Text mining chemical-protein interactions (CHEMPROT) corpus, including:

• ChemProt sample set
• ChemProt training set
• ChemProt development set
• ChemProt test set

The BioCreative VI workshop will be held at DoubleTree by Hilton Hotel Bethesda - Bethesda, Maryland during October 18-20, 2017.

• Registration
• Travel Awards
• Scientific Program
• Venue and Access
• Work Submissions
• Accommodations
• Visas
• Sponsors
• Proceedings

Registration

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Registration to BioCreative VI Workshop is now closed

Registration includes:

Breakfast

Attendance to workshop

Coffee breaks

Lunch

Tour to the National Library of Medicine

Registration is in US dollars:

Registration Type	Early fee (until September 18)	Late fee (after September 18)
Student/post-doc	$180	$250
Academic/non-profit/Government	$330	$400
Industry	$400	$470

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Travel Awards

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Funds are available for US participants for the amount up to $700 to participate in the BioCreative workshop. To apply complete the application available here by September 1st. Women, under-represented minorities, students, and post-doctoral fellows are encouraged to apply. Submissions are now closed

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Scientific Program

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Venue: DoubleTree by Hilton Hotel, Bethesda, Maryland
Talks: Ballroom D (2nd floor)
Posters: Balance room (2nd floor)

The scientific program includes the talks related to the individual tracks, a panel about Innovation in biomedical digital curation, a general session for BioCreative related topics, 2 keynote talks and a poster session. Detailed agenda is shown below

Wednesday, October 18, 2017

08:00 - 12:00	Registration (EMC foyer, 2nd floor)
08:00 - 09:00	Breakfast (EMC foyer, 2nd floor)
09:00 - 09:15	Workshop opening
09:15 - 10:40	TRACK 1 Interactive Bio-ID Assignment 9:15-9:25 Introduction to Bio_ID track (Cecilia Arighi, University of Delaware) 9:25-9:40 Introduction to SourceData and data set (Thomas Lemberger, SourceData) 9:40-9:55 Overview of Bio_ID results – batch results (Lynette Hirschman, MITRE) 9:55-10:05 A Neural Named Entity Recognition Approach to Biological Entity Identification (Emily Sheng, Information Sciences Institute/USC) 10:05-10:15 A Study on Identification of Organism and micro-RNA Mentions in Figure Captions (Po-Ting Lai, National Central University) 10:15-10:40 Next steps and discussion
10:40 - 11:00	Break
11:00 - 12:30	Panel on Innovation on Digital Curation (Moderators: Fabio Rinaldi and Cecilia Arighi) 11:00-11:10 Julio Collado-Vides, UNAM- Natural language processing to enhance accessibility to knowledge in RegulonDB 11:10-11:20 Thomas Lemberger, EMBO- Data transparency in scientific publishing 11:20-11:30 Zhiyong Lu, NCBI- Text mining for improving the prioritization, curation, and integration of knowledge for clinically relevant variants 11:30-11:40 Johanna McEntyre, EMBL-EBI- How can text mining scale to meet diverse and precise curation needs? 11:40-12:30 Open discussion
12:30 - 13:40	Lunch (Restaurant first floor)
13:40 - 15:40	TRACK 4 Mining protein interactions and mutations for precision medicine 1:40-2:10 Overview of the Precision Medicine Track (Rezarta Islamaj Dogan) 2:10-2:30 Identifying Relevant Literature for Precision Medicine Using Deep Neural Networks (Sergio Matos) 2:30- 2:50 Exploring a Deep Learning Pipeline for the BioCreative VI Precision Medicine Task (Tung Tran) 2:50- 3:10 Mining protein interactions affected by mutations using a NLP based machine learning approach (Albert Steppi and Jinchan Qu) 3:10-3:30 Document Triage and Relation Extraction for Protein-Protein Interactions affected by Mutations (Dina Demner Fushman for Karin Verspoor and team) 3:30-3:40 Poster spotlight and Open discussion
15:40 - 16:00	Break
16:00 - 17:00	Keynote- Dr. Patricia Flatley Brennan, Director of National Library of Medicine, NIH Towards a future of data-powered health Zip file
17:00 - 18:00	Panel on Funding Stakeholders (Moderator: Cathy Wu) Susan Gregurick, NIGMS, NIH Jennifer Weller, NSF Jane Ye, NLM, NIH Johanna McEntyre, EMBL-EBI

Thursday, October 19, 2017

08:00 - 12:00	Registration (EMC foyer, 2nd floor)
08:00 - 09:00	Breakfast (EMC foyer, 2nd floor)
09:00 - 10:15	General session 9:00-9:20 Efficient and Accurate Entity Recognition for Biomedical Text (Fabio Rinaldi, U. Zurich) 9:20-9:40 iTextMine: Integrated Text Mining System for Large-Scale Knowledge Extraction from Literature (Jia Ren, U. Delaware) 9:40-10:00 Large-scale Automated Reading with Reach Discovers New Cancer Driving Mechanisms (Dane Bell, U. Arizona) 10:00-10:20 Evaluating without a Gold Standard (Lynette Hirschman, MITRE)
10:20 - 10:40	Break
10:40 - 12:30	TRACK 2 Text-mining services for Kinome Curation 10:40-11:10 Kinome Track Overview (Julien Gobeill & Patrick Ruch, SIB) 11:10-11:35 Assisting Document Triage for Human Kinome Curation via Machine Learning (Alan Hsu, NCBI) 11:35-11:55 KinDER: A Biocuration Tool for Extracting Kinase Knowledge from Biomedical Literature (Adam Morrone & Daniel Dopp, Montana State University) 11:55-12:20 Discussion
12:30 - 13:45	Lunch (Restaurant first floor)
13:45 - 15:45	TRACK 3 Extraction of causal network information using the Biological Expression Language 1:45 - 2:15 BEL Track - Overview and Results (Sumit Madan, Fraunhofer SCAI, Germany) 2:15 - 2:30 Task 1 - BELMiner – Information extraction system to extract BEL relationships (Ravikumar Komandur Elayavilli, Mayo Clinic, USA) 2:30 - 2:45 Task 1 - Generating Biological Expression Language Statements with Pipeline Approach and Different Parsers (Po-Ting Lai, National Central University, Taiwan) 2:45 - 3:00 Task 1 - Automatic Extraction of BEL-Statements based on Neural Networks (Mehdi Ali, University of Bonn, Germany) 3:00 - 3:15 Task 2 - Semantic Information Retrieval: Exploring dependency and word embedding features in biomedical Information Retrieval (Majid Rastegar-Mojarad, Mayo Clinic, USA) 3:15 - 3:30 BEL Track - Next steps and discussion (Sumit Madan, Fraunhofer SCAI, Germany)
15:45 - 16:00	Break
16:00 - 17:00	Keynote- Dr. Hongfang Liu, Professor Biomedical Informatics, Mayo Clinic Text mining in precision medicine: opportunities and challenges
17:00 - 19:00	Poster session and Reception

Friday, October 20, 2017

08:00 - 09:00	Breakfast (EMC foyer, 2nd floor)
08:30 - 10:30	TRACK 5 Text mining chemical-protein interactions 8:30-9:00 Overview of the Chemical-Protein relation extraction track (Martin Krallinger / Saber A. Akhondi (CNIO / Elsevier) 9:00-9:15 Chemical-protein relation extraction with SVM, CNN, RNN and ensemble systems (Yifan Peng, NCBI, NLM, NIH) 9:15-9:30 Extracting Chemical-Protein Interactions using Long Short-Term Memory Networks (Sérgio Matos, University of Aveiro, Portugal) 9:30-9:45 Attention based Neural Networks for Chemical Protein Relation Extraction (Ravikumar Komandur Elayavilli, Mayo Clinic, USA) 9:45-10:00 Extracting protein-chemical compound interactions from literature (Pei-Yau Lung, Florida State University) 10:00-10:15 Knowledge-base-enriched relation extraction (Ignacio Tripodi, University of Colorado, Boulder) 10:15 - 10:30 CTCPI - Convolution Tree Kernel-based Chemical-Protein interaction detection (Po-Ting Lai, National Tsing-Hua University, Hsinchu, Taiwan)
10:30 - 10:45	Break
10:45 - 12:00	Tracks open discussion/closing
12:00 - 13:00	Lunch (Restaurant first floor)
13:00 - 15:30	Tour to the National Library of Medicine

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Work Submissions

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Submission of abstracts/papers should be done via Easychair at the following URL: https://easychair.org/conferences/?conf=bc6. Format for submission:PDF.

BioCreative VI proceedings will be published online and will be available at the time of the meeting.

We will invite selected works for full publication in the Database Journal Special Issue for BioCreative.

Track presentation submissions: Track participants should submit their work in the form of a short paper (up to 4 pages). See template with instructions here. Although template is a word document, the format for submission should be in PDF.

Submission deadline: please follow the dates described in the track you are participating

General session submissions: BioCreative VI will host a general session to provide an opportunity to discuss related work to BioCreative topics, including data set preparation, evaluation, biomedical information extraction. Then, we are soliciting submission of your bioNLP work that is related to any of these topics in the form of a 2 page abstracts (see template with instructions can be found here). Although template is a word document, the format for submission should be in PDF. Abstracts will be selected for oral presentation during the corresponding session.

Submission deadline September 17, 2017

POSTERS
Poster size 32"x40"

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Venue and Access

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Conference venue | Map

DoubleTree by Hilton Hotel Bethesda - Washington DC
8120 Wisconsin Avenue, Bethesda, Maryland 20814
Phone: (301) 652-2000

Accommodations

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There are a number of rooms reserved for this event at the DoubleTree hotel with a special rate of US$219 per night. This special rate is available through September 22, 2017.
Guests can go online to the BioCreative hotel page reservation http://doubletree.hilton.com/en/dt/groups/personalized/W/WASBHDT-BC0-20171017 (Preferred)
OR
Guests can call 1-800-955-7359 and request the group rate for the BioCreative VI Conference or the Group SRP/Code: BC0.
OR
Go to the hotel main page www.bethesda.doubletree.com, click on the Reservations Tab, enter dates and on the Special Accounts Section enter BC0 for the Group/Convention Code.
The special rate applies for the nights 10/17/2017 through 10/20/2017.

Directions

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Map & Directions to the hotel from local airports:

The Doubletree Hotel in Bethesda is conveniently located near 3 airports. It is just 15 miles from Ronald Reagan Washington National Airport (DCA), 27 miles from Washington Dulles International Airport (IAD), and 38 miles from Baltimore Washington International Airport (BWI). All three airports should have private shuttle services available. Fees for these services vary based on distance to the hotel.

Transportation options from DCA
Transportation options from IAD
Transportation options from BWI

Maps and directions

Parking

The hotel offers paid parking (rate $12 for day parking and $23 for overnight). There are also meter spaces and public parking throughout Bethesda area. To check parking places and rates click here

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Visas

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You are responsible to inquire about visa requirements to enter the US. General information about US visas can be found here. If you need a letter of invitation to attend the workshop please send email to bcviworkshop@gmail.com with subject: visa letter request.

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Sponsors

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BioCreative workshop is sponsored by

NIH/MIGMS Conference grant 1R13GM109648-01A1

NIH/MIGMS Supplement 2R01GM08064

Database, Oxford University Press

International Society for Biocuration

Elsevier

OpenMinted (654021) H2020 project

encomienda MINETAD-CNIO/OTG Sanidad Plan TL

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BioCreative VI Workshop Proceedings

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The proceedings is now available here

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Co-located: BioCreative V.5 Challenge Evaluation Workshop and ELIXIR-EXCELERATE Workshop Text-mining infrastructure requirements

Table of Contents: BC V.5 - Workshop Proceedings

Editorial and track overview papers

1. The BioCreative V.5 evaluation workshop: tasks, organization, sessions and topics . Krallinger et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 8-10
2. Evaluation of chemical and gene/protein entity recognition systems at BioCreative V.5: the CEMP and GPRO patents tracks. Pérez-Pérez et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 11-18
3. Benchmarking biomedical text mining web servers at BioCreative V.5: the technical Interoperability and Performance of annotation Servers - TIPS track . Pérez-Pérez et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 19-27

Chemical/gene entity recognition tracks: CEMP & GPRO

4. DUTIR at the BioCreative V.5.BeCalm Tasks: A BLSTM-CRF Approach for Biomedical Entity Recognition in Patents. Luo et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 28-39
5. HITextracter System for Chemical and Gene/Protein Entity Mention Recognition in Patents. Liu et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 40-46
6. CRFVoter: Chemical Entity Mention, Gene and Protein Related Object recognition using a conglomerate of CRF based tools. Liu et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 47-53
7. Neji: Recognition of Chemical and Gene Mentions in Patent Texts. Santos and Matos. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 54-60
8. Chemlistem - chemical named entity recognition using recurrent neural networks. Corbett and Boyle. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 61-68
9. Recognition of Chemical Entity Mention in Patents Using Feature-rich CRF. Guo et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 69-72
10. Towards Robust Chemical Recognition with TaggerOne at the BioCreative V.5 CEMP Task. Leaman and Lu. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 73-80
11. A hybrid text mining system for chemical entity recognition and classification using dictionary look-up and pattern matching @ BeCalm challenge evaluation workshop. Raja et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 81-88
12. IBEnt: Chemical Entity Mentions in Patents using ChEBI. Lamurias et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 89-95
13. ChemGrab: Identification of Chemical Names Using a Combined Negative-Dictionary and Rule-Based Approach. Sharma and Sarkar. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 96-103
14. Combining the BANNER tool with the DINTO ontology for the CEMP task of BioCreative V.5. Colon-Ruiz et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 104-107
15. An Ensemble Algorithm for Sequential Labelling: A Case Study in Chemical Named Entity Recognition. Wang et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 108-114
16. Statistical Principle-based Approach for Gene and Protein Related Object Recognition. Lai et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 115-121

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TIPS (Technical interoperability and performance of annotation servers) Track

17. Tagger: BeCalm API for rapid named entity recognition. Jensen. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 122-129
18. MER: a Minimal Named-Entity Recognition Tagger and Annotation Server. Couto et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 130-137
19. SIA: Scalable Interoperable Annotation Server. Kirschnick and Thomas. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 138-145
20. High-throughput, interoperability and benchmarking of text-mining with BeCalm biomedical metaserver. Madrid and Valencia. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 146-155
21. Performance and interoperability assessment of Disease Extract Annotation Server (DEAS). Jonnagaddala et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 156-162
22. TextImager as an interface to BeCalm. Hemati et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 163-166
23. Olelo’s named-entity recognition web service in the BeCalm TIPS task. Folkerts and Neves. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 167-174
24. OGER: OntoGene’s Entity Recogniser in the BeCalm TIPS Task. Furrer and Rinaldi. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 175-182
25. READ-Biomed-Server: A Scalable Annotation Server Using the UIMA Concept Mapper. Teng and Verspoor. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 183-190
26. Neji: DIY web services for biomedical concept recognition. Santos and Matos. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 191-195
27. NTTMU-SCHEMA BeCalm API in BioCreative V.5. Dai et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 196-204
28. Micro-RNA Recognition in Patents in BioCreative V.5. Wang et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 205-209