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- Baker, Christopher, et al.
(author)
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Slicing through the scientific literature
- 2009. - 1
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In: DILS: International Workshop on Data Integration in the Life Sciences Data Integration in the Life Sciences 6th International Workshop, DILS 2009, Manchester, UK, July 20-22, 2009. Proceedings. - Berlin, Heidelberg : Springer. - 9783642028786 ; , s. 127-140
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Conference paper (peer-reviewed)abstract
- Success in the life sciences depends on access to information in knowlegde bases and literature. Finding and extracting the relevant information depends on a user’s domain knowledge and the knowledge of the search technology. In this paper we present a system that helps users formulate queries and search the scientific literature. The system coordinates ontologies, knowledge representation, text mining and NLP techniques to generate relevant queries in response to keyword input from the user. Queries are presented in natural language, translated to formal query syntax and issued to a knowledge base of scientific literature, documents or aligned document segments. We describe the components of the system and exemplify using real-world examples.
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2. |
- Edberg, Anna, et al.
(author)
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Assessing Relative Bioactivity of Chemical Substances Using Quantitative Molecular Network Topology Analysis
- 2012
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In: Journal of Chemical Information and Modeling. - : American Chemical Society (ACS). - 1549-9596 .- 1549-960X. ; 52:5, s. 1238-1249
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Journal article (peer-reviewed)abstract
- Structurally different chemical substances may cause similar systemic effects in mammalian cells. It is therefore necessary to go beyond structural comparisons to quantify similarity in terms of their bioactivities. In this work, we introduce a generic methodology to achieve this on the basis of Network Biology principles and using publicly available molecular network topology information. An implementation of this method, denoted QuantMap, is outlined and applied to antidiabetic drugs, NSAIDs, 17 beta-estradiol, and 12 substances known to disrupt estrogenic pathways. The similarity of any pair of compounds is derived from topological comparison of intracellular protein networks, directly and indirectly associated with the respective query chemicals, via a straightforward pairwise comparison of ranked proteins. Although output derived from straightforward chemical/structural similarity analysis provided some guidance on bioactivity, QuantMap produced substance interrelationships that align well with reports on their respective perturbation properties. We believe that QuantMap has potential to provide substantial assistance to drug repositioning, pharmacology evaluation, and toxicology risk assessment.
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3. |
- Hammerling, Ulf, et al.
(author)
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Consumption of Red/Processed Meat and Colorectal Carcinoma : Possible Mechanisms Underlying the Significant Association
- 2016
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In: Critical reviews in food science and nutrition. - : Informa UK Limited. - 1040-8398 .- 1549-7852. ; 56:4, s. 614-634
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Research review (peer-reviewed)abstract
- Epidemiology and experimental studies provide an overwhelming support of the notion that diets high in red or processed meat accompany an elevated risk of developing pre-neoplastic colorectal adenoma and frank colorectal carcinoma (CRC). The underlying mechanisms are disputed; thus several hypotheses have been proposed. A large body of reports converges, however, on haem and nitrosyl haem as major contributors to the CRC development, presumably acting through various mechanisms. Apart from a potentially higher intestinal mutagenic load among consumers on a diet rich in red/processed meat, other mechanisms involving subtle interference with colorectal stem/progenitor cell survival or maturation are likewise at play. From an overarching perspective, suggested candidate mechanisms for red/processed meat-induced CRC appear as three partly overlapping tenets: (i) increased N-nitrosation/oxidative load leading to DNA adducts and lipid peroxidation in the intestinal epithelium, (ii) proliferative stimulation of the epithelium through haem or food-derived metabolites that either act directly or subsequent to conversion, and (iii) higher inflammatory response, which may trigger a wide cascade of pro-malignant processes. In this review, we summarize and discuss major findings of the area in the context of potentially pertinent mechanisms underlying the above-mentioned association between consumption of red/processed meat and increased risk of developing CRC.
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4. |
- Ivanova, Valentina, et al.
(author)
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Debugging Taxonomies and their Alignments: the ToxOntology - MeSH Use Case
- 2012
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In: Proceedings of the First International Workshop on Debugging Ontologies and Ontology Mappings. - : Linköping University Electronic Press. ; , s. 25-36
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Conference paper (peer-reviewed)abstract
- As part of an initiative to facilitate adequate identification and display of substance-associated health effects a toxicological ontology - ToxOntology - was created. Further, an alignent with MeSH was accomplished to obtain an indirect index to the scientific literature.To arrive at satisfactory results in the semantically-enabled applications, high-quality ontologies and alignments are both necessary. A key step towards high quality in this area is debugging the ontologies and their alignments. In this paper we present an experience report on the debugging of ToxOntology and MeSH as well as an alignment.
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