
• Virginia herbarium digitization
• How you can become involved
Vast amounts of
Vast amounts of
Herbarium specimens from 1699-1702
Herbarium specimens from 19th century
Happy birthday, Darwin!
Centuries of data about plant species
Isolated online databases
Natural history specimens
• uses modern technologies to
• convert vast amount of data on biodiversity into
• knowledge, wisdom, and environmental outcomes
Arthur Chapman: https://www.youtube.com/watch?v=w5_y6o9G
"A world in which biodiversity information is freely and
universally available for science, society and a
sustainable future." 2007
• Species discovery
• Retrospective distribution mapping: Climate change
• Predictive distribution modeling: Climate change
Natural History Museums are Teeming with
Undiscovered Species. (February 8, 2016)
Bebber DP, Carine MA, Wood JRI, et al. 2010. Herbaria are a major frontier for species
discovery. PNAS 107: 22169 – 22171. doi:10.1073/pnas.1011841108.
Herbaria are a major frontier for species
Between 1970 - 2010
• 84% new species based on >5 y old specimens, with nearly
one-quarter of new species descriptions involving specimens
>50 y old.
• Of the estimated 70,000 species still to be described,
more than 35,000 already have been collected and are
stored in herbaria, unnoticed.
Altitudinal shifts of the native and
introduced flora of California in the
context of 20th century warming‐
681,609 herbarium records
between 1895 - 2009
4426 native & exotic species
15% native shifted up in elevation
27% exotic shifted up in elevation
Global Ecology and Biogeography
20 JAN 2016 DOI: 10.1111/geb.12423
Using museum specimens to
refine models of species
distribution in Florida
• Herbarium records of 1,548
Florida plant species tied to yearly
• Refined contemporary potential
• Future plant diversity under two
Hot spots of plant endemism in the southeast (Estill & Cruzan 2001)Hot spots of plant endemism in the southeast (Estill & Cruzan 2001)
A biodiverse region with intense human
A rich tradition of botanical collection yet
many herbaria under-resourced.
Estill, J. C., & Cruzan, M. B.. (2001). Phytogeography of Rare Plant Species Endemic to the Southeastern
United States. Castanea, 66(1/2), 3–23.
State of Herbaria in the Southeast USA
Data derived from Index Herbariorum
• 233 collections vary in size from 3,000 to 750,000 specimens.
• Curators are taxonomists, ecologists, paleobotanists, population biologists.
• Some institutions with significant budgets, IT support and curatorial staff.
• Some institutions are single person operations without budgets or IT support.
• ESTIMATED 15 MILLION SPECIMENS FROM THE SOUTHEAST.
The Key to the Cabinets: Building and
Sustaining a Research Database for a
Global Biodiversity Hotspot
A new NSF-Advancing Digitization in Biological Collections (ADBC)
collaborative project in the southeast
NSF ADBC #1410069 (plus collaborative awards (1410077 1410081
1410086 1410087 1410092 1410094 1410098 1410143 1410200
1410288 1410439 1410445)
• Southeastern U.S. vascular plants
• 93 collections will be digitized
• 12 states
• 28 hubs
• 6 partners
• 4.5M herbarium
specimens will be
served to GBIF.
Data Contributors in the SE US (yellow diamonds)
www.sernecportal.org is our central hub of digitization in the SE US
11 Virginian herbaria are covered under NSF grant.
Data Management Workflow
Specimen Image Capture
Texas Advanced Computing
Metadata to Portal
Batch Georeferenced Data to Portal
Metadata to Local
VA progress to date: May 2015 – February 2016
2015 Virginia Native Plant Society Research Grant awarded
0 records accessible 94,207 online database entries
0 images available 40,689 online specimen images
11 15 Virginian herbaria using our infrastructure
Training documents created
At least 22 curators, staff & students trained
A selection of herbaria already on sernecportal.org
Online database fostering new
conversations, e.g. nativity of
Magnolia tripetala in Fairfax Co.
Challenges & Opportunities for 2016
Notes From Nature platform, although fully functional, may
not be serving Virginian specimens for transcription until 2017.
We have a great alternative: SERNEC transcription portal.
We need beta testers for SERNEC transcription portal.
Step 1: login by following private hyperlink (see handout)
Step 2: Select one of GMUF’s specimens to transcribe
Step 3: Set up your transciption window
Step 4: Transcribe 8 database fields & Save Edits