ChrisDS Consulting

Sweden

ChrisDS Consulting

Sweden
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Southan C.,ChrisDS Consulting | Williams A.J.,Royal Society of Chemistry | Ekins S.,Collaborations in Chemistry
Drug Discovery Today | Year: 2013

There is an expanding amount of interest directed at the repurposing and repositioning of drugs, as well as how in silico methods can assist these endeavors. Recent repurposing project tendering calls by the National Center for Advancing Translational Sciences (USA) and the Medical Research Council (UK) have included compound information and pharmacological data. However, none of the internal company development code names were assigned to chemical structures in the official documentation. This not only abrogates in silico analysis to support repurposing but consequently necessitates data gathering and curation to assign structures. Here, we describe the approaches, results and major challenges associated with this. © 2012 Elsevier Ltd.


Gaudet P.,Swiss Institute of Bioinformatics | Gaudet P.,Northwestern University | Bairoch A.,Swiss Institute of Bioinformatics | Field D.,UK Center for Ecology and Hydrology | And 37 more authors.
Database | Year: 2011

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources; and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. © The Author(s) 2011.


Gaudet P.,Swiss Institute of Bioinformatics | Gaudet P.,Northwestern University | Bairoch A.,Swiss Institute of Bioinformatics | Field D.,UK Center for Ecology and Hydrology | And 40 more authors.
Nucleic Acids Research | Year: 2011

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. © The Author(s) 2010.


Eriksson M.,Astrazeneca | Nilsson I.,Astrazeneca | Kogej T.,Astrazeneca | Southan C.,Astrazeneca | And 5 more authors.
Molecular Informatics | Year: 2012

The access and use of large-scale structure-activity relationships (SAR) is increasing as the range of targets and availability of bioactive compound-to-protein mappings expands. However, effective exploitation requires merging and normalisation of activity data, mappings to target classifications as well as visual display of chemical structure relationships. This work describes the development of the application "SARConnect" to address these issues. We discuss options for delivery and analysis of large-scale SAR data together with a set of use-cases to illustrate the design choices and utility. The main activity sources of ChEMBL,1 GOSTAR2 and AstraZeneca's internal system IBIS, had already been integrated in Chemistry Connect.3 For target relationships we selected human UniProtKB/Swiss-Prot4 as our primary source of a heuristic target classification. Similarly, to explore chemical relationships we combined several methods for framework and scaffold analysis into a unified, hierarchical classification where ease of navigation was the primary goal. An application was built on TIBCO Spotfire to retrieve data for visual display. Consequently, users can explore relationships between target, activity and structure across internal, external and commercial sources that encompass approximately 3 million compounds, 2000 human proteins and 10 million activity values. Examples showing the utility of the application are given. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


PubMed | ChrisDS Consulting
Type: Journal Article | Journal: Drug discovery today | Year: 2012

There is an expanding amount of interest directed at the repurposing and repositioning of drugs, as well as how in silico methods can assist these endeavors. Recent repurposing project tendering calls by the National Center for Advancing Translational Sciences (USA) and the Medical Research Council (UK) have included compound information and pharmacological data. However, none of the internal company development code names were assigned to chemical structures in the official documentation. This not only abrogates in silico analysis to support repurposing but consequently necessitates data gathering and curation to assign structures. Here, we describe the approaches, results and major challenges associated with this.

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