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Linking the Resource Description Framework to cheminformatics and proteochemometrics
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. (Wikberg group)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. (Farmaceutisk bioinformatik)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Cancer Pharmacology and Computational Medicine. (Onkologisk farmakologi och informatik)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. (Farmaceutisk bioinformatik; Wikberg group)
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2011 (English)In: Journal of Biomedical Semantics, ISSN 2041-1480, E-ISSN 2041-1480, Vol. 2, no Suppl 1, 6- p.Article in journal (Refereed) Published
Abstract [en]

BACKGROUND :

Semantic web technologies are finding their way into the life sciences. Ontologies and semantic markup have already been used for more than a decade in molecular sciences, but have not found widespread use yet. The semantic web technology Resource Description Framework (RDF) and related methods show to be sufficiently versatile to change that situation.

RESULTS :

The work presented here focuses on linking RDF approaches to existing molecular chemometrics fields, including cheminformatics, QSAR modeling and proteochemometrics. Applications are presented that link RDF technologies to methods from statistics and cheminformatics, including data aggregation, visualization, chemical identification, and property prediction. They demonstrate how this can be done using various existing RDF standards and cheminformatics libraries. For example, we show how IC50 and Ki values are modeled for a number of biological targets using data from the ChEMBL database.

CONCLUSIONS :

We have shown that existing RDF standards can suitably be integrated into existing molecular chemometrics methods. Platforms that unite these technologies, like Bioclipse, makes this even simpler and more transparent. Being able to create and share workflows that integrate data aggregation and analysis (visual and statistical) is beneficial to interoperability and reproducibility. The current work shows that RDF approaches are sufficiently powerful to support molecular chemometrics workflows.

Place, publisher, year, edition, pages
2011. Vol. 2, no Suppl 1, 6- p.
Keyword [en]
cheminformatics, bioclipse, chembl, chemometrics
National Category
Bioinformatics (Computational Biology) Telecommunications Probability Theory and Statistics Bioinformatics and Systems Biology Pharmacology and Toxicology
Research subject
Chemistry with specialization in Analytical Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-147589DOI: 10.1186/2041-1480-2-S1-S6PubMedID: 21388575OAI: oai:DiVA.org:uu-147589DiVA: diva2:400543
Available from: 2011-02-26 Created: 2011-02-26 Last updated: 2017-12-11Bibliographically approved

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Willighagen, EgonAlvarsson, JonathanAndersson, AnnsofieEklund, MartinLampa, SamuelLapins, MarisSpjuth, OlaWikberg, Jarl

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Willighagen, EgonAlvarsson, JonathanAndersson, AnnsofieEklund, MartinLampa, SamuelLapins, MarisSpjuth, OlaWikberg, Jarl
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Department of Pharmaceutical BiosciencesCancer Pharmacology and Computational Medicine
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Journal of Biomedical Semantics
Bioinformatics (Computational Biology)TelecommunicationsProbability Theory and StatisticsBioinformatics and Systems BiologyPharmacology and Toxicology

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