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The GENIA Project

Nigel Collier, Hideki Mima, San Zoo Lee, Tomoko Ohta, Yuka Tateisi, Akane Yakushiji, Jun'ichi Tsujii
2000 Genome Informatics Series  
In addition to processing methods, we are developing an annotated corpus in which the structure of a text, the structure of sentences, and the semantics of terms based on a domain ontology [7] are marked  ...  We intend that while the methods are customized for application in the micro-biology domain, the basic methods should be generalisable to knowledge acquisition in other scientific and engineering domains  ...  In addition to processing methods, we are developing an annotated corpus in which the structure of a text, the structure of sentences, and the semantics of terms based on a domain ontology [7] are marked  ... 
doi:10.11234/gi1990.11.448 fatcat:6sb2e6vrcvdg3hssa2rqn622jm

Part-of-Speech Tagging in Molecular Biology Scientific Abstracts Using Morphological and Contextual Statistical Information [chapter]

Gavrilis Dimitris, Dermatas Evangelos
2004 Lecture Notes in Computer Science  
The system consists of three modules: a rule based molecular-biology names detector, an unknown words handler, and a Hidden Markov model based tagger which are used to annotate the corpus with an extended  ...  The F-score for the molecular-biology names detector was 0.95, and the annotation rate was greater than 93% in all experiments using the Viterbi algorithm.  ...  In this corpus the 2000 molecular biology abstracts, annotated using the 6 biological categories, where added to the training corpus.  ... 
doi:10.1007/978-3-540-24674-9_39 fatcat:272gczr4ovh4fhwsourvmkvh7e

Building Domain-Specific Taggers without Annotated (Domain) Data

John E. Miller, Manabu Torii, K. Vijay-Shanker
2007 Conference on Empirical Methods in Natural Language Processing  
We present a method for developing taggers for new domains without requiring POS annotated text in the new domain.  ...  We evaluate the method by applying it in the Biology domain and show that we achieve results that are comparable with some taggers developed for this domain.  ...  Degradation of accuracy in a new domain can be overcome by developing an annotated corpus for that specific domain, e.g., as in the Biology domain.  ... 
dblp:conf/emnlp/MillerTV07 fatcat:j7jadxmppzbdhotoip7dc5v44y

Ontology Based Corpus Annotation and Tools

Tomoko Ohta, Yuka Tateisi, Jin-Dong Kim, Hideki Mima, Jun'ichi Tsujii
2001 Genome Informatics Series  
Introduction With the explosion of results in molecular biology there is an increased need for IE to extract knowledge to support database building and to search intelligently for information in online  ...  As a part of a project on information extraction from the research papers in biology domain, we are creating an expert-tagged corpus of MEDLINE abstracts, which will be used for training and testing the  ... 
doi:10.11234/gi1990.12.469 fatcat:m72t3yajsfguzbmwhmvtlyew2y

Building an allergens ontology and maintaining it using machine learning techniques

Alexandros G. Valarakos, Vangelis Karkaletsis, Dimitra Alexopoulou, Elsa Papadimitriou, Constantine D. Spyropoulos, George Vouros
2006 Computers in Biology and Medicine  
The application of this methodology in the allergen domain is then discussed in detail presenting the ontology built, the specific techniques used and the evaluation settings.  ...  Ontologies are becoming increasingly important in the biomedical domain since they enable knowledge sharing in a formal, homogeneous and unambiguous way.  ...  Acknowledgements The authors are grateful to Prof. Brusic and his team at the Institute for Infocomm.  ... 
doi:10.1016/j.compbiomed.2005.09.007 pmid:16253221 fatcat:oftekuignjg2hgyepxh5tyidiq

PASBio: predicate-argument structures for event extraction in molecular biology

Tuangthong Wattarujeekrit, Parantu K Shah, Nigel Collier
2004 BMC Bioinformatics  
The exploitation of information extraction (IE), a technology aiming to provide instances of structured representations from free-form text, has been rapidly growing within the molecular biology (MB) research  ...  In this article, we explore the need to adapt PAS for the MB domain and specify PAS frames to support IE, as well as outlining the major issues that require consideration in their construction.  ...  Acknowledgements We gratefully acknowledge the kind support of Yoko Mizuta, Ai Kawazoe and Tony Mullen (NII) for useful discussions on the linguistic aspects of the examples discussed in this paper.  ... 
doi:10.1186/1471-2105-5-155 pmid:15494078 pmcid:PMC535924 fatcat:nbjbhwj2d5adlki6bjc4vlyo64

Exploring variation across biomedical subdomains

Thomas Lippincott, Diarmuid Ó Séaghdha, Lin Sun, Anna Korhonen
2010 International Conference on Computational Linguistics  
In this paper we identify the related issue of subdomain variation, i.e., differences between subsets of a domain that might be expected to behave homogeneously.  ...  We conclude that an awareness of such variation is necessary when deploying NLP systems for use in single or multiple subdomains.  ...  Acknowledgements This work was supported by EPSRC grant EP/G051070/1, the Royal Society (AK) and a Dorothy Hodgkin Postgraduate Award (LS).  ... 
dblp:conf/coling/LippincottSSK10 fatcat:o7mvynte3reazclqiwndncpssa

ISMB 2003 Text Mining SIG Meeting Report

Christian Blaschke, Alexander Yeh, Lynette Hirschman, Alfonso Valencia
2003 Comparative and Functional Genomics  
Society for Computational Biology) for organizing the logistics and the infrastructure, and the EU projects ORIEL (Contract number: IST-2001-32688) and TEMBLOR (Contract number: VEQLRT 2001 00015) for  ...  Acknowledgements The organizers of the workshop would like to thank especially all the speakers for their presentations, Marc Light for co-organizing the event, Steven Leard and the ISCB (The International  ...  Procter & Gamble, USA An overview of text mining in the biology domain at P&G George Demetriou, Robert Gaizauskas. Univ.  ... 
doi:10.1002/cfg.338 pmid:18629019 pmcid:PMC2447301 fatcat:vmqqau3myrgsfdfhwotqljapje

Overview of the Regulatory Network of Plant Seed Development (SeeDev) Task at the BioNLP Shared Task 2016

Estelle Chaix, Bertrand Dubreucq, Abdelhak Fatihi, Dialekti Valsamou, Robert Bossy, Mouhamadou Ba, Louise Delėger, Pierre Zweigenbaum, Philippe Bessières, Loïc Lepiniec, Claire Nėdellec
2016 Proceedings of the 4th BioNLP Shared Task Workshop  
We analyze and discuss the final results of the seven participant systems to the test. The best F-score is 0.432, which is similar to the scores achieved in similar tasks on molecular biology.  ...  In this paper, we describe the organization of the SeeDev task, the corpus characteristics, and the metrics used for the evaluation of participant systems.  ...  The IJPB benefits from the support of the Labex Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS).  ... 
doi:10.18653/v1/w16-3001 dblp:conf/bionlp/ChaixDFVBBDZBLN16 fatcat:z5pm4gaakbca3j4l6eauu2k4jq

Information Extraction from Bibliography for Marker-Assisted Selection in Wheat [chapter]

Claire Nédellec, Robert Bossy, Dialekti Valsamou, Marion Ranoux, Wiktoria Golik, Pierre Sourdille
2014 Communications in Computer and Information Science  
Improvement of most animal and plant species of agronomical interest in the near future has become an international stake because of the increasing demand for feeding a growing world population and to  ...  The recent advent of genomic tools contributed to improve the discovery of linkage between molecular markers and genes that are involved in the control of traits of agronomical interest such as grain number  ...  recent progress of RE in molecular biology as evaluated in shared tasks open up possibilities of large scale extraction of complex events in the wheat MAS domain.  ... 
doi:10.1007/978-3-319-13674-5_28 fatcat:jiznl6qz2fdpzahwsk42yvgsmi

Relation Mining over a Corpus of Scientific Literature [chapter]

Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess, Christos Andronis, Andreas Persidis, Ourania Konstanti
2005 Lecture Notes in Computer Science  
The amount of new discoveries (as published in the scientific literature) in the area of Molecular Biology is currently growing at an exponential rate.  ...  Molecular Biology.  ...  Introduction The amount of research results in the area of molecular biology is growing at such a pace that it is extremely difficult for individual researchers to keep track of them.  ... 
doi:10.1007/11527770_70 fatcat:bwmczbjm2jg2pabj3tvngami74

Text mining and protein annotations: the construction and use of protein description sentences

Martin Krallinger, Rainer Malik, Alfonso Valencia
2006 Genome Informatics Series  
The steps used for the corpus construction and its features are presented.  ...  Moreover, some of the potential applications of the Prodisen corpus for biomedical text mining purposes are explored and the obtained results are presented.  ...  The diculty of interpretation is particularly obvious in domain specic literature, such as the molecular biology literature.  ... 
pmid:17503385 fatcat:6uuve2sddjfhrgbfxeqzqgikaq

Text Mining and Protein Annotations

Martin Krallinger, Rainer Malik, Alfonso Valencia
2006 Genome Informatics Series  
The steps used for the corpus construction and its features are presented.  ...  Moreover, some of the potential applications of the Prodisen corpus for biomedical text mining purposes are explored and the obtained results are presented.  ...  The difficulty of interpretation is particularly obvious in domain specific literature, such as the molecular biology literature.  ... 
doi:10.11234/gi1990.17.2_121 fatcat:bjmblz4kmnezzcsatcd2lmzdci

Page 138 of Computational Linguistics Vol. 33, Issue 1 [page]

2007 Computational Linguistics  
Chapter 9, “Evaluation of text mining in biology” by Lynette Hirschman and Christian Blaschke, begins by explaining how the MUC and TREC evaluation challenges and similar efforts in molecular biology inspired  ...  From their own ex- perience in the development of the GENIA corpus (Kim et al. 2003), the authors provide practical advice on how to compile a representative corpus, prepare annotation schemes and guidelines  ... 

Proceedings of the Second International Symposium for Semantic Mining in Biomedicine

Sophia Ananiadou, Juliane Fluck
2006 BMC Bioinformatics  
The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2105/7?issue=S3.  ...  Acknowledgements This article has been published as part of BMC Bioinformatics Volume 7, Supplement 3, 2006: Second International Symposium on Semantic Mining in Biomedicine.  ...  and a manually annotated corpus.  ... 
doi:10.1186/1471-2105-7-s3-s1 fatcat:h26jwoukezbvtgt73qlrfhyapy
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