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What once took months, now takes seconds – an interview with the Open PHACTS project coordinators


Derek Marren of Eli Lilly

IMI Programme Office: Why was the Open PHACTS Discovery Platform needed in the first place?

Derek Marren: Industry needed it because it was potentially spending a great deal of time, effort and indirectly money to connect, find and join data to answer scientific questions. Some of them are basic questions, such as where this compound is being tested or what the results of a drug actually are in various different scientific experiments. With the help of the Open PHACTS Discovery Platform, researchers in industry and academia can test their scientific hypothesis, without having to run the experiment, because someone else has already done it.

IMI Programme Office: Your project also did a lot of work to standardise data across different databases so that it is more easily searchable. Why was that important?

Gerhard Ecker: When you search database by database manually, you will find that in different data sources, whatever you are searching for could be named differently. For example, in one database your protein could appear as ‘P-glycoprotein 1’, in the next one as ‘multidrug resistance protein 1’, and in the third one as ‘ABCB1’. If you do that manually, you may not even realise that you are talking about the same protein. The Open PHACTS platform puts that together for you in the background. So irrespective of whether you start your search with P-glycoprotein 1, or ABCB1, you get the results together.

From an academic perspective, it used to take two post-docs three days to answer our top business questions. Via the Open PHACTS system, it is done automatically with one click.

IMI Programme Office: How many different data sources does the Open PHACTS platform now contain?

Gerhard Ecker: Between 10 and 12. It’s all public data sources, and they contain different data domains: proteins, diseases, etc.

IMI Programme Office: Which project achievement are you most proud of? Which ones stand out the most?

Derek Marren: The fact that we did it at all. This is the first evidence of that technological approach to deliver anything of this magnitude. It wasn’t theoretical, it wasn’t on paper, it was real and usable. This is a significant achievement.

Gerhard Ecker: Having the platform up and running, and seeing that it really works in real time. With some systems you can submit your search, leave your office in the evening and come back in the morning, hoping that your result will be there. There are internet platforms like that, you submit your search and then you have to wait. Our platform is doing it on the fly.

Derek Marren: It’s a click and review rather than a click and go have coffee.

IMI Programme Office: So this platform is now available for anyone. Is it free access?

Derek Marren: Yes it’s free and open access. And we have set up a foundation to develop and maintain it beyond the lifetime of the project.

IMI Programme Office: Can you give me some examples how this platform is being used?

Gerhard Ecker: In my group, having the platform available changed a lot how we work. For example, for one of our projects it took my

Gerhard Ecker of the University of Vienna

PhD student 3 months to compile a dataset of around 1 000 compounds, to make a decent computational model. With Open PHACTS, you can immediately create a dataset of around 2 000, 3 000 compounds.

As another example, recently I was approached by a colleague from oncology, they are working on a certain target, and it had a pathway with 10 proteins. We pushed it through Open PHACTS and we immediately saw what is out there. When we get any request to work together with someone, our first access point now is checking via Open PHACTS what is out there.

IMI Programme Office: And what kind of research are we talking about?

Derek Marren: Drug discovery, pre-clinical early-stage research but it doesn’t preclude you looking into the clinical data. So when Gerhart was talking about using Open PHACTS as the first door, it’s the first door to set your foundation of what you’re then going to pour more into. You evolve your understanding of that business space.

It is also a way of creating a reproducible science space, one person does the analysis and they get answer A, another research facility does that same experiment and get the same answer. You can now start to compare your divergent science because your foundation is the same – you’re not arguing where you started from because you all started from the same point.

IMI Programme Office: How has the industry benefitted from this project?

Derek Marren: The collaboration has gone up, because of the intellectual network. The people angle of this project has been phenomenal and the social network that we now have has continued beyond the project in many different spheres and projects. In terms of direct benefits, it’s probably re-ignited the debate about the reproducibility of data.

IMI Programme Office: And what about the academic community? How did it benefit?

Gerhard Ecker: We benefitted from the industry network and getting to know how industry is working. This exposure to industry was especially beneficial for my PhD students: at least three of them were hired by pharmaceutical companies.

For me personally it changed the way I am teaching, because I am closer to what the real industry problems are. For example, I never thought that data integration is an issue for a pharmaceutical company.

IMI Programme Office: Open PHACTS also resulted in at least one spin off. Could you tell us more about it?

Gerhard Ecker: Yes, we are in the process of creating the spin-off. It is called Phenaris and will develop ToxPHACTS, a software that will combine what we learned in IMI’s eTOX project with the Open PHACTS discovery platform.

It will allow toxicologists to do the very early assessment of the risk of a certain compound, even before they do the first animal experiments. According to estimations you can lose 250 million euro on average when you overlook compounds toxicity in the early phase of drug discovery because you have to go back and re-do everything. ToxPHACTS will allow you to do a very early assessment, saving money and time, and reducing the use of animals in research.

IMI Programme Office: Would all of this have been possible without the public-private partnership brought by IMI?

Gerhard Ecker: No. It would have not been impossible.

Derek Marren: I agree. Good luck trying to set up a multi-party precompetitive arrangement that’s legally binding and doesn’t cause a problem with that many members.

Gerhard Ecker: You can do it with one pharmaceutical company. But as Derek was saying, having 10 pharmaceutical companies and 10 academics, without the framework that IMI is providing simply wouldn’t work.

Derek Marren: Nobody would have the willpower to see it to the end.

IMI Programme Office: Anything else you would like to add?

Derek Marren: I think it’s important from an EFPIA perspective, if you are going to be in one of those projects, be in the project. You won’t get the value from it, if you are just a passenger.

Gerhard Ecker: For an academic it’s being open towards industry, so the pharmaceutical industry is not our enemy. If you go in with that mindset it is extremely beneficial. And I am not talking about follow-up contracts, there was not a single follow-up contract with the pharmaceutical companies. The main benefit is just getting exposed to this mindset to how drugs are really discovered and developed, and realising the problems which are there.

Project factsheet