View source for Cohen and Hersh Briefings in Bioinformatics 2005

== Citation ==

Aaron M. Cohen and William R. Hersh. 2005. A Survey of Current Work in Biomedical Text Mining. Briefings in Bioinformatics. Vol 6. No 1. 57-71.

== Online version ==

[http://bib.oxfordjournals.org/content/6/1/57.full.pdf oxfordjournals]

== Summary ==
This is a survey paper about biomedical text mining in 2005. 

* Named entity recognition
** Problems
*** No complete dictionary for most types of biological named entities
*** ambiguous words and phrases
*** multi names
** approaches are mainly categorized into three below
*** lexicon based
*** rule based
*** statistically based
** performance
*** overall, the performance of gene and protein NER systems is F-scores between 75 and 85 percent.

* Text classification


* Synonym and abbreviation extraction
** Synonym
*** use dictionary
*** automatic extraction of gene name synonyms from biomedical free text
*** SVM classifier-based
*** pattern-based
** abbreviation
*** either the full form or the abbreviation is often enclosed in parentheses.
*** a variety of alignment and scoring methods

* Relationship extraction
** detect occurrences of a prespecified type of relationship between a pair of entities of given types
** manually generated template-based methods
** automatic template methods
** statistical methods
** NLP-based methods
mostly are about the relationships between genes and proteins

* Hypothesis generation
** uncover relationships that are not present in the text but instead are inferred by the presence of other more explicit relationships. uncover previously unrecognized relationships

* Integration frameworks
** integrated text-mining frameworks
** still in the research and development phrase.

* The authors' suggestions
** Access to full text is required
** Additional analytical methods with possible features are required for a particular application
** Researchers should consider actual users' needs. The performance of a system with certain metrics does not guarantee users' satisfaction.
** Shared challenge tasks should be continued