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BioCreative V

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

Table of Contents

BioC Track

Overview of BioCreative V BioC Track. Kim et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 1-9
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
Neji: a BioC compatible framework for biomedical concept recognition. Matos et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 17-21
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
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
Identifying genetic interaction evidence passages in biomedical literature. Dogan et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 36-41
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
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
A Visual Tool for Displaying Annotations in BioC. Shin et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 57-62

CHEMDNER Patents Track

Overview of the CHEMDNER patents task. Krallinger et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 63-75
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
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
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
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
NCU-IISR System for the CHEMDNER-patents Track at BioCreative V. Hsiao et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 94-95
CLRG ChemTMiner @ Biocreative V. Devi et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 96-101
Patent mining: combining dictionary-based and machine-learning approaches. Akhondi et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 102-109
Comparison of different strategies for utilizing two CHEMDNER corpora. Dieb et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 110-115
HTSZ_CEM System for Chemical Entity Mention Recognition in Patents. Bu et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 116-118
OCMiner for Patents. Extracting Chemical Information from Patent Texts. Irmer et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 119-123
Identifying chemical entities in patents using brown clustering and semantic similarity. Lamurias et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 124-128
Recognition of chemical entities in patents using LeadMine. Lowe et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 129-134
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
Mining Patents with tmChem, GNormPlus and an Ensemble of Open Systems. Leaman et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 140-146
UTH-CCB@BioCreative V Track 2: Recognizing Chemical Entities in Patents. Zhang et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 147-148
Adapting ChER for the recognition of chemical mentions in patents. Batista-Navarro et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 149-153

Chemical Disease Relation Track

Overview of the BioCreative V Chemical Disease Relation (CDR) Task. Wei et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 154-166
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
Annotating chemicals, diseases and their interactions in biomedical literature. Li et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 173-182
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
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
ExB Medical Text Miner. Hänig et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 202-207
The UET-CAM System in the BioCreAtIvE V CDR Task. Le et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 208-213
Chemical-disease Relations Extraction Based on The Shortest Dependency Path Tree. Zhou et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 214-219
Chemical-induced Disease Relation Extraction with Lexical Features. Gu et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 220-225
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
Recognition and normalization of disease mentions in PubMed abstracts. Jonnagaddala et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 234-239
LeadMine: Disease identification and concept mapping using Wikipedia. Lowe et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 240-246
RELigator: Chemical-disease relation extraction using prior knowledge and textual information. Pons et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 247-253
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
A Hybrid System for Extracting Chemical-Disease Relationships from Scientific Literature. Kilicoglu et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 260-265
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
A Knowledge-Poor Approach to BioCreative V DNER and CID Tasks. Alam et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 274-279
Resolution of Chemical Disease Relations with Diverse Features and Rules. Li et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 280-285
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
Extracting structured chemical-induced disease relations from free text via crowdsourcing. Li et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 292-298
Word Embedding Clustering for Disease Named Entity Recognition. Suarez-Paniagua et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 299-304
Ontogene Term and Relation Recognition for CDR. Ellendorff et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 305-310
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
A CRD-WEL System for Chemical-disease Relations Extraction. Jiang et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 317-326
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

Biological Expression Language Track

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
NCU-IISR System for BioCreative BEL Task 1. Lai et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 347-350
Integrating Coreference Resolution for BEL Statement Generation. Choi et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 351-355
Retrieving evidence sentences for BEL statements. Rastegar-Mojarad et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 356-359
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

Interactive Track

Overview of the Interactive Task in BioCreative V . Wang et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 364-383
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
Assisted Mining and Curation of Genomic Variants using Egas. Matos et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 396-402
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
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
MET Pathway in PubMed: A Pathway Visualization and Curation System. Dai et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 418-426
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
Biocuration of microRNAs in idiopathic pulmonary fibrosis. Balderas-Martinez et al. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 435-441