| 1. |
- Dura, Elzbieta, et al.
(author)
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Towards Information Fusion in Pathway Evaluation : Encoding Relations in Biomedical Texts
- 2006
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In: 9th International Conference on Information Fusion. - : IEEE. - 9781424409532
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Conference paper (peer-reviewed)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.
(author)
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Towards an Automated Analysis of Biomedical Abstracts
- 2006
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In: Data Integration in the Life Sciences. - Berlin, Heidelberg : Springer. - 9783540365938 ; , s. 50-65
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Conference paper (other academic/artistic)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 language technology methods, in particular by automatic text understanding. Since it is becoming increasingly difficult to keep up with the vast number of scientific articles being published, there is a need for more easily accessible representations of the current knowledge. The goal of the research described in this paper is to develop a system aimed to support the large-scale research on metabolic and regulatory pathways by extracting relations between biological objects from descriptions found in literature. We present and evaluate the procedures for semantico-syntactic tagging, dividing the text into parts concerning previous research and current research, syntactic parsing, and transformation of syntactic trees into logical representations similar to the pathway graphs utilized in the Kyoto Encyclopaedia of Genes and Genomes.
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| 3. |
- Gawronska, Barbara, et al.
(author)
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Tracking biological relations in texts : a Referent Grammar based approach
- 2005
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In: Proceedings of the workshop Biomedical Ontologies and Text Processing, in connection to ECCB/05. ; , s. 15-22
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Conference paper (peer-reviewed)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. |
- Idström, Alexander, et al.
(author)
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Dissolution of cellulose in tetrabutylammonium acetate/dimethyl sulfoxide
- 2016
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In: The 7th Workshop on cellulose, regenerated cellulose and cellulose derivatives. ; , s. 15-18
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Conference paper (other academic/artistic)abstract
- The dissolution of cellulose in tetrabutylammonium acetate (TBAAc)/dimethyl sulfoxide (DMSO) was studied combining experimental and simulation techniques. It was found that the dissolution limit at 40 °C corresponded to a molar ratio close to one acetate per cellulose anhydroglucose units. MD simulations suggested that the acetate ions bind to cellulose by dual hydrogen bonds. This effectively turns cellulose into a polyelectrolyte, attracting the bulky tetrabutylammonium (TBA+) counter ions, which prevent close contact between chains in the dissolved state. This hypothesis was tested by 1H- and 13C-NMR spectroscopy, which confirmed that acetate forms hydrogen bonds to cellulose, and by diffusion NMR spectroscopy, which demonstrated a strong dynamic correlation between bound acetate and tetrabutylammonium in near-quantitative agreement with simulation. The present results suggest that offering hydrogen bonding to the acetate ions is the main driving force for dissolving cellulose and that the TBA+ counter ions form a diffuse layer around the acetate-decorated cellulose chains.
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| 5. |
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| 6. |
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| 7. |
- Olsson, Björn, et al.
(author)
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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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In: 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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Conference paper (other academic/artistic)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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| 8. |
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| 9. |
- Olsson, Björn, et al.
(author)
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Förutsättningar och styrmedel för ökad elsjöfart
- 2024
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In: Sammanställning av referat från Transportforum 2024. - Linköping : Statens väg- och transportforskningsinstitut. ; , s. 43-44
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Conference paper (other academic/artistic)abstract
- Det finns potential att öka elektrifieringen i svensk sjöfart. Inom ramen för ett regeringsuppdrag föreslår Trafikanalys nya styrmedel för elsjöfart, bland annat skattereduktion för landström, klimatpremie för elfartyg och stöd till land- och laddinfrastruktur i hamnar. Under 2022 har Trafikanalys haft i uppdrag att dels utreda förutsättningarna för en ökad användning av helt eller delvis eldrivna fartyg i Sverige, dels utreda möjliga incitament för att åstadkomma ökad användning av land- och laddström. Resultaten från båda uppdragen redovisas här gemensamt.Vi har studerat litteraturen och utvecklingen avseende elektrifieringen av sjöfart inom Sverige, Norge och Nederländerna. Marknadspotentialen för elektrifieringen har analyserats genom energiförbrukningen för fartyg som anlöper svenska hamnar. Vi beskriver de tekniska förutsättningarna och vilka problem som är specifika för elektrifiering av sjöfart jämfört med andra trafikslag. Vi har också studerat vilka styrmedel som finns idag för elektrifiering inom sjöfart såväl som andra trafikslag. Baserat på detta har vi pekat på möjliga styrmedel med potential att öka användningen av land- och laddström, samt öka användningen av helt eller delvis eldrivna fartyg i Sverige. Vi har också låtit en referensgrupp med representanter från branschen ha synpunkter och kommentarer på vårt arbete och våra förslag till styrmedel. De förslag till styrmedel vi lyfter fram är:Skattereduktion för elanslutning för mindre fartygKlimatpremie för elfartygStöd till elanslutning för fartygUndantag från kravet på nätkoncession för hamnarTydligare klimatkrav på nationella fartygUnderlätta processen för certifiering av fartyg vid konvertering till eldriftInnovationsupphandling i regionalt upphandlad färjetrafikDet ingick i uppdraget att göra en bedömning av införande av miljözoner i hamnar. Vår uppfattning är att marknaden i Sverige idag inte är mogen för införande av miljözoner. Vi efterlyser en vidare diskussion om miljödifferentierade sjöfartsavgifter för att stimulera introduktionen av elsjöfart.
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| 10. |
- Olsson, Björn, 1962-, et al.
(author)
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Running research-oriented final year projects for CS and IS students
- 2003
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In: SIGCSE '03. - New York, NY, USA : ACM Special Interest Group on Computer Science Education. - 158113648X ; , s. 79-83
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Conference paper (peer-reviewed)abstract
- In this paper we discuss the difficulties of designing and running a final year project course for computer science and information systems students. In particular, we present the design of a research-oriented final year project course, where the aim is to develop the student's critical thinking and research skills. We also discuss the lessons learnt during the seven years that the course has been given.
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