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research.md

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title: "A sample Research article title" author:

  • Jane E. Doe [1,*,orcid:0000-0002-0778-8115]
  • John R.S. Smith [1,2,orcid:0000-0001-0002-0003] link-citations: yes output: html_document: pandoc_args:
    • --lua-filter=filters/extract-cito.lua
    • --citeproc
    • --lua-filter=filters/insert-cito-in-ref.lua pdf_document: pandoc_args:
    • --lua-filter=filters/extract-cito.lua
    • --citeproc
    • --lua-filter=filters/insert-cito-in-ref.lua word_document: pandoc_args:
    • --lua-filter=filters/extract-cito.lua
    • --citeproc
    • --lua-filter=filters/insert-cito-in-ref.lua

RStudio: cito-bibliography: bibliography.bib

Other: bibliography: bibliography.bib

cito-bibliography: bibliography.bib csl: journal-of-cheminformatics.csl ...

Abstract

Background: Text for this section. Research articles should include an abstract that does not exceed 350 words.

Methods: Text for this section.

Results: Text for this section.

Keywords: sample; article; author

Introduction

This Markdown template is for a Research article in the Journal of Cheminformatics. It requires pandoc 2.12 or later to be converted to a Word .docx or PDF, with the provided Makefile. See the pandoc manual for more information on pandoc.

Methods

Information about software and data

Reviewers and readers of a research paper must be able to use the used software and data to reach the same Results. Journal of Cheminformatics will only publish research or software that is entirely reproducible by third parties. This means that any datasets, software and algorithms that are required to reach the conclusions stated in the paper must be provided as supplemental materials, or be otherwise accessible without the need for registration, login or agreement with license terms other than Creative Commons licenses for data and text and OSI-approved Open Source Licenses for software. For any software, the source code must be provided @agrees_with:Guha_Willighagen_2017.

Adding References

References are added to the content in a similar way as LaTeX and there is a bibliography.bib in this folder in the BibTeX format. A citation is made by including an @ followed by the BibTeX key, for example like @Upper_writers_1974 for Ref. @Upper_writers_1974.

Now, the Journal of Cheminformatics support citation typing ontology annotations using the CiTO @uses_method_in:Willighagen_2020. Adding an annoted citation is done by prepending the BibTeX key with the intention, e.g. \@agrees_with:Guha_Willighagen_2017 or \@uses_method_in:Willighagen_2020.

Results

Figures are easy to add in Markdown, and can be done with the ![](images/cito_in_Word.png) syntax.

Figure 1: Reference list as converted into Word, including CiTO annotation.

Discussion

In this section we examine the growth rate of the mean of $Z_0$, $Z_1$ and $Z_2$. And we can have LaTeX equations:

$$ x+1 = 2 $$

Conclusions

List of abbreviations

Availability of data and materials

Text for this section.

Competing interests

Text for this section.

Funding

Text for this section.

Authors' contributions

Text for this section.

Acknowledgements

Text for this section.

Authors' information (optional)

Text for this section.

References