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Thursday, May 07, 2020

new project: "COVID-19 Disease Maps"

Project logo by Marek Ostaszewski.
CC-BY.
Already started a few weeks ago, but the COVID-19 Disease Maps project now has a sketch published, outlining the ambitions: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms  (doi:10.1038/s41597-020-0477-8).

I've been focusing on the experimental knowledge we have about the components of the SARS-CoV-2 virion and how they interact with the human cell. I'm at least two weeks behind on reading literature, but hope to catch up a bit this week. The following diagram shows one of the pathways on the WikiPathways COVID-19 Portal:

wikipathways:WP4846, CC0
This has led to collaborations with Andra Waagmeester, Jasper Koehorst and others, resulting in this preprint that needs some tweaking before submission, to an awesome collaboration with Birgit Meldal around the Complex Portal (preprint pending), and a Japanese translation of a book around a number search queries against Wikidata (CC-BY/CC0). The latter two were started at the recent online BioHackathon.

Oh, boy, do I love Open Science.

Monday, April 27, 2020

new paper: "NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment"

Fig. 1. Schematic overview of the workflow for toxicogenomics
modelling and how these models feed into the subsequent
materials modelling and IATA. Open Access.
NanoSolveIT is a H2020 project that started last year. Our BiGCaT group is involved in the data integration to support systems biology part of the Integrated Approaches to Testing and Assessment (IATA) for engineered nanomaterials in Work Package 1. This paper gives an overview of the project, the work, and the goals.

Of course, doing this is not trivial at all. And we have to bridge a lot of different research data, concepts, etc. As such, it is clear how it relates to the other nanosafety projects we have been involved in, such as eNanoMapper, NanoCommons, and RiskGONE.

Sunday, March 29, 2020

Tackling SARS-CoV-2 with big data

This blog post will contain a translation I made of this short "our story" Coronavirus te lijf met big data at the MUMC+ website written by André Leblanc. The Maastricht University Medical Center+ (MUMC+) is a collaboration of our our Maastricht University Faculty of Health, Medicine, and Life Science, of which our BiGCaT research group is part.

Wikidata is a community project and I only use and contribute to it. Scholia is a project started by Finn Nielsen (Technical University of Denmark - DTU), and now has funding from the Alfred P. Sloan Foundation, coordinated by Daniel Mietchen and Lane Rasberry (University of Virginia). Further acknowledgements to Andra Waagmeester (Micelio) and Jasper Koehorst (Wageningen University) for a great collaboration on corona virus information (see also Wikidata:WikiProject_COVID-19). WikiPathways colleagues including, of course, Prof. Chris Evelo and Dr. Martina Kutmon in Maastricht, but also Dr. Alex Pico and others in San Francisco. For me it was one of the selling points of the research group when I joined in 2012.

Tackling the corona virus with big data


Scholars around the world are working relentlessly on the development of a vaccine against the new SARS-CoV-2 coronavirus. Chemist and assistant professor Egon Willighagen contributes in collaboration with colleagues at the BiGCaT Department of Bioinformatics in Maastricht to make data and knowledge easier to find for other scholars. How does that work?

Big data is the new buzz words in the scholarly community. For example, collecting worldwide data around the treatment of cancer, and extracting from the best personal, unique treatment. In the case of the new coronavirus there is a more general need to just have access to data. Since the virus outbreak in Wuhan, China, there has been an explosion of new research articles on the COVID19 and the causing SARS-CoV-2 virus. The total number of scientific publications about corona viruses itself has reached some 29 thousand. These are not only about the new virus, but also the corona viruses that roamed the world before, like SARS and MERS. Either way, this makes it practically impossible to read all these articles. Instead, access to this literature has to be provided in a different way, allowing researchers to find the knowledge and data they need for their research.

Filter
Willighagen does this by organizing scientific literature, linking information, and filtering the collection of data and publications, making it searchable for scholars. He annotates publications with search terms and author names, and uses unique, global identifiers (like personal identification numbers) to support this. This is not unlike the use of phone numbers or dictionaries.

Various tools

Wikidata is the database used by Willighagen to link the information resources, along with Scholia to visualize the results. For example, Wikidata organizes data around the new virus with the https://tools.wmflabs.org/scholia/topic/Q82069695 entry. Willighagen uses these two tools to visualize what this database knows about specific topics.

Research can take advantage of a new open access resource edited by Willighagen: https://egonw.github.io/SARS-CoV-2-Queries/. Also social media are used: Twitter is used to increase awareness and mobilize people. Willighagen: "That is from a personal motivation. I tweet articles that show important changes. Or if they emphasize aspects that show how unique and urgent the situation". And finally there is WikiPathways, a project initiated by colleagues of Willighagen, to collect even more specific knowledge about the COVID19 virus. Here's the pathway about the SARS-CoV-2 virion: https://www.wikipathways.org/index.php/Pathway:WP4846

Thursday, March 19, 2020

new paper: "Wikidata as a knowledge graph for the life sciences"

A figure from the article, outlining the idea
of using SPARQL queries to extract data
from the open knowledge base.
As a reader of my blog, you know I have been doing quite some research where Wikidata has some role. I am preparing a paper on the work I have done around chemicals in Wikidata, based on what I presented at the ICCS with a poster. So, I was delighted when Andra and Andrew asked me to contribute to a paper outline the importance of Wikidata to the life sciences. The paper was published in eLife, which I'm excited about to, as they do a significant amount of publishing innovation.

I'll keep this post brief, as I have plenty of work to do, among which is SARS-CoV-2 data in Wikidata. Join this project, after you read the paper: Wikidata as a knowledge graph for the life sciences (doi:10.7554/eLife.52614, or in Scholia):



I'll write up some more queries for this eBook now: Wikidata Queries around the SARS-CoV-2 virus and pandemic.

Sunday, March 15, 2020

SARS-CoV-2, stuck at home, flu, and snowstorms

Scholia linking articles about the COVID19 disease.
Okay, okay, the snowstorm was ten years ago, when we were living in Sweden. We had two snowstorms, each time stuck at home, unable to leave our house. That was okay. We knew the next days the streets were cleaned, and we could continue living our lives.

Now it's different. I've been in 'social distancing' mode since the evening of Friday the 6th, so a bit over a week now. Because I have a flu. Presumably. Testing for SARS-CoV-2 is not routinely done and saved for risk groups and patients with severe COVID19 symptoms.

But the current situation is once in a lifetime. In the bad way. My generation has not had a situation like this yet. A real national emergency. But The Netherlands is coping. The data is scary. The situation in North Italy shows that humans are humans, and the virus doesn't care where it is surviving. It is how each country deals with it. And let me make clear, we must be learning from the countries that have been in the fire line already.

(North) Italy has a health care system in the top 5% according to OECD guidelines. Still, they were taken by surprise. But even the warned countries have been hesitant. The discussion is complex. A smaller economy (a 1% shrink is estimated right now) also means (as a Dutch professor pointed out 2, 3 days ago) there is less tax money to spend on the health care system.

Sad fact is, where are no longer talking about how to stop SARS-CoV-2. We are now talking about minimizing the number of causalities. A storm it is.

Keep safe, keep electronically in contact with the people around you (mental health), and foremost, wash your hands and practice social distancing. Let the storm not grow much further. This storm is not over the next morning. We're in for a rough ride.