| 1. |
- Dura, Elzbieta, et al.
(författare)
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Towards Information Fusion in Pathway Evaluation : Encoding Relations in Biomedical Texts
- 2006
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Ingår i: 9th International Conference on Information Fusion. - : IEEE. - 9781424409532
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Konferensbidrag (refereegranskat)abstract
- 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
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| 2. |
- Olsson, Björn, et al.
(författare)
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Automated text analysis of biomedical abstracts applied to the extraction of signaling pathways involved in plant cold-adaptation
- 2006
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Ingår i: Proceedings of the Fifth International Conference on Bioinformatics of Genome Regulation and Structure. - : Russian Academy of Sciences. - 5769208481 - 9785769208485 ; , s. 296-299
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- 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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