Posts tagged ‘NCBI’

Collaborative Intelligence for Biomed

This post will not be about personal genomics, and I apologize for this… but still, it will be about personal-something and also still about biomed. I read those two last days, post about ‘Pubmed Fight’ [1] [2]. And it made me smile because I designed such an application previous winter, but slightly different. My tool is a mix between a social network and Pubmed. Let’s see what are the limitations of those:

  • Limitations of Pubmed: while being the most complete database of biomed publications, it has a major drawback: it is just publications-centered, not people centered. Even Hubmed, which is a re-engineering of Pubmed do not cover the people aspect. However the connection between people is an essential element for future collaboration, for knowing who works in the same area as who, etc.
  • Limitations of social networks: Every member of any social network knows it, the “friend” or “contact” status doesn’t always reflect a real-life situation. In my LinkedIn profile or in my Facebook profile, I have “friends” and “contacts” I never saw once in my life. A tool centered only on true relation between people could be welcome.

My tools at interMedi group both aspects. With the “Search for collaborators” applications, you can find who worked with who. With the “Fight” application, you can compare two researchers on the basis of their publication number but also the number of collaborators they’ve had until now.

How does it work?

It is based on the Pubmed API. Based on a writer’s name “A”, you can retrieve all his articles. Based on those articles, you can retrieve all the co-authors. You then have the collaborator’s list of “A”. This tool is in beta version and will/should be developed in the next few months.

By the way, I seize the opportunity to give a link to my personal page.

Pubmed API

This little known API is open, free, and very useful. It is well explained in the NCBI Handbook. I read on another blog post a nice script to get all the chapters of the NCBI Handbook and make just one nice pdf book of them. Read my comments on that post to update the proposed script.

Keep on reading, have fun!


July 4, 2008 at 10:26 am 3 comments


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