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Evaluating the botanical coverage of PATO using an unsupervised learning algorithm

Authors:

Alyssa Janning,

Hong CuiAuthors Info & Claims

iConference '12: Proceedings of the 2012 iConference

Pages 504 - 505

https://doi.org/10.1145/2132176.2132265

Published: 07 February 2012 Publication History

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Abstract

In this paper, we explore issues in adopting PATO as a standard phenotypic quality ontology for the biological community. Using CharaParser's unsupervised learning algorithm and the Stanford Parser, we extract morphological descriptions from Flora of North America to be matched to terms in PATO. Using the resulting data, we examine PATO's coverage of botanically interesting terms in order to find gaps and to determine accuracy. To maintain PATO's neutrality, we recommend that term definitions be reevaluated and propose that complimentary ontologies be enhanced to close any outstanding gaps in terminology.

References

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Cui, H. (Submitted). CharaParser for Fine-Grained Semantic Annotation of Taxonomic Descriptions. Journal of American Society of Information Science and Technology.

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[2]

Cui, H. (2010). Evaluating Plant Character Ontologies Against Domain Literature. Journal of American Society of Information Science and Technology. 61(6):1144--1165.

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Klein, D. and Manning, C. D. 2003. Accurate Unlexicalized Parsing. In Proceedings of the 41st Meeting of the Association for Computational Linguistics, 423--430.

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Knowlton, M. N., Li, T., Ren, Y. et. al. (2008). A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information. BMC Bioinformatics, 9, 7 (January 2008). DOI= 10.1186/1471-2105-9-7.

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PATO: http://www.bioontology.org/wiki/index.php/PATO:Main_Page

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Smith B, Ashburner M, Rosse C, et. al. (2007). The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology, 25, 1251--1255.

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Schindelman, G., Fernandes, J. S., Bastiani, C. A, Yook, K. and Sternberg, P. W. 2011. Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community. BMC Bioinformatics, 12, 3.

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Index Terms

Evaluating the botanical coverage of PATO using an unsupervised learning algorithm
1. Computing methodologies
  1. Artificial intelligence
    1. Knowledge representation and reasoning
      1. Semantic networks
  2. Machine learning
    1. Machine learning approaches
      1. Rule learning

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Published In

iConference '12: Proceedings of the 2012 iConference

February 2012

667 pages

ISBN:9781450307826

DOI:10.1145/2132176

Conference Chair:
Jens-Erik Mai
University of Toronto

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Association for Computing Machinery

New York, NY, United States

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Published: 07 February 2012

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iConference '12

iConference '12: iConference 2012

February 7 - 10, 2012

Ontario, Toronto, Canada

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Competency evaluation of plant character ontologies against domain literature

Using SPARQL to query bioportal ontologies and metadata

A semantic metrics suite for evaluating modular ontologies

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