Frontiers of discovery with Encyclopedia of LifeTraitBank research and other case studies

Cyndy ParrSmithsonian Institution National Museum of Natural Historyparrc@si.edu @cydparr http://www.slideshare.net/csparr

Central challenges• What are all the organisms on the planet?• What do we know about them?• How can we build new knowledge about

them?

GenBank 60 million DNA sequence records

900,000 species 4,000 genomes

How are these related to traits?

Phenomes: the next frontierIn 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

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

Outline

eol.org

Third party applications

How EOL is different

How EOL gets used

http://www.notesfromnature.org/

http://www.onezoom.org/ http://yanwong.me/

PhyloTilerhttp://viburnum.peabody.yale.edu/~piel/Tree_4_color/

Links and images…what about research?

Search groups for “EOL papers”at Mendeley.com

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.

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

BioNames.orgRod Page

But can we do more?

Introducing TraitBank

Search & Download

Data Sources

Data Summaries on EOL Taxon

Pages

Which plants grow well in acidic soil?

What do water bears eat?

What is the biggest species of whale?

Structured Data

TraitBank

JSON-LD API

• 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

TraitBank Quick facts

TraitBank Data tab

TraitBank Metadata

TraitBank Search & download

TraitBank Search & download

TraitBank Data glossaryhttp://eol.org/data_glossary

Download

TraitBank Data model

TraitBank Uploading Darwin Core Archives

Common names | Taxa | References | MeasurementsOrFacts | Associations | Events | Occurrences

Term URIs from existing ontologies bioportal.bioontologies.org

Term URIs from existing ontologies

•Where necessary: request terms•Last resort: create provisional terms with http://eol.org/schema/terms/xxxx

•Still to do• create “equivalentTo” or “similarTo” relations• even more fancy inference

JSON-LD e.g. http://eol.org/api/traits/1045608? cache_ttl=2419200

Google Knowledge Graph

TraitBank data sources

Sources include: Databases (OBIS, AnAge, Paleodb, Phenoscape)

Literature(Dryad, Ecological Archives, Data tables)

Natural History Collections(Label data)

Legacy/unpublished data

Loading up TraitBank

TraitBank

~7 million records326 traits 1.2 million taxa40+ datasetshttp://eol.org/collections/97700

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

Text mining

Automated annotation Manual annotation

Morphological Data from NMNH catalogAbi Nishimura

Project: Clean-up morphological data from NMNH KE-Emu 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

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

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

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. Taxon Tree Tool (Lin) 6. Global Biotic Interactions (GLoBI, Poelen & Mungall et al)

http://www.globalbioticinteractions.org/

7. Reol: An R interface for EOL (Banbury, O’Meara)Banbury, B. L., & O’Meara, B. C. (2014). Ecology and Evolution, 4(12). doi:10.1002/ece3.1109

Chang crowdsourcingJonathan Chang, UCLAhttp://jonathanchang.org/

Amazon Mechanical Turk

EOL-BHL Research Sprint

1. Character displacement across the Tree of Life2. Illuminating the Dark Parts of the Tree of Life3. Evolution in the usage of anatomical concepts in the biodiversity literature

4. Planning for global change: using species interactions in conservation5. No place like home: Defining “habitat” for biodiversity science6. Assessing risk status of Mexican amphibians7. Quantifying color from digital imagery: color may determine species’

responses to habitat edges and to climate change8. More is less - Identifying global trends in species’ niche width9. Identifying key species traits associated with climate change vulnerability

NESCent-EOL-BHL Research Sprint

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

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

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

• Decorate trees with traits• NSF Genealogy of Life• NSF Big Data• NSF ABI Isotopes and Interactions• Microsoft/WCMC Global Ecosystem Models

TraitBank future plans

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

Annotation of a specimen record

Ovary size and reproductive stateAge markersFat statusBody mass and other size attributes

Annotation of an observation record

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

• Open source code https://github.com/EOL/• APIs at http://eol.org/api• Become an EOL Curator

Take home messages• EOL can be useful for research• TraitBank is already awesome• Mutualism between collections,

EOL, citizen science• Let’s collaborate

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 curatorsSteve Cairnes • John Keltner • Katie Barker • Jonathan Coddington • Sean Brady • Tom Orrell • Chris Meyers • Yan Wong • Jon Norenburg • Torsten Dikow • Yurong He • Jenny Preece and others on BioTracker team • Pensoft Publishing • EOL Science Advisory BoardKatja 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 @cydparr 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.

1. Terms are not in any existing ontologye.g., seawater oxygen saturation, eutrophic pond, north-facing bluff

2. Synonyms are not includede.g., vernal pond/intermittent pond

3. Standard classifications should be mappede.g., NatureServe, NOAA

4. Environment estimates vs. well-documented niche

parameterse.g., text mining results vs. NatureServe habitats, OBIS data vs. niche analyses

Challenges

14 datasets with 25k taxa, 422k interactions, for 3k locationsalpha version of ingestion, normalization, aggregationalpha version of web APIalpha version of data exports

GLoBI http://globalbioticinteractions.wordpress.com/Jorrit Poelen, Chris Mungall, James Simon GoMexSi