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

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.

Publications

BC IV - CHEMDNER: Journal of Cheminformatics special issue (Resources) [2015-03-31]

BC IV - CHEMDNER: Journal of Cheminformatics special issue

The entire special issue is available at: here.

Table of Contents

  1. CHEMDNER: The drugs and chemical names extraction challenge Martin Krallinger, Florian Leitner, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, Alfonso Valencia. Journal of Cheminformatics 2015, 7(Suppl 1):S1 (19 January 2015)[ PUBMED]
  2. The CHEMDNER corpus of chemicals and drugs and its annotation principles Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M Lowe, Roger A Sayle, Riza Batista-Navarro, Rafal Rak, Torsten Huber, Tim Rocktäschel, Sérgio Matos, David Campos, Buzhou Tang, Hua Xu, Tsendsuren Munkhdalai, Keun Ryu, SV Ramanan, Senthil Nathan, Slavko Žitnik, Marko Bajec, Lutz Weber, Matthias Irmer, Saber A Akhondi, Jan A Kors, Shuo Xu, Xin An, Utpal Sikdar, Asif Ekbal, Masaharu Yoshioka, Thaer M Dieb, Miji Choi, Karin Verspoor, Madian Khabsa, C Giles, Hongfang Liu, Komandur Ravikumar, Andre Lamurias, Francisco M Couto, Hong-Jie Dai, Richard Tsai, Caglar Ata, Tolga Can, Anabel Usié, Rui Alves, Isabel Segura-Bedmar, Paloma Martínez, Julen Oyarzabal, Alfonso Valencia et al. Journal of Cheminformatics 2015, 7(Suppl 1):S2 (19 January 2015) [ PUBMED]
  3. tmChem: a high performance approach for chemical named entity recognition and normalization Robert Leaman, Chih-Hsuan Wei, Zhiyong Lu Journal of Cheminformatics 2015, 7(Suppl 1):S3 (19 January 2015) [ PUBMED]
  4. CHEMDNER system with mixed conditional random fields and multi-scale word clustering Yanan Lu, Donghong Ji, Xiaoyuan Yao, Xiaomei Wei, Xiaohui Liang Journal of Cheminformatics 2015, 7(Suppl 1):S4 (19 January 2015) [ PUBMED]
  5. LeadMine: a grammar and dictionary driven approach to entity recognition Daniel M Lowe, Roger A Sayle Journal of Cheminformatics 2015, 7(Suppl 1):S5 (19 January 2015) [ PUBMED]
  6. Optimising chemical named entity recognition with pre-processing analytics, knowledge-rich features and heuristics Riza Batista-Navarro, Rafal Rak, Sophia Ananiadou Journal of Cheminformatics 2015, 7(Suppl 1):S6 (19 January 2015) [ PUBMED]
  7. A document processing pipeline for annotating chemical entities in scientific documents David Campos, Sérgio Matos, José L Oliveira Journal of Cheminformatics 2015, 7(Suppl 1):S7 (19 January 2015) [ PUBMED]
  8. A comparison of conditional random fields and structured support vector machines for chemical entity recognition in biomedical literature Buzhou Tang, Yudong Feng, Xiaolong Wang, Yonghui Wu, Yaoyun Zhang, Min Jiang, Jingqi Wang, Hua Xu Journal of Cheminformatics 2015, 7(Suppl 1):S8 (19 January 2015) [ PUBMED]
  9. Incorporating domain knowledge in chemical and biomedical named entity recognition with word representations Tsendsuren Munkhdalai, Meijing Li, Khuyagbaatar Batsuren, Hyeon Park, Nak Choi, Keun Ryu Journal of Cheminformatics 2015, 7(Suppl 1):S9 (19 January 2015) [ PUBMED]
  10. Recognition of chemical entities: combining dictionary-based and grammar-based approaches Saber A Akhondi, Kristina M Hettne, Eelke van der Horst, Erik M van Mulligen, Jan A Kors Journal of Cheminformatics 2015, 7(Suppl 1):S10 (19 January 2015) [ PUBMED]
  11. A CRF-based system for recognizing chemical entity mentions (CEMs) in biomedical literature Shuo Xu, Xin An, Lijun Zhu, Yunliang Zhang, Haodong Zhang Journal of Cheminformatics 2015, 7(Suppl 1):S11 (19 January 2015) [ PUBMED]
  12. Chemical entity extraction using CRF and an ensemble of extractors Madian Khabsa, C Giles Journal of Cheminformatics 2015, 7(Suppl 1):S12 (19 January 2015) [ PUBMED]
  13. Improving chemical entity recognition through h-index based semantic similarity Andre Lamurias, João D Ferreira, Francisco M Couto Journal of Cheminformatics 2015, 7(Suppl 1):S13 (19 January 2015) [ PUBMED]
  14. Enhancing of chemical compound and drug name recognition using representative tag scheme and fine-grained tokenization Hong-Jie Dai, Po-Ting Lai, Yung-Chun Chang, Richard Tsai Journal of Cheminformatics 2015, 7(Suppl 1):S14 (19 January 2015) [ PUBMED]
  15. CheNER: a tool for the identification of chemical entities and their classes in biomedical literature Anabel Usié, Joaquim Cruz, Jorge Comas, Francesc Solsona, Rui Alves Journal of Cheminformatics 2015, 7(Suppl 1):S15 (19 January 2015) [ PUBMED]