Nanopub 101

Christian Meesters

Johannes Gutenberg University Mainz

Saranjeet Kaur Bhogal

Imperial College London

What is a Nanopub?

Think of a Nanopub as a little knowledge container

This is an example Nanopub, a dataset description

Register your account

If you have don’t have an account yet, please register at nanodash using your ORCID iD.

Registration page

Interlude: What is an ORCID?

ORCID stands for Open Researcher and Contributor ID.

  • free, unique & persitent ID
  • show your research interest, funding, employment and publications (sometimes they add automagically with crossref)
  • useful in research to be found:
    • for agencies to look you up during proposal reviews
    • to find colleagues (and see how actively they are engaged and in which topics)

Interlude: What is an ORCID? II

Example screenshot with links and research interests.

Example screenshot of papers linked in an ORCID profile.

Authorise ORCID iD and enter your Nanodash account

Authorise ORCID

Landing page

Introduction of an User

Click on the profile icon in the top right corner to access your profile page.

Profile page

Then click on the “See Your Profile Details” button to access your profile details.

Create Introduction

Inside the Profile Details page, click on the “Create Introduction” button to create your introduction.

Create introduction

And then …

Once inside the introduction page, you will see a “Create Nanopublication” form.

Create nanopublication

Complete your introduction

Under the “Introducing a user” section, add your name as you would like it to appear on your profile.

Complete introduction

Finally, after you are happy to check the publication button, you should be able to click on the “Publish” button to publish your introduction.

A published introduction …

Once the introduction is published, you should now be able to view your name on it.

Published introduction

View latest nanopub

Finally, your name will appear under the latest nanopublications on your profile page.

Latest Nanopublications

Add “view display” to your profile

To add display sections to your profile, click on the “+ view display” button and it will open a new page for adding a new display section.

View display

Create a view display

Approval of an User

Next on our list: approval of a user. Users can be approved by approved users.

Task: approve your neighbour(s)!

Publish using a Template

Select “Publish” from the menu.

Then you can choose from the list of templates. (We are going to publish together. Please wait.)

Your first Nanopub!

Let’s select an easy template: Search for “Announcing a paper I have read”

Select and enter a DOI of a recently read paper.

Modifying a Template

There are many templates for different purposes and disciplines. But, sometimes you need some new template …

First look, then leap

It is better not to “pollute” the nanopub template space. First look or ask for existing templates.

Note

We are not going to create a new template in this workshop. But we will briefly show you how its done.

Modifying a Template II

  1. start by selecting a suitable (similar) template and select the little blue caret
  2. then select “edit as derived nanopublication”

Modifying a Template III

Start small

Creating a new assertion template can be difficult. Start with an easy (or small) one.

Ask for input!

If you need substantial changes, ask for help. (In the end we show some resources.)

What can you do with Nanopubs?

Construct knowledgegraphs for your paper!

Example knowledgefrage for a data analysis workflow (which nanopub IDs)

Created with the Snakemake reporter plugin for posting workflow metadata.

Citing Nanopubs

Remember: nanopubs are unique persistent identifiers, worldwide accessible.

What can you do with Nanopubs? II

More & more Citation Ontologies become available in Scholia:

https://scholia.toolforge.org/cito/

Nanopub has a Template for your CiTOs

Declare CiTOs with this template.

And now? Where to go from here?

This workshop merely gave an overview. There is so much more: