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README.md

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+# 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.
+

paper/paper.bib

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+@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},
+}

paper/paper.md

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+---
+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