Next Generation Cancer Data Discovery, Access, and Integration Using Prizms and Nanopublications

McCusker, James P.; Lebo, Timothy; Krauthammer, Michael; McGuinness, Deborah L.

doi:10.1007/978-3-642-39437-9_9

Cited by 5 publications

(3 citation statements)

References 7 publications

(7 reference statements)

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“…A more generic conversion approach is provided by Prizms [9]. According to the authors, the tool converts several formats into a nanopublication model called 'datapub', to describe the integrated datasets.…”

Section: Related Workmentioning

confidence: 99%

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COEUS 2.0: automated platform to integrate and publish biomedical data as nanopublications

Sernadela

Oliveira

2018

IET softw.

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Publishing, analysing or properly accessing the abundant information resulting largely from experimental studies in the biomedical domain are current challenges for the research community. Problems with the extraction of relevant information, redundant data, and lack of associations or provenance are good examples of the main concerns. The innovative nanopublication publishing strategy tries to overcome these issues by representing the essential pieces of publishable information on the Semantic Web. However, existing methods to create these Resource Description Framework-based data snippets are based on complex scripting procedures, hindering their use by the community. Therefore, novel and automated strategies are needed to explore the evident value of nanopublications and to enable data attribution mechanisms, an important feature for data owners. To solve these challenges, the authors introduce the second generation of the COEUS open-source application framework (http://bioinformatics.ua.pt/coeus/), an automated platform to integrate heterogeneous scientific outcomes into nanopublications. This results in seamless integration, making data accessible and citable at the same time. No additional scripting methods are needed. A validation of a nanopublishing pipeline is described to demonstrate the system functionalities, integrating and publishing common biomedical achievements into the Semantic Web ecosystem.

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Section: Related Workmentioning

confidence: 99%

“…However, even with the adoption of standards, some data‐sharing issues persist. The major reason is the lack of expertise to convert local data into accepted data standards [9]. Moreover, the inexistence of adequate tools and systems are obstacles to data‐publishing as nanopublications.…”

Section: Introductionmentioning

confidence: 99%

COEUS 2.0: automated platform to integrate and publish biomedical data as nanopublications

Sernadela

Oliveira

2018

IET softw.

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“…Nanopublications have been applied to a number of domains, so far mostly from the life sciences including pharmacology [28], genomics [23], and proteomics [6]. An increasing number of datasets formatted as nanopublications are openly available, including neXtProt [5] and DisGeNET [25], and the nanopublication concept has been combined with and integrated into existing frameworks for data discovery and integration, such as CKAN [19].…”

Section: Introductionmentioning

confidence: 99%

Publishing Without Publishers: A Decentralized Approach to Dissemination, Retrieval, and Archiving of Data

Kuhn

Chichester

Krauthammer

et al. 2015

Lecture Notes in Computer Science

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Abstract. Making available and archiving scientific results is for the most part still considered the task of classical publishing companies, despite the fact that classical forms of publishing centered around printed narrative articles no longer seem well-suited in the digital age. In particular, there exist currently no efficient, reliable, and agreed-upon methods for publishing scientific datasets, which have become increasingly important for science. Here we propose to design scientific data publishing as a Web-based bottom-up process, without top-down control of central authorities such as publishing companies. Based on a novel combination of existing concepts and technologies, we present a server network to decentrally store and archive data in the form of nanopublications, an RDF-based format to represent scientific data. We show how this approach allows researchers to publish, retrieve, verify, and recombine datasets of nanopublications in a reliable and trustworthy manner, and we argue that this architecture could be used for the Semantic Web in general. Evaluation of the current small network shows that this system is efficient and reliable.

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A Nanopublishing Architecture for Biomedical Data

Sernadela

Horst

Thompson

et al. 2014

8th International Conference on Practical Applications of Computational Biology &Amp; Bioinformatics (PACBB 2014)

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Next Generation Cancer Data Discovery, Access, and Integration Using Prizms and Nanopublications

Cited by 5 publications

References 7 publications

COEUS 2.0: automated platform to integrate and publish biomedical data as nanopublications

COEUS 2.0: automated platform to integrate and publish biomedical data as nanopublications

Publishing Without Publishers: A Decentralized Approach to Dissemination, Retrieval, and Archiving of Data

A Nanopublishing Architecture for Biomedical Data

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