Using Workflows to Explore and Optimise Named Entity Recognition for Chemistry

Chemistry text mining tools should be interoperable and adaptable regardless of system-level implementation, installation or even programming issues. We aim to abstract the functionality of these tools from the underlying implementation via reconfigurable workflows for automatically identifying chemical names. To achieve this, we refactored an established named entity recogniser (in the chemistry domain), OSCAR and studied the impact of each component on the net performance. We developed two reconfigurable workflows from OSCAR using an interoperable text mining framework, U-Compare. These workflows can be altered using the drag-&-drop mechanism of the graphical user interface of U-Compare. These workflows also provide a platform to study the relationship between text mining components such as tokenisation and named entity recognition (using maximum entropy Markov model (MEMM) and pattern recognition based classifiers). Results indicate that, for chemistry in particular, eliminating noise generated by tokenisation techniques lead to a slightly better performance than others, in terms of named entity recognition (NER) accuracy. Poor tokenisation translates into poorer input to the classifier components which in turn leads to an increase in Type I or Type II errors, thus, lowering the overall performance. On the Sciborg corpus, the workflow based system, which uses a new tokeniser whilst retaining the same MEMM component, increases the F-score from 82.35% to 84.44%. On the PubMed corpus, it recorded an F-score of 84.84% as against 84.23% by OSCAR

Mining metabolites: extracting the yeast metabolome from the literature

Text mining methods have added considerably to our capacity to extract biological knowledge from the literature. Recently the field of systems biology has begun to model and simulate metabolic networks, requiring knowledge of the set of molecules involved. While genomics and proteomics technologies are able to supply the macromolecular parts list, the metabolites are less easily assembled. Most metabolites are known and reported through the scientific literature, rather than through large-scale experimental surveys. Thus it is important to recover them from the literature. Here we present a novel tool to automatically identify metabolite names in the literature, and associate structures where possible, to define the reported yeast metabolome. With ten-fold cross validation on a manually annotated corpus, our recognition tool generates an f-score of 78.49 (precision of 83.02) and demonstrates greater suitability in identifying metabolite names than other existing recognition tools for general chemical molecules. The metabolite recognition tool has been applied to the literature covering an important model organism, the yeast Saccharomyces cerevisiae, to define its reported metabolome. By coupling to ChemSpider, a major chemical database, we have identified structures for much of the reported metabolome and, where structure identification fails, been able to suggest extensions to ChemSpider. Our manually annotated gold-standard data on 296 abstracts are available as supplementary materials. Metabolite names and, where appropriate, structures are also available as supplementary materials

Stringent response of Escherichia coli: revisiting the bibliome using literature mining

Understanding the mechanisms responsible for cellular responses depends on the systematic collection and analysis of information on the main biological concepts involved. Indeed, the identification of biologically relevant concepts in free text, namely genes, tRNAs, mRNAs, gene products and small molecules, is crucial to capture the structure and functioning of different responses. Results In this work, we review literature reports on the study of the stringent response in Escherichia coli. Rather than undertaking the development of a highly specialised literature mining approach, we investigate the suitability of concept recognition and statistical analysis of concept occurrence as means to highlight the concepts that are most likely to be biologically engaged during this response. The co-occurrence analysis of core concepts in this stringent response, i.e. the (p)ppGpp nucleotides with gene products was also inspected and suggest that besides the enzymes RelA and SpoT that control the basal levels of (p)ppGpp nucleotides, many other proteins have a key role in this response. Functional enrichment analysis revealed that basic cellular processes such as metabolism, transcriptional and translational regulation are central, but other stress-associated responses might be elicited during the stringent response. In addition, the identification of less annotated concepts revealed that some (p)ppGpp-induced functional activities are still overlooked in most reviews. Conclusions In this paper we applied a literature mining approach that offers a more comprehensive analysis of the stringent response in E. coli. The compilation of relevant biological entities to this stress response and the assessment of their functional roles provided a more systematic understanding of this cellular response. Overlooked regulatory entities, such as transcriptional regulators, were found to play a role in this stress response. Moreover, the involvement of other stress-associated concepts demonstrates the complexity of this cellular response

Interleukin 1Β proinflammatory genotypes protect against gastro‐oesophageal reflux disease through induction of corpus atrophy

BACKGROUND AND AIMS: The relationship between Helicobacter pylori infection and gastro‐oesophageal reflux disease (GORD) is controversial but it is accepted that GORD is associated with increased exposure to gastric acidity. The proinflammatory interleukin (IL)‐1B polymorphisms increase the risk of hypochlorhydria and gastric atrophy. We examined the association between proinflammatory cytokine gene polymorphisms, presence of gastric atrophy, and risk of GORD in H pylori positive and negative subjects in Japan. METHODS: We studied 320 consecutive dyspeptic patients without peptic ulcers or cancers. GORD symptoms were scored using the Carlsson‐Dent questionnaire and erosive oesophagitis was assessed endoscopically. H pylori infection was diagnosed by urea breath test, histological examination, and serology. Gastric atrophy was assessed histologically, and polymorphisms in the IL‐1B, IL‐10, and tumour necrosis factor α (TNF‐A) genes were genotyped. RESULTS: Two hundred and eight patients were H pylori positive and 112 were negative. One hundred and eight (34%) were found to have erosive oesophagitis by endoscopic criteria (grade A: 78; grade B: 23; grade C: 6; grade D: 1). Erosive oesophagitis and GORD symptoms were significantly more common in H pylori negative compared with H pylori positive subjects (p<0.05). H pylori positive subjects were more likely to have corpus gastric atrophy than H pylori negative subjects (p<0.001). Among H pylori positive patients, those without erosive oesophagitis or GORD symptoms were significantly more likely to have corpus atrophy than subjects with erosive oesophagitis or GORD symptoms (p<0.05). Among H pylori positive patients, subjects homozygous for the proinflammatory allele IL‐1B−511T had a significantly lower risk of erosive oesophagitis (odds ratio (OR) 0.06 (95% confidence interval (CI) 0.006–0.51); p = 0.01) and GORD symptoms (OR 0.10 (95% CI 0.01–0.85); p = 0.04) compared with those homozygous for the −511C allele, while none of the two other proinflammatory cytokine gene polymorphisms had significant correlations with erosive oesophagitis or GORD symptoms. CONCLUSIONS: A proinflammatory IL‐1B genotype is associated with increased risk of atrophy and decreased risk of GORD in H pylori infected subjects in Japan. These data indicate that in some genetically predisposed subjects, H pylori infection may protect against GORD through induction of gastric atrophy

Establishment and validation of an aquarium system to evaluate salinity preference in conscious rainbow trout

Anadromous salmon migrate between fresh water (FW) and seawater (SW) during their life cycle, which most likely is driven by changes in salinity preference. There have been some studies examining salinity preference in juveniles during downstream migration, but no study has yet been reported in homing adults. In this study, we established an aquarium system to evaluate salinity preference that is usable not only for juveniles but for adult fish. The aquarium consists of three areas of different salinities, a FW area, a SW area and a brackish water (BW) area, among which fish can voluntarily move. By modifying the flow rate of FW/SW and other parameters, we could maintain the salinity of the FW area at <0.5 ppt (part per thousand) and that of the SW area at >20 ppt irrespective of the depth, but the salinity varies considerably by depth between the surface and bottom layer in the BW area. Two aquaria with the same system were prepared side by side, an acclimation aquarium that allowed fish to learn the system before the experiment and an experimental aquarium that was insulated from the environment and observed by a video system. Using this aquarium system, we found that cultured rainbow trout, Oncorhynchus mykiss, of ca. 200g preferred areas in the order of BW≥FW>>SW. To further validate this system, we injected various hormones that have been implicated in osmoregulation/smoltification such as angiotensin II (Ang II), cortisol, thyroid hormone (T3), arginine vasotocin (AVT) and prolactin into the third brain ventricle of the trout and observed their preference behavior. There was a tendency toward high salinity preference after injection of hormones that promote SW acclimation and/or smoltification (Ang II, cortisol T3 and AVT), but fish tended to prefer a low salinity area after injection of prolactin that promotes FW adaptation. These results suggest that the newly established aquarium system can be used to evaluate salinity preference in salmonids and will contribute to future studies in identidying key factors that motivate downstream migration of juveniles and upstream migration of mature chum salmon, O. keta, homing to natal rivers in the Tohoku area of Japan