Table of Contents: BC VI - Workshop Proceedings

1. Preface Proceedings of the BioCreative VI Challenge Evaluation Workshop, 3
2. BioCreative VI Committees and Sponsors Proceedings of the BioCreative VI Challenge Evaluation Workshop, 4
3. BioCreative VI Scientific Program Proceedings of the BioCreative VI Challenge Evaluation Workshop, 5

Keynotes and Panels

4. Keynote 1: Towards a future of data-powered health Patricia Flatley Brennan, RN, PhD (NLM/NIH) Proceedings of the BioCreative VI Challenge Evaluation Workshop, 7
5. Keynote 2: Text mining in precision medicine: opportunities and challenges Hongfang Liu, PhD (Mayo Clinic) Proceedings of the BioCreative VI Challenge Evaluation Workshop, 8

Panel: Innovation on Digital Curation

6. Natural language processing to enhance accessibility to knowledge in RegulonDB Collado-Vides J (UNAM) Proceedings of the BioCreative VI Challenge Evaluation Workshop, 9
7. Data transparency in scientific publishing Lemberger T (EMBO) Proceedings of the BioCreative VI Challenge Evaluation Workshop, 10
8. Text Mining for Improving the Prioritization, Curation, and Integration of Knowledge for Clinically Relevant Variants Lu Z (NLM/NIH) Proceedings of the BioCreative VI Challenge Evaluation Workshop, 11
9. How can text mining scale to meet diverse and precise curation needs? McEntyre J (ePMC/EMBL) Proceedings of the BioCreative VI Challenge Evaluation Workshop, 12

Track 1 Bio-ID Assignment

10. Bio-ID track overview Arighi et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 14-19
11. A Study on Identification of Organism and micro-RNA Mentions in Figure Captions Chang et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 20-23
12. A Neural Named Entity Recognition Approach to Biological Entity Identification Sheng et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 24-27
13. SPRENO: A BioC Module for Recognizing and Normalizing Species and Their Model Organisms Singh et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 28-31
14. TurkuNLP Entry for Interactive Bio-ID Assignment Kaewphan et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 32-35
15. Organism named entity recognition on an enhanced CRF-based model and normalization for BioCreative VI bioentity normalization task Yang et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 36-39

Track 2 Text-Mining Services for Kinome Curation

16. Overview of BioCreative VI Kinome Track Gobeill et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 41-45
17. Assisting Document Triage for Human Kinome Curation via Machine Learning Hsu et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 46-50
18. KinDER: A Biocuration Tool for Extracting Kinase Knowledge from Biomedical Literature Dopp et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 51-55

Track 3 Extraction of causal network information using BEL

19. Overview of BEL Track: Extraction of Complex Relationships and their Conversion to BEL Madan et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 57-61
20. BELMiner – Information extraction system to extract BEL relationships Elayavilli et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 62-65
21. Generating Biological Expression Language Statements with Pipeline Approach and Different Parsers Lai et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 66-69
22. Automatic Extraction of BEL-Statements based on Neural Networks Ali et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 70-73
23. Semantic Information Retrieval: Exploring Dependency and Word Embedding Features in Biomedical Information Retrieval Rastegar-Mojarad et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 74-77
24. A Hierarchical Sequence Labeling System for BioCreative VI BEL task Liu et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 78-81

Track 4 Mining protein interactions and mutations for precision medicine

25. Overview of the BioCreative VI Precision Medicine Track Doğan et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 83-87
26. The BioCreative VI Precision Medicine Track corpus Doğan et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 88-93
27. Hierarchical Bidirectional Attention-Based RNN in BioCreative VI Precision Medicine Track, Document Triage Task Fergadis et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 94-98
28. Identifying Relevant Literature for Precision Medicine Using Deep Neural Networks Matos et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 99-101
29. Document Triage and Relation Extraction for Protein-Protein Interactions affected by Mutations Chen Q et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 102-105
30. Exploring a Deep Learning Pipeline for the BioCreative VI Precision Medicine Task Tran et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 106-109
31. Text Classification using Ontology and Semantic Values of Terms for Mining Protein Interactions and Mutations Altinel et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 110-114
32. Leveraging Prior Knowledge for Protein-Protein Interaction Extraction with Memory Network Zhou et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 115-118
33. DUTIR at the BioCreative VI Precision Medicine Track: Document Triage for Identifying PPIs Affected by Genetic Mutations Luo et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 119-122
34. Identifying Mutation-induced Protein-Protein Interactions in Scientific Literature Chen E et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 123-126
35. MayoNLP at the BioCreative VI PM Track: Entity-enhanced Hierarchical Attention Neural Networks for Mining Protein Interactions from Biomedical Text Wang et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 127-130
36. Mining protein interactions affected by mutations using a NLP based machine learning approach Qu et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 131-134
37. WBI@BioCreative Track 4: Mining protein interactions and mutations for precision medicine (PM) Ševa et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 135-139

Track 5 Text mining chemical-protein interactions

38. Overview of the BioCreative VI chemical-protein interaction Track Krallinger et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 141-146
39. Chemical-protein relation extraction with ensembles of SVM, CNN, and RNN models Peng et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 147-150
40. Extracting Chemical-Protein Interactions using Long Short-Term Memory Networks Matos et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 151-154
41. Attention-based Neural Networks for Chemical Protein Relation Extraction Liu et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 155-158
42. Extracting chemical-protein interactions from literature Lung et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 159-162
43. Knowledge-base-enriched relation​extraction Tripodi et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 163-166
44. CTCPI – Convolution Tree Kernel-based Chemical-Protein Interaction Detection Warikoo et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 167-170
45. Extracting Chemical-protein interactions via bidirectional long short-term memory network Wang et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 171-174
46. Combining Support Vector Machines and LSTM Networks for Chemical-Protein Relation Extraction Mehryary et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 175-179
47. Improving the learning of chemical-protein interactions from literature using transfer learning and word embeddings. Corbett et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 180-183
48. CNN-based Chemical-Protein Interactions Classification Yuksel et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 184-186
49. Predicting Chemical Protein Relations with Biaffine Relation Attention Networks Verga et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 187-189
50. Chemical-Gene Relation Extraction Using Recursive Neural Network Lim et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 190-193

General Session

51. Efficient and Accurate Entity Recognition for Biomedical Text Rinaldi et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 195-197
52. iTextMine: Integrated Text Mining System for Large- Scale Knowledge Extraction from Literature Ren et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 198-199
53. Large-scale Automated Reading with Reach Discovers New Cancer Driving Mechanisms Valenzuela-Escarcega et al. Proceedings of the BioCreative VI Challenge Evaluation Workshop, 200-202

Poster Session

54. Poster Session List Proceedings of the BioCreative VI Challenge Evaluation Workshop, 203