April 27, 2020

Data science against Covid-19

Martin Hofmann-Apitius is using some of the technologies that he brought to the Human Brain Project (in particular semantic technologies such as text mining and terminology / ontology construction) to address the COVID-19 challenge.

martin-h.png

https://www.fraunhofer-innovisions.de/experten/prof-dr-martin-hofmann-apitius/

Prof. Dr. Martin Hofmann-Apitius

Institution: Head of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing SCAI

HBP research areas: Medical Informatics Platform, Leader Comprehensive Ontologies for Brain Disease

Q: What are you doing at the moment to help address the challenges posed by the novel Coronavirus?

Martin Hofmann-Apitius: we are using some of the technologies that we brought also to the Human Brain Project (in particular semantic technologies such as text mining and terminology / ontology construction) to address the COVID-19 challenge. In the HBP, we have used ontologies to structure knowledge about human brain diseases; in the COVID-19 context, semantic technologies allow us to automatically read thousands of relevant publications every day and to extract relevant information on chemical entities from the flood of scientific papers dealing with COVID-19.

During the last two weeks of time, we have:

  • generated a first version of a COVID-19 terminology which will be developed into a full-blown COVID-19 ontology
  • generated a first version of the “COVID-19 PHARMACOME”, which is in essence a comprehensive drug target network model of SARS-CoV-2 pathophysiology integrated with pharmaceutical chemistry knowledge

Let me add one important point: all this was only possible because the Fraunhofer Headquarters supports our COVID-related work with internal funding. We are really grateful to the administration in Munich, who allowed us to throw a lot of resources on this new topic.

Q: How has the current shutdown affected your work?

Martin Hofmann-Apitius: the entire team is working remotely from home; so far, this works surprisingly well. On my side, I manage to get much more done in isolation, as I do not get disturbed during reading and writing. However, we all miss the opportunities to talk directly to each other. Motivation and spirits in the team are high, despite the fact that all exchange of ideas takes place in “virtual” meeting rooms.