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Träfflista för sökning "WFRF:(Erlendsson Björn) ;conttype:(refereed)"

Sökning: WFRF:(Erlendsson Björn) > Refereegranskat

  • Resultat 1-6 av 6
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1.
  • Dura, Elzbieta, et al. (författare)
  • Towards Information Fusion in Pathway Evaluation : Encoding Relations in Biomedical Texts
  • 2006
  • Ingår i: 9th International Conference on Information Fusion. - : IEEE. - 9781424409532
  • 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.
  • Gawronska, Barbara, et al. (författare)
  • Tracking biological relations in texts : a Referent Grammar based approach
  • 2005
  • Ingår i: Proceedings of the workshop Biomedical Ontologies and Text Processing, in connection to ECCB/05. ; , s. 15-22
  • Konferensbidrag (refereegranskat)abstract
    • In this paper, we describe a method for extracting biological relations (in the first place, relations used in the KEGG ontology of biological pathways) from scientific texts. The main assumption is that correct syntactic analysis combined with domain-specific heuristics provides a good basis for relation extraction. We propose an algorithm that searches through the syntactic trees produced by a parser based on a formalism called Referent Grammar (inspired by Categorial Grammar), identifies relations mentioned in the sentence, and classifies them with respect to their semantic class and epistemic status (facts, counterfactuals, hypotheses).
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4.
  • Olsson, Björn, et al. (författare)
  • Deriving pathway maps from automated text analysis using a grammar-based approach
  • 2006
  • Ingår i: Journal of Bioinformatics and Computational Biology. - : World Scientific. - 0219-7200 .- 1757-6334. ; 4:2, s. 483-501
  • 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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5.
  • Erlendsson, Lýður S, et al. (författare)
  • Barley as a green factory for the production of functional Flt3 ligand
  • 2009
  • Ingår i: Biotechnology Journal. - Weinheim : Wiley-VCH Verlag GmbH & Co. KGaA. - 1860-7314 .- 1860-6768. ; 5:2, s. 163-171
  • Tidskriftsartikel (refereegranskat)abstract
    • Biologically active recombinant human Flt3 ligand was expressed and isolated from transgenic barley seeds. Its expression is controlled by a tissue specific promoter that confines accumulation of the recombinant protein to the endosperm tissue of the seed. The recombinant Flt3 ligand variant expressed in the seeds contains an HQ-tag for affinity purification on immobilized metal ion affinity chromatography (IMAC) resin. The tagged protein was purified from seed extracts to near homogeneity using sequential chromatography on IMAC affinity resin and cation exchange resin. We also show that the recombinant Flt3 ligand protein undergoes posttranslational modifications: it is a glycoprotein containing alpha-1,3-fucose and alpha-1,2-xylose. The HQ-tagged Flt3 ligand variant exhibits comparable biological activity to commercial Flt3 ligand. This is the first report showing expression and accumulation of recombinant human growth factor in barley seeds with a yield of active protein similar to a bacterial expression system. The present results demonstrate that plant molecular farming is a viable approach for the bioproduction of human-derived growth factors.
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6.
  • Gawronska, Barbara, et al. (författare)
  • Syntactic, Semantic and Referential Patterns in Biomedical Texts : towards in-depth text comprehension for the purpose of bioinformatics
  • 2005
  • Ingår i: Natural Language Understanding and Cognitive Science, Proceedings of the 2nd International Workshop on Natural Language Understanding and Cognitive Science, NLUCS 2005, In conjunction with ICEIS 2005, Miami, FL, USA, May 2005. - : INSTICC Press. - 9728865236 - 9789728865238 ; , s. 68-77
  • Konferensbidrag (refereegranskat)abstract
    • An essential part of bioinformatic research concerns the iterative process of validating hypotheses by analyzing facts stored in databases and in published literature. This process can be enhanced by automatic in-depth text understanding. A prerequisite for this is an adequate syntactic and semantic analysis. The paper presents the results of syntactic, semantic, and textual analysis of a corpus of biomedical abstracts. It focuses on the ways in which relevant molecular interactions are referred to in the abstracts, and proposes a strategy for linking natural language expressions to the standard notation used in Kyoto Encyclopedia of Genes and Genomes. The syntactic and semantic regularities observed in the language of biomedicine are also discussed from the cognitive point of view.
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  • Resultat 1-6 av 6

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