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Instructions for authors

Database

See 'About this journal' for descriptions of different article types and information about policies and the refereeing process.

Criteria

Database should describe a novel database likely to be of broad utility. The database must be readily accessible and data within the database should be attributed to a source.

Should a description of a database be submitted as a Database or a Research article?

An article describing a database but also including research that merits publication in its own right should either be submitted as a Research article or should be split into a Research article and a separate Database.

Availability of Database to reviewers and other researchers

The Database described in the manuscript must be available for testing by reviewers in a way that preserves their anonymity. If published, the described databases must be accessible by any researcher wishing to use them for non-commercial purposes, without restrictions such as the need for a material transfer agreement. We may require an archive copy of the database to be held by BioMed Central as a safeguard.

Submission process

Manuscripts must be submitted by one of the authors of the manuscript, and should not be submitted by anyone on their behalf. The submitting author takes responsibility for the article during submission and peer review. Chemistry Central journals are covered by the Membership scheme.

Please note that Journal of Cheminformatics levies an article-processing charge on all accepted Database; if the submitting author's institution is a Chemistry Central member the cost of the article-processing charge may be covered by the membership (see About page for detail). Please note that the membership is only automatically recognised on submission if the submitting author is based at the member institution.

To facilitate rapid publication and to minimize administrative costs, Journal of Cheminformatics prefers online submission.

Files can be submitted as a batch, or one by one. The submission process can be interrupted at any time; when users return to the site, they can carry on where they left off.

See below for examples of word processor and graphics file formats that can be accepted for the main manuscript document by the online submission system. Additional files of any type, such as movies, animations, or original data files, can also be submitted as part of the manuscript.

During submission you will be asked to provide a cover letter. Use this to explain why your manuscript should be published in the journal, to elaborate on any issues relating to our editorial policies in the 'About Journal of Cheminformatics' page, and to declare any potential competing interests. You will be also asked to provide the contact details (including email addresses) of potential peer reviewers for your manuscript. These should be experts in their field, who will be able to provide an objective assessment of the manuscript. Any suggested peer reviewers should not have published with any of the authors of the manuscript within the past five years, should not be current collaborators, and should not be members of the same research institution. Suggested reviewers will be considered alongside potential reviewers recommended by the Editor-in-Chief and/or Editorial Board members.

Assistance with the process of manuscript preparation and submission is available from Chemistry Central customer support team.

We also provide a collection of links to useful tools and resources for scientific authors on our Useful Tools page.

File formats

The following word processor file formats are acceptable for the main manuscript document:

  • Microsoft word (DOC, DOCX)
  • Rich text format (RTF)
  • Portable document format (PDF)
  • TeX/LaTeX (use Chemistry Central's TeX template)
  • DeVice Independent format (DVI)

TeX/LaTeX users: Please use BioMed Central's TeX template and BibTeX stylefile if you use TeX format. During the TeX submission process, please submit your TeX file as the main manuscript file and your bib/bbl file as a dependent file. Please also convert your TeX file into a PDF and submit this PDF as an additional file with the name 'Reference PDF'. This PDF will be used by internal staff as a reference point to check the layout of the article as the author intended. Please also note that all figures must be coded at the end of the TeX file and not inline.

If you have used another template for your manuscript, or if you do not wish to use BibTeX, then please submit your manuscript as a DVI file. We do not recommend converting to RTF.

For all TeX submissions, all relevant editable source must be submitted during the submission process. Failing to submit these source files will cause unnecessary delays in the publication procedures.

Publishing Datasets

Through a special arrangement with LabArchives, LLC, authors submitting manuscripts to Journal of Cheminformatics can obtain a complimentary subscription to LabArchives with an allotment of 100MB of storage. LabArchives is an Electronic Laboratory Notebook which will enable scientists to share and publish data files in situ; you can then link your paper to these data. Data files linked to published articles are assigned digital object identifiers (DOIs) and will remain available in perpetuity. Use of LabArchives or similar data publishing services does not replace preexisting data deposition requirements, such as for nucleic acid sequences, protein sequences and atomic coordinates.

Instructions on assigning DOIs to datasets, so they can be permanently linked to publications, can be found on the LabArchives website. Use of LabArchives’ software has no influence on the editorial decision to accept or reject a manuscript.

Authors linking datasets to their publications should include an Availability of supporting data section in their manuscript and cite the dataset in their reference list.

Preparing main manuscript text

General guidelines of the journal's style and language are given below.

Manuscript sections for Database

Manuscripts for Database submitted to Journal of Cheminformatics should be divided into the following sections (in this order):

The Accession Numbers of any nucleic acid sequences, protein sequences or atomic coordinates cited in the manuscript should be provided, in square brackets and include 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).

Title page

The title page should list the title of the article, the full names, institutional addresses, email addresses for all authors. The corresponding author should also be indicated.

Abstract

The Abstract of the manuscript should not exceed 350 words and must be structured into separate sections: Background, the context and purpose of the study; Description, the main findings; Conclusions, brief summary and potential implications.

Please do not use abbreviations or references in the abstract. Please see also our guide for writing an easily accessible abstract.

Keywords

Three to ten keywords representing the main content of the article.

Background

The Background section should be written in a way that is accessible to researchers without specialist knowledge in that area and must clearly state - and, if helpful, illustrate - the background to the research and its aims. It should clearly describe the perceived need for the database, mentioning forerunners and competitors, and stating its potential value.

Construction and content

The database schema and implementation should be described in this section, together with information on data sources, the informatics of data generation and quality control.

Utility and Discussion

These may be combined into a single section or presented separately. They may also be broken into subsections with short, informative headings. The user interface should be described and a discussion of the intended uses of the database, and the benefits that are envisioned, should be included, together with data on how its performance and functionality compare with and improve on functionally similar existing databases. A case study of the use of the database may be presented. The planned future development of new features, if any, should be mentioned.

Conclusions

This should state clearly the main conclusions of the article and give a clear explanation of the importance and relevance of the database.

Availability and requirements

This should state the web/ftp address at which the database is available and any restrictions to its use by non-academics.

List of abbreviations

If abbreviations are used in the text they should be defined in the text at first use, and a list of abbreviations can be provided, which should precede the competing interests and authors' contributions.

Competing interests

A competing interest exists when your interpretation of data or presentation of information may be influenced by your personal or financial relationship with other people or organizations. Authors must disclose any financial competing interests; they should also reveal any non-financial competing interests that may cause them embarrassment were they to become public after the publication of the manuscript.

Authors are required to complete a declaration of competing interests. 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'.

When completing your declaration, please consider the following questions:

Financial competing interests

  • In the past five years have you received reimbursements, fees, funding, or salary from an organization that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Is such an organization financing this manuscript (including the article-processing charge)? If so, please specify.
  • Do you hold any stocks or shares in an organization that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? If so, please specify.
  • Do you hold or are you currently applying for any patents relating to the content of the manuscript? Have you received reimbursements, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript? If so, please specify.
  • Do you have any other financial competing interests? If so, please specify.

Non-financial competing interests

Are there any non-financial competing interests (political, personal, religious, ideological, academic, intellectual, commercial or any other) to declare in relation to this manuscript? If so, please specify.

If you are unsure as to whether you, or one your co-authors, has a competing interest please discuss it with the editorial office.

Authors' contributions

In order to give appropriate credit to each author of a paper, the individual contributions of authors to the manuscript should be specified in this section.

According to ICMJE guidelines, An 'author' is generally considered to be someone who has made substantive intellectual contributions to a published study. To qualify as an author one should 1) have made substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data; 2) have been involved in drafting the manuscript or revising it critically for important intellectual content; 3) have given final approval of the version to be published; and 4) agree to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. Each author should have participated sufficiently in the work to take public responsibility for appropriate portions of the content. Acquisition of funding, collection of data, or general supervision of the research group, alone, does not justify authorship.

We suggest the following kind of format (please use initials to refer to each author's contribution): AB carried out the catalyst design and ligand screening studies. JY carried out the synthesis, purification and characterization of the compounds. MT carried out the computational experiments. FG conceived of the study, and participated in its design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.

All contributors who do not meet the criteria for authorship should be listed in an acknowledgements section. Examples of those who might be acknowledged include a person who provided purely technical help, writing assistance, or a department chair who provided only general support.

Description of additional data files (if any)

Please provide a brief summary of the additional data files that are accompany the manuscript; this should be done in the form of an "Additional data file" section; the details and descriptions you have provided in the additional data file could be included in this section. This should be in the format of the following example:

"The following additional data are available with the online version of this paper. Additional data file 1 is a table listing the reaction optimization conditions. Additional data file 2 contains full characterization data for the compounds synthesized. Additional data file 3 contains the CIF for compound 1... etc."

Authors' information

You may choose to use this section to include any relevant information about the author(s) that may aid the reader's interpretation of the article, and understand the standpoint of the author(s). This may include details about the authors' qualifications, current positions they hold at institutions or societies, or any other relevant background information. Please refer to authors using their initials. Note this section should not be used to describe any competing interests.

Acknowledgements

Please acknowledge anyone who contributed towards the article by making substantial contributions to conception, design, acquisition of data, or analysis and interpretation of data, or who was involved in drafting the manuscript or revising it critically for important intellectual content, but who does not meet the criteria for authorship. Please also include the source(s) of funding for each author, and for the manuscript preparation. Authors must describe the role of the funding body, if any, in design, in the collection, analysis, and interpretation of data; in the writing of the manuscript; and in the decision to submit the manuscript for publication. Please also acknowledge anyone who contributed materials essential for the study. If a language editor has made significant revision of the manuscript, we recommend that you acknowledge the editor by name, where possible.

Authors should obtain permission to acknowledge from all those mentioned in the Acknowledgements section.

Endnotes

Endnotes should be designated within the text using a superscript lowercase letter and all notes (along with their corresponding letter) should be included in the Endnotes section. Please format this section in a paragraph rather than a list.

References

All references, including URLs, must be numbered consecutively, in square brackets, in the order in which they are cited in the text, followed by any in tables or legends. Each reference must have an individual reference number. Please avoid excessive referencing. If automatic numbering systems are used, the reference numbers must be finalized and the bibliography must be fully formatted before submission.

Only articles and abstracts that have been published or are in press, or are available through public e-print/preprint servers, may be cited; unpublished abstracts, unpublished data and personal communications should not be included in the reference list, but may be included in the text and referred to as "unpublished observations" or "personal communications" giving the names of the involved researchers. Obtaining permission to quote personal communications and unpublished data from the cited colleagues is the responsibility of the author. Footnotes are not allowed, but endnotes are permitted. Journal abbreviations follow Index Medicus/MEDLINE. Citations in the reference list should include all named authors, up to the first 30 before adding 'et al.'..

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.

Examples of the Journal of Cheminformatics reference style are shown below. Please ensure that the reference style is followed precisely; if the references are not in the correct style they may have to be retyped and carefully proofread.

Examples of the Journal of Cheminformatics reference style


Article within a journal
Mihovilovic MD, Leisch HG, Mereiter K: Microwave-mediated intramolecular Diels-Alder cyclization of biodihydroxylated benzoic acid derivatives. Tetrahedron Lett 2004, 45:7087-7090

Article within a journal supplement
Fubini B: Surface reactivity in the pathogenic response to particulates. Environ Health Perspect 1997, 105(Suppl 5):1013–1020.

In press article
Van Damme S, Langenaeker W, Bultinck P: Prediction of Blood-brain partitioning: a model based on ab initio calculated quantum chemical descriptors. Journal of Molecular graphics and modeling, in press

Published abstract
Herres-Pawlis S, Haase R, Bienemann O: Dissecting the role of guanidine copper complexes in atom transfer radical polymerization by density functional theory [abstract]. J Cheminf 2011, 3(Suppl1):P28.

Article within conference proceedings
Schurath U, Wipprecht V: Reactions of peroxiacyl radicals. In Proceedings of the 1st European Symposium on the Physico-Chemical Behavior of Atmospheric Pollutants, Concerted Action EEC-COST 61A bis. Edited by Versino B. Commission European Community; 1980:157-166.

Book chapter, or article within a book
Ellis GP: The chemistry of heterocyclic compounds. In Chromene, Chromanes and Chromone. Volume 2. Edited by Weissberger A, Taylor ECE. John Wiley: New York; 1977:13

Whole issue of journal
Weckhuysen B (Ed): In-situ characterisation of heterogeneous catalysts. In Chem Soc Rev 2010, 39:4541-5072.

Whole conference proceedings
Brown S, Clarke I, Williams P (Eds): Proceedings of the 14th International Symposium on Ceramics in Medicine. Palm Springs, California, USA; 2001.

Complete book
Görög S: Ultraviolet-Visible Spectrophotometry in Pharmaceutical Analysis. CRC Press, New York; 1994.

Monograph or book in a series
Fujiki M: Helix Generation, Amplification, Switching, and Memory of Chromophoric Polymers. In Amplification of Chirality. Edited by Soai K. Springer: Heidelberg; 2008:119-186. [Balzani V, deMeijere A, Houk KN, Kessler J, Lehn JM, Ley SV, Schreiber SL, Thiem J, Trost BM, Vögtle F, Yamamoto H (Series Editors): Topics in Current Chemistry, vol 284.]

Book with institutional author
IUPAC: Nomenclature of Organic Chemistry. Pergamon Press, Oxford; 1979.

PhD thesis
Ravi Kishore VVN: Photo-luminescence and electron-luminescence of hydroxy quinoline based organic semiconductors. PhD Thesis. Tata Institute of Fundamental Research, Department of Chemical Sciences; 2004.

Link / URL
The Chemistry Development Kit [http://sourceforge.net/projects/cdk]

Link / URL with author(s)
Pichon A: Debating cyclobutadiene. [http:// blogs.nature.com/thescepticalchymist/2010/11/debating_cyclobutadiene.html]

Dataset with persistent identifier
Bradley JC, Neylon C, Guha R, Williams AJ, Hooker B, Lang ASID, Friesen B, Bohinski T, Bulger D, Federici M, Hale J, Mancinelli J, Mirza KB, Moritz MJ, Rein D, Tchakounte C, Truong HT (2010): Open Notebook Science Challenge: Solubilities of Organic Compounds in Organic Solvents. Nature Precedings. http://dx.doi.org/10.1038/npre.2010.4243.3

Preparing figures and schemes

Figures and schemes should be provided as separate files and should not be included in the main text of the submitted manuscript, although they may also be embedded in appropriate locations in the text file. Figures should always be cited in text in consecutive numerical order. Schemes must only be embedded in the text file. Each figure or scheme should comprise only a single file. There is no charge for the use of color.

Please read our figure preparation guidelines for detailed instructions on maximising the quality of your figures, and schemes.

Illustrations should be provided as separate files, not embedded in the text file. Each figure should include a single illustration and should fit on a single page in portrait format. If a figure consists of separate parts, it is important that a single composite illustration file be submitted which contains all parts of the figure. There is no charge for the use of color figures.

Please read our figure preparation guidelines for detailed instructions on maximising the quality of your figures.

Formats

The following file formats can be accepted:

  • PDF (preferred format for diagrams)
  • DOCX/DOC (single page only)
  • PPTX/PPT (single slide only)
  • EPS
  • PNG (preferred format for photos or images)
  • TIFF
  • JPEG
  • BMP
  • CDX (ChemDraw: preferred format for chemical structures)
  • SKC, TGF (ISIS/Draw, Symyx Draw: Accelrys Draw preferred format for chemical structures)

Figure legends

The legends should be included in the main manuscript text file at the end of the document, rather than being a part of the figure file. For each figure, the following information should be provided: Figure number (in sequence, using Arabic numerals - i.e. Figure 1, 2, 3 etc); short title of figure (maximum 15 words); detailed legend, up to 300 words.

Please note that it is the responsibility of the author(s) to obtain permission from the copyright holder to reproduce figures or tables that have previously been published elsewhere.

Preparing tables

Each table should be numbered and cited in sequence using Arabic numerals (i.e. Table 1, 2, 3 etc.). Tables should also have a title (above the table) that summarizes the whole table; it should be no longer than 15 words. Detailed legends may then follow, but they should be concise. Tables should always be cited in text in consecutive numerical order.

Smaller tables considered to be integral to the manuscript can be pasted into the end of the document text file, in A4 portrait or landscape format. These will be typeset and displayed in the final published form of the article. Such tables should be formatted using the 'Table object' in a word processing program to ensure that columns of data are kept aligned when the file is sent electronically for review; this will not always be the case if columns are generated by simply using tabs to separate text. Columns and rows of data should be made visibly distinct by ensuring that the borders of each cell display as black lines. Commas should not be used to indicate numerical values. Color and shading may not be used; parts of the table can be highlighted using symbols or bold text, the meaning of which should be explained in a table legend. Tables should not be embedded as figures or spreadsheet files.

Larger datasets or tables too wide for a portrait page can be uploaded separately as additional files. Additional files will not be displayed in the final, laid-out PDF of the article, but a link will be provided to the files as supplied by the author.

Tabular data provided as additional files can be uploaded as an Excel spreadsheet (.xls or .xlsx) or comma separated values (.csv). As with all files, please use the standard file extensions.

Preparing additional files

Although Journal of Cheminformatics does not restrict the length and quantity of data included in an article, we encourage authors to provide datasets, tables, movies, or other information as additional files.

Please note: All Additional files will be published along with the article. Do not include files such as certificates of language editing, or revised versions of the main manuscript document with tracked changes. Such files should be sent by email to editor@jcheminf.com, quoting the Manuscript ID number.

Results that would otherwise be indicated as "data not shown" can and should be included as additional files. Since many weblinks and URLs rapidly become broken, Journal of Cheminformatics requires that supporting data are included as additional files, or deposited in a recognized repository. Please do not link to data on a personal/departmental website. The maximum file size for additional files is 20 MB each, and files will be virus-scanned on submission.

Additional files can be in any format, and will be downloadable from the final published article as supplied by the author. We recommend CSV rather than PDF for tabular data.

Certain supported files formats are recognized and can be displayed to the user in the browser. These include most movie formats (for users with the Quicktime plugin), mini-websites prepared according to our guidelines, chemical structure files (MOL, PDB), geographic data files (KML).

If additional material is provided, please list the following information in a separate section of the manuscript text:

  • File name (e.g. Additional file 1)
  • File format including the correct file extension for example .pdf, .xls, .txt, .pptx (including name and a URL of an appropriate viewer if format is unusual)
  • Title of data
  • Description of data

Additional files should be named "Additional file 1" and so on and should be referenced explicitly by file name within the body of the article, e.g. 'An additional movie file shows this in more detail [see Additional file 1]'.

Additional file formats

Ideally, file formats for additional files should not be platform-specific, and should be viewable using free or widely available tools. The following are examples of suitable formats.

  • Additional documentation
    • PDF (Adode Acrobat)
  • Animations
    • SWF (Shockwave Flash)
  • Movies
    • MP4 (MPEG 4)
    • MOV (Quicktime)
  • Tabular data
    • XLS, XLSX (Excel Spreadsheet)
    • CSV (Comma separated values)

As with figure files, files should be given the standard file extensions.

Mini-websites

Small self-contained websites can be submitted as additional files, in such a way that they will be browsable from within the full text HTML version of the article. In order to do this, please follow these instructions:

  1. Create a folder containing a starting file called index.html (or index.htm) in the root.
  2. Put all files necessary for viewing the mini-website within the folder, or sub-folders.
  3. Ensure that all links are relative (ie "images/picture.jpg" rather than "/images/picture.jpg" or "http://yourdomain.net/images/picture.jpg" or "C:\Documents and Settings\username\My Documents\mini-website\images\picture.jpg") and no link is longer than 255 characters.
  4. Access the index.html file and browse around the mini-website, to ensure that the most commonly used browsers (Internet Explorer and Firefox) are able to view all parts of the mini-website without problems, it is ideal to check this on a different machine.
  5. Compress the folder into a ZIP, check the file size is under 20 MB, ensure that index.html is in the root of the ZIP, and that the file has .zip extension, then submit as an additional file with your article.

Style and language

General

Currently, Journal of Cheminformatics can only accept manuscripts written in English. Spelling should be US English or British English, but not a mixture.

There is no explicit limit on the length of articles submitted, but authors are encouraged to be concise.

Journal of Cheminformatics will not edit submitted manuscripts for style or language; reviewers may advise rejection of a manuscript if it is compromised by grammatical errors. Authors are advised to write clearly and simply, and to have their article checked by colleagues before submission. In-house copyediting will be minimal. Non-native speakers of English may choose to make use of a copyediting service.

Help and advice on scientific writing

The abstract is one of the most important parts of a manuscript. For guidance, please visit our page on Writing titles and abstracts for scientific articles.

Tim Albert has produced for Chemistry Central a list of tips for writing a scientific manuscript. American Scientist also provides a list of resources for science writing.

Abbreviations

Abbreviations should be used as sparingly as possible. They should be defined when first used and a list of abbreviations can be provided following the main manuscript text.

Typography

  • Please use double line spacing.
  • Type the text unjustified, without hyphenating words at line breaks.
  • Use hard returns only to end headings and paragraphs, not to rearrange lines.
  • Capitalize only the first word, and proper nouns, in the title.
  • All pages should be numbered.
  • Use the Journal of Cheminformatics reference format.
  • Footnotes are not allowed, but endnotes are permitted.
  • Please do not format the text in multiple columns.
  • Greek and other special characters may be included. If you are unable to reproduce a particular special character, please type out the name of the symbol in full. Please ensure that all special characters used are embedded in the text, otherwise they will be lost during conversion to PDF.

Units

SI units should be used throughout (liter and molar are permitted, however).

Mathematical notation

Please use the standard mathematical notation for formulae, symbols, etc.:

  • Italic for single letters that denote mathematical constants, variables, and unknown quantities
  • Roman/upright for numerals, operators, and punctuation, and commonly defined functions or abbreviations, e.g., cos, det, e or exp, lim, log, max, min, sin, tan, d (for derivative)
  • Bold italics for vectors, tensors, and matrices.