1.
Frontiers of discovery with
Encyclopedia of Life
TraitBank research and other case studies
Cyndy Parr
Smithsonian Institution National Museum of Natural History
parrc@si.edu @cydparr http://www.slideshare.net/csparr

2.
• How is EOL different
• How EOL gets used
• Introducing TraitBank
• Loading up TraitBank
• EOL & TraitBank in research
• Future of EOL & TraitBank
Outline

3.
Take home messages
• EOL can be useful for research
• TraitBank is already awesome
• Mutualism between collections,
EOL, citizen science
• Let us know how we can help

4.
EOL
Crowds
Harvest
Third party applications
How EOL is different

5.
started 2008
text, media, literature
all species, genera, etc.
names infrastructure
data curation
2.6 million images
1.3 million taxa with content
Over 5 million visitors/year
75,000 registered members
eol.org

6.
How EOL gets used
http://www.notesfromnature.org/

7.
http://www.onezoom.org/ http://yanwong.me/
Links and images…what about research?

8.
Search groups for
“EOL papers”
at Mendeley.com

9.
Anatolia Zooarchaeology Case Study led
by Alexandria Archive Institute
1. 14 different sites
2. 34+ zooarchaeologists
3. Decoding, cleanup, metadata documentation
4. 220,000+ specimens
5. 450 entities linked to 143 EOL taxon concepts
6. Anatomical entities linked to Uberon.org
7. Biometrics linked to measurement ontology
8. Collaborative analysis
http://opencontext.org/
Kansa, E., Kansa, S. W., & Arbuckle, B. (2014). Publishing and Pushing:
Mixing Models for Communicating Research Data in Archaeology.
International Journal for Digital Curation, 9.

10.
Page, R. D. M. (2013). BioNames: linking taxonomy,
texts, and trees. PeerJ, 1, e190. doi:10.7717/peerj.190
BioNames.org
Rod Page

11.
But can we do more?
Introducing TraitBank

12.
GenBank
60 million DNA sequence records
900,000 species
4,000 genomes
How are these related to traits?

13.
Quick math
In Phenoscape
57 publications had 565,158 anatomical trait
descriptions for 2,527 kinds of organisms
= 223 traits/organism
In ZFIN
38,189 trait descriptions for 4,727 genes for
Zebrafish
1.9 million species on the planet
= LOTS OF TRAITS

14.
Why Smithsonian + EOL

15.
• Numeric data
(measurements)
• Categorical data
(controlled vocabulary)
• Species interactions
• Mostly summaries for
populations, species
• Individual specimens
• Higher taxa
http://eol.org/traitbank
released January 2014

16.
TraitBank Quick facts

17.
TraitBank Data tab

18.
TraitBank Metadata

19.
TraitBank Search & download

20.
TraitBank Search & download

21.
TraitBank Data glossary
http://eol.org/data_glossary

22.
Download

23.
Making TraitBank data available to
Google Knowledge Graph and
anyone

24.
TraitBank data sources
Sources include:
Databases
(OBIS, AnAge, Paleodb, Phenoscape)
Literature
(Dryad, Pangaea, Ecological Archives)
Natural History Collections
(Label data)
Legacy/unpublished data
Loading up TraitBank

25.
TraitBank
~7 million records
326 traits
1.2 million taxa
40+ datasets
http://eol.org/collections/97700

26.
Text mining
Environments-EOL
Evangelos Pafilis, Hellenic Centre for Marine Research (HCMR), Institute of
Marine Biology, Biotechnology and Aquaculture (IMBBC), Crete, Greece
491,616 habitat terms for 136,548 taxa

27.
Text mining
Automated annotation Manual annotation

28.
Morphological Data from NMNH KE-Emu
Abi Nishimura
Project: Clean-up morphological data from
NMNH catalog and publish to TraitBank
Goal: Make it easier to access and analyze
this valuable morphological data
Sakurai Midori,
http://eol.org/data_objects/26918624
Raw data from Spectral Tarsier Tarsius tarsier
database search

29.
RESULTS
• Primate data published (320 taxa)
• Comprehensive mammals data to
be published soon (4662 taxa)
• Bird catalog currently being mined
Wan Hong, http://eol.org/data_objects/29203274

30.
Mineralization of tissue in
marine organisms
Jen Hammock with Steve Cairns
For modeling impacts of ocean acidification
143,000 records for 119,000 species and subspecies of Micro- and Macroalgae,
Cnidaria, Polychaetes, Bryozoans, Brachiopods, Sponges, Mollusks,
Echinoderms and Arthropods
Mineralized tissue =
● Biogenic silica
● Calcium carbonate
○ Calcite
○ and/or Aragonite

31.
Other work in progress at NMNH
• Sarah Miller: growth form, habitat, and
elevation data from botany collection
specimen labels, summarizing elevation
• Reid Rumelt: behavior and other data
from Cornell University Macaulay Library
sound files and captions
• Katja Schulz:
PaleoBiology DataBase
• BHL-MoBot: IMLS
Mining biodiversity
© Donald E. Hurlbert/Smithsonian National
Museum of Natural History

32.
2013-14 EOL Rubenstein Fellows
EOL & TraitBank research
1. EnvO habitat terms (Pafilis et al.)
2. Altitude Specificity of Flower Coloration (Wright & Seltmann)
3. Morphological impacts of extinction risk in fish (Chang)
4. Butterfly-host plant associations (Ferrer-Parris et al.)
5. Global Biotic Interactions (GLoBI, Poelen & Mungall et al)
6. Reol: An R interface for EOL (Banbury, O’Meara)
7. Taxon Tree Tool (Lin)

33.
Chang crowdsourcingJonathan Chang, UCLA
http://jonathanchang.org/
Amazon Mechanical Turk

34.
EOL-BHL
Research Sprint

35.
1. Character displacement across the Tree of Life
2. Illuminating the Dark Parts of the Tree of Life
3. Evolution in the usage of anatomical concepts in the biodiversity
literature
4. Planning for global change: using species interactions in
conservation
5. No place like home: Defining “habitat” for biodiversity science
6. Assessing risk status of Mexican amphibians
7. Quantifying color from digital imagery: color may determine
species’ responses to habitat edges and to climate change
8. More is less - Identifying global trends in species’ niche width
9. Identifying key species traits associated with climate change
vulnerability
NESCent-EOL-BHL Research Sprint

36.
Quantifying color from digital imagery
1. Automate processing of almost 300k images (of EOL’s 2.4 million)
2. Identify pinned specimen images
3. Process these for color and pattern information
4. Put this info into TraitBank
Elise Larsen, Yan Wong

37.
Illuminating the Dark Parts of the Tree of Life
Jessica Oswald, Karen Cranston, Gordon Burleigh, Cyndy Parr
1. Query EOL, GBIF,
GenBank for # records
2. Create score for amount
of information available
3. Map score to phylogeny

38.
Global Genome Initiative Data Portal
For every family:
• Use TraitBank to assemble counts of records in repositories
• Compute a score (percentile) to assess knowledge available
relative to other families
• Make it easy to browse to find families that require effort
Beta launch end of June

39.
• NSF Genealogy of Life
• NSF Big Data
• TMON themed portals & traits
• Bocas del Toro revisionary taxonomy workshops
• NSF ABI Isotopes and Interactions
• Microsoft/WCMC Global Ecosystem Models
• And more mutualisms…
EOL & TraitBank future plans

40.
Leveraging social networks
Ahn, J., et al.. (2012). Visually Exploring Social Participation in Encyclopedia of
Life. In 2012 International Conference on Social Informatics (pp. 149–156). IEEE.
Rotman, D., et al. (2014). Motivations affecting initial and long-term participation in
citizen science projects in three countries. In iConference 2014 Proceedings (pp.
110-124).
http://biotracker.umd.edu
• motivation model for citizen scientists
• international attitudes of scientists and
citizens to working together
• factors that increase curation network
activity
• currently working on motivations of EOL
content partners

41.
Annotation of a specimen record
Ovary size and reproductive state
Age markers
Fat status
Body mass and other size
attributes

42.
Annotation of an observation record

43.
For more
information
• See & cite Parr, et al. 2014 Biodiv. Data Journal
• See our TraitBank paper (in review)
http://www.semantic-web-journal.net/content/traitbank-
practical-semantics-organism-attribute-data
• Talk to your favorite EOL person
• Become an EOL Curator
• See our NMNH collection of collections
http://eol.org/collections/743

44.
Take home messages
• EOL can be useful for research
• TraitBank is already awesome
• Mutualism between collections,
EOL, citizen science
• Let us know how we can help

45.
Atlas of Living Australia • Biodiversity Heritage Library Consortium • Chinese
Academy of Sciences • La Comisión Nacional para el Conocimiento y Uso de la
Biodiversidad (CONABIO) • The Field Museum • Harvard University • El Instituto
Nacional de Biodiversidad (INBio) • Marine Biological Laboratory • Missouri
Botanical Garden • Muséum National d’histoire Naturelle • Naturalis Netherlands
• New Library of Alexandria • Smithsonian Institution • South African National
Biodiversity Institute • All of our content providers and curators
Steve Cairnes • John Keltner • Katie Barker • Jonathan Coddington • Sean Brady •
Tom Orrell • Chris Meyers • Patricia Gentilis • Sylvia Orli • Kate Lyons • Yan Wong •
Jon Norenburg • Torsten Dikow • Yurong He • Jenny Preece and others on
BioTracker team • Pensoft Publishing • EOL Science Advisory Board
Katja Schulz, Jen Hammock, Marie Studer, Jeff Holmes, Nathan Wilson, Patrick
Leary, Jeremy Rice, Lisa Walley, Bob Corrigan, Erick Mata, Dmitry Mozzherin, Abi
Nishimura • Sarah Miller • Anthony Goddard, Mark Westneat and former BioSynC
staff
http://eol.org @eol parrc@si.edu
Major Funding for TraitBank provided by the Alfred P. Sloan
Foundation. Fellows program supported by Daniel M.
Rubenstein, Research sprint by Richard Lounsbery
Foundation.