What’s the answer? (Publishing apps)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week the highlighted question is different. It’s MINE! After exploring the new embedded browser app that Elsevier added and we discussed the other day, I began to think about what exactly would make the interactions of scientists easier when they mine the literature. So I posed this question:

Question of the week:

What features from publishers would help bioinformatics folks?

So I was looking into the new browser/viewer that’s been integrated into Elsevier’s papers. There was some discussion of it on our blog yesterday. But it’s got me thinking about what would be really useful for taking data in a paper further, more easily and fluidly.

What tools and features would you want in an app from publishers that would make the lives of bioinformatics folks easier?

For me, better text mining tool integration would be great. I can’t even believe how bad the search is just for authors sometimes. I like the idea of gene lists too, which could be quickly obtained in one fell swoop and used with other tools. It also stuns me that “big data” sets are not always easily linked to where they can be found in a live browser.


There were some good responses, some were more philosophical about the state of scientific publishing. Check out the answers in the current discussion. I haven’t selected one yet as correct–because it’s still percolating. But I may choose the top vote-getter as it winds down.

I was sorta thinking more about working with the system we have, and what tools could we overlay to add value to the papers and ease to our interactions with it.

For me it was interesting because I found out that publishers are now keen to let us add helpful stuff. Elsevier has a whole developer access program–so if you had a great text mining tool (Casey, I’m looking at you…) you can add it as an app to their system.  People could then choose to add it to their interface and use it from multiple points. And then I saw a tweet that something similar is possible via PLoS and Medeley thanks to Steven Turner: RT @genetics_blog: . @PLoS and @mendeley_com Call for Apps: http://bit.ly/oc2NGL and http://bit.ly/nHYqNa

So many instead of just complaining about the lack of tools, maybe it’s our job to build them…What do you think? Discuss at BioStar. Or tell me here what apps you want publishers to add to make your life easier. I’m really curious.

What would make your interactions with the literature better?