Biological Pathways in the Open

A spotlight on WikiPathways, a 2018 Global Sprint project

Alex Pico (@xanderpico) is the Associate Director of Bioinformatics at The Gladstone Institutes in San Francisco where he develops biomedical data visualization, analysis and collaboration software. Alex was selected to join the current round of Mozilla Open Leaders with his work on WikiPathways.

I interviewed Alex to learn more about WikiPathways and how you can help at the Global Sprint 2018.

What is WikiPathways?

It’s a wiki, like Wikipedia, but focused on biological pathways. Basically, we ripped out the text editor in Wikipedia and replaced it with a drawing tool to let folks diagram pathways of biochemical reactions. Importantly, the diagrams you draw are more than just pictures; they are also fully annotated computational models. Also like Wikipedia, the content and code are all free, open access and open source. WikiPathways has been practicing open science for the past 10 years.

Why did you start WikiPathways?

At the time we came up with idea, we were using wikis for project management and shared documents, but not directly as a publicly accessible database. We had been maintaining a traditional database of pathways models for many years, but were having trouble keeping up with edits, corrections and new discoveries. Applying the concepts of a wiki to our pathway database challenges turned out to be a perfect match.

Why is a database of biological pathways useful for scientists?

Pathways are used in a few different ways by folks interested in biology. Research scientists use them to represent models of biological activity associated with diseases, like cancer, heart disease or diabetes. They can be used one-at-a-time as figures or for data visualization; or they can be used in bulk for computational analysis. Pathways are also useful for education. These diagrams pack a lot of knowledge acquired by multiple labs over many years into a single picture. Drawing a pathway is itself a learning experience!

What will you be working on during the Sprint?

We have a variety of tasks lined up for MozSprint. We will be drawing pathways, as well as fixing and updating existing pathway diagrams. We will be updating our tutorials and help documents for new contributors. And we will also be squashing bugs in our code and working on contained feature development.

What challenges have you faced working on this project?

The first challenge was the realizing the fallacy of “build it and they will come.” This is distinctly not true for many wiki projects in science. It was almost a year before we saw new contributors from outside our group. Fortunately, WikiPathways was so useful even to us using it “internally” that the project survived this initial challenge. Ongoing challenges include maintaining a core of stable, supported functionality while still going after exciting new features. Oh, and funding!

What kind of skills do I need to help you? Do I need to be a scientist?

We are ready to welcome a broad range of backgrounds. We’ve had high school students contribute some amazing content. You don’t need to be recognized as an “expert” or brandish a particular degree. If you have an interest in science, biochemistry, biology or pathways, then we could use your help.

How can others join your project at #mozsprint 2018?

Our MozSprint effort is summarized on the Pulse site:

https://www.mozillapulse.org/entry/621

You can also start with our brief README file and follow the links from there:

https://github.com/wikipathways/wikipathways.org/blob/master/README.md

And our list of starter tasks for MozSprint are listed here:

https://github.com/wikipathways/wikipathways.org/issues?q=is%3Aissue+is%3Aopen+label%3Amozsprint

Join us wherever you are May 10–11 at Mozilla’s Global Sprint to work on many amazing open projects! Join a diverse network of scientists, educators, artists, engineers and others in person and online to hack and build projects for a health Internet. Register today