RSS 2.0
Critical Assessment of Information Extraction in Biology - data sets are available from Resources/Corpora and require registration.

BioCreative IV

Workshop [2013-09-16]

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 to BioCreative IV Workshop is now open.

Register Here!

Registration includes:

  • Attendance to workshop
  • Coffee breaks
  • Evening reception on Tuesday
  • Lunch
  • Registration is in US dollars:

  • Regular registration $250
  • Student/post-doc $125
  • Organizer/Advisory Group Member free
  • Back to top


    Place: DoubleTree Hotel, Bethesda, Maryland
    Talks: Ballroom A
    Poster/Demo: Harmony room

    Monday, October 7, 2013

    08:00 - 12:00Registration
    09:00 - 09:15Workshop opening (W. J. Wilbur/C. Arighi)
    09:15 - 11:15TRACK 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 - 11:35Break
    11:35 - 12:35TRACK 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 - 13:40Lunch
    13:40 - 14:40TRACK 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 - 15:00Break
    15:00 - 17:00TRACK 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
        • Posters and Demos for Interoperablity, GO, and CTD tracks

    Tuesday, October 8, 2013

    08:00 - 12:00Registration
    09:00 - 09:45Plenary 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 - 11:15DOE PANEL (moderator: L. Hirschman)
        • 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 - 11:30Break
    11:30 - 12:45TRACK 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 - 13:45Lunch
    13:45 - 15:45TRACK 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 - 16:00Break
    16:00 - 18:00POSTER/DEMO SESSION II
        • Posters and Demos for ChemDNER track and other posters (including IAT)

    Wednesday, October 9, 2013

    09:00 - 11:00TRACK 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 - 11:20Break
    11:20 - 12:50TRACK 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 - 13:50Lunch
    13:50 - 14:50BioCreative - next steps
    14:50 - 15:00Workshop closing

    Back to top

    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.


    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


    The hotel offers paid parking. There are also meter spaces and public parking throughout Bethesda area. To check parking places and rates click here

    Back to top


    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: 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.


    Back to top