com.aliasi.corpus.parsers
Class AbstractMedTagParser

java.lang.Object
  com.aliasi.corpus.Parser<H>
      com.aliasi.corpus.StringParser<TagHandler>
          com.aliasi.corpus.parsers.AbstractMedTagParser

Direct Known Subclasses:

GeneTagParser, MedPostPosParser

public abstract class AbstractMedTagParser
extends StringParser<TagHandler>

The AbstractMedTagParser class provides an adapter for NCBI's MedTag corpora, including GeneTag and MedPost. The MedTag format is sentence based, consisting of a number of pairs of lines of the following form:

 P00073344A0367
 tok_tag tok_tag ... tok_tag
 P00083846T0000
 tok_tag tok_tag ... tok_tag
 ...
 

The initial part of the first line, P00073344, provides the PubMed identifier from which the text was abstracted. The second part of the first line, A0367 indicates that the sentence was from the abstract, beginning at character offset 367. The text may be extracted from titles or abstracts; the third line indicates a line beginning with the first character (index 0000) of the title (T) of the citation with PubMed ID 83846.

The second (and fourth) line consist of a sequence of tokens and tags, separated by an underscore. The tags are part-of-speech tags in the MedPost corpus and chunk entity tags in the GeneTag corpus. Note that with this format, whitespace information is lost.

Subclasses must override the parseTokensTags(String[],String[],String[]) method to actually do the parsing of a sentence once its tags are extracted.

For more information on the MedTag project, see:

• LH Smith, L Tanabe, T Rindflesch and WJ Wilbur. 2005. 2005. MedTag: a collection of biomedical annotations. Proceedings of ACL-ISMB Workshop on Linking Biological LIterature, Ontologies and Databases. Detroit.

Since:

LingPipe2.1

Version:

3.8

Author:

Bob Carpenter

Constructor Summary

AbstractMedTagParser()
Construct an abstract MedTag parser with no handler specified.

AbstractMedTagParser(TagHandler handler)
Construct an abstract MedTag parser with the specified tag handler.

Method Summary

void	parseString(char[] cs, int start, int end) Parse the specified input source and send extracted taggings to the current handler.
protected abstract void	parseTokensTags(String[] tokens, String[] whitespaces, String[] tags) This method handles the raw tokens and tags pulled from a MedTag corpus.
TagHandler	tagHandler() Deprecated. Use generic Parser.getHandler() instead.

Methods inherited from class com.aliasi.corpus.StringParser

parse

Methods inherited from class com.aliasi.corpus.Parser

getHandler, parse, parse, parseString, setHandler

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AbstractMedTagParser

public AbstractMedTagParser()

Construct an abstract MedTag parser with no handler specified.

AbstractMedTagParser

public AbstractMedTagParser(TagHandler handler)

Construct an abstract MedTag parser with the specified tag handler.

Parameters:

handler - Tag handler.

Method Detail

tagHandler

@Deprecated
public TagHandler tagHandler()

Deprecated. Use generic Parser.getHandler() instead.

Returns the tag handler for this parser.

Returns:

The tag handler for this parser.

parseString

public void parseString(char[] cs,
                        int start,
                        int end)

Parse the specified input source and send extracted taggings to the current handler. This string should correspond to the contents of an input file.

Specified by:

parseString in class Parser<TagHandler>

Parameters:

cs - Character array underlying string.

start - First character of string.

end - Index of one past the last character in the string.

parseTokensTags

protected abstract void parseTokensTags(String[] tokens,
                                        String[] whitespaces,
                                        String[] tags)

This method handles the raw tokens and tags pulled from a MedTag corpus. This method must be implemented by subclasses, and it must call the contained handler on the result.

Parameters:

tokens - Raw tokens to handle.

whitespaces - Raw whitespaces to handle.

tags - Raw tags to handle.