Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance

Frey, Jeremy G.; Bird, Colin

doi:10.1002/wcms.1127

Cited by 24 publications

(19 citation statements)

References 86 publications

(152 reference statements)

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“…This initiated ac onsiderable amounto fc hemical informatics research within Southampton. Particularly relevant for this papera re the research themes on chemical information and the Semantic Web [6][7][8][9][10][11][12][13] and the work on Electronic Laboratory Notebooks. [14,15] The e-Science programme was not the only driver for the Southampton Chemical Information group.…”

Section: Navigationmentioning

confidence: 99%

The Evolution of Digital Chemistry at Southampton

Bird

Coles

Frey

2015

Molecular Informatics

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In this paper we take a historical view of e‐Science and e‐Research developments within the Chemical Sciences at the University of Southampton, showing the development of several stages of the evolving data ecosystem as Chemistry moves into the digital age of the 21st Century. We cover our research on aspects of the representation of chemical information in the context of the world wide web (WWW) and its semantic enhancement (the Semantic Web) and illustrate this with the example of the representation of quantities and units within the Semantic Web. We explore the changing nature of laboratories as computing power becomes increasing powerful and pervasive and specifically look at the function and role of electronic or digital notebooks. Having focussed on the creation of chemical data and information in context, we finish the paper by following the use and reuse of this data as facilitated by the features provided by digital repositories and their importance in facilitating the exchange of chemical information touching on the issues of open and or intelligent access to the data.

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Section: Navigationmentioning

confidence: 99%

The Evolution of Digital Chemistry at Southampton

Bird

Coles

Frey

2015

Molecular Informatics

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“…ELNs for specific needs are designed for life sciences and chemistry laboratories in industry, academic institutions, and hospitals (Beato et al, 2011;Christ et al, 2012;Elliott, 2013;Frey and Bird, 2013;John et al, 2011;Lagoze et al, 2012;Oleksik et al, 2014). Many pharmaceutical companies have implemented ELNs or have created their own ELNs for drug discovery (Machina and Wild, 2013b).…”

Section: Specific Elnsmentioning

confidence: 99%

“…Many pharmaceutical companies have implemented ELNs or have created their own ELNs for drug discovery (Machina and Wild, 2013b). Some ELNs were built to serve the needs of chemists (Christ et al, 2012;Frey and Bird, 2013;Lagoze et al, 2012;MacNeil, 2011;Milsted et al, 2013;Rajarao and Weiss, 2011;Rudolphi and Goossen, 2011).…”

Section: Specific Elnsmentioning

confidence: 99%

Managing research data

Baykoucheva¹

2015

Managing Scientific Information and Research Data

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“…Frey and Bird have recently reviewed [6] the progress made by cheminformatics towards the goals of integration, owing to the influence of Semantic Web technologies.…”

Section: Introductionmentioning

confidence: 99%

Usage and applications of Semantic Web techniques and technologies to support chemistry research

Borkum

Frey

2014

J Cheminform

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BackgroundThe drug discovery process is now highly dependent on the management, curation and integration of large amounts of potentially useful data. Semantics are necessary in order to interpret the information and derive knowledge. Advances in recent years have mitigated concerns that the lack of robust, usable tools has inhibited the adoption of methodologies based on semantics.ResultsThis paper presents three examples of how Semantic Web techniques and technologies can be used in order to support chemistry research: a controlled vocabulary for quantities, units and symbols in physical chemistry; a controlled vocabulary for the classification and labelling of chemical substances and mixtures; and, a database of chemical identifiers. This paper also presents a Web-based service that uses the datasets in order to assist with the completion of risk assessment forms, along with a discussion of the legal implications and value-proposition for the use of such a service.ConclusionsWe have introduced the Semantic Web concepts, technologies, and methodologies that can be used to support chemistry research, and have demonstrated the application of those techniques in three areas very relevant to modern chemistry research, generating three new datasets that we offer as exemplars of an extensible portfolio of advanced data integration facilities. We have thereby established the importance of Semantic Web techniques and technologies for meeting Wild’s fourth “grand challenge”.

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Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance

Cited by 24 publications

References 86 publications

The Evolution of Digital Chemistry at Southampton

The Evolution of Digital Chemistry at Southampton

Managing research data

Usage and applications of Semantic Web techniques and technologies to support chemistry research

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