The BioCreative IV workshop will be held at DoubleTree by Hilton Hotel Bethesda - Bethesda, Maryland during October 7-9, 2013.
IMPORTANT!!!!The workshop will be held at DoubleTree by Hilton Hotel Bethesda - Bethesda, Maryland, 8120 Wisconsin Avenue, Bethesda, Maryland 20814
We will keep you posted on the final venue. Thank you for your patience.
Registration
Registration to BioCreative IV Workshop is now open.
Register Here!
Registration includes:
Registration is in US dollars:
Agenda
Place: DoubleTree Hotel, Bethesda, Maryland
Talks: Ballroom A
Poster/Demo: Harmony room
Monday, October 7, 2013
| 08:00 - 12:00 | Registration |
| 09:00 - 09:15 | Workshop opening (W. J. Wilbur/C. Arighi) |
| 09:15 - 11:15 | TRACK 1 BioC: Interoperability • 9:15 Overview of BioC and BioCreative IV - Interoperability track (D.C. Comeau/K. Cohen) • 9:45 BioC for NER Web Services-Based Inter-process Communications (T. Wiegers) • 10:00 PyBioC: a python implementation of the BioC core (F. Rinaldi) • 10:15 Enhancing the Interoperability of iSimp by Using the BioC Format (Y.Peng) • 10:30 Improving Interoperability of Text Mining Tools with BioC (C-H.Wei/K. Cohen) • 10:45 Addressing common challenges in biomedical text processing with BioC: some processing tools and corpora (R.I.Dogan/W. Liu) • 11:00 Questions, Discussion and Conclusion (D.C.Comeau/K. Cohen and R.I.Dogan/W. Liu) |
| 11:15 - 11:35 | Break |
| 11:35 - 12:35 | TRACK 3 CTD (session 1) • 11:35 Overview and results of the BioCreative IV – CTD track (T. Wiegers) • 12:05 NaCTeM CTD Web Services (R. Batista-Navarro) • 12:20 Morning Discussion |
| 12:35 - 13:40 | Lunch |
| 13:40 - 14:40 | TRACK 3 CTD (session 2) • 13:40 OntoGene: CTD entity and action term recognition (F. Rinaldi) • 13:55 Adapting a multi-class biomedical tagger for the CTD task (S.V. Ramanan) • 14:10 A Web Service Annotation Framework for CTD Using the UIMA Concept Mapper (K. Verspoor) • 14:25 Afternoon Discussion |
| 14:40 - 15:00 | Break |
| 15:00 - 17:00 | TRACK 4 GO • 15:00 Overview and results of the BioCreative IV – GO track (Z. Lu/K. Van-Auken) • 15:30 Closing the loop: from paper to protein annotation using automatic text categorization (J. Gobeill) • 15:45 Integrating Information Retrieval with Distant Supervision for Gene Ontology Annotation (D. Zhu) • 16:00 Unsupervised Information Extraction for Finding Gene Functions (E. Emadzadeh) • 16:15 A Robust Data-Driven Approach for Gene Ontology Annotation (Y. Li) • 16:30 Discussion |
| 17:00 - 19:00 | POSTER/DEMO SESSION I AND RECEPTION • Posters and Demos for Interoperablity, GO, and CTD tracks |
Tuesday, October 8, 2013
| 08:00 - 12:00 | Registration |
| 09:00 - 09:45 | Plenary Talk: Evangelos Pafilis Institute of Marine Biology Biotechnology and Aquaculture Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece • SPECIES and ENVIRONMENTS: taxonomic name and environment descriptive term identification in text |
| 09:45 - 11:15 | DOE PANEL (moderator: L. Hirschman) Panelists: • Jim Cole, Michigan State University • George Garrity, Names for Life Folker Meyer, Argonne National Laboratory • Nikos Kyrpides, Joint Genome Institute • Tatiana Tatusova, NCBI |
| 11:15 - 11:30 | Break |
| 11:30 - 12:45 | TRACK 2 CHEMDNER (session 1) • 11:30 Overview and results of the BioCreative IV – CHEMDNER task (M. Krallinger) • 12:00 PA dictionary- and grammar-based name entity recognizer for chemical name entity recognition (E. van Mulligen) • 12:15 tmChem: a machine-learning approach for recognizing chemical names in PubMed articles (R. Leaman/K.Vespoor) • 12:30 Extended Feature Set for Chemical Named Entity Recognition and Indexing (M. Neves) |
| 12:45 - 13:45 | Lunch |
| 13:45 - 15:45 | TRACK 2 CHEMDNER (session 2) • 13:45 Chemistry-specific Features and Heuristics for Developing a CRF-based Chemical Named Entity Recogniser (R. Batista-Navarro) • 14:00 In grammars we trust: LeadMine, a knowledge driven solution (D. Lowe) • 14:15 Chemical name recognition with harmonized feature-rich conditional random fields (D. Campos) • 14:30 Recognizing Chemical Named Entities using CRF and SSVM (H. Xu) • 14:45 Adapting Cocoa, a multi-class entity detector, for the CHEMDNER task of BioCreative IV ( S.V. Ramanan) • 15:00 BANNER-CHEMDNER: Incorporating Domain Knowledge in Chemical and Drug Named Entity Recognition (T. Munkhdalai) • 15:15 An Ensemble Information Extraction Approach to the BioCreative CHEMDNER Task (T. M. Khabsa) • 15:30 CHEMDNER discussion: organizers & all participanting teams |
| 15:45 - 16:00 | Break |
| 16:00 - 18:00 | POSTER/DEMO SESSION II • Posters and Demos for ChemDNER track and other posters (including IAT) |
Wednesday, October 9, 2013
| 09:00 - 11:00 | TRACK 5 IAT • 9:00 Overview and results of the BioCreative IV – (C. Arighi) • 9:20 Evaluation of the CellFinder pipeline in the BioCreative IV User Interactive task (M. Neves) • 9:30 Ontogene curation pipelines (F. Rinaldi) • 9:40 MarkerRIF: An interactive curation system for biomarker (H-J Dai) • 9:50 Supporting Document Triage with the SciKnowMine System in the Mouse Genome Informatics (MGI) Curation Process (G. Burns) • 10:00 BioQRator: a web-based interactive biomedical literature curating system (S. Kim/C. Arighi) • 10:10 RLIMS-P: Literature-based curation of protein phosphorylation information (M. Torii) • 10:20 Egas – Collaborative Biomedical Annotation as a Service ( S. Matos) • 10:30 tagtog: Interactive Human and Machine Annotation of Gene Mentions in PLOS Full-Text Articles (J. M. Cejuela) • 10:40 Customizable Curation Workflows in Argo (R. Batista-Navarro) • 10:50 Discussion:organizers & all participanting teams |
| 11:00 - 11:20 | Break |
| 11:20 - 12:50 | TRACK 5 IAT demo session • 11:20 CellFinder (M. Neves) • 11:30 Ontogene (F. Rinaldi) • 11:40 MarkerRIF (H-J Dai) • 11:50 SciKnowMine (G. Burns) • 12:00 BioQRator (S. Kim/C. Arighi) • 12:10 RLIMS-P (G. Li) • 12:20 EGAS (D. Campos) • 12:30 tagtog (J. M. Cejuela) • 12:40 Argo (R. Batista-Navarro) |
| 12:50 - 13:50 | Lunch |
| 13:50 - 14:50 | BioCreative - next steps |
| 14:50 - 15:00 | Workshop closing |
Venue and Access
Conference venue | Map
DoubleTree by Hilton Hotel Bethesda - Washington DC
8120 Wisconsin Avenue, Bethesda, Maryland 20814
Phone: (301) 652-2000
There are a number of rooms reserved for this event with a special rate of US$209 per night.
For reservations online, please use the code B40.
The special rate applies for the nights 10/06/13 through 10/09/13.
Directions
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
http://www.doubletreebethesda.com/map_and_directions/
Parking
The hotel offers paid parking. There are also meter spaces and public parking throughout Bethesda area. To check parking places and rates click here
Proceedings
For track participants, descriptions of their activities will be published in the workshop proceedings. Submission of documents should be done via Easychair at the following URL: https://www.easychair.org/conferences/?conf=bioc2013. The authors are required to submit a paper for each track in which they participate. They should verify with the individual tracks for additional requirements and other deadlines. Paper submissions should follow the style described below in download section.
We also accept poster submissions from any workshop attendee who would like to show related work. For submission use same URL as above but make sure to specify that the submission is for a poster. Poster submissions are restricted to 500 words. The size of posters should be: 4 ft wide x 3 ft high (48 in x 36 in or 122 cm x 91 cm).
The deadline for paper submissions and poster submissions is on September 26, 2013.
