Sunday, May 03, 2015

Pathways as summaries: Nature Review Disease Primers and Open Source Malaria

A P.falciparum isoprenoid
biosynthesis pathway (WP2918).
Event 1
The Nature Publishing Group (NPG) has launched a new journal, which you probably did not miss. There is founding editorial titles From mechanisms to management (doi:10.1038/nrdp.2015.1) as the goal of the journal. Very noble and very needed, indeed! They write:
Each Primer article includes the same major sections: epidemiology, mechanisms, pathophysiology, diagnosis, screening, prevention, management and patient quality of life.
The complement the articles with PrimerViews and even animations:
Together, we hope that the Primer and PrimeView will provide readily accessible introductions to each topic for readers from all disciplines.
Very exciting! The mechanistic diagrams in the papers are perhaps even better, but, it wouldn't be a proper chem-bla-ics post had I not something to bitch about. And I do; read on.

Event 2
This weekend Christopher Southan asked if the Plasmodium falciparum pathway for isoprenoid biosynthesis was to be found in WikiPathways (related to this blog post about MMV008138). It was not at the time. But other resources did, including literature (of course), Wikipedia, and the excellent Malaria Parasite Metabolic Pathways resource.

In related news, about a year ago, Patricia Zaandam worked in our group on pathway analysis related to malaria. At the time, we selected human data from ArrayExpress because of the abundance of human pathways in WikiPathways (>600 now, of which the Curated Collection and Reactome Approved are subsets). So, on a weekend where I really needed a break from working and with some time free, I decided to make that pathway. One of the first observations was that you cannot create Plasmodium pathways on WikiPathways yet. Second, we also do not have a BridgeDb gene identifier mapping database for this organism either. But that is not needed for drawing the pathway.

So, I am digitizing the pathway from the various sources that I can find, added MMV008138, and will probably add more malaria drugs and drug leads along the way. The idea of the project of Patricia last year was indeed possible drug targets. This resulted in this current outcome (with MMV008138 highlighted in red):

The new NPG journal realized we need high quality summaries, and they are correct. This is why the periodic table of elements has been so useful, and the purpose of physical laws expressed as mathematical equations: it puts emphasis on what we think matters. This is also why I believe WikiPathways is so important.

But that's where the parallel between WikiPathways and NatRevDiseasePrimers about ends. The goal of WikiPathways is not just to summarize the knowledge, but to make it manageable. We are talking about data management here. I don't care that much about nice graphics; if we really want to make the science and the industry going forward, then we cannot hide behind a knowledge publishing system that doesn't scale and that doesn't integrate. That is not the kind of management we need.

New readers of my blog - welcome! - can browse my past writings to read what the publishing industry should have done. I have explored many different solutions, and only few of them are being picked up. The Nature Publishing Group has repeatedly experimented with new technologies to make the flood of knowledge manageable, and it find it rather disappointing that this editorial does not manage to go beyond nice graphics. I hope the journal will quickly pick up speed, and add the missing machine readability and APIs. Because a new journal is for years, and we really cannot wait another 15 years.

I am not claiming this new journal is not useful, but it could have been so much more.

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