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Critical Assessment of Information Extraction in Biology - data sets are available from Resources/Corpora and require registration.

Publications

BC IV - CHEMDNER Proceedings Volume 2 [2013-10-15]

Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2.

The entire proceedings (volume 2) are available here.

Table of Contents

  1. Overview of the chemical compound and drug name recognition (CHEMDNER) task. Krallinger et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,2-33 PDF
  2. NCBI at the BioCreative IV CHEMDNER Task: Recognizing chemical names in PubMed articles with tmChem. Leaman et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,34-41 PDF
  3. DBCHEM: A Database Query Based Solution for the Chemical Compound and Drug Name Recognition Task. Ata et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,42-46 PDF
  4. LeadMine: A grammar and dictionary driven approach to chemical entity recognition. Lowe et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,47-54 PDF
  5. Chemistry-specific Features and Heuristics for Developing a CRF-based Chemical Named Entity Recogniser. Batista-Navarro et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,55-59 PDF
  6. Adapting Cocoa a multi-class entity detector for the CHEMDNER task of BioCreative IV. Ramanan et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,60-65 PDF
  7. A tool for the identification of chemical entities (CheNER-BioC). Usie et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,66-69 PDF
  8. Recognizing Chemical Entities in Biomedical Literature using Conditional Random Fields and Structured Support Vector Machines. Tang et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,70-74 PDF
  9. Chemical compound and drug name recognition using CRFs and semantic similarity based on ChEBI. Lamurias et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,75-81 PDF
  10. Chemical name recognition with harmonized feature-rich conditional random fields. Campos et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,82-87 PDF
  11. Extended Feature Set for Chemical Named Entity Recognition and Indexing. Huber et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,88-91 PDF
  12. Chemical Named Entity Recognition with OCMiner. Irmer et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,92-96 PDF
  13. NEROC: Named Entity Recognizer of Chemicals. Choi et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,97-104 PDF
  14. An Ensemble Information Extraction Approach to the BioCreative CHEMDNER Task. Khabsa et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,105-112 PDF
  15. A dictionary- and grammar-based chemical named entity recognizer. Akhondi et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,113-120 PDF
  16. Recognizing Chemical Compounds and Drugs: a Rule-Based Approach Using Semantic Information. Lana-Serrano et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,121-128 PDF
  17. WHU-BioNLP CHEMDNER System with Mixed Conditional Random Fields and Word Clustering. Lu et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,129-134 PDF
  18. BANNER-CHEMDNER: Incorporating Domain Knowledge in Chemical and Drug Named Entity Recognition. Munkhdalai et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,135-139 PDF
  19. An ensemble approach for chemical entity mention detection and indexing. Ravikumar et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,140-143 PDF
  20. Token- and Constituent-based Linear-chain CRF with SVM for Named Entity Recognition. Zitnik et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,144-151 PDF
  21. A CRF-Based System for Recognizing Chemical Entities in Biomedical Literature. Xu et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,152-157 PDF
  22. Domain-independent Model for Chemical Compound and Drug Name Recognition. Sikdar et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,158-161 PDF
  23. Ensemble Approach to Extract Chemical Named Entity by Using Results of Multiple CNER Systems with Different Characteristic. Yoshioka et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,162-167 PDF
  24. A Chemical Compound and Drug Named Recognizer for BioCreative IV. Shu et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,168-170 PDF
  25. Combining Machine Learning with Dictionary Lookup for Chemical Compound and Drug Name Recognition Task. Li et al. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2 ,171-177 PDF