Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data

Kuhn, Tobias; Meroño‐Peñuela, Albert; Malic, Alexander; Poelen, Jorrit; Hurlbert, Allen H.; Ortiz, Emilio Centeno; Furlong, Laura I.; Queralt-Rosiñach, Núria; Chichester, Christine; Banda, Juan M.; Willighagen, Egon; Ehrhart, Friederike; Evelo, Chris T.; Malas, Tareq B.; Dumontier, Michel

doi:10.1109/escience.2018.00024

Cited by 30 publications

(20 citation statements)

References 30 publications

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“…Nanopublications for WikiPathways have been released for several years now in collaboration with their international community ( 35 ). The nanopublications are created using a combination of nanopub-java library ( 36 ) and SPARQL queries against the WikiPathways RDF (see https://github.com/wikipathways/nanopublications ).…”

Section: Connections To Other Initiativesmentioning

confidence: 99%

WikiPathways: connecting communities

Martens

Ammar

Riutta

et al. 2020

Nucleic Acids Research

Self Cite

584

502

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WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the core idea of the scientific community developing and curating biological knowledge in pathway models, WikiPathways lowers all barriers for accessing and using its content. Increasingly more content creators, initiatives, projects and tools have started using WikiPathways. Central in this growth and increased use of WikiPathways are the various communities that focus on particular subsets of molecular pathways such as for rare diseases and lipid metabolism. Knowledge from published pathway figures helps prioritize pathway development, using optical character and named entity recognition. We show the growth of WikiPathways over the last three years, highlight the new communities and collaborations of pathway authors and curators, and describe various technologies to connect to external resources and initiatives. The road toward a sustainable, community-driven pathway database goes through integration with other resources such as Wikidata and allowing more use, curation and redistribution of WikiPathways content.

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Section: Connections To Other Initiativesmentioning

confidence: 99%

WikiPathways: connecting communities

Martens

Ammar

Riutta

et al. 2020

Nucleic Acids Research

Self Cite

584

502

View full text Add to dashboard Cite

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“…In this paper we were motivated to replicate some of the analysis presented in [3] and [5]. This involves reusing a subset of the data on the nanopublication network.…”

Section: Data and Experiments Methodsologymentioning

confidence: 99%

“…We will now briefly describe the data used with a summary given in Table 1. Full details of the datasets and how they are generated can be found in [3], [5]. We will provide a fuller discussion of Table 1 [8], OpenBEL large and small corpus 5 version 20131211 [10], and LIDDI 6 version 1.02 [11].…”

Section: Data and Experiments Methodsologymentioning

confidence: 99%

“…In this paper we look to repeat the analysis of Kuhn et al [3]. However, we found ourselves asking more questions about the collection of nanopublications and thus present our extended analysis of the nanopublication collection.…”

Section: Introductionmentioning

confidence: 95%

“…http://npmonitor.inn.ac/ accessed 21 June 2019 of the nanopublication approach is that it significantly increases the size of the dataset. However, Kuhn et al [3] have shown that for versioned datasets this overhead is actually less than publishing each complete version of the claims in the dataset as done by traditional data publishing with the advantage of the increased provenance of the data.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Data Quality Issues in Current Nanopublications

Asif¹,

Chen-Burger²,

Gray³

2019

2019 15th International Conference on eScience (eScience)

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Nanopublications are a granular way of publishing scientific claims together with their associated provenance and publication information. More than 10 million nanopublications have been published by a handful of researchers covering a wide range of topics within the life sciences. We were motivated to replicate an existing analysis of these nanopublications, but then went deeper into the structure of the existing nanopublications. In this paper, we analyse the usage of nanopublications by investigating the distribution of triples in each part and discuss the data quality issues raised by this analysis. From this analysis we argue that there is a need for the community to develop a set of community guidelines for the modelling of nanopublications.

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A Framework for Citing Nanopublications

Fabris

Kuhn

Silvello

2019

Digital Libraries for Open Knowledge

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Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data

Cited by 30 publications

References 30 publications

WikiPathways: connecting communities

WikiPathways: connecting communities

Data Quality Issues in Current Nanopublications

A Framework for Citing Nanopublications

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