Workflow for query and visualization in R

[bw4sz]

Hello,

Thanks for your work on this really interesting package. Before i get too deep into exploring i wanted your opinion, plus @sckott , on the best framework for what i'm trying to do. I've been playing around with downloading pubmed records to look at affiliation and topic for ecology departments. What would your suggestion be if i had a list of journal titles and a list of academic departments, for querying pubmed from R. I've been using the direct api, but its a bit ugly (source: https://github.com/bw4sz/FacultyNetwork/blob/master/FacultySource.R and markdown example for one department: https://github.com/bw4sz/sandbox/blob/master/FacultyAbstracts.md ). Looking at your package, i don't see a query tool, the fetch tool takes in already known ids?

The major challenge will be associating authors with departments, so your geolocating idea could be very powerful.

I appreciate your time, plus all the work that ROpenSci has done to push the field forward.

Plus thanks Scott, taxize is the best.

Cheers,

Ben Weinstein Stony Brook University

[bw4sz]

One more doc from this morning, on the direction i'm going, in case i was unclear:

http://htmlpreview.github.io/?https://github.com/bw4sz/FacultyNetwork/blob/master/FacultyNetwork.html

[DASpringate]

Hi Ben,

I think you want to use the rentrez package that I used in building rpubmed (http://cran.r-project.org/web/packages/rentrez/index.html). This is a wrapper for the entrez api and has the query tool you require. Have a look at the example section for my fetch_in_chunks() function.

If there are any futher features you would like to see in rpubmed, feel free to let me know or put in a pull request.

Cheers,

David

From: Ben Weinstein [mailto:notifications@github.com] Sent: 01 November 2014 16:49 To: rOpenHealth/rpubmed Subject: [rpubmed] Workflow for query and visualization in R (#18)

Hello,

Thanks for your work on this really interesting package. Before i get too deep into exploring i wanted your opinion, plus @sckott https://github.com/sckott , on the best framework for what i'm trying to do. I've been playing around with downloading pubmed records to look at affiliation and topic for ecology departments. What would your suggestion be if i had a list of journal titles and a list of academic departments, for querying pubmed from R. I've been using the direct api, but its a bit ugly (source: https://github.com/bw4sz/FacultyNetwork/blob/master/FacultySource.R and markdown example for one department: https://github.com/bw4sz/sandbox/blob/master/FacultyAbstracts.md ). Looking at your package, i don't see a query tool, the fetch tool takes in already known ids?

The major challenge will be associating authors with departments, so your geolocating idea could be very powerful.

I appreciate your time, plus all the work that ROpenSci has done to push the field forward.

Plus thanks Scott, taxize is the best.

Cheers,

Ben Weinstein Stony Brook University

— Reply to this email directly or view it on GitHub https://github.com/rOpenHealth/rpubmed/issues/18 . https://github.com/notifications/beacon/AAztFyJ4l5PjkA7IxT_8EblKtuD1a90fks5nJQZwgaJpZM4C15pe.gif

[sckott]

@bw4sz thanks for the kind words, Agreed that rentrez is what you are looking for.