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

Cristina-Iulia Bucur1 , Tobias Kuhn2 , Davide Ceolin 3
1, 2 Vrije Universiteit Amsterdam, 3 Centrum Wiskunde & Informatica (CWI)

September 2020

These slides: http://bit.do/Linkflows-EKAW-Sept-2020

Scientific publishing: ancient paradigms still in place

  • Long texts in natural language in formats like PDF
  • Digitized, but not machine-interpretable
  • Quality checking with peer reviews which are also long texts in natural language

A nanopublication-style communication interaction

Previous work[1]:
Reviews can be made more structured and precise

[1] Bucur, C.I., Kuhn, T., Ceolin, D.: Peer reviewing revisited: Assessing research with interlinked semantic comments. K-CAP 2019.

Research question

Can we use the concept of nanopublications as a unifying model to represent in a semantic and fine-grained way the elements of publications, their interrelations as well as their provenance and their assessments?

A nanopublication[2]:
a fine-grained provenance-aware Linked Data format

[2] Groth, P., Gibson, A., Velterop, J.: The anatomy of a nanopublication. Information Services & Use 30, 51–56 (2010).

Nanopublication of a review comment

Nanopublication assertion of a review comment

Research questions (1)

  • RQ1: Can we use nanopublications as a unifying data model to represent the structure, links and assessments of manuscripts in a precise, transparent, and provenance-aware manner?

  • Evaluation:
    • descriptive analysis on a small case study applying the model

Use case data: recent publications with their reviews from the Semantic Web Journal

Elements of publication
articles 3
reviewers 9
sections 89
paragraphs 279
figures 11
tables 10
formula 8
footnote 2
review comments 213
Nanopublications 627
RDF triples 10 437
Total download time 11.66s
Download time per nanopublication 18.6ms

Research questions (2)

  • RQ2: Is a fine-grained semantic publishing and reviewing model able to provide editors with answers to common competency questions?

  • Evaluation: competency questions (CQs)
    • formalizations as SPARQL queries
    • prototype of a fine-grained semantic analysis interface for editors

Competency questions from the editor's point of view:

  • CQ1: What is the number of positive and negative comments per reviewer?
  • CQ2: What is the number of and negative comments per section?
  • CQ3: What is the distribution of review comments with respect to the content or presentation of the article?
  • CQ4: What is the nature of the review comments with respect to whether they refer to a specific paragraph or a larger structure like a section?
  • CQ5: What are the critical points raised by the reviewers?
  • CQ6: How many points were raised that need to be addressed by the authors?
  • CQ7: How do the review comment cover the different sections and paragraphs?
Query CQ1: What is the number of positive and negative comments per reviewer?

Research questions (3)

  • RQ3: Can we design an intuitive and effective interface based on a fine-grained semantic publishing and reviewing model that supports journal editors?

  • Evaluation: user study
    • perceived importance of the defined CQs for editors
    • perceived usefulness of the prototype for answering CQs

User study with editors

  • Invitations sent to editors of Computer Science journals: PeerJ CS, Semantic Web, Data Science Journal
  • 401 invitations sent, received a total of 42 answers (10.5%)

User study with editors: importance of CQs

User study interface: reviewer-oriented view

User study interface: section-oriented view

User study with editors: interface usefulness

Most of the CQs are considered important, while our interface is considered useful

Competency Question Importance Usefulness
average p-value≥3 average p-value≥3
CQ1: comments per reviewer 3.17 0.044 * 3.48 1.36e-4 *
CQ2: comments per section 2.36 0.860 3.83 2.22e-7 *
CQ3: content or presentation 3.64 1.36e-4 * 3.40 1.47e-3 *
CQ4: paragraph or a larger structure 3.05 0.022 * 3.26 0.022 *
CQ5: critical points 4.58 <e-12 * 3.21 1.36e-4 *
CQ6: need to be addressed 3.57 1.41e-6 * 3.43 3.44e-5 *
CQ7: coverage sections and paragraphs 2.79 0.220 3.62 2.22e-7 *


  • The different elements of scientific publishing can be represented in a fine-grained and semantic manner with nanopublications (RQ1)
  • We can answer a set of CQs for editors using SPARQL queries (RQ2)
  • Editors mostly find the defined CQs important and our prototype useful (RQ3)

Future work

  • Extending our approach to represent the content of research findings
  • Linking it to article quality
  • Interfaces for reviewers and authors

Acknowledgements: thank you!

  • IOS Press: Maarten Fröhlich, Stephanie Delbeque
  • Sound and Vision Institute: Erwin Verbruggen, Johan Oomen
  • Vrije Universiteit Amsterdam: Jacco van Ossenbruggen