frontiers of discovery with encyclopedia of life
DESCRIPTION
Presented at the National Museum of Natural History, Smithsonian Institution 18 June 2014 Describes, among other things, development of the TraitBank repository of species attributes, and the use of EOL and TraitBank in scientific research.TRANSCRIPT
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Frontiers of discovery with Encyclopedia of LifeTraitBank research and other case studies
Cyndy ParrSmithsonian Institution National Museum of Natural [email protected] @cydparr http://www.slideshare.net/csparr
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• How is EOL different• How EOL gets used• Introducing TraitBank • Loading up TraitBank• EOL & TraitBank in research• Future of EOL & TraitBank
Outline
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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
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Third party applications
How EOL is different
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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
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How EOL gets used
http://www.notesfromnature.org/
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http://www.onezoom.org/ http://yanwong.me/
Links and images…what about research?
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Search groups for “EOL papers”at Mendeley.com
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Anatolia Zooarchaeology Case Study led by Alexandria Archive Institute1. 14 different sites2. 34+ zooarchaeologists3. Decoding, cleanup, metadata documentation4. 220,000+ specimens5. 450 entities linked to 143 EOL taxon concepts6. Anatomical entities linked to Uberon.org7. Biometrics linked to measurement ontology 8. Collaborative analysis
Anatolia Zooarchaeology Case Study led by Alexandria Archive Institute1. 14 different sites2. 34+ zooarchaeologists3. Decoding, cleanup, metadata documentation4. 220,000+ specimens5. 450 entities linked to 143 EOL taxon concepts6. Anatomical entities linked to Uberon.org7. 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.
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Page, R. D. M. (2013). BioNames: linking taxonomy, texts, and trees. PeerJ, 1, e190. doi:10.7717/peerj.190
BioNames.orgRod Page
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But can we do more?
Introducing TraitBank
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GenBank 60 million DNA sequence records
900,000 species 4,000 genomes
How are these related to traits?
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Quick math
In Phenoscape57 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
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Why Smithsonian + EOL
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• 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
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TraitBank Quick facts
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TraitBank Data tab
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TraitBank Metadata
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TraitBank Search & download
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TraitBank Search & download
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TraitBank Data glossaryhttp://eol.org/data_glossary
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Download
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Making TraitBank data available to Google Knowledge Graph and anyone
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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
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TraitBank
~7 million records
326 traits
1.2 million taxa
40+ datasetshttp://eol.org/collections/97700
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Text miningEnvironments-EOLEvangelos 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
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Text mining
Automated annotation Manual annotation
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Morphological Data from NMNH KE-EmuAbi Nishimura
Project: Clean-up morphological data from NMNH catalog and publish to TraitBankGoal: 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 tarsierdatabase search
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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
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Mineralization of tissue in marine organismsJen 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
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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
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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)
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Chang crowdsourcingJonathan Chang, UCLAhttp://jonathanchang.org/
Amazon Mechanical Turk
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EOL-BHL Research Sprint
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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
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Quantifying color from digital imagery1. Automate processing of almost 300k images (of EOL’s 2.4 million)2. Identify pinned specimen images3. Process these for color and pattern information4. Put this info into TraitBank
Elise Larsen, Yan Wong
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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
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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
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• 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
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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
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Annotation of a specimen record
Ovary size and reproductive stateAge markersFat statusBody mass and other size attributes
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Annotation of an observation record
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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
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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
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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 [email protected]
Major Funding for TraitBank provided by the Alfred P. Sloan Foundation. Fellows program supported by Daniel M. Rubenstein, Research sprint by Richard Lounsbery Foundation.