Who's interested in Pubmed for Drupal
We are working on the specification for a module that will be able to integrate content from PubMed, a service of the U.S. National Library of Medicine that includes over 18 million citations from MEDLINE and other life science journals for biomedical articles back to 1948.
I found the following blog post written in 2003(?) that is talking about a PubMed module but I couldn't find it in the repository. I contacted the author, but I thought I could already post a first spec stump while I wait for his answer.
In a first use case we imagine the module could be used to auto-generate reference lists for scientist's profile pages:
- The module would do regular queries to the PubMed database to verify if any new articles for a given person/keyword have been published.
- All new articles would end up in a download queue (to keep within the connection restraints set by PubMed)
- The module downloads the articles and stores them as unpublished nodes
- All scientists with a profile on the site receive an email with a notification that a new publication has been found for his/her name/query
- The scientist reviews the article and approves it's publication on his/her profile
- Depending on the settings a title, co-authors and abstract with a link to the full text article are published
- With a block view these articles can be shown on the scientist's profile page
If you would want to do this for only a couple of profiles you could build RSS feeds in the PubMed user interface for the consecutive queries and use FeedAPI to pull in the content. But you wouldn't want to do this for more than 50 scientists (duplicate downloads, lot of manual work)...
If you have any other use cases or if you would like to contribute to the development of this project, post a comment or send us a mail at info {at} pronovix.com.
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I posted a video on our blog that explains how this can be done with existing modules in Drupal, it's not perfect, but for smaller groups it might be good enough.
Check it out at:
http://www.pronovix.com/solution/importing-rss-feeds-pubmed-drupal
A student from our Drupal class also started working on the module so stay tuned.
I had to integrate PUBMED and a drupal install way back in 2005 back in drupal 4.5
I'd be interested on how you might integrate the two better
I was only using for basic screen scraping with a user drop down
email if you would like a like
keep us posted
We need to work with PubMed for some Science Collaboration Framework projects.
I think our main use cases are a bit different, but please keep us up on your approaches and progress. Thanks for making your plans known, and we'll let you know any moves we make also.
Thanks,
benjamin, Agaric Design Collective
Would love to see this done in a modular way so that it could be easily modified to work with any source database. And would be very interested in seeing this setup to be designed to work with the bibliography module. Perhaps there will be cases where folks want to publish the bibliography in some format but perhaps not make the article itself available for whatever reason.
The problem is that the bibliography module doesn't play well with CCK (it has hard coded nodes). Maybe a rewrite of it's data structure is due?
This sounds most promising. At work, we were just talking about the need to find or generate a master list of publications for our scientists, and of course we're thinking about ways to best use PubMed.