Pathways4Life: Crowdsourcing Pathway Modeling from Published Figures [pathways4life]

Thinklab specific comments

I will provide my comments related to formatting and visual improvements here — feedback that is unrelated to any substantial aspect of the proposal.

  1. Misspelling of most:

    mosst pathway information is still published solely as static

  2. I would use the markdown list feature for the paragraph beginning with

    Several caveats to this survey ...

  3. Figure 3 is too low resolution — specific gene names are not visible. The human/machine difficultly aspect of the image is discernible, but I would like to see the actual images, especially to gain familiarity with examples of pathway figures.

  4. Thinklab citations would improve online readability. Minimal extra work would be needed if you use the Citation Key method. I would use crossref for doi lookup when needed. The intelligent citations will help with readability and hopefully spur discussions on referenced works.

Figure 3 is too low resolution

Just FYI, people will soon be able to insert figures and have them appear somewhat like they do on PLOS and other websites. There will be an option to insert figures at a smaller size that can be clicked to zoom, and an option to have the figure full width. There will also be a button to download the original. This should help things.

Thinklab citations would improve online readability

@alexanderpico we'd be happy to take care of this for you.

  1. Fixed
  2. I think I prefer the paragraph form here.
  3. Looking forward to the PLoS-like feature. The goal of this figure, though, isn't really to inspect the details of the image. Honestly, I'd simply recommend searching pubmed central for "signaling pathway" and you'll see exactly what we're working with.
  4. Thanks Jesse. The help with formatting would be appreciated. I'm going to stick with Endnote in Word for the final version, so I'm not too motivated to markdown all the refs...

I've gone ahead and converted the references in your proposal to a native ThinkLab format. In the future we may actually be able to automate this process.

I also took the liberty to convert your figures to use our new figures feature. If you'd like to edit the figures, you can find them by clicking "edit figures" from the project manager page. If you'd like to go ahead and upload a higher resolution version of the figure that @dhimmel commented on I think that would be a good idea. We currently don't have a click to zoom or download feature but those will be added soon.

Cite this as
Daniel Himmelstein, Jesse Spaulding, Alexander Pico (2015) Thinklab specific comments. Thinklab. doi:10.15363/thinklab.d77

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