The Seven Stones

A visual wiki for biological notation?

What standards are needed in computational systems biology? The results of a survey on this topic have been recently summarized by Edda Klipp and colleagues (Klipp et al, 2007, Nat Biotech 4:390). Even if it is somewhat unclear how representative the sample of respondents were with respect to the larger systems biology community, some of the top priorities identified are interesting (I list only the three first):

Respondents expressed most strongly the need for standardization in the following fields: first, graphical representation of biochemical networks; second, experimental procedures; third, model encoding and model exchange;…

How to encourage standards in biological graphical notations? One way would be to provide tools that facilitate the use of standardized notations by a wide range of users, beyond the circle of modelers. I was wondering whether a visual wiki could not help in this regard. An idea would be to have an open-source plugin for a common wiki software that would allow embedding of editable diagrams and would be specially tailored to draw biological diagrams, for example as Kitano’s process diagrams or Kohn’s interaction maps.

Gliffy proposes a graphical plugin for the Confluence wiki software and mxGraph is a Javascript library for web-based diagramming. Unfortunately, none of them are open-source. Cumulatedraw (see illustration) is perhaps less sophisticated but is licensed under a Creative Commons Attribution-Non Commercial-Share Alike license.

Would it be possible or easy to customize such software to specialize it for drawing biological diagrams? What are the existing solutions for visual wikis? Would a visual encyclopedia of biological processes be something that may drive biologists to use standardized notations?


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    Keith said:

    If you want to encourage the use of a standardized way of graphically representing biological networks, i think it would be better to start with agreeing on a standard, and then work to get software to support the standard. Otherwise you may end up with different people with different ideas on how they want to display things, and simply go off and write their own wiki plugins. Why not email a few researchers who care about the issue and come together online in a forum or wiki to discuses what kinds of properties and abilities an ideal graphical representation should have, give it a name and a homepage, and go from there?

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    Dylan Morris said:

    Keith, such an effort is already underway, brought to you by the same people who created SBML — they’re calling it SBGN (Systems Biology Graphical Notation):

    however, creating a standard and getting people to adopt that standard are two very different things. i think having software that supports a standard is the only way to really drive adoption and use. there are currently plenty of software packages out there for diagramming biological networks; how many of them will adopt the future SBGN standard is an open question…

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    Thomas Lemberger said:

    It is true that there are already great packages out there to create diagrams. The idea was rather to embed this into a (hopefully) useful “social” software context to share diagrams.

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    Keith said:

    This is a little off-topic, but something interesting to me…

    “…however, creating a standard and getting people to adopt that standard are two very different things.”

    That’s an good point. It’s a shame there is no central place where people can come together to decide on and develop standards on all different issues. Right now, for any given technology, there may be a host of groups each with their own proposed standards (e.g. for web standards you have W3C, The Web Standards Project, and WSG ), each with their own set of goals & recommendationsm but no central place for all of them, and any other standards, to be compared and evaluated.

    Right now, if i want to get an idea of what kind of standards are out there any some given technology, i normally start with one i know of, and look it up on wikipedia to see if other comparable standards are listed.To find out the best way to represent a graph in xml for example i can start with one i’ve heard of (GraphML), and pull up it’s Wikipedia article. From there i see that there are several other alternative including GML, GXL, and XGMML. I Can then go and compare each standard before deciding on which one seems to be the most-supported, and best suited for what i want to do.

    It would be neat if there was a web-site devoted to dealing with standards on all different topics, and contrasting standards with one another.

    This i suppose still would not solve the issue of getting people to follow any one standard among a handful of choices, but at least it would let people know what the choices are.

    Anyways, just a thought.


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    Alexander Pico said:

    10 months later…

    I just stumbled across this thread and identified with the perspective and need expressed almost 1 year ago. Around that time, I happened to be working with wikis and with biological pathway drawing tools, and decided to try to put the two together. This led very quickly to WikiPathways, a free and open source community resource where the users are the curators. We worked on this as part of the Google Summer of Code 2007 and are continuing to ramp it up.

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    Dario said:

    Curiously – someone in our user community came up with a very similar suggestion in reply to my question – what killer feature people would like to see implemented in our wiki engine.

    WikkaWiki was the first wiki engine to introduce support for mindmaps via FreeMind – this proved to be a very popular feature among mindmap enthusiasts.

    I am sure the idea of collaboratively editing/revising diagrams via a wiki would be appealing for lot of users.

    We are going to send an application for the Google Summer of Code 2008 for projects related to WikkaWiki and it’d be great to see someone interested in developing a plugin to implement this functionality join in, especially if there are already standards for visual markup for specific scientific fields.

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