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Educational Article

Criteria

Journal of Cheminformatics publishes Educational articles that describe an aspect of cheminformatics. This aspect may be about cheminformatics theory and methods, but also like a tutorial explaining in detail how to perform some cheminformatics. Journal of Cheminformatics will only publish research or software that taken an open science approach and that is entirely reproducible by third parties. All algorithms, data, and source code needed to follow the paper to the end should be open. This means that any datasets, software and algorithms that are required must be provided as supplemental materials, or be otherwise accessible without the need for registration, login or agreement with open license terms that allow use, modification, and redistribution, such as the Creative Commons licenses for data and text and OSI-approved Open Source Licenses for software.

Educational articles can roughly be divided into two categories:

  • Articles that describe in detail how common cheminformatics tasks can be performed using a particular open source toolkit. Data, standards, and code used in this type must be fully open source.
  • Articles that describe in detail a cheminformatics algorithms, must provide enough detail that it can be fully implemented with open source software. Data and standards used in this type must be fully open source.

Scientific contribution statement
The abstract should contain a section titled "Scientific Contribution". In this section, please use a maximum of 3 sentences to specifically highlight the scientific contributions that advance the field and what differentiates your contribution from prior work on this topic.

Preparing your manuscript

Title page

The title page should:

  • present a title that includes, if appropriate, the research design or for non-research studies: a description of what the article reports
  • list the full names and institutional addresses for all authors
    • if a collaboration group should be listed as an author, please list the group name as an author  and include the names of the individual members of the group in the “Acknowledgements” section in accordance with the instructions below
    • Large Language Models (LLMs), such as ChatGPT, do not currently satisfy our authorship criteria. Notably an attribution of authorship carries with it accountability for the work, which cannot be effectively applied to LLMs. Use of an LLM should be properly documented in the Methods section (and if a Methods section is not available, in a suitable alternative part) of the manuscript
  • indicate the corresponding author

Abstract

The abstract should briefly summarize the aim, findings or purpose of the article. Please minimize the use of abbreviations and do not cite references in the abstract.

Keywords

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

Main text

This should contain the body of the article, and may also be broken into subsections with short, informative headings.

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 should be provided.

Declarations

All manuscripts must contain the following sections under the heading 'Declarations':

  • Availability of data and materials
  • Competing interests
  • Funding
  • Authors' contributions
  • Acknowledgements
  • Authors' information (optional)

Please see below for details on the information to be included in these sections.

If any of the sections are not relevant to your manuscript, please include the heading and write 'Not applicable' for that section.

Availability of data and materials

For all journals, BioMed Central strongly encourages all datasets on which the conclusions of the manuscript rely to be either deposited in publicly available repositories (where available and appropriate) or presented in the main paper or additional supporting files, in machine-readable format (such as spreadsheets rather than PDFs) whenever possible. Please see the list of recommended repositories in our editorial policies.

For some journals, deposition of the data on which the conclusions of the manuscript rely is an absolute requirement. Please check the Criteria section for this article type (located at the top of this page) for journal specific policies.

For all journals, authors must include an “Availability of data and materials” section in their article detailing where the data supporting their findings can be found. If you do not wish to share your data, please state that data will not be shared, and state the reason.

For instructions on how to cite your data and format this section see preparation/style and formatting.

If you wish to co-submit a data note describing your data to be published in BMC Research Notes, you can do so by visiting our submission portal. Data notes support open data and help authors to comply with funder policies on data sharing. Co-published data notes will be linked to the research article the data support (example).

Competing interests

All financial and non-financial competing interests must be declared in this section. See our editorial policies for a full explanation of competing interests. If you are unsure whether you or any of your co-authors have a competing interest please contact the editorial office.

Funding

All sources of funding for the research reported should be declared. If the funder has a specific role in the conceptualization, design, data collection, analysis, decision to publish, or preparation of the manuscript, this should be declared.

Authors' contributions

The individual contributions of authors to the manuscript should be specified in this section.

Acknowledgements

Please acknowledge anyone who contributed towards the article who does not meet the criteria for authorship including anyone who provided professional writing services or materials.

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

See our editorial policies for a full explanation of acknowledgements and authorship criteria.

Group authorship: if you would like the names of the individual members of a collaboration Group to be searchable through their individual PubMed records (where applicable), please ensure that the title of the collaboration Group is included on the title page and in the submission system and also include collaborating author names as the last paragraph of the “Acknowledgements” section. Please add authors in the format First Name, Middle initial(s) (optional), Last Name. You can add institution or country information for each author if you wish, but this should be consistent across all authors.

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.

Footnotes

Footnotes should be designated within the text using a superscript number. It is not allowed to use footnotes for references/citations.

Examples of the Basic Springer reference style are shown below. 

See our editorial policies for author guidance on good citation practice.

Web links and URLs: All web links and URLs, including links to the authors' own websites, should be given a reference number and included in the reference list rather than within the text of the manuscript. They should be provided in full, including both the title of the site and the URL, as well as the date the site was accessed, in the following format: The Mouse Tumor Biology Database. http://tumor.informatics.jax.org/mtbwi/index.do. Accessed 20 May 2013. If an author or group of authors can clearly be associated with a web link, such as for weblogs, then they should be included in the reference.

​​​​​​​Example reference style:

Article within a journal

Smith J, Jones M Jr, Houghton L (1999) Future of health insurance. N Engl J Med 965:325-329.

Article by DOI (with page numbers)

Slifka MK, Whitton JL (2000) Clinical implications of dysregulated cytokine production. J Mol Med 78:74-80. doi:10.1007/s001090000086.

Article by DOI (before issue publication and with page numbers)

Slifka MK, Whitton JL (2000) Clinical implications of dysregulated cytokine production. J Mol Med. doi:10.1007/s001090000086.

Article in electronic journal by DOI (no paginated version)

Slifka MK, Whitton JL (2000) Clinical implications of dysregulated cytokine production. Dig J Mol Med. doi:10.1007/s801090000086.

Journal issue with issue editor

Smith J (ed) (1998) Rodent genes. Mod Genomics J 14(6):126-233.

Journal issue with no issue editor

Mod Genomics J (1998) Rodent genes. Mod Genomics J 14(6):126-233.

Book chapter, or an article within a book

Brown B, Aaron M (2001) The politics of nature. In: Smith J (ed) The rise of modern genomics, 3rd edn. Wiley, New York.

Complete book, authored

South J, Blass B (2001) The future of modern genomics. Blackwell, London.

Complete book, edited

Smith J, Brown B (eds) (2001) The demise of modern genomics. Blackwell, London.

Complete book, also showing a translated edition [Either edition may be listed first.]

Adorno TW (1966) Negative Dialektik. Suhrkamp, Frankfurt. English edition: Adorno TW (1973) Negative Dialectics (trans: Ashton EB). Routledge, London.

Chapter in a book in a series without volume titles

Schmidt H (1989) Testing results. In: Hutzinger O (ed) Handbook of environmental chemistry, vol 2E. Springer, Heidelberg, p 111.

Chapter in a book in a series with volume titles

Smith SE (1976) Neuromuscular blocking drugs in man. In: Zaimis E (ed) Neuromuscular junction. Handbook of experimental pharmacology, vol 42. Springer, Heidelberg, pp 593-660.

OnlineFirst chapter in a series (without a volume designation but with a DOI)

Saito, Yukio, and Hyuga, Hiroyuki. (2007) Rate equation approaches to amplification of enantiomeric excess and chiral symmetry breaking. Topics in Current Chemistry. doi:10.1007/128_2006_108.

Proceedings as a book (in a series and subseries)

Zowghi D (1996) A framework for reasoning about requirements in evolution. In: Foo N, Goebel R (eds) PRICAI'96: topics in artificial intelligence. 4th Pacific Rim conference on artificial intelligence, Cairns, August 1996. Lecture notes in computer science (Lecture notes in artificial intelligence), vol 1114. Springer, Heidelberg, p 157.

Article within conference proceedings with an editor (without a publisher)

Aaron M (1999) The future of genomics. In: Williams H (ed) Proceedings of the genomic researchers, Boston, 1999.

Article within conference proceedings without an editor (without a publisher)

Chung S-T, Morris RL (1978) Isolation and characterization of plasmid deoxyribonucleic acid from Streptomyces fradiae. In: Abstracts of the 3rd international symposium on the genetics of industrial microorganisms, University of Wisconsin, Madison, 4-9 June 1978.

Article presented at a conference

Chung S-T, Morris RL (1978) Isolation and characterization of plasmid deoxyribonucleic acid from Streptomyces fradiae. Paper presented at the 3rd international symposium on the genetics of industrial microorganisms, University of Wisconsin, Madison, 4-9 June 1978.

Patent

Norman LO (1998) Lightning rods. US Patent 4,379,752, 9 Sept 1998.

Dissertation

Trent JW (1975) Experimental acute renal failure. Dissertation, University of California.

Book with institutional author

International Anatomical Nomenclature Committee (1966) Nomina anatomica. Excerpta Medica, Amsterdam.

In press article

Major M (2007) Recent developments. In: Jones W (ed) Surgery today. Springer, Dordrecht (in press). 

Online document

Doe J (1999) Title of subordinate document. In: The dictionary of substances and their effects. Royal Society of Chemistry. Available via DIALOG. http://www.rsc.org/dose/title of subordinate document. Accessed 15 Jan 1999.

Online database

Healthwise Knowledgebase (1998) US Pharmacopeia, Rockville. http://www.healthwise.org. Accessed 21 Sept 1998.

Supplementary material/private homepage

Doe J (2000) Title of supplementary material. http://www.privatehomepage.com. Accessed 22 Feb 2000.

University site

Doe J (1999) Title of preprint. http://www.uni-heidelberg.de/mydata.html. Accessed 25 Dec 1999.

FTP site

Doe J (1999) Trivial HTTP, RFC2169. ftp://ftp.isi.edu/in-notes/rfc2169.txt. Accessed 12 Nov 1999.

Organization site

ISSN International Centre (2006) The ISSN register. http://www.issn.org. Accessed 20 Feb 2007.

Figures, tables and additional files

See General formatting guidelines for information on how to format figures, tables and additional files.

Submit manuscript

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Annual Journal Metrics

  • Citation Impact 2023
    Journal Impact Factor: 7.1
    5-year Journal Impact Factor: 9.3
    Source Normalized Impact per Paper (SNIP): 2.078
    SCImago Journal Rank (SJR): 1.745

    Speed 2023
    Submission to first editorial decision (median days): 8
    Submission to acceptance (median days): 116

    Usage 2023
    Downloads: 1,414,777
    Altmetric mentions: 1,319

    Citations
    Click here to see citation distribution in recent years