Request about Pubnet

I am looking for an easy-to-handle application to analyse collaborative networks in science, and I am very interested by Pubnet, that you published quite a while ago. Unfortunately, event if it looks very simple to use the web interface, after submitting a query with a author name, I always have a page indicating the pubmed xml was generated, but it is never analysed. It always blocks as this: (see image)

We’ve managed to revive pubnet. Please check it out.

Help regarding co-authorship network (PubNet)

I am trying to perform the comparison of my co-authors network with PubNet submitted network of consortium’s.

Can you please provide the PMID’s for the individual centers you have used.

It will ne easy to compare using same input you have provided.

Can you please provide PubNet access with more than 20 papers.

Actually I did the work on pubnet over 10 years ago as an undergraduate student. So I am no longer in the lab.

If you have additional questions you should direct them to Mark Gerstein. I believe the TopNet tool can be accessed here: (it seems to have been renamed to TYNA)

I am trying to access TopNet from PubNet, its not working.

Can you provide a working link for same.

I will use PMID information from PubNet gallery section for each center’s.

If I also get same network properties as in PubNet paper, than I can say created co-author network is also correct

If you click on the text label (e.g. "NESG") it will show you PMIDs for the query:

You can explore further in the “text view” link near the bottom.

subway network maps


I’ve really enjoyed seeing your subway network maps. Our institute at Duke has an external review coming up, and I was wondering if any of the code you’ve developed might be applicable to visualize the published interactions within our institute as well as outside with other investigators across the Duke campus.

Thoughts, or is this still too early?

And I bet I’m not the only one who would be interested in this. Are you planning to publish this method? I would think many universities/groups would find this informative to understand where the interactions are happening across campus and where they aren’t happening enough.

I am very enthusiastic that you find our analysis of publication
networks interesting. We just sent out a more extensive description
of this to the analysis group.

In relation to the software, we actually constructed a package for
doing literature networks and distributed some software associated
with it. It is called PubNet and it is available at Unfortunately the web server does not work
that well as of late, mostly due to changes in the NCBI’s PubMed
system, but you can still download the software and do the queries
manually if you want to. I hope this is of use.



I just tried to access Pubnet again and it stopped at the parsing XML stage. Please let me know if this is my error or if the site is no longer functional.


PubNet stopped functioning when NCBI changed their data APIs. We are working on fixing it.