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33 Publications visible to you, out of a total of 33
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: Booklet

Issue Cover (September 2017)

Abstract

Not specified

Editor:

Date Published: 1st Sep 2017

Publication Type: Journal

Inhibition of the mitochondrial calcium uniporter rescues dopaminergic neurons in pink1 − / − zebrafish

Abstract

Not specified

Authors: Smijin Soman, Marcus Keatinge, Mahsa Moein, Marc Da Costa, Heather Mortiboys, Alexander Skupin, Sreedevi Sugunan, Michal Bazala, Jacek Kuznicki, Oliver Bandmann

Date Published: 24th Nov 2016

Publication Type: Journal

Toward Community Standards and Software for Whole-Cell Modeling.

Abstract

Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells.

Authors: Dagmar Waltemath, Jonathan R Karr, Frank T Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K Aranganathan, Kambiz Baghalian, Arne T Bittig, Paulo E Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S Costa, Joseph Cursons, Tobias Czauderna, Arthur P Goldberg, Harold F Gomez, Jens Hahn, Tuure Hameri, Daniel F Hernandez Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knupfer, Matthias Konig, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie J Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Toure, Jannis Uhlendorf, Thawfeek M Varusai, Leandro H Watanabe, Florian Wendland, Markus Wolfien, James T Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber

Date Published: 24th Sep 2016

Publication Type: Not specified

Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum

Abstract

Not specified

Authors: Gerald Penkler, Francois du Toit, Waldo Adams, Marina Rautenbach, Daniel C. Palm, David D. van Niekerk, Jacky L. Snoep

Date Published: 1st Apr 2015

Publication Type: Not specified

Reconstruction of a high-quality metabolic model enables the identification of gene overexpression targets for enhanced antibiotic production in Streptomyces coelicolor A3(2)

Abstract

Not specified

Authors: Minsuk Kim, Jeong Sang Yi, Joonwon Kim, Ji-Nu Kim, Min Woo Kim, Byung-Gee Kim

Date Published: 1st Sep 2014

Publication Type: Not specified

Is health-related quality of life associated with upper and lower airway inflammation in asthmatics

Abstract (Expand)

Background. Allergic diseases impair health-related quality of life (HR-QoL). However, the relationship between airway inflammation and HR-QoL in patients with asthma and rhinitis has not been fully … investigated. We explored whether the inflammation of upper and lower airways is associated with HR-QoL. Methods. Twenty-two mild allergic asthmatics with concomitant rhinitis (10 males, 38 +/- 17 years) were recruited. The Rhinasthma was used to identify HR-QoL, and the Asthma Control Test (ACT) was used to assess asthma control. Subjects underwent lung function and exhaled nitric oxide (eNO) test, collection of exhaled breath condensate (EBC), and nasal wash. Results. The Rhinasthma Global Summary score (GS) was 25 +/- 11. No relationships were found between GS and markers of nasal allergic inflammation (% eosinophils: r = 0.34, P = 0.24; ECP: r = 0.06, P = 0.87) or bronchial inflammation (pH of the EBC: r = 0.12, P = 0.44; bronchial NO: r = 0.27, P = 0.22; alveolar NO: r = 0.38, P = 0.10). The mean ACT score was 18. When subjects were divided into controlled (ACT >/= 20) and uncontrolled (ACT < 20), the alveolar NO significantly correlated with GS in uncontrolled asthmatics (r = 0.60, P = 0.04). Conclusions. Upper and lower airways inflammation appears unrelated to HR-QoL associated with respiratory symptoms. These preliminary findings suggest that, in uncontrolled asthma, peripheral airway inflammation could be responsible for impaired HR-QoL.

Authors: N. Scichilone, F. Braido, S. Taormina, E. Pozzecco, A. Paterno, I. Baiardini, V. Casolaro, G. W. Canonica, V. Bellia

Date Published: 31st Aug 2013

Publication Type: Not specified

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