Building on 8 years of highly productive work in technology development that included the creation of the Colorado Richly Annotated Full Text corpus (CRAFT), we hypothesize that text mining resources and methods are approaching the level of maturity required to productively process a significant proportion of the full text biomedical literature to create a well-represented formal knowledge base of molecular biology. We propose a detailed, integrated plan to achieve this long-standing goal. Success in this effort will make possible a transformative new way for the biomedical research community to identify access and integrate existing knowledge, breaking down disciplinary boundaries and other silos that have kept scientists from fully exploiting relevant prior results in their research. Our successes in the prior funding period broadened the applicability of biomedical concept identification systems to a much wider set of tasks, demonstrating the ability to target multiple community-curated ontologies in text mining, and generate scientifically significant insights from the results. The proposed work would take advantage of the resources we produced to transcend several of the limitations of previous efforts. We propose innovative new approaches to formal knowledge representation and to characterizing relationships between textual elements and semantic content. We will design, implement and evaluate computational systems that have the potential to transform enormous text collections into semantically rich, logic-based, standards-compliant, formal representations of biomedical knowledge with clearly identified provenance. The resulting representations will express complex assertions about a very wide range of entities, processes, qualities, and, most importantly, their specific relationships with one another.

Public Health Relevance

Hunter, Lawrence E. Project narrative This project will affect public health by increasing the access of physicians, researchers, and the general public to highly targeted information from published research and electronic health records. PHS 398/2590 (Rev. 06/09) Page Continuation Format Page

Agency
National Institute of Health (NIH)
Institute
National Library of Medicine (NLM)
Type
Research Project (R01)
Project #
5R01LM008111-12
Application #
9306202
Study Section
Biomedical Library and Informatics Review Committee (BLR)
Program Officer
Ye, Jane
Project Start
2004-09-30
Project End
2018-06-30
Budget Start
2017-07-01
Budget End
2018-06-30
Support Year
12
Fiscal Year
2017
Total Cost
Indirect Cost
Name
University of Colorado Denver
Department
Pharmacology
Type
Schools of Medicine
DUNS #
041096314
City
Aurora
State
CO
Country
United States
Zip Code
80045
Boguslav, Mayla; Cohen, K Bretonnel; Baumgartner, William A et al. (2018) Improving precision in concept normalization. Pac Symp Biocomput 23:566-577
Cohen, K Bretonnel; Xia, Jingbo; Zweigenbaum, Pierre et al. (2018) Three Dimensions of Reproducibility in Natural Language Processing. LREC Int Conf Lang Resour Eval 2018:156-165
Callahan, Tiffany J; Baumgartner, William A; Bada, Michael et al. (2018) OWL-NETS: Transforming OWL Representations for Improved Network Inference. Pac Symp Biocomput 23:133-144
Cohen, K Bretonnel; Lanfranchi, Arrick; Choi, Miji Joo-Young et al. (2017) Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles. BMC Bioinformatics 18:372
Kao, David P; Stevens, Laura M; Hinterberg, Michael A et al. (2017) Phenotype-Specific Association of Single-Nucleotide Polymorphisms with Heart Failure and Preserved Ejection Fraction: a Genome-Wide Association Analysis of the Cardiovascular Health Study. J Cardiovasc Transl Res 10:285-294
Hunter, Lawrence E (2017) Knowledge-based biomedical Data Science. EPJ Data Sci 1:19-25
Greene, Casey S; Garmire, Lana X; Gilbert, Jack A et al. (2017) Celebrating parasites. Nat Genet 49:483-484
Hooper, Joan E; Feng, Weiguo; Li, Hong et al. (2017) Systems biology of facial development: contributions of ectoderm and mesenchyme. Dev Biol 426:97-114
Oellrich, Anika; Collier, Nigel; Groza, Tudor et al. (2016) The digital revolution in phenotyping. Brief Bioinform 17:819-30
Cohen, K Bretonnel; Fort, Karën; Adda, Gilles et al. (2016) Ethical Issues in Corpus Linguistics And Annotation: Pay Per Hit Does Not Affect Effective Hourly Rate For Linguistic Resource Development On Amazon Mechanical Turk. LREC Int Conf Lang Resour Eval 2016:8-12

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