Bridging Biodiversity and Biomedical Knowledge Through Literature

Indra Neil Sarkar, PhD

Divisions of Invertebrate Zoology & Library Services

American Museum of Natural History

Refactoring Digital Natural History Texts

University of Illinois at Urbana-Champaign

April 17, 2006

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Life on Earth

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Biomedical Literature

• Medline

• 17 Million+ Records

• Citations back to 1960's

• Free, Web-based Interface

• Organized/Indexed According to MeSH

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Biodiversity Literature

• Natural History Collections

• PDF or Image Files

• Free*, Institution Specific Search

• Minimal Meta-data

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Exploring Literature

• Meet Information Needs

• Map to Other Knowledge

• Extract Domain Specific Features

• Perform Data Mining for Novel Correlations

• Automated Methods

• Biomedical (Yes!)

• Biodiversity (No!)

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Biological Data Revolution

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"Modernizing" Biodiversity Literature

• Digitization

• Optical Character Recognition

• First Pass Markup

• Domain Specific Markup

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TaxonX

• Designed as a W3C XML Schema

• Identify Taxonomic Treatments

• Major Structural Components

• Open Source (http://sourceforge.net/projects/taxonx)

• Stable

• Consistent

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TaxonX

• Iterative Markup

1. Identify Taxonomic Treatments

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TaxonX

• Iterative Markup

1. Identify Taxonomic Treatments

2. Identify Lower Level Meta-Data

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TaxonX Goals

• Describe Structure of Systematics Publications

• Enable Specific Queries

• Taxa: Ant Literature since 1995

• Fauna: Ant Literature from Madagascar

(http://antbase.org/databases/xml_publications.htm)

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TaxonX Integration

• Currently Stand-Alone Schema

• Designed to Link with Other Schemata

• XHTML

• NLM Journal Archiving

• TEI

• Publisher-specific

• Mash-ups: e.g., http://www.ispecies.org

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TaxonX Going Forward

• Plausible Intermediate Step

• Biodiversity Heritage Library

• Amenable to Automated Methods

• Linkages to Molecular, Distributional, and Nomenclatural Resources

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TaxonX Summary

• Lightweight Schema

• Small Learning Curve

• General Applicability to Heritage Literature

• Allows External Linkages

• MODS for File-Level Bibliographic Metadata

• Enables Iterative Deployment

• Accommodates Differing Granularities

• Darwin Core, Linnaean Core, SDD, etc.

• ITIS, GUID, LSID, etc.

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More Details to Come...

• taXMLit, INOTAXA

• Biodiversity Heritage Library

• Unifying Thread:

• Bringing Legacy Data into A Digital Commons For Sharing Knowledge

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Then?

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Taxonomic Knowledge

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Extracting Taxonomic Names

• Name Entity Recognition

• Taxonomic Name Recognition (TNR)

• Rule-based TNR Tools

• TaxonGrab (AMNH)

• FindIT (uBio)

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Rule-Based TNR

• Reverse-Lexical Lookup

• Non-Taxon Name Words

• Genus Species Nomenclature

• Genus Capitalized

• Suffix Patterns (e.g., -ia, -us)

• Other Features

• Infra-species, Strain

• Authority Designation

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Extracting Taxonomic Names

• Medline

• Digitized Text

• Zoological Record

• Chapin's Birds of the Congo

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Why Not Just Look up Names?

Scientific Names

Escherichia coli

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Federate Scientific Names

• Collect Scientific Names

• Digital Taxonomy Resources

• Data Marts

• Natural Language Text

• Scientific Name Reconciliation

• Many Names for Same Organism

• Objective: Escherichia coli, Bacterium coli, Bacillus coli

• Subjective: Brucella melitensis, Brucella canis, Brucella ovis

• Many Organisms for Same Name

• Agathis montana is both a wasp and plant

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uBio

• 6 Million+ Name Strings

• Reconciliation Groups

• http://www.ubio.org

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Scientific Names in Medline

• Medline Is Indexed With MeSH Terms

• MeSH Contains Some Scientific Names

• How Many Medline Documents Contain Scientific Names?

• How Many Scientific Names are Contained in Medline?

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Scientific Names in Medline

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Medline vs. Biodiversity Literature

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Medline vs. Catalogue Lists

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Remaining Questions

• How many species overlap?

• Are there valid linkages to be drawn?

• Biomedical (e.g., molecular)

• Biodiversity (e.g., biogeography)

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Tracking Prospective Knowledge

• WSDL/SOAP Integration

• Taxonomic Intelligence

• Google

• RSS

• http://portal.ubio.org

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Concluding Remarks

• Retrospective Biological Knowledge

• Not Just PDF's!

• Biodiversity Heritage Library

• Contemporary Biological Knowledge

• Titles, Abstracts, Meta-Data (MeSH)

• Medline

• Prospective Biological Knowledge

• Track New Publications via RSS

• Services Integrated Into Interfaces

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Acknowledgments

NSF/AMNH Team
Terry Catapano
Drew Koning
Bob Morris
Donat Agosti
Tom Moritz
Christie Stephenson

MBL/WHOI uBio
David Remsen
Patrick Leary
David Patterson
Cathy Norton

National Science Foundation (IIS-0241229)

Lewis B. & Dorothy Program for Molecular Systematics

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Indra Neil Sarkar, PhD
sarkar@amnh.org

Pacific Symposium on Biocomputing - Biodiversity Informatics Track

http://psb.stanford.edu