| 21. |
- 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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| 22. |
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| 23. |
- Olsson, Björn, et al.
(författare)
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Deriving pathway maps from automated text analysis using a grammar-based approach
- 2006
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Ingår i: Journal of Bioinformatics and Computational Biology. - : World Scientific. - 0219-7200 .- 1757-6334. ; 4:2, s. 483-501
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate how automated text analysis can be used to support the large-scale analysis of metabolic and regulatory pathways by deriving pathway maps from textual descriptions found in the scientific literature. The main assumption is that correct syntactic analysis combined with domain-specific heuristics provides a good basis for relation extraction. Our method uses an algorithm that searches through the syntactic trees produced by a parser based on a Referent Grammar formalism, identifies relations mentioned in the sentence, and classifies them with respect to their semantic class and epistemic status (facts, counterfactuals, hypotheses). The semantic categories used in the classification are based on the relation set used in KEGG (Kyoto Encyclopedia of Genes and Genomes), so that pathway maps using KEGG notation can be automatically generated. We present the current version of the relation extraction algorithm and an evaluation based on a corpus of abstracts obtained from PubMed. The results indicate that the method is able to combine a reasonable coverage with high accuracy. We found that 61% of all sentences were parsed, and 97% of the parse trees were judged to be correct. The extraction algorithm was tested on a sample of 300 parse trees and was found to produce correct extractions in 90.5% of the cases.
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| 24. |
- Sigurd, Bengt, et al.
(författare)
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Modals as a problem for MT
- 1994
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Ingår i: COLING '94 : Proceedings of the 15th conference on Computational linguistics - Proceedings of the 15th conference on Computational linguistics. - Morristown, NJ, USA : Association for Computational Linguistics. ; 1, s. 120-124
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The paper demonstrates the problem of translating modal verbs and phrases and shows how some of these problems can be overcome by choosing semantic representations which look like representations of passive verbs. These semantic representations suit alternative ways of expressing modality by e.g. passive constructions, adverbs and impersonal constructions in the target language. Various restructuring rules for English, Swedish and Russian are presented.
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| 25. |
- Sigurd, Bengt, et al.
(författare)
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Morphology in referent grammar and in the automatic translation system SWETRA
- 1989
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Most of the work in Referent Grammar so far has focused on syntax, but it is clear that the syntactic rales must rely on some kind of lexical information about the form, meaning and category of the words to be used in the rules. As the lexicon cannot include all possible forms, at least not in such languages as Swedish, Russian and Georgian, some kind of moiphological rules are needed. Such rules also reflect the morphological competence of the language users, as demonstrated e.g. when new loan-words are to be inflected. This joint paper is a discussion of the problems met when morphological rules are to be integrated in Referent Grammar and when morphological rules are to be localized in the whole multi-lingual translation system SWETRA.
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| 26. |
- Sigurd, Bengt, et al.
(författare)
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Reflexivization in referent grammar
- 1990
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The interpretation of reflexive pronouns has been the topic of extensive linguistic research. This paper illustrates how different types of reflexive pronouns can be inter-preted and generated within the framework of Referent Grammar, a grammar which can be run directly on the computer. The rules illustrated are to be used in the machine translation project SWETRA which translates between English, Russian, Swedish and German (Sigurd & Gawroriska-Werngren 1988). Some of the translation problems are also discussed.
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| 27. |
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| 28. |
- Sigurd, Bengt, et al.
(författare)
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The potential of Swetra - A multilanguage MT system
- 1988
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Ingår i: Computers and Translation. - 0884-0709. ; 3, s. 237-250
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Tidskriftsartikel (refereegranskat)abstract
- One may indicate the potentials of an MT system by stating what text genres it can process, e.g., weather reports and technical manuals. This approach is practical, but misleading, unless domain knowledge is highly integrated in the system. Another way to indicate which fragments of language the system can process is to state its grammatical potentials, or more formally, which languages the grammars of the system can generate. This approach is more technical and less understandable to the layman (customer), but it is less misleading, since it stresses the point that the fragments which can be translated by the grammars of a system need not necessarily coincide exactly with any particular genre. Generally, the syntactic and lexical rules of an MT system allow it to translate many sentences other than those belonging to a certain genre. On the other hand it probably cannot translate all the sentences of a particular genre. Swetra is a multilanguage MT system defined by the potentials of a formal grammar (standard referent grammar) and not by reference to a genre. Successful translation of sentences can be guaranteed if they are within a specified syntactic format based on a specified lexicon. The paper discusses the consequences of this approach (Grammatically Restricted Machine Translation, GRMT) and describes the limits set by a standard choice of grammatical rules for sentences and clauses, noun phrases, verb phrases, sentence adverbials, etc. Such rules have been set up for English, Swedish and Russian, mainly on the basis of familiarity (frequency) and computer efficiency, but restricting the grammar and making it suitable for several languages poses many problems for optimization. Sample texts — newspaper reports — illustrate the type of text that can be translated with reasonable success among Russian, English and Swedish.
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| 29. |
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