Dataset Information

Molecule database framework: a framework for creating database applications with chemical structure search capability.

ABSTRACT:

Background

Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time.

Results

Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:•Support for multi-component compounds (mixtures)•Import and export of SD-files•Optional security (authorization)For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures).Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files.

Conclusions

By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework.

SUBMITTER: Kiener J

PROVIDER: S-EPMC3892073 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature

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Publications

Molecule database framework: a framework for creating database applications with chemical structure search capability.

Kiener Joos J

Journal of cheminformatics 20131211 1

<h4>Background</h4>Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of ...[more]

PMID: 24325762

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Project description:BackgroundInterest in value-based healthcare, generally defined as providing better care at lower cost, has grown worldwide, and learning health systems (LHSs) have been proposed as a key strategy for improving value in healthcare. LHSs are emerging around the world and aim to leverage advancements in science, technology and practice to improve health system performance at lower cost. However, there remains much uncertainty around the implementation of LHSs and the distinctive features of these systems. This paper presents a conceptual framework that has been developed in Canada to support the implementation of value-creating LHSs.MethodsThe framework was developed by an interdisciplinary team at the Institut national d'excellence en santé et en services sociaux (INESSS). It was informed by a scoping review of the scientific and grey literature on LHSs, regular team discussions over a 14-month period, and consultations with Canadian and international experts.ResultsThe framework describes four elements that characterise LHSs, namely (1) core values, (2) pillars and accelerators, (3) processes and (4) outcomes. LHSs embody certain core values, including an emphasis on participatory leadership, inclusiveness, scientific rigour and person-centredness. In addition, values such as equity and solidarity should also guide LHSs and are particularly relevant in countries like Canada. LHS pillars are the infrastructure and resources supporting the LHS, whereas accelerators are those specific structures that enable more rapid learning and improvement. For LHSs to create value, such infrastructures must not only exist within the ecosystem but also be connected and aligned with the LHSs' strategic goals. These pillars support the execution, routinisation and acceleration of learning cycles, which are the fundamental processes of LHSs. The main outcome sought by executing learning cycles is the creation of value, which we define as the striking of a more optimal balance of impacts on patient and provider experience, population health and health system costs.ConclusionsOur framework illustrates how the distinctive structures, processes and outcomes of LHSs tie together with the aim of optimising health system performance and delivering greater value in health systems.

Dataset Information

Molecule database framework: a framework for creating database applications with chemical structure search capability.

Background

Results

Conclusions

Publications

Molecule database framework: a framework for creating database applications with chemical structure search capability.

Similar Datasets

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