BACKGROUND As we are witnessing a great interest in identifying and extracting chemical entities in academic articles, many approaches have been proposed to solve this problem. In this work we describe a probabilistic framework that allows for the output of multiple information extraction systems to be combined in a systematic way. The identified entities are assigned a probability score that r...

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A lipidome is the set of lipids in a given organism, cell or cell compartment and this set reflects the organism's synthetic pathways and interactions with its environment. Recently, lipidomes of biological model organisms and cell lines were published and the number of functional studies of lipids is increasing. In this study we propose a homology metric that can quantify systematic difference...

We describe the development of a chemical entity recognition system and its application in the CHEMDNER-patent track of BioCreative 2015. This community challenge includes a Chemical Entity Mention in Patents (CEMP) recognition task and a Chemical Passage Detection (CPD) classification task. We addressed both tasks by an ensemble system that combines a dictionary-based approach with a statistic...

We present a program, named Promega, to predict the Xaa-Pro peptide bond conformation on the basis of backbone chemical shifts and the amino acid sequence. Using a chemical shift database of proteins of known structure together with the PDB-extracted amino acid preference of cis Xaa-Pro peptide bonds, a cis/trans probability score is calculated from the backbone and (13)C(beta) chemical shifts ...

Introduction: Dietary diversity score (DDS) and Food variety score (FVS) are the appropriate measures used to evaluate the overall quality of dietary patterns. However, their associations with the serum levels of micronutrients remain unclear. The present study aimed to investigate the correlations between DDS/FVS and serum ferritin and magnesium status in the non-athlete femal...

in this research, the effect of different levels of carrageenan gum (0.05– 0.2%) and whey protein concentrate (0.5 - 1.5%) on physical, chemical and sensory properties of low fat mozzarella cheese have been investigated. use of these fat replacers cause significant differences (p ≤ 0.05) on chemical properties as increase in gum and wpc resulted moisture and protein content to increase but ph t...

We propose a hybrid system for extracting chemical-disease relationships from Medline abstracts. At the core of our approach is a general, rule-based system that extracts causal relations from text, using a combination of trigger lists and syntactic dependencies. We augmented this system with supervised learning. We trained two binary classifiers: one extracts intra-sentential relationships bet...