Skip to content

Instantly share code, notes, and snippets.

@hubgit
Last active June 3, 2019 14:26
Show Gist options
  • Save hubgit/7359278 to your computer and use it in GitHub Desktop.
Save hubgit/7359278 to your computer and use it in GitHub Desktop.
Useful URLs for working with the PMC Open Access Subset via EUtils
Search PubMed for articles in the PMC Open Access Subset for which free full text (i.e. XML) is available:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmode=xml&term=pubmed+pmc+open+access%5Bfilter%5D+AND+free+full+text%5Bfilter%5D
Find the PMCID for an article by PMID:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=pmc&retmode=xml&linkname=pubmed_pmc&id=24191168
Fetch full text article XML from PMC by PMCID:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=3804407
A PMC article for which the full text XML is not available:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=380440
Search PMC for an article by DOI:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pmc&retmax=1&term=10.1155%2F2013%2F248349%5BDOI%5D
Get XML for an article from the PMC OAI server by PMCID (namespaces <3):
http://www.pubmedcentral.nih.gov/oai/oai.cgi?verb=GetRecord&metadataPrefix=pmc&identifier=oai:pubmedcentral.nih.gov:3628370
Search PMC for articles with a certain license:
http://www.pubmedcentral.nih.gov/utils/oa/oa.fcgi?term=cc+by+nc+license%5Bfilter%5D
License vagueness:
http://www.ncbi.nlm.nih.gov/books/NBK159964/
http://oag.cottagelabs.com/
Macrodocs:
search PMC Open Access Subset, list matching articles, pick an article by DOI or PMC ID, fetch and render the XML
http://macrodocs.org/
@Klortho
Copy link

Klortho commented Feb 18, 2015

See also http://www.ncbi.nlm.nih.gov/pmc/about/new-in-pmc/#day8 for a pretty comprehensive description of PMC URLs, including, for example, going directly to an article via its DOI.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment