Open AccessProceedings Article
Overview of BioNLP Shared Task 2013
Claire Nédellec,Robert Bossy,Jin-Dong Kim,Jung-Jae Kim,Tomoko Ohta,Sampo Pyysalo,Pierre Zweigenbaum +6 more
- pp 1-7
TLDR
The BioNLP Shared Task 2013 shows advances in the state of the art and demonstrates that extraction methods can be successfully generalized in various aspects.Citations
More filters
Journal ArticleDOI
One, no one and one hundred thousand events: Defining and processing events in an inter-disciplinary perspective*
Rachele Sprugnoli,Sara Tonelli +1 more
TL;DR: An overview of event definition and processing spanning 25 years of research in NLP is presented, where the notion of event for historians is put in relation to the NLP perspective and the results of a questionnaire are presented.
Journal ArticleDOI
Using text mining techniques to extract phenotypic information from the PhenoCHF corpus
TL;DR: PhenoCHF is the first annotated corpus aimed at encoding detailed phenotypic information, and the unique heterogeneous composition of the corpus has been shown to be advantageous in the training of systems that can accurately extract phenotypes from a range of different text types.
Posted Content
CrossNER: Evaluating Cross-Domain Named Entity Recognition
Zihan Liu,Yan Xu,Tiezheng Yu,Wenliang Dai,Ziwei Ji,Samuel Cahyawijaya,Andrea Madotto,Pascale Fung +7 more
TL;DR: Results show that focusing on the fractional corpus containing domain-specialized entities and utilizing a more challenging pre-training strategy in domain-adaptive pre- training are beneficial for the NER domain adaptation, and the proposed method can consistently outperform existing cross-domain NER baselines.
Journal ArticleDOI
BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language.
Fabio Rinaldi,Tilia Renate Ellendorff,Sumit Madan,Simon Clematide,Adrian van der Lek,Theo Mevissen,Juliane Fluck +6 more
TL;DR: The aim of this evaluation method is to help identify the characteristics of the systems which, if combined, would be most useful for achieving the overall goal of automatically constructing causal biological networks from text.
Proceedings ArticleDOI
Predicting Future Scientific Discoveries Based on a Networked Analysis of the Past Literature
Meenakshi Nagarajan,Angela D. Wilkins,Benjamin J. Bachman,Ilya B. Novikov,Shenghua Bao,Peter J. Haas,María E. Terrón-Díaz,Sumit Bhatia,Anbu Karani Adikesavan,Jacques Joseph Labrie,Sam Regenbogen,Christie M. Buchovecky,Curtis R. Pickering,Linda Kato,Andreas Martin Lisewski,Ana Lelescu,Houyin Zhang,Stephen K. Boyer,Griff Weber,Ying Chen,Lawrence A. Donehower,Scott Spangler,Olivier Lichtarge +22 more
TL;DR: KnIT, the Knowledge Integration Toolkit, a system for accelerating scientific discovery and predicting previously unknown protein-protein interactions is presented, a step towards automated hypothesis generation from text, with potential application to other scientific domains.
References
More filters
Proceedings ArticleDOI
Coarse-to-Fine n-Best Parsing and MaxEnt Discriminative Reranking
Eugene Charniak,Mark Johnson +1 more
TL;DR: This paper describes a simple yet novel method for constructing sets of 50- best parses based on a coarse-to-fine generative parser that generates 50-best lists that are of substantially higher quality than previously obtainable.
Proceedings ArticleDOI
Overview of BioNLP'09 Shared Task on Event Extraction
TL;DR: The design and implementation of the BioNLP'09 Shared Task is presented, indicating that state-of-the-art performance is approaching a practically applicable level and revealing some remaining challenges.
Performance measures for information extraction
TL;DR: An error measure is defined, the slot error rate, which combines the different types of error directly, without having to resort to precision and recall as preliminary measures.
Book ChapterDOI
PANTHER Pathway: An Ontology-Based Pathway Database Coupled with Data Analysis Tools
Huaiyu Mi,Paul Thomas +1 more
TL;DR: This chapter first discusses how biological knowledge is represented, particularly the importance of ontologies or standards in systems biology research, and uses PANTHER Pathway as an example to illustrate how ontologies and standards play a role in data modeling, data entry, and data display.
Journal ArticleDOI
Evaluating temporal relations in clinical text: 2012 i2b2 Challenge.
TL;DR: A corpus of discharge summaries annotated with temporal information was provided to be used for the development and evaluation of temporal reasoning systems, and the best systems overwhelmingly adopted a rule based approach for value normalization.