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Querying NeXtProt Nanopublications and Their Value for Insights on Sequence Variants and Tissue Expression

24 Pages Posted: 10 Jul 2018 First Look: Accepted

See all articles by Christine Chichester

Christine Chichester

University of Lausanne - CALIPHO Group

Pascale Gaudet

University of Lausanne - CALIPHO Group

Oliver Karch

Merck & Co., Inc. - Biomarker Technologies, Discovery Bioinformatics

Paul Groth

Elsevier - Elsevier Labs

Lydie Lane

University of Lausanne - CALIPHO Group

Amos Bairoch

University of Lausanne - CALIPHO Group

Barend Mons

Netherlands Bioinformatics Centre

Antonis Loizou

VU University Amsterdam - Department of Computer Science

Abstract

Understanding how genetic differences between individuals impact the regulation, expression, and ultimately function of proteins is an important step toward realizing the promise of personal medicine. There are several technical barriers hindering the transition of biological knowledge into the applications relevant to precision medicine. One important challenge for data integration is that new biological sequences (proteins, DNA) have multiple issues related to interoperability potentially creating a quagmire in the published data, especially when different data sources do not appear to be in agreement. Thus, there is an urgent need for systems and methodologies to facilitate the integration of information in a uniform manner to allow seamless querying of multiple data types which can illuminate, for example, the relationships between protein modifications and causative genomic variants. Our work demonstrates for the first time how semantic technologies can be used to address these challenges using the nanopublication model applied to the neXtProt data set, a curated knowledgebase of information about human proteins. We have appliedĀ the nanopublication model to demonstrate querying over several named graphs, including the provenance information associated with the curated scientific assertions from neXtProt. We show by the way of use cases using sequence variations, post-translational modifications and tissue expression, that querying the neXtProt nanopublication implementation is a credible approach for expanding biological insight.

Keywords: biological databases, linked data, semantic web, nanopublication, post-translation modification, single nucleotide polymorphisms, tissue expression

Suggested Citation

Chichester, Christine and Gaudet, Pascale and Karch, Oliver and Groth, Paul and Lane, Lydie and Bairoch, Amos and Mons, Barend and Loizou, Antonis, Querying NeXtProt Nanopublications and Their Value for Insights on Sequence Variants and Tissue Expression (2014). Journal of Web Semantics First Look . Available at SSRN: https://ssrn.com/abstract=3199138 or http://dx.doi.org/10.2139/ssrn.3199138

Christine Chichester (Contact Author)

University of Lausanne - CALIPHO Group ( email )

CMU-RueMichel-Servet1
1211Geneva4
Switzerland

Pascale Gaudet

University of Lausanne - CALIPHO Group

CMU-RueMichel-Servet1
1211Geneva4
Switzerland

Oliver Karch

Merck & Co., Inc. - Biomarker Technologies, Discovery Bioinformatics

Frankfurter Str. 250
Darmstadt, 64271
Germany

Paul Groth

Elsevier - Elsevier Labs

United States

Lydie Lane

University of Lausanne - CALIPHO Group

CMU-RueMichel-Servet1
1211Geneva4
Switzerland

Amos Bairoch

University of Lausanne - CALIPHO Group

CMU-RueMichel-Servet1
1211Geneva4
Switzerland

Barend Mons

Netherlands Bioinformatics Centre

P.O. Box 9101
6500 HB Nijmegen
Netherlands

Antonis Loizou

VU University Amsterdam - Department of Computer Science ( email )

De Boelelaan 1081
1081 HV Amsterdam
Netherlands

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