What are the APIs available to retrieve PubMed or PMC articles?
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6.1 years ago

When a keyword is searched in PubMed or PMC database, how can I retrieve the documents that are shown in results?

Latest text mining information retrieval • 3.3k views
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"When a keyword is searched" : using e-utils ?

"How can I retrieve the documents": do you want the pdf ?

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I'm building a text mining application. When a keyword is entered in the system, it should automatically search it in PubMed or PMC and get all the articles. (Title, content etc) I'm exactly not sure how to do it. Can I do it using e-utils? Does it have an API?

No, I don't want Pdf. I want either in ASCII or HTML,since I have to perform text mining.  

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Can I use e-utils for that?

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Just google "NCBI text mining", you will get some articles whose Materials and Methods section can be of assistance.

Otherwise, check out http://www.ncbi.nlm.nih.gov/pmc/tools/get-full-text/.

You will be limited to open access reviews, I fear, due to copyright issues.

Good luck!

PS: pdftotext -layout input.pdf output.txt will let you process pdf files as text files.You will almost certainly want a quick way to access the articles under a human readable form.

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6.1 years ago
cvu ▴ 180

yes you can use NCBI e-utils

check out this API:

change pmid and rettype

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=pmid&retmode=text&rettype=MEDLINE
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Be careful not to hammer the NCBI website with your requests. This will likely result in your institute being blacklisted and make your colleagues quite unhappy.

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