Journal of Cheminformatics is an open-access journal publishing original peer-reviewed research in all aspects of cheminformatics and molecular modelling.
Welcome
Featured article - Learning chemistry: exploring the suitability of machine learning for the task of structure-based chemical ontology classification
Chemical data is increasingly openly available in databases such as PubChem, which contains approximately 110 million compound entries as of February 2021. With the availability of data at such scale, the burden has shifted to organisation, analysis and interpretation. Chemical ontologies provide structured classifications of chemical entities that can be used for navigation and filtering of the large chemical space. ChEBI is a prominent example of a chemical ontology, widely used in life science contexts. However, ChEBI is manually maintained and as such cannot easily scale to the full scope of public chemical data. There is a need for tools that are able to automatically classify chemical data into chemical ontologies, which can be framed as a hierarchical multi-class classification problem. In this paper, the authors evaluate machine learning approaches for this task, comparing different learning frameworks including logistic regression, decision trees and long short-term memory artificial neural networks, and different encoding approaches for the chemical structures, including cheminformatics fingerprints and character-based encoding from chemical line notation representations.
Michael Schwarzenberger from Pixabay (CC0)
Featured Collection - In Silico Structure Generation: Recent Developments, Applications, and Challenges
This special collection showcases recent advances, applications, challenges in the enumeration of chemical structures: from the design to the analysis and use of either small, focused data sets, to large compound libraries. Analysis and handling of the newly constructed chemical structures include the storage, mining, integration of the constructed structures with other existing data sets, and curation.
Articles
2020
In Silico Structure Generation: Recent Developments, Applications, and Challenges
Edited by José L. Medina-Franco, Emma Schymanski, Christoph Steinbeck
Collection published: 27 October 2020
Citation Typing Ontology (CiTO) Pilot
Edited by Egon Willighagen
Collection published: 28 July 2020
2019
Big Data in Chemistry
Edited by Igor V. Tetko
Collection published: 8 August 2019
Proceedings of the 11th International Conference on Chemical Structures
Edited by Gerard van Westen and Markus Wagener
Collection published: 14 February 2019
Programming Languages for Chemical Information
Edited by Rajarshi Guha
Collection published: 5 February 2019
2018
BioCreative V.5
Edited by Martin Krallinger, Obdulia Rabal, Anália Lourenço, Alfonso Valencia
Collection published: 14 December 2018
Novel applications of machine learning in cheminformatics
Edited by Ola Spjuth
Collection published: 21 February 2018
2015
Cross journal collection
Jean-Claude Bradley Memorial Series
Edited by Andrew SID Lang, Antony Williams
Collection published: 22 March 2015
2013
6th Joint Sheffield Conference on Chemoinformatics
Collection published: 29 July 2013
2012
The IUPAC International Chemical Identifier (InChI) and its influence on the domain of chemical information
Edited by Antony Williams
Collection published: 13 December 2012
Semantic physical science
Edited by Henry Rzepa, Peter Murray-Rust
Collection published: 3 August 2012
2011
Visions of a semantic molecular future
Collection published: 14 October 2011
RDF technologies in chemistry
Edited by Egon Willighagen, Martin Paul Braendle
Collection published: 13 May 2011
PubChem3D
Collection published: 27 January 2011
2021
What is the role of cheminformatics in a pandemic?
Rajarshi Guha, Egon Willighagen, Barbara Zdrazil & Nina Jeliazkova
2 March 2021
2020
From Big Data to Artificial Intelligence: chemoinformatics meets new challenges
Igor V. Tetko & Ola Engkvist
18 December 2020
Adoption of the Citation Typing Ontology by the Journal of Cheminformatics
Egon Willighagen
28 July 2020
Learning cheminformatics
Rajarshi Guha & Egon Willighagen
20 January 2020
2019
Journal of Cheminformatics, ORCID, and GitHub
Egon Willighagen, Nina Jeliazkova & Rajarshi Guha
8 July 2019
Implementing cheminformatics
Rajarshi Guha
5 February 2019
2018
Novel applications of Machine Learning in cheminformatics
Ola Spjuth
6 September 2018
2017
Helping to improve the practice of cheminformatics
Rajarshi Guha & Egon Willighagen
2013
Cheminformatics for the masses: a chance to increase educational opportunities for the next generation of cheminformaticians
David J Wild
5 July 2013
2012
InChI: connecting and navigating chemistry
Antony J Williams
13 December 2012
Semantic physical science
Peter Murray-Rust & Henry S Rzepa
3 August 2012
2011
Semantic science and its communication - a personal view
Peter Murray-Rust
14 October 2011
Resource description framework technologies in chemistry
Egon L Willighagen & Martin P Brändle
13 May 2011
2009
Grand challenges for cheminformatics
David J Wild
Upcoming Special Issues
Learn more about open Calls for Papers and upcoming Special Issues here.
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Featured Collection - Big Data in Chemistry
The increasing volume of biomedical data in chemistry and life sciences requires the development of new methodologies and approaches for their analysis. Artificial intelligence (AI) and machine learning, especially neural networks, are increasingly used in the chemical industry, in particular with respect to big data. The collection presents progress and exemplifies the current needs, trends and requirements for machine learning in chemical data analysis.
Steve Buissinne from Pixabay (CC0)
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. To learn more about how, please click through to our dedicated page on the CiTO pilot and to see published papers already participating in the pilot.
COVID-19 and peer review
As a result of the significant disruption that is being caused by the COVID-19 pandemic we are very aware that many researchers will have difficulty in meeting the timelines associated with our peer review process during normal times. Please do let us know if you need additional time. Our systems will continue to remind you of the original timelines but we intend to be highly flexible at this time.
Benefit from our free funding service
We offer a free open access support service to make it easier for you to discover and apply for article-processing charge (APC) funding.
Learn more here.
Editor profiles
Editors-in-Chief:
Egon Willighagen is a researcher in the BiGCaT Department for Bioinformatics and teacher at Maastricht University in the Netherlands.
Rajarshi Guha is the Associate Director of Informatics at Vertex Pharmaceuticals, USA, where he leads the cheminformatics group that is responsible for informatics needs in high throughput screening.
Associate Editors:
Nina Jeliazkova is a founder and co-owner of Ideaconsult Ltd, Bulgaria, and has been technical manager of the company since 2009.
Barbara Zdrazil is a group leader at the University of Vienna, Austria, and works as a safety data scientist for the European Bioinformatics Institute (EMBL-EBI), UK.
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47 days to first decision for reviewed manuscripts only
32 days to first decision for all manuscripts
124 days from submission to acceptance
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