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

BioCreative VI

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BioCreative VI Workshop Registration and Information (Events) [2017-07-05]

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

Registration


Registration to BioCreative VI Workshop is now open. Please register in our secure website http://www.udel.edu/biocreative6

Registration includes:

  • Breakfast
  • Attendance to workshop
  • Coffee breaks
  • Lunch
  • Tour to the National Library of Medicine
  • Registration is in US dollars:

    Registration TypeEarly fee (before September 10)Late fee (on or after September 10)
    Student/post-doc$180$250
    Academic/non-profit/Government$330$400
    Industry$400$470

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    Travel Awards


    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.

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    Scientific Program


    Venue: DoubleTree by Hilton Hotel, Bethesda, Maryland
    Talks: Ballroom B
    Posters: Wisdom room

    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 - 12:00Registration
    09:00 - 09:15Workshop opening
    09:15 - 11:15TRACK 1 Interactive Bio-ID Assignment
    11:15 - 11:35Break
    11:35 - 12:35Panel on Innovation on Digital Curation
    12:35 - 13:40Lunch
    13:40 - 15:40TRACK 2 Text-mining services for Kinome Curation
    15:40 - 16:00Break
    16:00 - 17:00Keynote- Dr. Patricia Flatley Brennan, Director of National Library of Medicine, NIH
    17:00 - 18:00Panel on Funding Agencies
    18:00 - 19:30Poster session and Reception

    Thursday, October 19, 2017

    08:00 - 12:00Registration
    08:00 - 10:15General session
    10:15 - 10:30Break
    10:30 - 12:30TRACK 3 Extraction of causal network information using the Biological Expression Language
    12:30 - 13:45Lunch
    13:45 - 15:45TRACK 4 Mining protein interactions and mutations for precision medicine
    15:45 - 16:00Break
    16:00 - 17:00Keynote- Dr. Hongfang Liu, Professor Biomedical Informatics, Mayo Clinic
    17:00 - 19:00Poster session

    Friday, October 20, 2017

    08:30 - 10:30TRACK 5 Text mining chemical-protein interactions
    10:30 - 10:45Break
    10:45 - 12:00Tracks open discussion/closing
    12:00 - 13:00Lunch
    13:00 - 15:30Tour to the National Library of Medicine

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    Work Submissions


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

    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.

    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). Abstracts will be selected for oral presentation during the corresponding session.

    Submission deadline September 10, 2017

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    Venue and Access


    Conference venue | Map

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

    Accommodations


    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 17, 2017.
    Guests can call 1-800-955-7359 and request the group rate for the BioCreative VI Conference or the Group SRP/Code: BCO.
    Guests can go online to www.bethesda.doubletree.com, click on the Reservations Tab, enter dates and on the Special Accounts Section enter BCO for the Group/Convention Code.
    The special rate applies for the nights 10/17/2017 through 10/20/2017.

    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

    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


    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


    BioCreative workshop is sponsored by

  • NIH/MIGMS Conference grant 1R13GM109648-01A1
  • NIH/MIGMS Supplement 2R01GM08064
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    Downloads

    PM-task Training Data (Tasks) [2017-05-31]

    Please download the training data for the Precision Medicine Task. (JSON and XML formats)

    • Triage training dataset consists of 4082 annotated PubMed documents as relevant or not relevant. The file contains a BioC collection of documents. Each document contains two passages: the title and abstract, and has a document ID corresponding to the article's PubMed ID. Each document is characterized with an infon tag marking the document as relevant or not.
    • Relations training dataset consists of 597 PubMed articles marked relevant in the Triage set. This set of articles is annotated with PPI relations that are affected by a mutation. The mentions of these interacting genes/proteins in the PubMed title and abstract are also annotated and linked to their corresponding Gene ID. The non-relevant interactions are not annotated.

      You can use this link to visualize the relations training dataset.
    Feel free to contact task organizers for questions:

    Task organizers:

    Rezarta Islamaj Dogan (NCBI)
    Andrew Chatr-aryamontri (BioGrid)
    Sun Kim (NCBI)
    Don Comeau (NCBI)
    Zhiyong Lu (NCBI)

    Downloads

    Publications

    BC V.5 - Workshop Proceedings (Resources) [2017-05-19]

    PDF

    Co-located: BioCreative V.5 Challenge Evaluation Workshop PDF and ELIXIR-EXCELERATE Workshop Text-mining infrastructure requirements PDF
    PDF
    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 PDF
    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 PDF
    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 PDF
    4. Chemical/gene entity recognition tracks: CEMP & GPRO

    5. 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 PDF
    6. 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 PDF
    7. 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 PDF
    8. Neji: Recognition of Chemical and Gene Mentions in Patent Texts. Santos and Matos. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 54-60 PDF
    9. Chemlistem - chemical named entity recognition using recurrent neural networks. Corbett and Boyle. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 61-68 PDF
    10. 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 PDF
    11. 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 PDF
    12. 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 PDF
    13. IBEnt: Chemical Entity Mentions in Patents using ChEBI. Lamurias et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 89-95 PDF
    14. 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 PDF
    15. 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 PDF
    16. 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 PDF
    17. 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 PDF

    18. TIPS (Technical interoperability and performance of annotation servers) Track

    19. Tagger: BeCalm API for rapid named entity recognition. Jensen. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 122-129 PDF
    20. MER: a Minimal Named-Entity Recognition Tagger and Annotation Server. Couto et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 130-137 PDF
    21. SIA: Scalable Interoperable Annotation Server. Kirschnick and Thomas. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 138-145 PDF
    22. 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 PDF
    23. Performance and interoperability assessment of Disease Extract Annotation Server (DEAS). Jonnagaddala et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 156-162 PDF
    24. TextImager as an interface to BeCalm. Hemati et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 163-166 PDF
    25. 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 PDF
    26. OGER: OntoGene’s Entity Recogniser in the BeCalm TIPS Task. Furrer and Rinaldi. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 175-182 PDF
    27. 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 PDF
    28. Neji: DIY web services for biomedical concept recognition. Santos and Matos. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 191-195 PDF
    29. NTTMU-SCHEMA BeCalm API in BioCreative V.5. Dai et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 196-204 PDF
    30. Micro-RNA Recognition in Patents in BioCreative V.5. Wang et al. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 205-209 PDF

    Downloads