Peter Murray-Rust, (Chemistry), Gita Yadav (Plant Sciences) and interns in India

openVirus is a team of Young Indian Scientists who have built tools to mine the scientific literature for new insights into Viral Epidemics.
Solutions to COVID may be lying in the literature of previous epidemics or the vast new output of COVID papers. The project has many facets and is very suitable for anyone interested in extracting and analysing masses of scientific articles.

Our facets (X in “viral epdemics and X”) include:

  • what countries are epidemics reported in?
  • what drugs are used?
  • what comorbidities occur
  • who funds research into viruses?
  • what viruses are involved?
  • what is the role of zoonosis (animal hosts)
  • who reports Test and Trace strategies
  • what non-pharma interventions are used (quarantine, social distancing, masks)

We build “minicorpora” for all of these using EuropePMC, and ontologies using Wikidata.

Among the skills that delegates can learn without previous programming

  • repositories (EuropePMC) and searching (including REST)
  • creation of ontologies (dictionaries) using Wikidata and SPARQL
  • Dockerised containers
  • Jupyter notebooks

A mini-review can be carried out in 2-3 hours.

If you’re interested in developing technology (probably scripting – R, Python, KNIME) we’d love contributions on

  • text-based search (Lucene)
  • Natural Language Processing (nltk, OpenNLP)
  • data display (e.g. matplotlib, D3.js)
  • Machine Learning (Keras, word2vec)
  • multilingual documents (Hindi, Urdu, Tamil, and Portuguese / Spanish – we have a collaboration with Redalyc repository in Latin America)

There is extensive documentation and there will be project members available for the working day (up to say 1700 BST, 2130 India Standard Time and PMR till later in UK).

overview slides at: https://github.com/petermr/openVirus/blob/master/outreach/OpenVirus_18.pptx

openVirus is a team of Young Indian Scientists who have built tools to mine the scientific literature for new insights into Viral Epidemics.
Solutions to COVID may be lying in the literature of previous epidemics or the vast new output of COVID papers. The project has many facets and is very suitable for anyone interested in extracting and analysing masses of scientific articles.

Steven Wingett
Author: Steven Wingett

Bioinformatician at The Babraham Institute and organiser of the Online Cambridge Bioinformatics Hackathon 2020.

Categories: Project

Steven Wingett

Steven Wingett

Bioinformatician at The Babraham Institute and organiser of the Online Cambridge Bioinformatics Hackathon 2020.

5 Comments

Padmini Rai · September 18, 2020 at 2:45 pm

That’s an amazing achievement by the youth , I’d love to contribute on my part.

    Sana Saifi

    Sana Saifi · September 21, 2020 at 7:24 am

    lets meet today to talk about some details!

Eliel Godsent

Eliel Godsent · September 19, 2020 at 9:40 am

i’ll like to be a part of this

    Sana Saifi

    Sana Saifi · September 21, 2020 at 7:23 am

    Happy to Hear! lets meet today to talk on the same 🙂

Peter Murray-Rust

Peter Murray-Rust · September 21, 2020 at 9:24 am

NOTE:
(Steven is not the author – that’s a technical glitch)

The coordinators are:
* Sana Saifi (coordinator)
* Shweata Hegde (Documentation)

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