About Journal of Cheminformatics

This page includes information about the aims and scope of Journal of Cheminformatics, editorial policies, open access, the peer review process and other information. For details of how to prepare and submit a manuscript through the online submission system, please see the instructions for authors.

Aims & scope

Journal of Cheminformatics is an open access journal publishing original peer-reviewed research in all aspects of cheminformatics and molecular modelling.

Coverage includes, but is not limited to:

• chemical information systems, software and databases, and molecular modelling
• chemical structure representations and their use in structure, substructure, and similarity searching of chemical substance and chemical reaction databases
• computer and molecular graphics, computer-aided molecular design, expert systems, QSAR, and data mining techniques

Open access

All articles published by Journal of Cheminformatics are made freely and permanently accessible online immediately upon publication, without subscription charges or registration barriers. Further information about open access can be found here.

Authors of articles published in Journal of Cheminformatics are the copyright holders of their articles and have granted to any third party, in advance and in perpetuity, the right to use, reproduce or disseminate the article, according to the Chemistry Central copyright and license agreement.

Article-processing charges

Open access publishing is not without costs. Journal of Cheminformatics therefore levies an article-processing charge of £806/$1280/€980 for each article accepted for publication. We routinely waive charges for authors from low-income countries. Generally, if the submitting author's institution is a Member the cost of the article-processing charge is covered by the membership, and no further charge is payable. In the case of authors whose institutions are Supporter Members, however, a discounted article-processing charge is payable by the author. For further details, see our article-processing charge page. A limited number of waivers for article-processing charges are also available at the editors' discretion, and authors wishing to apply for these waivers should contact the editors.

Indexing services

Journal of Cheminformatics's articles are archived in e-Depot, the National Library of the Netherlands' digital archive of all electronic publications. The journal is also participating in the British Library's e-journals pilot project, and plans to deposit copies of all articles with the British Library.

Chemistry Central is working closely with Thomson Reuters (ISI) to ensure that citation analysis of articles published in Journal of Cheminformatics will be available.

Publication and peer review process

Authors will be able to check the progress of their manuscript through the submission system at any time by logging into My Journal of Cheminformatics, a personalized section of the site.

Portability of peer review

In order to support efficient and thorough peer review, we aim to reduce the number of times a manuscript is re-reviewed after rejection from Journal of Cheminformatics, thereby speeding up the publication process and reducing the burden on peer reviewers. Therefore, please note that, if a manuscript is not accepted for publication in Journal of Cheminformatics and the authors choose to submit a revised version to another Chemistry Central journal, we will pass the reviews on to the other journal's editors at the authors' request. We will reveal the reviewers' names to the handling editor for editorial purposes unless reviewers let us know when they return their report that they do not wish us to share their report with another Chemistry Central journal.

Reprints

High-quality, bound reprints can be purchased for all articles published. Please see our reprints website for further information about ordering reprints, and to enquire about further details, including fees, please contact BioMed Central's reprint service.

Supplements

Journal of Cheminformatics will consider supplements based on proceedings (full articles or meeting abstracts), reviews or research. All articles submitted for publication in supplements are subject to peer review. Published supplements are fully searchable and freely accessible online and can also be produced in print. All full length articles (proceedings, reviews or research articles) are indexed by PubMed. PubMed displays the title of the supplement only in the case of meeting abstract collections. For further information, please contact us.

Editorial policies

Any manuscript, or substantial parts of it, submitted to the journal must not be under consideration by any other journal. In general, the manuscript should not have already been published in any journal or other citable form, although it may have been deposited on a preprint server. Information on duplicate/overlapping publications can be found here. Authors are required to ensure that no material submitted as part of a manuscript infringes existing copyrights, or the rights of a third party.

Correspondence concerning articles published in Journal of Cheminformatics is encouraged. A 'post a comment' feature is available on all articles published by Journal of Cheminformatics. Comments will be moderated by the editorial office (see our Comment policy for further information) and linked to the full-text version of the article, if suitable.

Editorial standards

Chemistry Central is a member of the Committee on Publication Ethics (COPE).

Characterization of compounds and Data deposition

For known compounds used in syntheses the methods of preparation and the literature data used to confirm the material's identity should be cited. For all new compounds sufficient evidence to establish the identity and the degree of purity of the compound must be provided.

Experimental data should generally be included within the Additional Material rather than within the main text of the paper and should include relevant yields, elemental analyses, spectral data, melting point analyses and other data. Chemical structure data, X-ray crystallographic data, atomic co-ordinates, nucleic acid sequences and protein sequences should be deposited in an appropriate open access database in time for any relevant accession numbers to be included in the published data.

Submission of a manuscript to Journal of Cheminformatics implies that readily reproducible materials described in the manuscript, including all relevant raw data, will be freely available to any scientist wishing to use them for non-commercial purposes.

Any 'in press' articles cited within the references and necessary for the reviewers' assessment of the manuscript should be made available if requested by the editorial office.

Chemical structures and assays

Structures of chemical substances and in reaction schemes should be produced using structure drawing software such as ChemDraw. Chemical substances can be deposited with PubChem Substance and/or PubChem Compound. Bioactivity screens of chemical substances can be deposited with PubChem BioAssay.

X-ray crystallographic data

A Crystallographic Information File (CIF) for any crystal structure should be included. CIFs should be provided as an additional file, and should be accompanied by a checkCIF report and include an explanation for any level A alerts in the report. checkCIF reports can be obtained by using the International Union of Crystallography's free checkCif service.

Crystallographic data should be deposited in the Cambridge Structural Database (free deposition; pay access) and the Crystallography Open Database (free access), and relevant accession numbers should be included in the published data.

Spectral data

Copies of spectra used in the characterization of compounds should be reproduced as figures in the Additional Materials. Copies of spectra in JCAMP-DX format which can be viewed using JSpecView software can also be submitted as additional files. Spectra can be deposited in an appropriate open access database; for example NMR spectra should be deposited in NMRShiftDB.

Nucleotide sequences

Nucleotide sequences can be deposited with the DNA Data Bank of Japan (DDBJ), European Molecular Biology Laboratory (EMBL/EBI) Nucleotide Sequence Database, or GenBank (National Center for Biotechnology Information).

Protein sequences and structures

Protein sequences can be deposited with SwissProt or the Protein Information Resource (PIR). Protein structures can be deposited with one of the members of the Worldwide Protein Data Bank. Nucleic Acids structures can be deposited with the Nucleic Acid Database at Rutgers.

The accession numbers of any nucleic acid sequences, protein sequences or atomic coordinates cited in the manuscript should be provided, in square brackets with the corresponding database name; for example, [EMBL:AB026295, EMBL:AC137000, DDBJ:AE000812, GenBank:U49845, PDB:1BFM, Swiss-Prot:Q96KQ7, PIR:S66116].

The databases for which we can provide direct links are: EMBL Nucleotide Sequence Database (EMBL), DNA Data Bank of Japan (DDBJ), GenBank at the NCBI (GenBank), Protein Data Bank (PDB), Protein Information Resource (PIR) and the Swiss-Prot Protein Database (Swiss-Prot).

Appeals and complaints

Authors who wish to appeal a rejection or make a complaint should, in the first instance, contact the Editor-in-Chief who will provide details of the journal's complaints procedure.

Competing interests

Journal of Cheminformatics requires authors to declare any competing financial or other interest in relation to their work. All competing interests that are declared will be listed at the end of published articles. Where an author gives no competing interests, the listing will read 'The author(s) declare that they have no competing interests'.

Plagiarism detection

Journal of Cheminformatics's publisher, Chemistry Central, is a member of the CrossCheck plagiarism detection initiative. In cases of suspected plagiarism CrossCheck is available to the editors of Journal of Cheminformatics to detect instances of overlapping and similar text in submitted manuscripts. CrossCheck is a multi-publisher initiative allowing screening of published and submitted content for originality.

Citing articles in Journal of Cheminformatics

Articles in Journal of Cheminformatics should be cited in the same way as articles in a traditional journal. Because articles are not printed, they do not have page numbers; instead, they are given a unique article number.

Article citations follow this format:

Authors: Title. J Cheminf [year], [volume number]:[article number].

e.g. Roberts LD, Hassall DG, Winegar DA, Haselden JN, Nicholls AW, Griffin JL: Increased hepatic oxidative metabolism distinguishes the action of Peroxisome Proliferator-Activated Receptor delta from Peroxisome Proliferator-Activated Receptor gamma in the Ob/Ob mouse. J Cheminf 2009, 1:115.

refers to article 115 from Volume 1 of the journal.

Why publish your article in Journal of Cheminformatics?

High visibility

Journal of Cheminformatics's open access policy allows maximum visibility of articles published in the journal as they are available to a wide, global audience. Articles that have been especially highly accessed are highlighted with a 'Highly accessed' graphic, which appears on the journal's contents pages and search results.

Speed of publication

Journal of Cheminformatics offers a fast publication schedule whilst maintaining rigorous peer review; all articles must be submitted online, and peer review is managed fully electronically (articles are distributed in PDF form, which is automatically generated from the submitted files). Articles are published with their final citation immediately upon acceptance in a provisional PDF form. The article will subsequently be published in both fully browsable web form, and as a formatted PDF; the article will then be available through Journal of Cheminformatics, Chemistry Central and PubMed Central and will also be included in PubMed.

Flexibility

Online publication in Journal of Cheminformatics gives authors the opportunity to publish large datasets, large numbers of color illustrations and moving pictures, to display data in a form that can be read directly by other software packages so as to allow readers to manipulate the data for themselves, and to create all relevant links (for example, to PubMed, to sequence and other databases, and to other papers).

Promotion and press coverage

Articles published in Journal of Cheminformatics are included in article alerts and regular email updates. Some may be included in abstract books mailed to academics and are highlighted on Journal of Cheminformatics's pages and on the Chemistry Central homepage.

In addition, articles published in Journal of Cheminformatics may be promoted by press releases to the general or scientific press. These activities increase the exposure and number of accesses for articles published in Journal of Cheminformatics.

Copyright

Authors of articles published in Journal of Cheminformatics retain the copyright of their articles and are free to reproduce and disseminate their work (for further details, see the Chemistry Central copyright and license agreement).

For further information about the advantages of publishing in a journal from Chemistry Central, please click here.