BioCreAtIvE publications

BioCreAtIvE II publications

Will be provided as soon as ready!

BioCreAtIvE I publications

BioCreAtIvE I workshop proceedings

Task 1A
Yu Song, Eunji Yi, Eunju Kim and Gary Geunbae Lee: POSBIOTMNER: A Machine Learning Approach for BioNamed Entity Recognition.
[PDF]

Tomohiro Mitsumori, Sevrani Fation, Masaki Murata, Kouichi Doi and Hirohumi Doi: Gene/protein name recognition using Support Vector Machine after dictionary matching
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Ryan McDonald and Fernando Pereira: Identifying Gene and Protein Mentions in Text Using Conditional Random Fields
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Yikun Guo, Henk Harkema, Ian Roberts, Rob Gaizauskas and Mark Hepple: University of Sheffield: Preliminary investigation of a dictionarybased approach to the Biocreative gene and protein identification task
[PDF]

Steffen Bickel, Ulf Brefeld, Lukas Faulstich, Jörg Hakenberg, Ulf Leser, Conrad Plake and Tobias Scheffer: A Support Vector Machine Classifier for Gene Name Recognition
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Zhou GuoDong, Shen Dan, Zhang Jie, Su Jian, Tan Soon Heng and Tan Chew Lim: Recognition of Protein/Gene Names from Text using an Ensemble of Classifiers and Effective Abbreviation Resolution
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Shuhei Kinoshita, K. Bretonnel Cohen, Philip Ogren and Lawrence Hunter: Entity identification in the molecular biology domain with a stochastic POS tagger: the BioCreative task
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Harald Kirsch and Dietrich Rebholz: Method used for BioCreAtIvE Task 1A
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Shipra Dingare, Jenny Finkel, Christopher Manning, Malvina Nissim and Beatrice Alex: Exploring the Boundaries: Gene and Protein Identification in Biomedical Text
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Task 1A/B
Javier Tamames: Text Detective: BioAlma's gene annotation tool
[PDF]

Task 1B

Daniel Hanisch, Katrin Fundel, HeinzTheodor Mevissen, Ralf Zimmer and Juliane Fluck: ProMiner: Organismspecific protein name detection using approximate string matching
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Jeremiah Crim, Ryan McDonald and Fernando Pereira: Automatically Annotating Documents with Normalized Gene Lists
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Ben Hachey, Huy Nguyen, Malvina Nissim, Bea Alex and Claire Grover: Grounding Gene Mentions with Respect to Gene Database Identifiers
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Hongfang Liu, Cathy Wu and Carol Friedman: BioTagger: A Biological Entity Tagging System
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Katrin Fundel, Daniel G¸ttler, Ralf Zimmer, Joannis Apostolakis : Exact versus approximate string matching for protein name identification
[PDF]

Task 2
Soumya Ray and Mark Craven: Learning Statistical Models for Annotating Proteins with Function Information using Biomedical Text
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JungHsien Chiang and HsuChun Yu: Extracting Functional Annotations of Proteins Based on Hybrid Text Mining Approaches
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Francisco M. Couto, Mário J. Silva and Pedro Coutinho: FiGO: Finding GO Terms in Unstructured Text
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Frédéric Ehrler and Patrick Ruch: Preliminary Report on the BioCreative Experiment: Task Presentation, System Description and Preliminary Results.
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Simon B. Rice, Goran Nenadic and Benjamin J. Stapley: Protein function assignment using termbased support vector machines ­ BioCreative Task Two 2003
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Martin Krallinger and María Magdalena Padron: Prediction of GO annotation by combining entity specific sentence sliding window profiles
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Yuval Krymolowski, Beatrice Alex and Jochen L. Leidner: BioCreative Task 2.1: The EdinburghStanford system
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Karin Verspoor, Judith Cohn, Cliff Joslyn, Sue Mniszewski, Andreas Rechtsteiner, Luis M. Rocha and Tiago Simas: Protein Annotation as Term Categorization in the Gene Ontology
[PDF]

BioCreAtIvE I - BMC Bioinformatics special issue
The BioCreAtIvE I articles were published in volume 6 supplement 1 of the journal BMC Bioinformatics.

BioCreAtIvE I contest overview:
Overview of BioCreAtIvE: critical assessment of information extraction for biology Lynette Hirschman, Alexander Yeh, Christian Blaschke, Alfonso Valencia BMC Bioinformatics 2005, 6(Suppl 1):S1 (24 May 2005)
[PDF] [PubMed]

Task 1:
BioCreAtIvE Task 1A: gene mention finding evaluation Alexander Yeh, Alexander Morgan, Marc Colosimo, Lynette Hirschman BMC Bioinformatics 2005, 6(Suppl 1):S2 (24 May 2005)
[PDF] [PubMed]

GENETAG: a tagged corpus for gene/protein named entity recognition Lorraine Tanabe, Natalie Xie, Lynne H Thom, Wayne Matten, W John Wilbur BMC Bioinformatics 2005, 6(Suppl 1):S3 (24 May 2005)
[PDF] [PubMed]

BioCreAtIvE Task1A: entity identification with a stochastic tagger Shuhei Kinoshita, K Bretonnel Cohen, Philip V Ogren, Lawrence Hunter BMC Bioinformatics 2005, 6(Suppl 1):S4 (24 May 2005)
[PDF] [PubMed]

Exploring the boundaries: gene and protein identification in biomedical text Jenny Finkel, Shipra Dingare, Christopher D Manning, Malvina Nissim, Beatrice Alex, Claire Grover BMC Bioinformatics 2005, 6(Suppl 1):S5 (24 May 2005)
[PDF] [PubMed]

Identifying gene and protein mentions in text using conditional random fields Ryan McDonald, Fernando Pereira BMC Bioinformatics 2005, 6(Suppl 1):S6 (24 May 2005)
[PDF] [PubMed]

Recognition of protein/gene names from text using an ensemble of classifiers GuoDong Zhou, Dan Shen, Jie Zhang, Jian Su, SoonHeng Tan BMC Bioinformatics 2005, 6(Suppl 1):S7 (24 May 2005)
[PDF] [PubMed]

Gene/protein name recognition based on support vector machine using dictionary as features Tomohiro Mitsumori, Sevrani Fation, Masaki Murata, Kouichi Doi, Hirohumi Doi BMC Bioinformatics 2005, 6(Suppl 1):S8 (24 May 2005)
[PDF] [PubMed]

Systematic feature evaluation for gene name recognition Jörg Hakenberg, Steffen Bickel, Conrad Plake, Ulf Brefeld, Hagen Zahn, Lukas Faulstich, Ulf Leser, Tobias Scheffer BMC Bioinformatics 2005, 6(Suppl 1):S9 (24 May 2005)
[PDF] [PubMed]

Text Detective: a rule-based system for gene annotation in biomedical texts Javier Tamames BMC Bioinformatics 2005, 6(Suppl 1):S10 (24 May 2005)
[PDF] [PubMed]

Overview of BioCreAtIvE task 1B: normalized gene lists Lynette Hirschman, Marc Colosimo, Alexander Morgan, Alexander Yeh BMC Bioinformatics 2005, 6(Suppl 1):S11 (24 May 2005)
[PDF] [PubMed]

Data preparation and interannotator agreement: BioCreAtIvE Task 1B Marc E Colosimo, Alexander A Morgan, Alexander S Yeh, Jeffrey B Colombe, Lynette Hirschman BMC Bioinformatics 2005, 6(Suppl 1):S12 (24 May 2005)
[PDF] [PubMed]

Automatically annotating documents with normalized gene lists Jeremiah Crim, Ryan McDonald, Fernando Pereira BMC Bioinformatics 2005, 6(Suppl 1):S13 (24 May 2005)
[PDF] [PubMed]

ProMiner: rule-based protein and gene entity recognition Daniel Hanisch, Katrin Fundel, Heinz-Theodor Mevissen, Ralf Zimmer, Juliane Fluck BMC Bioinformatics 2005, 6(Suppl 1):S14 (24 May 2005)
[PDF] [PubMed]

A simple approach for protein name identification: prospects and limits Katrin Fundel, Daniel Güttler, Ralf Zimmer, Joannis Apostolakis BMC Bioinformatics 2005, 6(Suppl 1):S15 (24 May 2005)
[PDF] [PubMed]

Task 2:
Evaluation of BioCreAtIvE assessment of task 2 Christian Blaschke, Eduardo Andres Leon, Martin Krallinger, Alfonso Valencia BMC Bioinformatics 2005, 6(Suppl 1):S16 (24 May 2005)
[PDF] [PubMed]

An evaluation of GO annotation retrieval for BioCreAtIvE and GOA Evelyn B Camon, Daniel G Barrell, Emily C Dimmer, Vivian Lee, Michele Magrane, John Maslen, David Binns, Rolf Apweiler BMC Bioinformatics 2005, 6(Suppl 1):S17 (24 May 2005)
[PDF] [PubMed]

Learning Statistical Models for Annotating Proteins with Function Information using Biomedical Text Soumya Ray, Mark Craven BMC Bioinformatics 2005, 6(Suppl 1):S18 (24 May 2005)
[PDF] [PubMed]

A sentence sliding window approach to extract protein annotations from biomedical articles Martin Krallinger, Maria Padron, Alfonso Valencia BMC Bioinformatics 2005, 6(Suppl 1):S19 (24 May 2005)
[PDF] [PubMed]

Protein annotation as term categorization in the gene ontology using word proximity networks Karin Verspoor, Judith Cohn, Cliff Joslyn, Sue Mniszewski, Andreas Rechtsteiner, Luis M Rocha, Tiago Simas BMC Bioinformatics 2005, 6(Suppl 1):S20 (24 May 2005)
[PDF] [PubMed]

Finding genomic ontology terms in text using evidence content Francisco M Couto, Mário J Silva, Pedro M Coutinho BMC Bioinformatics 2005, 6(Suppl 1):S21 (24 May 2005)
[PDF] [PubMed]

Mining protein function from text using term-based support vector machines Simon B Rice, Goran Nenadic, Benjamin J Stapley BMC Bioinformatics 2005, 6(Suppl 1):S22 (24 May 2005)
[PDF] [PubMed]

Data-poor categorization and passage retrieval for Gene Ontology Annotation in Swiss-Prot Frédéric Ehrler, Antoine Geissbühler, Antonio Jimeno, Patrick Ruch BMC Bioinformatics 2005, 6(Suppl 1):S23 (24 May 2005)
[PDF] [PubMed]


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