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Affirmer understands and acknowledges that Creative Commons is not a + party to this document and has no duty or obligation with respect to + this CC0 or use of the Work. diff --git a/README.md b/README.md new file mode 100644 index 0000000..e729e15 --- /dev/null +++ b/README.md @@ -0,0 +1,84 @@ +# BioHackrXiv Publication Template + +Minimal example of a [BioHackrXiv](https://biohackrxiv.org/) publication that can be generated with the +[Preview Service](http://preview.biohackrxiv.org/). + +## Step 1: Clone this Template Repository + +This repository is a template repository. This means that you can hit the green "Use this template" +button (after logging in) to use it as a template to start a new BioHackrXiv Publication: + +![Screenshot of the green "Use this template" button.](paper/use-this-template.png) + +## Step 2: Configuring the Markdown + +The publication Markdown is found in the `paper/paper.md` file. At the top you can edit the +YAML code with metadata. It is important to get this part correct, because otherwise the PDF +generation will fail. The metadata looks like this: + +```yaml +title: 'BioHackEU22 Report for Project 26: Shedding the light on unknown chemical substances' +title_short: 'BioHackEU22 #26: unknown chemical substances' +tags: + - cheminformatics + - PubChem + - unknown chemical substances +authors: + - name: Egon Willighagen + affiliation: 1 +affiliations: + - name: Dept of Bioinformatics - BiGCaT, NUTRIM, FHML, Maastricht University, Maastricht, NL + index: 1 +date: 7 November 2022 +cito-bibliography: paper.bib +event: BH22EU +biohackathon_name: "BioHackathon Europe 2022" +biohackathon_url: "https://biohackathon-europe.org/" +biohackathon_location: "Paris, France, 2022" +group: Unknown chemical substances group +# URL to project git repo --- should contain the actual paper.md: +git_url: https://github.com/biohackrxiv/publication-template +# This is the short authors description that is used at the +# bottom of the generated paper (typically the first two authors): +authors_short: Egon Willighagen \emph{et al.} +``` + +### Which metadata to update? + +#### To change + +The following fields should be changed: + +* title +* title_short +* tags +* authors +* affiliations +* date +* group +* authors_short + +Particularly important to update is the following field, which should point to +your clone of the template, instead of the template itself: + +* git_url: https://github.com/biohackrxiv/publication-template + +#### Only update for other BioHackathons + +The following fields should only be changed if you are not writing for the BioHackathon Europe 2022: + +* event: BH22EU +* biohackathon_name: "BioHackathon Europe 2022" +* biohackathon_url: "https://biohackathon-europe.org/" +* biohackathon_location: "Paris, France, 2022" + +## Step 3: Writing the article + +A full Markdown example is given in [paper/paper.md](paper/paper.md). This includes instructions how to include +figures, tables, and annotate citations with the Citation Typing Ontology. + +## Step 4: Previewing the paper as PDF + +This repository can be converted into a preview PDF with BioHackrXiv [Preview Server](http://preview.biohackrxiv.org/). +The preview website asks for the link to your repository and will automatically find the `paper.md` and create an PDF. + diff --git a/paper/biohackrxiv.png b/paper/biohackrxiv.png new file mode 100644 index 0000000..9aaff07 Binary files /dev/null and b/paper/biohackrxiv.png differ diff --git a/paper/paper.bib b/paper/paper.bib new file mode 100644 index 0000000..2856d05 --- /dev/null +++ b/paper/paper.bib @@ -0,0 +1,20 @@ +@article{Queralt2016, + author={Queralt-Rosinach, N. and Pinero, J. and Bravo, {\`A}lex and Sanz, F. and Furlong, L. I.}, + title={{DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases}}, + journal={Bioinformatics}, + year={2016}, + volume={32}, + number={14}, + pages={2236--2238}, + doi={10.1093/bioinformatics/btw214}, +} + +@article{CiTO, +author = {Shotton, David}, +journal = {Journal of Biomedical Semantics}, +number = {Suppl 1}, +year = {2010}, +pages = {S6}, +title = {CiTO, the {Citation} {Typing} {Ontology}}, +volume = {1 Suppl 1}, +} diff --git a/paper/paper.md b/paper/paper.md new file mode 100644 index 0000000..fa96766 --- /dev/null +++ b/paper/paper.md @@ -0,0 +1,114 @@ +--- +title: 'BioHackEU23 report: Template for the very long title' +title_short: 'BioHackEU23 #26: unknown chemical substances' +tags: + - cheminformatics + - PubChem + - unknown chemical substances +authors: + - name: First Author + affiliation: 1 + - name: Last Author + orcid: 0000-0000-0000-0000 + affiliation: 2 +affiliations: + - name: First Affiliation + index: 1 + - name: Second Affiliation + index: 2 +date: 8 November 2023 +cito-bibliography: paper.bib +event: BH23EU +biohackathon_name: "BioHackathon Europe 2023" +biohackathon_url: "https://biohackathon-europe.org/" +biohackathon_location: "Barcelona, Spain, 2023" +group: Project 26 +# URL to project git repo --- should contain the actual paper.md: +git_url: https://github.com/biohackrxiv/publication-template +# This is the short authors description that is used at the +# bottom of the generated paper (typically the first two authors): +authors_short: First Author \emph{et al.} +--- + + +# Introduction + +As part of the BioHackathon Europe 2023, we here report... + +# Formatting + +This document use Markdown and you can look at [this tutorial](https://www.markdowntutorial.com/). + +## Subsection level 2 + +Please keep sections to a maximum of only two levels. + +## Tables and figures + +Tables can be added in the following way, though alternatives are possible: + +Table: Note that table caption is automatically numbered and should be +given before the table itself. + +| Header 1 | Header 2 | +| -------- | -------- | +| item 1 | item 2 | +| item 3 | item 4 | + +A figure is added with: + +![Caption for BioHackrXiv logo figure](./biohackrxiv.png) + +# Other main section on your manuscript level 1 + +Lists can be added with: + +1. Item 1 +2. Item 2 + +# Citation Typing Ontology annotation + +You can use [CiTO](http://purl.org/spar/cito/2018-02-12) annotations, as explained in [this BioHackathon Europe 2021 write up](https://raw.githubusercontent.com/biohackrxiv/bhxiv-metadata/main/doc/elixir_biohackathon2021/paper.md) and [this CiTO Pilot](https://www.biomedcentral.com/collections/cito). +Using this template, you can cite an article and indicate _why_ you cite that article, for instance DisGeNET-RDF [@citesAsAuthority:Queralt2016]. + +The syntax in Markdown is as follows: a single intention annotation looks like +`[@usesMethodIn:Krewinkel2017]`; two or more intentions are separated +with colons, like `[@extends:discusses:Nielsen2017Scholia]`. When you cite two +different articles, you use this syntax: `[@citesAsDataSource:Ammar2022ETL; @citesAsDataSource:Arend2022BioHackEU22]`. + +Possible CiTO typing annotation include: + +* citesAsDataSource: when you point the reader to a source of data which may explain a claim +* usesDataFrom: when you reuse somehow (and elaborate on) the data in the cited entity +* usesMethodIn +* citesAsAuthority +* citesAsEvidence +* citesAsPotentialSolution +* citesAsRecommendedReading +* citesAsRelated +* citesAsSourceDocument +* citesForInformation +* confirms +* documents +* providesDataFor +* obtainsSupportFrom +* discusses +* extends +* agreesWith +* disagreesWith +* updates +* citation: generic citation + + +# Results + + +# Discussion + +... + +## Acknowledgements + +... + +## References diff --git a/paper/use-this-template.png b/paper/use-this-template.png new file mode 100644 index 0000000..2d67fe6 Binary files /dev/null and b/paper/use-this-template.png differ