Table 1 List of papers in the special issue on BioCreAtIvE
From: Overview of BioCreAtIvE: critical assessment of information extraction for biology
Ref | Task | Authors | Institution | Country | Title |
|---|---|---|---|---|---|
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 | |
1 | 1A | Yeh, A., Morgan, A., Colosimo, M. Hirschman, L. | MITRE | US | BioCreAtIvE task 1A: gene mention finding evaluation |
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 |
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 | |||
Hunter, L. | Center for Computational Pharmacology, University of Colorado School of Medicine | US | |||
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 |
5 | 1A | McDonald, R., Pereira, F. | University of Pennsylvania | US | Identifying Gene and Protein Mentions in Text using Conditional Random Fields |
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 | ||||
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 | ||||
Doi, K., Doi, H. | Nara Institute of Science and Technology | ||||
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 |
9 | 1A, 1B | Tamames, J. | BioAlma | Spain | Text Detective: A Rule-based System for Gene Annotation in Biomedical Texts |
10 | 1B | Hirschman, L., Colosimo, M., Morgan, A., Yeh, A. | MITRE | US | Overview of BioCreAtIvE task 1B: Normalized Gene Lists |
11 | 1B | Colosimo, M., Morgan, A., Yeh, A., Colombe, J., Hirschman, L. | MITRE | US | Data Preparation and Interannotator Agreement: BioCreAtIvE Task 1B |
12 | 1B | Crim, J., McDonald, R., Pereira, F. | University of Pennsylvania | US | Automatically Annotating Documents with Normalized Gene Lists |
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 |
14 | 1B | Fundel, K., Guttler, D., Zimmer, R., Apostolakis, J | Institute für Informatik | Germany | A Simple Approach for Protein Name Identification: Prospects and Limits |
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 |
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 |
17 | 2 | Ray, S., Craven, M. | University of Wisconsin | US | Learning Statistical Models for Annotating Proteins with Function Information using Biomedical Text |
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 |
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 | |||
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 | |||
21 | 2 | Rice, S., Nenadic, G., Stapley, G. | University of Manchester | UK | Mining Protein Function from Text using Term-based Support Vector Machines |
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 | ||||
Ruch, P | University Hospital of Geneva | ||||