An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.

In many databases, biocuration primarily involves literature curation, which usually involves retrieving relevant articles, extracting information that will translate into annotations and identifying new incoming literature. As the volume of biological literature increases, the use of text mining to assist in biocuration becomes increasingly relevant. A number of groups have developed tools for text mining from a computer science/linguistics perspective, and there are many initiatives to curate some aspect of biology from the literature. Some biocuration efforts already make use of a text mining tool, but there have not been many broad-based systematic efforts to study which aspects of a text mining tool contribute to its usefulness for a curation task. Here, we report on an effort to bring together text mining tool developers and database biocurators to test the utility and usability of tools. Six text mining systems presenting diverse biocuration tasks participated in a formal evaluation, and appropriate biocurators were recruited for testing. The performance results from this evaluation indicate that some of the systems were able to improve efficiency of curation by speeding up the curation task significantly (∼1.7- to 2.5-fold) over manual curation. In addition, some of the systems were able to improve annotation accuracy when compared with the performance on the manually curated set. In terms of inter-annotator agreement, the factors that contributed to significant differences for some of the systems included the expertise of the biocurator on the given curation task, the inherent difficulty of the curation and attention to annotation guidelines. After the task, annotators were asked to complete a survey to help identify strengths and weaknesses of the various systems. The analysis of this survey highlights how important task completion is to the biocurators' overall experience of a system, regardless of the system's high score on design, learnability and usability. In addition, strategies to refine the annotation guidelines and systems documentation, to adapt the tools to the needs and query types the end user might have and to evaluate performance in terms of efficiency, user interface, result export and traditional evaluation metrics have been analyzed during this task. This analysis will help to plan for a more intense study in BioCreative IV.

Fish oil induced hyperlipidemia and oxidative stress in BioF1B hamsters is attenuated by elderberry extract.

We have previously reported fish oil induced hyperlipidemia in BioF1B hamsters compared with Golden Syrian (GS) hamsters. Elderberry (Sambucus nigra L.) extract is abundant in anthocyanins and is believed to exert cardioprotective effects primarily by virtue of its hypolipidemic and antioxidant potential. In the current study, high-fat fish oil feeding increased oxidative stress in BioF1B hamsters compared with GS hamsters; this increase was associated with increased levels of omega-3 polyunsaturated fatty acids in plasma and liver. We then investigated whether cosupplementation with anthocyanin-rich elderberry extract would reverse fish oil induced hyperlipidemia and reduce lipid peroxidation in BioF1B hamsters. Plasma and hepatic lipids decreased significantly when hamsters were fed diets containing elderberry extract along with fish oil. Both plasma and liver thiobarbituric acid reactive substances showed significant reductions upon cosupplementation with elderberry extract in fish oil fed BioF1B hamsters. Our findings demonstrate that cosupplementation with elderberry extract reverses hyperlipidemia and lipid peroxidation observed with dietary fish oil alone in BioF1B hamsters.

Diets Enriched in Fish-Oil or Seal-Oil have Distinct Effects on Lipid Levels and Peroxidation in BioF1B Hamsters.

AIM: Fish-oil omega-3 polyunsaturated fatty acids (n-3 PUFAs) are mostly esterified to the sn-2 position of triglycerides, while in seal-oil triglycerides, these are mostly esterified to the sn-1 and -3 positions. We investigated whether fish-oil and seal-oil feeding has a different effect on the regulation of lipid metabolism and oxidative stress in BioF1B hamsters. METHODS: BioF1B hamsters were fed high fat diets rich in fish-oil or seal-oil for 4 weeks, and fasted for 14 hours prior to blood and tissue collection. RESULTS: Plasma and hepatic lipids and lipid peroxidation levels were significantly lower in seal-oil-fed hamsters as compared to those fed fish-oil. There was a selective hindrance of clearance of lipids in fish-oil-fed hamsters as reflected by higher levels of plasma apoB48. CONCLUSION: Differences in the fatty acid composition and positional distribution of n-3 PUFAs in triglycerides of fish-oil and seal-oil are suggested to trigger metabolic differences.