BioIE statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool BioIE

Tool usage distribution map

This map represents all the scientific publications referring to BioIE per scientific context
info info

Associated diseases


Popular tool citations

chevron_left Bio-entity identification chevron_right
Want to access the full stats & trends on this tool?

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


Annotating patient clinical records with syntactic chunks and named entities: the Harvey Corpus

PMCID: 4983282
PMID: 27570501
DOI: 10.1007/s10579-015-9330-7

[…] as annotated using a modified version of the OntoNotes guidelines (Hovy et al. ), but later Verspoor et al. () added syntactic annotation following the Penn Treebank guidelines (Bies et al. ) and the BioIE addendum (Warner et al. ). At the same time, concept annotation was added, identifying all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies (Bada et al […]


Annotated Chemical Patent Corpus: A Gold Standard for Text Mining

PLoS One
PMCID: 4182036
PMID: 25268232
DOI: 10.1371/journal.pone.0107477

[…] oteins and less effort has been put into creating corpora for chemical terms . Among the latter efforts, Kim et al. in 2003 developed the GENIA corpus consisting of several classes of chemicals. The BioIE corpus by Kulick et al. was made available in 2004 and included annotations of chemicals and proteins. In 2008, Kolárik et al. released a small corpus of scientific abstracts annotated with ch […]


Improving protein coreference resolution by simple semantic classification

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

[…] perly 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 about BioNLP-S […]


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

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

[…] (VP to(VP (VP obtain(NP regulatory approval))and(VP complete(NP transaction))(PP by(NP year-end)))))))‘‘The company expects to obtain regulatory approval and complete transaction by year-end.'' (Penn BioIE guidelines)“by year-end” is shared by both VPs “obtain regulatory approval” and “complete transaction”, but is attached at the same level as those two VPs to form a flat structure. CRAFT adds a […]


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

BMC Bioinformatics
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

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

[…] sed 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. n-grams […]

Want to access the full list of citations?
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.

BioIE reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review BioIE