<NAME>

Bio::ExtractNE - Extract biological named entities from PUBMED abstracts

<DESCRIPTION>

This module can extract Named Entities from PUBMED online
abstracts. It recognizes protein names and gene names adapted from
SWISSPROT database. And it also tries to resolve on-the-spot
abbreviation reference, which means abbreviations in abstracts
bracketed between parentheses will be extracted too using a naive
looking-back method, though the technique is inelegant in some way
now.

For now, this package use GAPSCORE as its name guessing module. Both
an RPC interface and a self-implemented version are provided.

You can pass a PMID, a URL for abstract, an abstract passage, or an
abstract file to the extractNE() function. It then returns a list of
tokens, recognized named entities, abbreviations with their full
names, and sentence numbers in which there are potential
protein-protein interactions. But no categorical or synonym grouping
information of named entities is provided. Other classes of words,
such as disease names and virus names will be considered in future
versions.

Any suggestion or comment is always welcome. Contributions and
patches are wanted.

Email me if you have questions.

