Table 1

List of papers in the special issue on BioCreAtIvE

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


Hirschman et al. BMC Bioinformatics 2005 6(Suppl 1):S1   doi:10.1186/1471-2105-6-S1-S1

Open Data