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Authors: Chichester, Christine

Article Type: Position Paper

Abstract: Scientists from diverse backgrounds are joining the field of data science. This leads to advances in data science being actualized in the context of many different domains. Conclusions from datasets using innovative algorithms are obvious aspects but advances in data science can take on many different forms such as new methods for data interpretation, new data integration and processing technologies, or as will be the topic of this editorial, data visualization techniques. The parity and complementary relationship between techniques from all domains provide ways to improve discovery although quantifying the contributions to discovery process from each technique can be elusive. …The experiences described here come from visualizing life science multi-omics data, but most of the remarks can be associated with visualization methods in general. From the perspective that visualization serves as an important method for shaping data science interpretations, this paper sets out: 1) some of the necessary requirements for visualization tools due to the nature of multi-omics datasets and, 2) some of the difficulties encountered in creating and valorizing new visualization implementations for scientific discovery. Show more

Keywords: Multidimensional data, valorization, bias

DOI: 10.3233/DS-170009

Citation: Data Science, vol. 1, no. 1-2, pp. 131-137, 2017

Authors: Sheehan, Jerry | Hornbostel, Stefan | Brody, Tim | MacCallum, Catriona | Chichester, Christine

Article Type: Abstract

DOI: 10.3233/ISU-2008-0580

Citation: Information Services & Use, vol. 28, no. 3-4, pp. 229-242, 2008

Authors: Queralt-Rosinach, Núria | Kuhn, Tobias | Chichester, Christine | Dumontier, Michel | Sanz, Ferran | Furlong, Laura I.

Article Type: Research Article

Abstract: The increasing and unprecedented publication rate in the biomedical field is a major bottleneck for knowledge discovery in the Life Sciences. The manual curation of facts from published scientific papers is slow and inefficient, and therefore new approaches are needed that can enable the automatic, scalable and reliable extraction of assertions. While the publication of scientific assertions and datasets on the Semantic Web is gaining traction, it also creates new challenges such as the proper representation of provenance and versioning. Here, we address these issues and describe our efforts to represent the DisGeNET database of human gene-disease associations as permanent, …immutable, and provenance rich digital objects called nanopublications. Our nanopublications are the first instance of a Linked Data model that ensures stable interlinking of the assertion and its metadata by Trusty URIs. As DisGeNET integrates manually curated as well as text-mined data of different origins, the semantic description of the evidence for each assertion is important to provide trust and allow evidence-based hypothesis generation. Here, we describe our steps to ensure high quality and demonstrate the utility of linking our data to other datasets on the emerging Semantic Web. Show more

Keywords: Gene-disease associations, linked data, nanopublication, provenance, trusty URIs

DOI: 10.3233/SW-150189

Citation: Semantic Web, vol. 7, no. 5, pp. 519-528, 2016

Authors: Chichester, Christine | Karch, Oliver | Gaudet, Pascale | Lane, Lydie | Mons, Barend | Bairoch, Amos

Article Type: Research Article

Abstract: neXtProt provides a comprehensive knowledgebase on human proteins complemented by an extensive cross incorporation of annotations from many databases. With the diversity of published data, provenance information becomes critical to providing reliable and trustworthy services to scientists, thus the tracking of provenance in open, decentralized systems is especially important. Since the nanopublication system addresses many of these challenges, we have developed the neXtProt Linked Data by serializing in RDF/XML annotations specific to neXtProt and started employing the nanopublication model to give appropriate attribution to all data. Specifically, a use case demonstrates the handling of post-translational modification (PTM) data modeled as …nanopublications to illustrate how the different levels of provenance and data quality thresholds can be captured in this model. Show more

Keywords: Biological database, Linked Data, Semantic Web, nanopublication, post-translation modification

DOI: 10.3233/SW-140149

Citation: Semantic Web, vol. 6, no. 2, pp. 147-153, 2015

Authors: Gray, Alasdair J.G. | Groth, Paul | Loizou, Antonis | Askjaer, Sune | Brenninkmeijer, Christian | Burger, Kees | Chichester, Christine | Evelo, Chris T. | Goble, Carole | Harland, Lee | Pettifer, Steve | Thompson, Mark | Waagmeester, Andra | Williams, Antony J.

Article Type: Research Article

Abstract: The discovery of new medicines requires pharmacologists to interact with a number of information sources ranging from tabular data to scientific papers, and other specialized formats. In this application report, we describe a linked data platform for integrating multiple pharmacology datasets that form the basis for several drug discovery applications. The functionality offered by the platform has been drawn from a collection of prioritised drug discovery business questions created as part of the Open PHACTS project, a collaboration of research institutions and major pharmaceutical companies. We describe the architecture of the platform focusing on seven design decisions that drove its …development with the aim of informing others developing similar software in this or other domains. The utility of the platform is demonstrated by the variety of drug discovery applications being built to access the integrated data. An alpha version of the OPS platform is currently available to the Open PHACTS consortium and a first public release will be made in late 2012, see http://www.openphacts.org/ for details. Show more

Keywords: pharmacology, linked data, data integration

DOI: 10.3233/SW-2012-0088

Citation: Semantic Web, vol. 5, no. 2, pp. 101-113, 2014