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Title Finding Conflicting Statements in the Biomedical Literature
URL
Publication Date
Degree Level doctoral
University/Publisher University of Manchester
Abstract The main archive of life sciences literature currently contains more than 18,000,000 references, and it is virtually impossible for any human to stay up-to-date with this large number of papers, even in a specific sub-domain.Not every fact that is reported in the literature is novel and distinct. Scientists report repeat experiments, or refer to previous findings. Given the large number of publications, it is not surprising that information on certain topics is repeated over a number of publications. From consensus to contradiction, there are all shades of agreement between the claimed facts in the literature, and considering the volume of the corpus, conflicting findings are not unlikely. Finding such claims is particularly interesting for scientists, as they can present opportunities for knowledge consolidation and future investigations.In this thesis we present a method to extract and contextualise statements about molecular events as expressed in the biomedical literature, and to find those that potentially conflict each other. The approach uses a system that detects event negations and speculation, and combines those with contextual features (e.g. type of event, species, and anatomical location) to build a representational model for establishing relations between different biological events, including relations concerning conflicts. In the detection of negations and speculations, rich lexical, syntactic, and semantic features have been exploited, including the syntactic command relation.Different parts of the proposed method have been evaluated in a context of the BioNLP 09 challenge. The average F-measures for event negation and speculation detection were 63% (with precision of 88%) and 48% (with precision of 64%) respectively. An analysis of a set of 50 extracted event pairs identified as potentially conflicting revealed that 32 of them showed some degree of conflict (64%); 10 event pairs (20%) needed a more complex biological interpretation to decide whether there was a conflict.We also provide an open source integrated text mining framework for extracting events and their context on a large-scale basis using a pipeline of tools that are available or have been developed as part of this research, along with 72,314 potentially conflicting molecular event pairs that have been generated by mining the entire body of accessible biomedical literature.We conclude that, whilst automated conflict mining would need more comprehensive context extraction, it is feasible to provide a support environment for biologists to browse potential conflicting statements and facilitate data and knowledge consolidation.
Subjects/Keywords Text Mining; Natural Language Processing; Information Extraction; Biomedical Text Mining; Bioinformatics; Negation; Contradiction; Contrast; Literature-based discovery; Molecular Event Extraction
Contributors Nenadic, Goran
Language en
Country of Publication uk
Format 336 page(s)
Record ID oai:escholar.manchester.ac.uk:uk-ac-man-scw-157382
Repository manchester
Date Retrieved
Date Indexed 2019-01-09

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…distribution of the most common speculation cues.....................255 Figure 6.9: Event numbers in the literature over time..........................................256 Figure 6.10: The number of events reported per publication over time...............257…

…outputs..............................236 Table 6.13: Literature-scale event extraction counts...........................................237 Table 6.14: Supporting mention counts extracted by BioContext........................238 Table 6.15: Evaluation of…

…main archive of life sciences literature currently contains more than 18,000,000 references, and it is virtually impossible for any human to stay upto-date with this large number of papers, even in a specific sub-domain. Not every fact that is reported…

…in the literature is novel and distinct. Scientists report repeat experiments, or refer to previous findings. Given the large number of publications, it is not surprising that information on certain topics is repeated over a number of publications…

…From consensus to contradiction, there are all shades of agreement between the claimed facts in the literature, and considering the volume of the corpus, conflicting findings are not unlikely. Finding such claims is particularly interesting for…

…scientists, as they can present opportunities for knowledge consolidation and future investigations. In this thesis we present a method to extract and contextualise statements about molecular events as expressed in the biomedical literature, and to find those…

…been developed as part of this research, along with 72,314 potentially conflicting molecular event pairs that have been generated by mining the entire body of accessible biomedical literature. We conclude that, whilst automated conflict mining would…

…sciences literature currently contains more than 18,000,000 references and approximately 2,000 are added to this archive every day.1 It is virtually impossible for any human to stay up-to-date with this large number of papers, even in a specific sub-domain…

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