Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Download and query fulltext from PMC OASS #4

Open
DASpringate opened this issue Feb 5, 2013 · 3 comments
Open

Download and query fulltext from PMC OASS #4

DASpringate opened this issue Feb 5, 2013 · 3 comments
Labels
enhancement
Milestone
Version 1.0

Comments

@DASpringate
Copy link
Member

  • Get PMC IDs from downloaded PubMed files and pull down xml if it is in OASS
  • Convert XML to R objects / JSON
  • Add predicate functions for fulltext to rpubmed_textsearch.R
@DASpringate
Copy link
Member Author

So, we can potentially:

  • Scape pubmed for PMCID's and then use these to scape PMC for XML, convert to R objects which can be queried with get_articles_by_terms() + some new helper predicate functions. I am guessing that Pubmed frowns on this approach!
  • Download PMIDs from Entrez directly via a modified rentrez_search (Can you download full text XML from PMCOASS via entrez_fetch?), convert as above

Then we need to add functionality to fetch_in_chunks() to automate this...

@DASpringate
Copy link
Member Author

Info here: http://www.ncbi.nlm.nih.gov/pmc/tools/oa-service/

@sckott
Copy link
Contributor

sckott commented Jun 12, 2013

nice, sounds good

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
enhancement
Projects
None yet
Milestone
Version 1.0
Development

No branches or pull requests
2 participants
@sckott @DASpringate