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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