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BioIE specifications


Unique identifier OMICS_22303
Name BioIE
Interface Web user interface
Restrictions to use None
Programming languages Perl, CGI
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Anna Divoli <>

Publication for BioIE

BioIE citations


Improving protein coreference resolution by simple semantic classification

PMCID: 3582588
PMID: 23157272
DOI: 10.1186/1471-2105-13-304

[…] dealing with it, it is often difficult to capture important information pieces in text. it was also a lesson from the bionlp shared task (bionlp-st) 2009, which was a community-wide campaign of bioie system development and evaluation [-], that coreference structures in biomedical text substantially hinder the progress of fine-grained ie. readers are referred to [,] for details […]


A corpus of full text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools

PMCID: 3483229
PMID: 22901054
DOI: 10.1186/1471-2105-13-207

[…] negation., although craft is not the first corpus of syntactically annotated biomedical text, it provides the first constituent annotation of full-text biomedical journal articles. penn treebank’s bioie project provided much of the basic skeleton for the workflow of this type of annotation. however, we did have to make several new policies or expand existing ptb policies for syntactic […]


Resolving anaphoras for the extraction of drug drug interactions in pharmacological documents

PMCID: 3288782
PMID: 20406499
DOI: 10.1186/1471-2105-11-S2-S1

[…] the background section [] is the closest to ours. as discussed, such an approach addresses the issue of anaphora resolution in the domain of protein interactions, has developed an ad-hoc tool called bioie to deal with morphosyntactic complexity of this kind of documents and resolution problems have been faced with an approach that also used centering theory. as it can be seen in table , our work […]


The High Throughput Sequence Annotation Service (HT SAS) – the shortcut from sequence to true Medline words

PMCID: 2694793
PMID: 19445703
DOI: 10.1186/1471-2105-10-148

[…] by attwood and co-workers. metis [] also uses blast homology search to gather literature (abstracts), but the collected text is passed into two sentence classification components (set of svms and bioie []). they find and categorize informative sentences, relating them to: structure, function, disease and localization categories. metis also calculates simple statistical properties, i.e. […]


Nominalization and Alternations in Biomedical Language

PMCID: 2527518
PMID: 18779866
DOI: 10.1371/journal.pone.0003158

[…] 0.9 of the pennbioie corpus (kulick et al. 2004) and release 3.0p of the genia corpus (kim et al. 2003) . (due to space considerations, in all table captions we refer to the pennbioie corpus as the bioie corpus.) both of these corpora are composed of the titles and abstracts of scientific journal articles. the pennbioie corpus is divided into two parts reflecting two distinct semantic domains: […]


Benchmarking natural language parsers for biological applications using dependency graphs

PMCID: 1797812
PMID: 17254351
DOI: 10.1186/1471-2105-8-24

[…] we can make use of the larger and rapidly-growing body of treebank-annotated biological text. since this project was begun, the genia treebank has grown from 200 to 500 medline abstracts, and the bioie project [] has released 642 abstracts annotated in a similar format. the stanford algorithm provides a de facto standard for comparing a variety of constituent parsers and treebanks […]

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BioIE institution(s)
Faculty of Life Sciences and School of Computer Science, University of Manchester, Manchester, UK
BioIE funding source(s)
Supported by Inpharmatica Ltd. and BBSRC.

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