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

BioCreative 2016

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BioCreative Workshop 2016 (Events) [2016-03-02]

Call for Participation

August 1-2, 2016 Corvallis, Oregon, USA

BioCreative: Critical Assessment of Information Extraction in Biology is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. We are happy to announce that we will host BioCreative Workshop 2016 at Corvallis Oregon, USA on August 1-2, 2016, satellite to the International Conference on Biological Ontology (ICBO) 2016. The goal of this workshop is to provide a discussion forum for topics of interest to the BioCreative community and to encourage synergistic interactions with the ontology community.
BioCreative workshop 2016 second day session will run jointly with the ICBO meeting.

BioCreative 2016 will consist of sessions that were selected based on input from the community via a user survey recently conducted. A draft agenda can be found in agenda

Keynote Speaker
William Hersh
Professor and Chair
Department of Medical Informatics & Clinical Epidemiology
School of Medicine, Oregon Health & Science University
Title: Information Retrieval and Text Mining Evaluation Must Go Beyond “Users”: Incorporating Real-World Context and Outcomes

Meeting Topics

  • 1-Text mining-facilitated models of curation. Application of text mining methods in areas such as crowdsourcing, database curation, publication process, and metagenomics.
    Chairs: Lynette Hirschman
  • 2-Text mining in precision medicine. Methods for annotations such as disease, phenotype, and adverse reactions in different text sources literature, clinical records and social media.
    Chairs: Donald Comeau
  • 3-Domain portability or generalizability across medical literature. Methods to achieve interoperability, generalizability and scalability in text mining: BioC, RDF and semantic web, among others.
    Chairs:Kevin Bretonnel Cohen and Donald Comeau.
  • 4-Text mining and ontologies. Application of ontologies in text mining, and text mining as ontology builder. (with ICBO).
    Chairs: Cecilia Arighi and Pankaj Jaiswal
  • We are soliciting submission of your work in the form of a 2 page abstract (see instructions to authors). Abstracts will be selected for oral presentation during the corresponding session or poster.
    All information about this event is available at the ICBO conference website site

    Funds are available for US participants for the amount up to $700 to participate in BioCreative workshop 2016. To apply complete the application available here by May 15. Women, under-represented minorities, students, and post-doctoral fellows are encouraged to apply.

    Posters
    Poster dimension should be maximum Width 36" (inches) x Height 44" (inches).
    Works selected for talks are also encourage to bring a poster to foster further discussion.
    Posters should be set up on August 1 before the poster session time and be available throughout the meeting.

    Downloads

    BioCreative V

    Proceedings of the Fifth BioCreative Challenge Evaluation Workshop (Resources) [2015-09-09]

    Table of Contents

      BioC Track

    1. Overview of BioCreative V BioC Track. Kim et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 1-9 PDF
    2. Interaction Passage Extraction Using the Interaction Pattern Kernel Approach for the BioCreative 2015 BioC Track. Chang et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 10-16 PDF
    3. Neji: a BioC compatible framework for biomedical concept recognition. Matos et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 17-21 PDF
    4. NTTMUNSW BioC Modules for Recognizing and Normalizing Species and Gene/Protein Mentions in Full Text Articles. Singh et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 22-29 PDF
    5. Extended dependency graph for BioC-compatible protein-protein interaction (PPI) passage detection in full-text articles. Peng et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 30-35 PDF
    6. Identifying genetic interaction evidence passages in biomedical literature. Dogan et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 36-41 PDF
    7. Retrieving Passages Describing Experimental Methods using Ontology and Term Relevance based Query Matching. Aydın et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 42-50 PDF
    8. Development of bespoke machine learning and biocuration workflows in a BioC-supporting text mining workbench. Batista-Navarro et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 51-56 PDF
    9. A Visual Tool for Displaying Annotations in BioC. Shin et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 57-62 PDF

    10. CHEMDNER Patents Track

    11. Overview of the CHEMDNER patents task. Krallinger et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 63-75 PDF
    12. Identification of chemical and gene mentions in patent texts using feature-rich conditional random fields. Matos et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 76-81 PDF
    13. The System for Recognizing Chemical Names and Detecting Chemical Passages in Patent Documents. Xu et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 82-87 PDF
    14. FRCRF: A Feature-rich CRF-based Solution for Chemical Entity Mention in Patent Task. Qu et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 88-89 PDF
    15. Combining Conditional Random Fields and Word Embeddings for the CHEMDNER-patents task. Segura Bedmar et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 90-93 PDF
    16. NCU-IISR System for the CHEMDNER-patents Track at BioCreative V. Hsiao et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 94-95 PDF
    17. CLRG ChemTMiner @ Biocreative V. Devi et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 96-101 PDF
    18. Patent mining: combining dictionary-based and machine-learning approaches. Akhondi et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 102-109 PDF
    19. Comparison of different strategies for utilizing two CHEMDNER corpora. Dieb et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 110-115 PDF
    20. HTSZ_CEM System for Chemical Entity Mention Recognition in Patents. Bu et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 116-118 PDF
    21. OCMiner for Patents. Extracting Chemical Information from Patent Texts. Irmer et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 119-123 PDF
    22. Identifying chemical entities in patents using brown clustering and semantic similarity. Lamurias et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 124-128 PDF
    23. Recognition of chemical entities in patents using LeadMine. Lowe et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 129-134 PDF
    24. Recognition of Chemical Entity Mention in Patents using CRF, Domain Specific Dictionaries and Features. Nittala et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 135-139 PDF
    25. Mining Patents with tmChem, GNormPlus and an Ensemble of Open Systems. Leaman et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 140-146 PDF
    26. UTH-CCB@BioCreative V Track 2: Recognizing Chemical Entities in Patents. Zhang et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 147-148 PDF
    27. Adapting ChER for the recognition of chemical mentions in patents. Batista-Navarro et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 149-153 PDF

    28. Chemical Disease Relation Track

    29. Overview of the BioCreative V Chemical Disease Relation (CDR) Task. Wei et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 154-166 PDF
    30. Hybrid approaches for the DNER task at BioCreative V: the INRA/LIMSI system. Deleger et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 167-172 PDF
    31. Annotating chemicals, diseases and their interactions in biomedical literature. Li et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 173-182 PDF
    32. DUTIR at the BioCreative V CDR Task: Disease Named Entity Recognition and Normalization and the Chemical-Disease Relation Extraction from Biomedical Text. Li et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 183-195 PDF
    33. HITSZ_CDR System for Disease and Chemical Named Entity Recognition and Relation Extraction. Li et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 196-201 PDF
    34. ExB Medical Text Miner. Hänig et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 202-207 PDF
    35. The UET-CAM System in the BioCreAtIvE V CDR Task. Le et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 208-213 PDF
    36. Chemical-disease Relations Extraction Based on The Shortest Dependency Path Tree. Zhou et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 214-219 PDF
    37. Chemical-induced Disease Relation Extraction with Lexical Features. Gu et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 220-225 PDF
    38. An enhanced CRF-based system for disease name entity recognition and normalization on BioCreative V DNER Task. Lee et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 226-233 PDF
    39. Recognition and normalization of disease mentions in PubMed abstracts. Jonnagaddala et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 234-239 PDF
    40. LeadMine: Disease identification and concept mapping using Wikipedia. Lowe et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 240-246 PDF
    41. RELigator: Chemical-disease relation extraction using prior knowledge and textual information. Pons et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 247-253 PDF
    42. UTH-CCB@BioCreative V CDR Task: Identifying Chemical-induced Disease Relations in Biomedical Text. Xu et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 254-259 PDF
    43. A Hybrid System for Extracting Chemical-Disease Relationships from Scientific Literature. Kilicoglu et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 260-265 PDF
    44. Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text. Bravo et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 266-273 PDF
    45. A Knowledge-Poor Approach to BioCreative V DNER and CID Tasks. Alam et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 274-279 PDF
    46. Resolution of Chemical Disease Relations with Diverse Features and Rules. Li et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 280-285 PDF
    47. CoTri: extracting chemical-disease relations with co-reference resolution and common trigger words. Chen et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 286-291 PDF
    48. Extracting structured chemical-induced disease relations from free text via crowdsourcing. Li et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 292-298 PDF
    49. Word Embedding Clustering for Disease Named Entity Recognition. Suarez-Paniagua et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 299-304 PDF
    50. Ontogene Term and Relation Recognition for CDR. Ellendorff et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 305-310 PDF
    51. Augmenting the Medical Subject Headings vocabulary with semantically rich variants to improve disease mention normalisation. Batista-Navarro et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 311-316 PDF
    52. A CRD-WEL System for Chemical-disease Relations Extraction. Jiang et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 317-326 PDF
    53. Disease Named Entity Recognition and Normalization using Conditional Random Fields and Levenshtein Distance. Wei et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 327-332 PDF

    54. Biological Expression Language Track

    55. Track 4 Overview: Extraction of Causal Network Information in Biological Expression Language (BEL). Fluck et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 333-346 PDF
    56. NCU-IISR System for BioCreative BEL Task 1. Lai et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 347-350 PDF
    57. Integrating Coreference Resolution for BEL Statement Generation. Choi et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 351-355 PDF
    58. Retrieving evidence sentences for BEL statements. Rastegar-Mojarad et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 356-359 PDF
    59. Adapting a rule-based relation extraction system for BioCreative V BEL task. Komandur Elayavilli et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 360-363 PDF

    60. Interactive Track

    61. Overview of the Interactive Task in BioCreative V . Wang et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 364-383 PDF
    62. EXTRACT: Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. Pafilis et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 384-395 PDF
    63. Assisted Mining and Curation of Genomic Variants using Egas. Matos et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 396-402 PDF
    64. Semi-automatic curation of chronic obstructive pulmonary disease phenotypes using Argo. Batista-Navarro et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 403-408 PDF
    65. BELIEF Dashboard - a Web-based Curation Interface to Support Generation of BEL Networks. Madan et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 409-417 PDF
    66. MET Pathway in PubMed: A Pathway Visualization and Curation System. Dai et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 418-426 PDF
    67. An integrated text mining system based on network analysis for knowledge discovery of human gene-disease associations (GenDisFinder). Subramani et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 427-434 PDF
    68. Biocuration of microRNAs in idiopathic pulmonary fibrosis. Balderas-Martinez et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 435-441 PDF

    Downloads

    BioCreative V Workshop (Events) [2015-08-06]

    The BioCreative V Workshop website is now open for registration. The workshop agenda is available on this webpage.
    In case you participated in several BioCreative V tracks, remember that you are required to submit a separate paper for each track. Your paper should describe resources you used and your methodology. It should also give any evaluation results you were able to produce based on gold standard data applicable to your task. We recommend limiting the length of the paper to 4-6 pages. Assuming your efforts and innovation in doing your chosen Subtask(s) were significant, we expect these papers to eventually form the basis for a journal article describing your efforts in more detail.
    To make the preparation of your manuscript easier we provide some templates based on the formats for Lecture Notes of Computer Sciences that we think are suitable to proceedings paper styles. The latex and word templates are available at: proceedings template
    The deadline for the camera-ready paper submission various for the different track (in case of doubts cross check with the corresponding track organizer). Your paper will need to be submitted through EasyChair: EasyChair BioCreative V

    Travel awards to attend the BioCreative workshop are now available. For more information visit the Travel Award section in the workshop registration page.