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Citation Typing Ontology (CiTO) Pilot

The Journal of Cheminformatics is piloting use of the Citation Typing Ontology (CiTO) in its  papers. Any author wishing to submit to the journal is free to participate in the pilot, but we encourage them first to read the launch Editorial by Egon Willighagen.

Author should follow the Submission Guidelines for the journal as normal. CiTO annotations should be added in the reference list (not as inline citations) in square brackets and in bold at the end of the full reference, e.g. [cito:extends]. Multiple CiTO annotations can be added by using a space between them, e.g. [cito:citesAsAuthority] [cito:usesMethodIn]. See the Editorial for examples.

When submitting their paper, authors should make sure to answer “yes” to the question “Are you submitting to a Thematic Series?” They should then select the Citation Typing Ontology (CiTO) Pilot from the list of available options. We initially encourage authors to use the below subset of CiTO types: 

[cito:citesAsDataSource] (when you point the reader to a source of data which may explain a claim) 
[cito:usesDataFrom] (when you reuse somehow (and elaborate on) the data in the cited entity)
[cito:usesMethodIn]
[cito:citesAsAuthority]
[cito:discusses]
[cito:extends]
[cito:agreesWith]
[cito:disagreesWith]

In addition, there are specific annotations for letters, retraction and corrections to articles that authors can use:

[cito:repliesTo]
[cito:retracts]
[cito:updates]

However, authors are in principle also free to use any of the CiTO annotations available. For more information, see http://purl.org/spar/cito.

We are collating guidelines on how to add the annotations to the reference list when preparing your manuscript. These guidelines will be in development throughout the pilot phase, and we welcome feedback from authors on how to improve them: https://jcheminform.github.io/jcheminform-author-guidelines/cito

Articles participating in the pilot will be added below and will serve as examples to future authors on how to format their CiTO annotations.

If you have any questions, please contact the Editors-in-Chief or Editorial Office.


  1. A key concept in drug design is how natural variants, especially the ones occurring in the binding site of drug targets, affect the inter-individual drug response and efficacy by altering binding affinity. The...

    Authors: Ammar Ammar, Rachel Cavill, Chris Evelo and Egon Willighagen
    Citation: Journal of Cheminformatics 2022 14:8
  2. In polypharmacology drugs are required to bind to multiple specific targets, for example to enhance efficacy or to reduce resistance formation. Although deep learning has achieved a breakthrough in de novo des...

    Authors: Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Michael T. M. Emmerich, Adriaan P. IJzerman and Gerard J. P. van Westen
    Citation: Journal of Cheminformatics 2021 13:85
  3. The ability to access chemical information openly is an essential part of many scientific disciplines. The Journal of Cheminformatics is leading the way for rigorous, open cheminformatics in many ways, but the...

    Authors: Emma L. Schymanski and Evan E. Bolton
    Citation: Journal of Cheminformatics 2021 13:50

    The Letter Response to this article has been published in Journal of Cheminformatics 2021 13:49

  4. The Resource Description Framework (RDF), together with well-defined ontologies, significantly increases data interoperability and usability. The SPARQL query language was introduced to retrieve requested RDF ...

    Authors: Jakub Galgonek and Jiří Vondrášek
    Citation: Journal of Cheminformatics 2021 13:38
  5. Compound (or chemical) databases are an invaluable resource for many scientific disciplines. Exposomics researchers need to find and identify relevant chemicals that cover the entirety of potential (chemical a...

    Authors: Emma L. Schymanski, Todor Kondić, Steffen Neumann, Paul A. Thiessen, Jian Zhang and Evan E. Bolton
    Citation: Journal of Cheminformatics 2021 13:19
  6. Natural products (NPs) are small molecules produced by living organisms with potential applications in pharmacology and other industries as many of them are bioactive. This potential raised great interest in N...

    Authors: Maria Sorokina, Peter Merseburger, Kohulan Rajan, Mehmet Aziz Yirik and Christoph Steinbeck
    Citation: Journal of Cheminformatics 2021 13:2
  7. Biomedical information mining is increasingly recognized as a promising technique to accelerate drug discovery and development. Especially, integrative approaches which mine data from several (open) data sourc...

    Authors: Alzbeta Tuerkova and Barbara Zdrazil
    Citation: Journal of Cheminformatics 2020 12:71
  8. Sugar units in natural products are pharmacokinetically important but often redundant and therefore obstructing the study of the structure and function of the aglycon. Therefore, it is recommended to remove th...

    Authors: Jonas Schaub, Achim Zielesny, Christoph Steinbeck and Maria Sorokina
    Citation: Journal of Cheminformatics 2020 12:67
  9. Identifying and assessing ligand-target binding is a core component in early drug discovery as one or more unwanted interactions may be associated with safety issues.

    Authors: Laeeq Ahmed, Hiba Alogheli, Staffan Arvidsson McShane, Jonathan Alvarsson, Arvid Berg, Anders Larsson, Wesley Schaal, Erwin Laure and Ola Spjuth
    Citation: Journal of Cheminformatics 2020 12:62