BMC Bioinformatics Volume 6(Suppl 1); 2005

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Volume 6(Suppl 1); 2005

Introduction

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. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S1

PMCID:: PMC1869002

Abstract Full Text PDF–303K

Reports

BioCreAtIvE Task 1A: gene mention finding evaluation

Alexander Yeh, Alexander Morgan, Marc Colosimo, Lynette Hirschman

BMC Bioinformatics. 2005; 6(Suppl 1): S2. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S2

PMCID:: PMC1869012

Abstract Full Text PDF–322K

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. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S3

PMCID:: PMC1869017

Abstract Full Text PDF–312K

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. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S4

PMCID:: PMC1869018

Abstract Full Text PDF–257K

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. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S5

PMCID:: PMC1869019

Abstract Full Text PDF–260K

Identifying gene and protein mentions in text using conditional random fields

Ryan McDonald, Fernando Pereira

BMC Bioinformatics. 2005; 6(Suppl 1): S6. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S6

PMCID:: PMC1869020

Abstract Full Text PDF–280K

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. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S7

PMCID:: PMC1869021

Abstract Full Text PDF–245K

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. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S8

PMCID:: PMC1869022

Abstract Full Text PDF–287K

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. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S9

PMCID:: PMC1869023

Abstract Full Text PDF–352K

Text Detective: a rule-based system for gene annotation in biomedical texts

Javier Tamames

BMC Bioinformatics. 2005; 6(Suppl 1): S10. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S10

PMCID:: PMC1869003

Abstract Full Text PDF–384K

Overview of BioCreAtIvE task 1B: normalized gene lists

Lynette Hirschman, Marc Colosimo, Alexander Morgan, Alexander Yeh

BMC Bioinformatics. 2005; 6(Suppl 1): S11. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S11

PMCID:: PMC1869004

Abstract Full Text PDF–262K

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. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S12

PMCID:: PMC1869005

Abstract Full Text PDF–261K Supplementary Material

Automatically annotating documents with normalized gene lists

Jeremiah Crim, Ryan McDonald, Fernando Pereira

BMC Bioinformatics. 2005; 6(Suppl 1): S13. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S13

PMCID:: PMC1771968

Abstract Full Text PDF–226K

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. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S14

PMCID:: PMC1869006

Abstract Full Text PDF–284K

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. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S15

PMCID:: PMC1869007

Abstract Full Text PDF–276K

Evaluation of BioCreAtIvE assessment of task 2

Christian Blaschke, Eduardo Andres Leon, Martin Krallinger, Alfonso Valencia

BMC Bioinformatics. 2005; 6(Suppl 1): S16. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S16

PMCID:: PMC1869008

Abstract Full Text PDF–443K

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. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S17

PMCID:: PMC1869009

Abstract Full Text PDF–729K Supplementary Material

Learning Statistical Models for Annotating Proteins with Function Information using Biomedical Text

Soumya Ray, Mark Craven

BMC Bioinformatics. 2005; 6(Suppl 1): S18. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S18

PMCID:: PMC1869010

Abstract Full Text PDF–255K

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. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S19

PMCID:: PMC1869011

Abstract Full Text PDF–373K

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. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S20

PMCID:: PMC1869013

Abstract Full Text PDF–1022K

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. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S21

PMCID:: PMC1869014

Abstract Full Text PDF–228K

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. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S22

PMCID:: PMC1869015

Abstract Full Text PDF–290K

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. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S23

PMCID:: PMC1869016

Abstract Full Text PDF–305K

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