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Learning to recognize phenotype candidates in the auto-immune literature using SVM re-ranking
- Source :
- PLoS ONE, Vol 8, Iss 10, p e72965 (2013), PLoS ONE
- Publication Year :
- 2013
- Publisher :
- Public Library of Science (PLoS), 2013.
-
Abstract
- The identification of phenotype descriptions in the scientific literature, case reports and patient records is a rewarding task for bio-medical text mining. Any progress will support knowledge discovery and linkage to other resources. However because of their wide variation a number of challenges still remain in terms of their identification and semantic normalisation before they can be fully exploited for research purposes. This paper presents novel techniques for identifying potential complex phenotype mentions by exploiting a hybrid model based on machine learning, rules and dictionary matching. A systematic study is made of how to combine sequence labels from these modules as well as the merits of various ontological resources. We evaluated our approach on a subset of Medline abstracts cited by the Online Mendelian Inheritance of Man database related to auto-immune diseases. Using partial matching the best micro-averaged F-score for phenotypes and five other entity classes was 79.9%. A best performance of 75.3% was achieved for phenotype candidates using all semantics resources. We observed the advantage of using SVM-based learn-to-rank for sequence label combination over maximum entropy and a priority list approach. The results indicate that the identification of simple entity types such as chemicals and genes are robustly supported by single semantic resources, whereas phenotypes require combinations. Altogether we conclude that our approach coped well with the compositional structure of phenotypes in the auto-immune domain.
- Subjects :
- Male
Vocabulary
Support Vector Machine
Computer science
Entropy
media_common.quotation_subject
Science
MEDLINE
Scientific literature
computer.software_genre
Bioinformatics
Autoimmune Diseases
Mice
03 medical and health sciences
0302 clinical medicine
Named-entity recognition
Knowledge extraction
Artificial Intelligence
Controlled vocabulary
Animals
Data Mining
Humans
Entropy (information theory)
Gene
030304 developmental biology
media_common
0303 health sciences
Multidisciplinary
business.industry
Principle of maximum entropy
Models, Theoretical
Semantics
Support vector machine
Phenotype
Vocabulary, Controlled
030220 oncology & carcinogenesis
Medicine
Artificial intelligence
business
computer
Natural language processing
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 8
- Issue :
- 10
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....bfe81890da296fa0fe3db6479b215a1f