Get PubMed documents based on a list of pmids?

KNIME Analytics Platform
1

Hi

I have a list of pmids and i want to grap all the documents from PubMed that match those pmids?

Malik

2

Hi Malik,

you can use KNIME's REST Get Request node in association with Pubmed's EFetch API. Have a look here about how to use the API:

https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch

Cheers,
Marco.

3

HI Marco

What about using document grabber ? just post the id there ?

Also why the document grabber node is not working now and i'm getting -1 for every  keywords?

 

Malik

4

Sorry Malik, I am not that familiar with the Document Grabber node. I just tried to run it with a simple query which I would expect to work and I also get -1 as a result. It is possible that PUBMED changed something in their API's and the node has not been updated since then.

The method based on REST API above works.

Cheers,
Marco.

5

Who can help me with " Document Grabber " node? 

 

Malik

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