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