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Harmonizing semantic annotations for computational models in biology.

Abstract (Expand)

Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability … and reusability of such models as well as for the integration of the data needed for model parameterization and validation. Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent. These annotations help researchers find and repurpose models, accelerate model composition and enable knowledge integration across model repositories and experimental data stores. However, realizing the potential benefits of semantic annotation requires the development of model annotation standards that adhere to a community-based annotation protocol. Without such standards, tool developers must account for a variety of annotation formats and approaches, a situation that can become prohibitively cumbersome and which can defeat the purpose of linking model elements to controlled knowledge resource terms. Currently, no consensus protocol for semantic annotation exists among the larger biological modeling community. Here, we report on the landscape of current annotation practices among the COmputational Modeling in BIology NEtwork community and provide a set of recommendations for building a consensus approach to semantic annotation.

Authors: M. L. Neal, M. Konig, D. Nickerson, G. Misirli, R. Kalbasi, A. Drager, K. Atalag, V. Chelliah, M. T. Cooling, D. L. Cook, S. Crook, M. de Alba, S. H. Friedman, A. Garny, J. H. Gennari, P. Gleeson, M. Golebiewski, M. Hucka, N. Juty, C. Myers, B. G. Olivier, H. M. Sauro, M. Scharm, J. L. Snoep, V. Toure, A. Wipat, O. Wolkenhauer, D. Waltemath

Date Published: 22nd Mar 2019

Publication Type: InBook

[Inhibition effect of soybean isoflavones on the oxidative modification of low-density lipoprotein].

Abstract (Expand)

In order to investigate the effect of soybean isoflavones(SI) on the oxidative modification to low-density lipoprotein(LDL) and to differentiate the effect of SI and alpha-tocopherol, in vitro and in … vivo test were conducted. An in vitro model of LDL oxidative modification induced by copper-ion was established by monitoring the production of thiobarbituric acid-reactive substances (TBARS) and conjugated dienes after SI or alpha-tocopherol was added. The in vivo test was conducted by feeding rats with a high fat diet supplemented with SI and measured the sensitivity of LDL oxidative modification mediated by Cu2+ in vitro. The results revealed that when SI was added into the in vitro LDL oxidation system, the content of TBARS or conjugated dienes in the system was much reduced with a dose-effect relationship, whether lipid oxidation being initiated or not by copper-ion at 37 degrees C. In comparison with SI, only a significant inhibiting effect on lipid oxidation while alpha-tocopherol was added before the initiation of oxidation. High fat diet induced a rising of LDL sensitivity of oxidative stress, and adding SI to the high fat diet could counteract the sensitivity of LDL oxidative modification significantly. It is concluded that SI is a valuable natural antioxidant different from alpha-tocopherol in inhibiting LDL oxidative modification both in vitro and inv vivo.

Authors: X. Yan, J. Gu, C. Sun, D. Liu

Date Published: No date defined

Publication Type: Not specified

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