Dataset Information

Taking Open Innovation to the Molecular Level - Strengths and Limitations.

ABSTRACT: The ever-growing availability of large-scale open data and its maturation is having a significant impact on industrial drug-discovery, as well as on academic and non-profit research. As industry is changing to an 'open innovation' business concept, precompetitive initiatives and strong public-private partnerships including academic research cooperation partners are gaining more and more importance. Now, the bioinformatics and cheminformatics communities are seeking for web tools which allow the integration of this large volume of life science datasets available in the public domain. Such a data exploitation tool would ideally be able to answer complex biological questions by formulating only one search query. In this short review/perspective, we outline the use of semantic web approaches for data and knowledge integration. Further, we discuss strengths and current limitations of public available data retrieval tools and integrated platforms.

SUBMITTER: Zdrazil B

PROVIDER: S-EPMC3507005 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature

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Taking Open Innovation to the Molecular Level - Strengths and Limitations.

Zdrazil Barbara B Blomberg Niklas N Ecker Gerhard F GF

Molecular informatics 20120807 8

The ever-growing availability of large-scale open data and its maturation is having a significant impact on industrial drug-discovery, as well as on academic and non-profit research. As industry is changing to an 'open innovation' business concept, precompetitive initiatives and strong public-private partnerships including academic research cooperation partners are gaining more and more importance. Now, the bioinformatics and cheminformatics communities are seeking for web tools which allow the ...[more]

PMID: 23226167

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Project description:In order to develop a better understanding of the role environmental toxicants may play in the onset and progression of neurodegenerative diseases, it has become increasingly important to optimize sensitive methods for quickly screening toxicants to determine their ability to disrupt neuronal function. The nematode Caenorhabditis elegans can help with this effort. This species has an integrated nervous system producing behavioral function, provides easy access for molecular studies, has a rapid lifespan, and is an inexpensive model. This study focuses on methods of measuring neurodegeneration involving the dopaminergic system and the identification of compounds with actions that disrupt dopamine function in the model organism C. elegans. Several dopamine-mediated locomotory behaviors, Area Exploration, Body Bends, and Reversals, as well as Swimming-Induced Paralysis and Learned 2-Nonanone Avoidance, were compared to determine the best behavioral method for screening purposes. These behavioral endpoints were also compared to morphological scoring of neurodegeneration in the dopamine neurons. We found that in adult worms, Area Exploration is more advantageous than the other behavioral methods for identifying DA-deficient locomotion and is comparable to neuromorphological scoring outputs. For larval stage worms, locomotion was an unreliable endpoint, and neuronal scoring appeared to be the best method. We compared the wild-type N2 strain to the commonly used dat-1p::GFP reporter strains BY200 and BZ555, and we further characterized the dopamine-deficient strains, cat-2 e1112 and cat-2 n4547. In contrast to published results, we found that the cat-2 strains slowed on food almost as much as N2s. Both showed decreased levels of cat-2 mRNA and DA content, rather than none, with cat-2 e1112 having the greatest reduction in DA content in comparison to N2. Finally, we compared and contrasted strengths, limitations, cost, and equipment needs for all primary methods for analysis of the dopamine system in C. elegans.

Dataset Information

Taking Open Innovation to the Molecular Level - Strengths and Limitations.

Publications

Taking Open Innovation to the Molecular Level - Strengths and Limitations.

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