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A Nano(publication) Approach Towards Big Data in Biodiversity

Mariya Dimitrova, Teodor Georgiev, Lyubomir Penev
2021 Biodiversity Information Science and Standards  
In addition, we envision nanopublications to be useful for curation or peer-review of published knowledge by enabling any researcher to publish a nanopublication containing a comment of an assertion made  ...  in a previously published nanopublication.  ...  In addition, we envision nanopublications to be useful for curation or peer-review of published knowledge by enabling any researcher to publish a nanopublication containing a comment of an assertion made  ... 
doi:10.3897/biss.5.74351 fatcat:jczm4lvr4vasfbuycf2xridysi

Data Quality Issues in Current Nanopublications

Imran Asif, Jessica Chen-Burger, Alasdair J G Gray
2019 Zenodo  
Nanopublications are a granular way of publishing scientific claims together with their associated provenance and publication information.  ...  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.  ...  This involves reusing a subset of the data on the nanopublication network. We will now briefly describe the data used with a summary given in Table 1 .  ... 
doi:10.5281/zenodo.3268904 fatcat:a3sw2l62wzeuraei2inpiooxf4

Publishing without Publishers: a Decentralized Approach to Dissemination, Retrieval, and Archiving of Data [article]

Tobias Kuhn, Christine Chichester, Michael Krauthammer, Michel Dumontier
2015 arXiv   pre-print
used for the Semantic Web in general.  ...  data.  ...  We argue that data publishing and archiving can and should be done in a decentralized manner.  ... 
arXiv:1411.2749v2 fatcat:5u7qd7iquve33jr2uud7v2hha4

Data Quality Issues in Current Nanopublications

Imran Asif, Jessica Chen-Burger, Alasdair J G Gray
2019 Zenodo  
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.  ...  used, and data being represented in the nanopublication collection.  ... 
doi:10.5281/zenodo.3358983 fatcat:u44seu7xmjbrpl5ylfexke7xfe

Decentralized provenance-aware publishing with nanopublications

Tobias Kuhn, Christine Chichester, Michael Krauthammer, Núria Queralt-Rosinach, Ruben Verborgh, George Giannakopoulos, Axel-Cyrille Ngonga Ngomo, Raffaele Viglianti, Michel Dumontier
2016 PeerJ Computer Science  
used as a low-level data publication layer to serve the Semantic Web in general.  ...  data.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.7717/peerj-cs.78 fatcat:ppukzzrz25aazcurhs6yrtsaze

Semantic micro-contributions with decentralized nanopublication services

Tobias Kuhn, Ruben Taelman, Vincent Emonet, Haris Antonatos, Stian Soiland-Reyes, Michel Dumontier
2021 PeerJ Computer Science  
To address these problems, we present here an approach to use nanopublications and a decentralized network of services to allow users to directly publish small Linked Data statements through a simple and  ...  We show here that these two kinds of services are complementary and together allow us to query nanopublications in a reliable and efficient manner.  ...  Collectively, they published 81 nanopublications, not counting their introduction nanopublications, via the use of seven distinct templates.  ... 
doi:10.7717/peerj-cs.387 pmid:33817033 pmcid:PMC7959648 fatcat:he4vr6n2xfh75iigogpqludvqu

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

Tobias Kuhn, Christine Chichester, Michael Krauthammer, Michel Dumontier
2015 Lecture Notes in Computer Science  
used for the Semantic Web in general.  ...  data.  ...  We argue that data publishing and archiving can and should be done in a decentralized manner.  ... 
doi:10.1007/978-3-319-25007-6_38 fatcat:6pf4j3b725dzdmq25qxmd3ea3a

nanopub-java: A Java Library for Nanopublications [article]

Tobias Kuhn
2015 arXiv   pre-print
Its core features are stable, but it also contains unofficial and experimental extensions: for publishing to a decentralized server network, for defining sets of nanopublications with indexes, for informal  ...  assertions, and for digitally signing nanopublications.  ...  library can be a valuable resource for tools that use RDF data in the context of provenance recording, reproducibility, data publishing, data reuse, and reliable retrieval of Linked Data.  ... 
arXiv:1508.04977v1 fatcat:lhpr33j4frfq7odlrgttgtgr6e

Representing Physician Suicide Claims as Nanopublications [article]

Tiffany I Leung, Tobias Kuhn, Michel Dumontier
2020 medRxiv   pre-print
Here, we report on the use of nanopublications as a scientific publishing approach to establish a citation network of claims drawn from a variety of media concerning the rate of suicide of US physicians  ...  Data was extracted into a spreadsheet that was then used to create nanopublications.  ...  are themselves defined and published as nanopublications.  ... 
doi:10.1101/2020.05.16.20101881 fatcat:otqb74nkfjhgxp3n5jwjm5ixre

Publishing DisGeNET as nanopublications

Núria Queralt-Rosinach, Tobias Kuhn, Christine Chichester, Michel Dumontier, Ferran Sanz, Laura I. Furlong, Boyan Brodaric
2016 Semantic Web Journal  
Nanopublications are a new way of publishing structured data that consists of an assertion along with its provenance.  ...  We present the publication of DisGeNET nanopublications as a new Linked Dataset implemented in combination of the Trusty URIs approach.  ...  We published our de-referenceable nanopublications on the Web with a human-readable list of the vocabularies used.  ... 
doi:10.3233/sw-150189 fatcat:udefvr3rszeevdyrugmgtnxq24

Reliable Granular References to Changing Linked Data [chapter]

Tobias Kuhn, Egon Willighagen, Chris Evelo, Núria Queralt-Rosinach, Emilio Centeno, Laura I. Furlong
2017 Lecture Notes in Computer Science  
Nanopublications are a concept to represent Linked Data in a granular and provenance-aware manner, which has been successfully applied to a number of scientific datasets.  ...  We show that the total size and overhead of evolving scientific datasets is reduced, and typical subsets that researchers use for their analyses can be referenced and retrieved efficiently with optimized  ...  to let data producers publish incremental datasets, and to allow researchers to publish index nanopublications to precisely specify the subsets of existing Linked Data resources they are using for their  ... 
doi:10.1007/978-3-319-68288-4_26 fatcat:ropyjxarijgerg75lj6kb5a3qu

Provenance for Linguistic Corpora Through Nanopublications [article]

Timo Lek, Anna de Groot, Tobias Kuhn, Roser Morante
2020 arXiv   pre-print
This paper addresses this issue with a case study on event annotated corpora and by creating a new, more interoperable representation of this data in the form of nanopublications.  ...  We describe how such nanopublications can be created and demonstrate how SPARQL queries can be performed to extract interesting content from the new representations.  ...  Linked Data, Data Provenance and Nanopublications Linked Data is about connecting and publishing data in a structured way on the web, often on the basis of an ontology using the Web Ontology Language (  ... 
arXiv:2006.06341v2 fatcat:jlezlg5oxzexpjmta3myx2zsni

A Unified Nanopublication Model for Effective and User-Friendly Access to the Elements of Scientific Publishing [chapter]

Cristina-Iulia Bucur, Tobias Kuhn, Davide Ceolin
2020 Lecture Notes in Computer Science  
In order to address these problems and to better align scientific publishing with the principles of the Web and Linked Data, we propose here an approach to use nanopublications as a unifying model to represent  ...  a prototype of a user interface for that scenario that shows different views on the set of review comments provided for a given manuscript, and we show in a user study that editors find the interface useful  ...  We proposed a semantic model for reviewing at a finer-grained level called Linkflows and argued that Linked Data principles like dereferenceable URIs using open standards like RDF can be used for publishing  ... 
doi:10.1007/978-3-030-61244-3_7 fatcat:v7pmobjoa5aebpntwzknojcp7i

A Unified Nanopublication Model for Effective and User-Friendly Access to the Elements of Scientific Publishing [article]

Cristina-Iulia Bucur, Tobias Kuhn, Davide Ceolin
2020 arXiv   pre-print
In order to address these problems and to better align scientific publishing with the principles of the Web and Linked Data, we propose here an approach to use nanopublications as a unifying model to represent  ...  a prototype of a user interface for that scenario that shows different views on the set of review comments provided for a given manuscript, and we show in a user study that editors find the interface useful  ...  In order to address these problems and to better align scientific publishing with the principles of the Web and Linked Data, we propose here an approach to use nanopublications as a unifying model to represent  ... 
arXiv:2006.06348v1 fatcat:vcjprierm5bnrmkgodkxetmtpu

Nanopublication-Based Semantic Publishing and Reviewing: A Field Study with Formalization Papers [article]

Cristina-Iulia Bucur and Tobias Kuhn and Davide Ceolin and Jacco van Ossenbruggen
2022 arXiv   pre-print
high-level scientific claims in formal logic,and publish the results in a special issue of an existing journal.We use the concept and technology of nanopublications for this endeavor,and represent not  ...  automated fashion has been proposed as a solution to this problem,but the accuracy of such processing remains very poor for extraction tasks beyond the basic ones.Few approaches have tried to change how we publish  ...  Then the authors can publish their formalization in the form of a nanopublication using Nanobench (see Figure 1 ), and afterwards they needed to submit it to the special issue using another Nanobench  ... 
arXiv:2203.01608v1 fatcat:co46olju2zfsrhonqkhf2dtz34
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