BioHackJP 23 Report Template

Minimal example of a BioHackrXiv publication that can be generated with the Preview Service.

Step 1: Clone this Template Repository

This repository is a template repository. This means you can hit the green "Use this template" button to use it as a template to start a new BioHackrXiv Publication:

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:

title: 'BioHackJP 2023 Report R1: linked data standardization with LLMs'
title_short: 'BioHackJP 2023 LD-LLM'
tags:
  - Linked Data
  - Large Language Models
authors:
  - name: First Author
    orcid: 0000-0000-0000-0000
    affiliation: 1
  - name: Last Author
    orcid: 0000-0000-0000-0000
    affiliation: 2
affiliations:
  - name: First Affiliation
    index: 1
  - name: Second Affiliation
    index: 2
date: 30 June 2023
cito-bibliography: paper.bib
event: BH23JP
biohackathon_name: "BioHackathon Japan 2023"
biohackathon_url:   "https://2023.biohackathon.org/"
biohackathon_location: "Kagawa, Japan, 2023"
group: R1
# URL to project git repo --- should contain the actual paper.md:
git_url: https://github.com/biohackathon-jp/bh23-report-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.}

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/biohackathon-jp/bh23-report-template

Step 3: Previewing the paper as PDF

This repository can be converted into a preview PDF with BioHackrXiv Preview Server. The preview website asks for the link to your repository and will automatically find the paper.md and create an PDF.

Guide to edit the markdown

Formatting

The document uses Markdown and you can look at this tutorial.

Subsection

Please keep sections to a maximum of only two levels with ##.

Tables and figures

Tables can be added in the following way, though alternatives are possible:

Header 1	Header 2
item 1	item 2
item 3	item 4

Table: Note that table caption is automatically numbered.

A figure is added with:

Other main section on your manuscript level 1

Lists can be added with:

Item 1
Item 2

Citation Typing Ontology annotation

You can use CiTO annotations, as explained in this BioHackathon Europe 2021 write up and this CiTO Pilot. Using this template, you can cite an article and indicate why you cite that article, for instance DisGeNET-RDF [@citesAsAuthority:Queralt2016].

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
discusses
extends
agreesWith
disagreesWith

tfuji/bh23-visc