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  • 1.
    Dura, Elzbieta
    University of Skövde, School of Humanities and Informatics.
    Term ambiguity and variation in biomedical nomenclature and literature - problems for information extraction2009In: Proceedings of the 4th Language and Technology Conference / [ed] Zygmunt Vetulani, Fundacja Uniwersytetu im A. Mickiewicza , 2009, p. 492-496Conference paper (Refereed)
    Abstract [en]

    Named entity recognition in life sciences is reported to achieve up to 0.9 F-score when tested on test corpora. The results which are obtained for casually chosen texts are usually not as good. We believe that the task may still be underestimated, together with the basic tasks of tokenization. We present here the problems which we have encountered in our attempt to identify gene names and chemical substance names in research articles. The two problems which information extraction has to cope with are language variation and ambiguity. Both are present not only in unstructured texts but also in the nomenclature of life sciences. We also note the discrepancies between the nomenclature registered in terminologies and the actual use of terms in texts. These problems are intimately entangled with text segmentation problems.

  • 2.
    Dura, Elzbieta
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Gawronska, Barbara
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Natural Language Processing in Information Fusion Terminology Management2008In: Proceedings of the 11th International Conference on Information Fusion, IEEE , 2008, p. 1388-1395Conference paper (Refereed)
    Abstract [en]

     

    The dynamic development of information fusion research implies introduction of new terms and concepts, which in turn requires tools and methods for terminology organization and standardization, as well as tools for creating domain-specific ontology. In this paper, we show how natural language processing and corpus technology tools applied for term extraction from texts in biomedicine can successfully be used for the field of information fusion. We demonstrate term and information extraction from a corpus of research articles in information fusion, showing how a vision of a combined text retrieval and information extraction service can be made real.

     

  • 3.
    Dura, Elzbieta
    et al.
    University of Skövde, School of Humanities and Informatics.
    Gawronska, Barbara
    University of Skövde, School of Humanities and Informatics.
    Towards Automatic Translation of Support Verbs Constructions: the Case of Polish 'robić/zrobić' and Swedish 'göra'2005In: Human language technologies as a challenge for computer science and linguistics: 2nd Language & Technology Conference, April, 21-23, 2005, Poznań, Poland: proceedings / [ed] Zygmunt Vetulani, Poznań: Wydawnictwo Naukowe Uniwersytetu im. Adama Mickiewicza, 2005, p. 450-454Chapter in book (Refereed)
    Abstract [en]

    Support verb constructions range from idiosyncratic to predictable. Lexical functions provide a solution to translation of idiosyncratic constructions only. Our corpus research aims to contribute to automatic translation of support verb constructions where the verb selects certain semantic groups of collocates, and where novel collocations can be expected. We investigate samples of support verb constructions with Polish robić/zrobić and Swedish göra. Nouns attested on the Internet as objects of these verbs are subdivided into semantic groups. Translation rules are then proposed for each group, and the similarities and differences in the behaviour of the verbs in both languages are discussed.

  • 4. Dura, Elzbieta
    et al.
    Gawronska, Barbara
    University of Skövde, School of Humanities and Informatics.
    Olsson, Björn
    University of Skövde, School of Humanities and Informatics.
    Erlendsson, Björn
    University of Skövde, School of Humanities and Informatics.
    Towards Information Fusion in Pathway Evaluation: Encoding Relations in Biomedical Texts2006In: The 9th International Conference on Information Fusion: Florence, Italy, 10-13 July 2006, IEEE Press, 2006, p. 240-247Conference paper (Other academic)
    Abstract [en]

    The long-term goal of the research presented in this paper is to incorporate linguistic text analysis into a system for evaluation of biological pathways. In this system, relations extracted from biomedical texts will be compared with pathways encoded in existing specialized databases. In this way, the biologist's conclusions regarding the plausibility and/or novelty of a certain relation between genes, proteins, etc., can be supported by fused information from biological databases and biological literature. We aim at overcoming the shortcomings of existing systems for information retrieval by proposing a method based on thorough linguistic analysis of a large text corpus. In this paper, we present a comparative analysis of two corpora: one consisting of biomedical texts from PubMed, the other one of general English prose. The results stress the importance of taking multiword entries into account when constructing a system for extracting biological relations from texts

  • 5.
    Dura, Elżbieta
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Gawronska, Barbara
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Novelty extraction from special and parallel corpora2009In: Human Language Technology. Challenges of the Information Society: Third Language and Technology Conference, LTC 2007, Poznan, Poland, October 5-7, 2007, Revised Selected Papers / [ed] Zygmunt Vetulani, Hans Uszkoreit, Springer Berlin/Heidelberg, 2009, p. 291-302Chapter in book (Refereed)
    Abstract [en]

    How can corpora assist translators in ways in which resources like translation memories or term databases cannot? Our tests on English, Polish and Swedish parts of the JRC-Acquis Multilingual Parallel show that corpora can provide support for term standardization and variation, and, most importantly, for tracing novel expressions. A corpus tool with an explicit dictionary representation is particularly suitable for the last task. Culler is a tool which allows one to select expressions with words absent from its dictionary. Even if the extracted material may be stained with some noise, it has an undeniable value for translators and lexicographers. The quality of extraction depends in a rather obvious way on the dictionary and text processing but also on the query.

  • 6.
    Olsson, Björn
    et al.
    University of Skövde, School of Humanities and Informatics.
    Gawronska, Barbara
    University of Skövde, School of Humanities and Informatics.
    Erlendsson, Björn
    University of Skövde, School of Humanities and Informatics.
    Lindlöf, Angelica
    University of Skövde, School of Humanities and Informatics.
    Dura, Elzbieta
    University of Skövde, School of Humanities and Informatics.
    Automated text analysis of biomedical abstracts applied to the extraction of signaling pathways involved in plant cold-adaptation2006In: Proceedings of the Fifth International Conference on Bioinformatics of Genome Regulation and Structure: Volume 3 / [ed] N. Kolchanov, R. Hofestadt, Russian Academy of Sciences, 2006, p. 296-299Conference paper (Other academic)
    Abstract [en]

    Motivation: Automated text analysis is an important tool for facilitating the extraction of knowledge from biomedical abstracts, thereby enabling researchers to build pathway models that integrate and summarize information from a large number of sources. Advanced methods of in-depth analysis of texts using grammar-based approaches developed within the field of computational linguistics must be adapted to the special requirements and challenges posed by biomedical texts, so that these methods can be made available to the bioinformatics and computational biology communities. Results: Our system for automated text analysis and extraction of pathway information is here applied to a set of PubMed abstracts concerning the CBF signaling pathway, which is a key pathway involved in the cold-adaptation response of plants subjected to cold non-freezing temperatures. The system successfully and accurately re-discovers the main features of this pathway, while also pointing to interesting and plausible new hypotheses. The evaluation also reveals a number of issues which will be important targets in the continued development of the system, e.g. the need for an extended lexicon of taxonomic terms and an improved procedure for recognition of sentence boundaries.

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