Mining protein function from text using term-based support vector machines View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2005-05

AUTHORS

Simon B Rice, Goran Nenadic, Benjamin J Stapley

ABSTRACT

BACKGROUND: Text mining has spurred huge interest in the domain of biology. The goal of the BioCreAtIvE exercise was to evaluate the performance of current text mining systems. We participated in Task 2, which addressed assigning Gene Ontology terms to human proteins and selecting relevant evidence from full-text documents. We approached it as a modified form of the document classification task. We used a supervised machine-learning approach (based on support vector machines) to assign protein function and select passages that support the assignments. As classification features, we used a protein's co-occurring terms that were automatically extracted from documents. RESULTS: The results evaluated by curators were modest, and quite variable for different problems: in many cases we have relatively good assignment of GO terms to proteins, but the selected supporting text was typically non-relevant (precision spanning from 3% to 50%). The method appears to work best when a substantial set of relevant documents is obtained, while it works poorly on single documents and/or short passages. The initial results suggest that our approach can also mine annotations from text even when an explicit statement relating a protein to a GO term is absent. CONCLUSION: A machine learning approach to mining protein function predictions from text can yield good performance only if sufficient training data is available, and significant amount of supporting data is used for prediction. The most promising results are for combined document retrieval and GO term assignment, which calls for the integration of methods developed in BioCreAtIvE Task 1 and Task 2. More... »

PAGES

s22

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-6-s1-s22

DOI

http://dx.doi.org/10.1186/1471-2105-6-s1-s22

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1042479871

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/15960835


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