Conference Talk: A Distributed Framework for Computation on the Results of Large Scale NLP

1. A Distributed Framework for
Computation on the Results of
Large Scale NLP
Christophe Roeder, William A. Baumgartner Jr., Kevin Livingston,
Lawrence E. Hunter
(University of Colorado Anschutz Medial Campus)
Chris.Roeder@ucdenver.edu
http://compbio.ucdenver.edu

2. Motivation
• A vast amount of information is available
in journal articles
• Journal articles are unstructured text
• Many applications require structured
knowledge
– Curated ontologies (Gene Ontology)
– Databases (UniProt, EntrezGene)
• Challenge: extract structured knowledge
from unstructured text and integrate with
existing knowledge…at massive scale

3. Architecture
Journal RDF
Scaled NLP Pipeline
Articles(u Document
nstructured) s(structured)
Queries Sesam
Knowledge e/Hado
Base(Ontologi op
es,
Databases)
Knowledg
Applications
Applications
(Visualization
e Distilled
Applications
(Visualization
, (Visualization
NLP,…)
, NLP,…)
Output
, NLP,…) (structured)
Structured
Information

4. Example Application
• Concept annotation
trends over time
Insuli
n
NOS1
http://tinyurl.com/bio-trends

5. Summary
• NLP pipelines extract structured annotations
• Our framework provides massively parallel access
to these structured document annotations
• Structured representation is integrated with
knowledge base
• Affords parallelization when possible, and access
to knowledge base when necessary
• Provides integration of unstructured document text
with structured knowledge for enabling
applications such as:
– Visualization (BioJigsaw, Hanalyzer,…)
– Natural Language Understanding (OpenDMAP)
– Leveraging text data for validation and evaluation of
other methods

6. Thank You / Questions
• http://tinyurl.com/bio-trends
• Co-authors
– William A. Baumgartner Jr. for data generation
– Kevin Livingston for RDF and Clojure help
• Grants and PIs
– Lawrence E Hunter, UCDenver SOM
• NIH 2R01LM009254-04, NIH 2R01LM008111-04A1,
NIH 5R01GM083649-02
– Karin Verspoor, UCDenver SOM
• NIH R01 LM010120-01
– Gully Burns, ISI
• NSF 0849977