Table 1 |
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List of papers in the special issue on BioCreAtIvE |
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Ref |
Task |
Authors |
Institution |
Country |
Title |
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|
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all |
Hirschman, L., Yeh, A., Blaschke, C., Valencia, A. |
MITRE BioAlma National Center of Biotechnology, CNB-CSIC |
US Spain |
Overview of BioCreAtIvE: Critical Assessment of Information Extraction in Biology |
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1 |
1A |
Yeh, A., Morgan, A., Colosimo, M. Hirschman, L. |
MITRE |
US |
BioCreAtIvE task 1A: gene mention finding evaluation |
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2 |
1A |
Tanabe, L., Xie, T.N. Thom, L.H., Matten, W. Wilbur, W.J. |
NIH Consolidated Safety NIH |
US |
Genetag: A Tagged Corpus for Gene/Protein Named Entity Recognition |
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|
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3 |
1A |
Kinoshita, S. |
University of Colorado School of Medicine and Fujitsu |
US/Japan |
BioCreAtIvE Task 1A: Entity Identification with a Stochastic Tagger |
|
Cohen, K.B., Ogren, P.V. |
University of Colorado School of Medicine |
US |
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Hunter, L. |
Center for Computational Pharmacology, University of Colorado School of Medicine |
US |
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4 |
1A |
Finkel, J. Dingare, S. Manning, C.D. Nissim, M., Alex, B., Grover, C. |
Stanford University University of Edinburgh Stanford University University of Edinburgh |
US UK US UK UK |
Exploring the Boundaries: Gene and Protein Identification in Biomedical Text |
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5 |
1A |
McDonald, R., Pereira, F. |
University of Pennsylvania |
US |
Identifying Gene and Protein Mentions in Text using Conditional Random Fields |
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6 |
1A |
Zhou, G.D. |
Institute for Infocomm Research and the University of Singapore |
Singapore |
Recognition of Protein/Gene Names from Text using an Ensemble of Classifiers |
|
Shen, D., Zhang, J., Su, J., Tan, S.H. |
Institute for Infocomm Research |
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7 |
1A |
Mitsumori, T., Fation, S. |
Nara Institute of Science and Technology |
Japan |
Gene/Protein Name Recognition based on Support Vector Machine using Dictionary as Features |
|
Murata, M. |
National Institute of Information and Communications Technology |
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Doi, K., Doi, H. |
Nara Institute of Science and Technology |
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8 |
1A |
Hakenberg, J., Bickel, S., Plake, C., Brefeld, U., Zahn, H., Faulstich, L., Leser, U., Scheffer, T. |
Humboldt-Universität zu Berlin, Computer Science Department |
Germany |
Systematic Feature Evaluation for Gene Name Recognition |
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9 |
1A, 1B |
Tamames, J. |
BioAlma |
Spain |
Text Detective: A Rule-based System for Gene Annotation in Biomedical Texts |
|
|
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10 |
1B |
Hirschman, L., Colosimo, M., Morgan, A., Yeh, A. |
MITRE |
US |
Overview of BioCreAtIvE task 1B: Normalized Gene Lists |
|
|
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11 |
1B |
Colosimo, M., Morgan, A., Yeh, A., Colombe, J., Hirschman, L. |
MITRE |
US |
Data Preparation and Interannotator Agreement: BioCreAtIvE Task 1B |
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12 |
1B |
Crim, J., McDonald, R., Pereira, F. |
University of Pennsylvania |
US |
Automatically Annotating Documents with Normalized Gene Lists |
|
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13 |
1B |
Hanisch, D. Fundel, K. Mivissen, H.T. Zimmer, R. Fluck, J. |
Fraunhofer Institute SCAI Institute for Informatics Fraunhofer Institute SCAI Institute for Informatics Fraunhofer Institute SCAI |
Germany |
ProMiner: Rule-based Protein and Gene Entity Recognition |
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14 |
1B |
Fundel, K., Guttler, D., Zimmer, R., Apostolakis, J |
Institute für Informatik |
Germany |
A Simple Approach for Protein Name Identification: Prospects and Limits |
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15 |
2 |
Blaschke, C. Krallinger, M., Leon, E.A., Valencia, A. |
BioAlma National Center of Biotechnology, CNB-CSIC |
Spain |
Evaluation of BioCreAtIvE assessment of task 2 |
|
|
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16 |
2 |
Camon, E.B., Barrell, D.G., Dimmer, E.C., Lee, V., Magrane, M., Maslen, J., Binns, D., Apweiler, R. |
European Molecular Biology Laboratory-European Bioinformatics Institute |
UK |
An evaluation of GO annotation retrieval for BioCreAtIvE and GOA |
|
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17 |
2 |
Ray, S., Craven, M. |
University of Wisconsin |
US |
Learning Statistical Models for Annotating Proteins with Function Information using Biomedical Text |
|
|
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18 |
2 |
Krallinger, M., Padron, M., Valencia, A. |
National Center of Biotechnology, CNB-CSIC |
Spain |
A Sentence Sliding Window Approach to Extract Protein Annotations from Biomedical Articles |
|
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19 |
2 |
Verspoor, K., Cohn, J., Joslyn, C., Mniszewski, S., Rechsteiner, A. |
Los Alamos National Lab |
US |
Protein Annotation as Term Categorization in the Gene Ontology using Word Proximity Networks |
|
Rocha, L., Simas, T. |
Indiana University |
US |
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20 |
2 |
Couto, F., Silva, M. |
Faculdade de Ci¸ncias da Universidade de Lisboa, Lisbon, Portugal |
Portugal |
Finding Genomic Ontology Terms in Unstructured Text |
|
Coutinho, P. |
Architecture et Fonction des Macromolécules Biologiques, CNRS |
France |
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21 |
2 |
Rice, S., Nenadic, G., Stapley, G. |
University of Manchester |
UK |
Mining Protein Function from Text using Term-based Support Vector Machines |
|
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22 |
2 |
Ehrler, F. |
University of Geneva and University Hospital of Geneva |
Switzerland |
Data-poor Categorization and Passage Retrieval for Gene Ontology Annotation in Swiss-Prot |
|
Jimeno, A. |
University Hospital of Geneva and CERN, Geneva |
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Ruch, P |
University Hospital of Geneva |
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Hirschman et al. BMC Bioinformatics 2005 6(Suppl 1):S1 doi:10.1186/1471-2105-6-S1-S1 |
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