Indexing pubmed articles by data available?
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5 months ago
LauferVA 4.2k

Is there a way to query pubmed articles that includes the type of data included?

For instance, suppose I wanted to locate all pubmed articles where fludarabine was used in a clinical trial for a cancer (of any kind) ... but really i only want to see the ones where survival data and genotype data (of some kind) are both provided.

some of this can be done using the pubmed advanced search page, here: https://pubmed.ncbi.nlm.nih.gov/advanced/. But, I dont see a way to filter by data availability... its a bit tricky because those data might be provided in a table or in supplementary or extended data, or even via a link to anther ncbi site, a linked github site, etc...

of course programmatic tools exist for parsing pubmed articles. there are the eutils; efetch etc.; as well as similar functionality through the python package Bio.Entrez. I think that even if i rely heavily on these tools, I am looking at a custom script, but id just like to see how close I can get to the desired functionality before committing to that.

i can provide examples of target articles that would and would not fit the description of what i would like filtered if that helps.

thank you for any suggestions!

search data pubmed query • 576 views
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For fluradabine I chose "completed with results" studies for this search (530 results today) : https://clinicaltrials.gov/search?term=fludarabine&aggFilters=results:with&viewType=Table

I checked a few initial records and they seem to have a link for publications for some:

https://clinicaltrials.gov/study/NCT00933335?term=fludarabine&aggFilters=results:with&viewType=Table&tab=results&rank=4#publications

https://clinicaltrials.gov/study/NCT00381550?term=fludarabine&aggFilters=results:with&viewType=Table&tab=results&rank=10#publications

So grab the NCT* accessions and check with URL above.

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thanks geno. this will get me started :-)

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I have no knowledge of this area, so this is just an opinion. Don't know what fludarabine is, but I doubt there are that many articles about it of any kind that you need to do all this script customization. It strikes me as very doable to go through a few hundred articles manually, if that, to find out what type of data they contain. It might take longer to write and troubleshoot a custom script than to go through them by hand.

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fludarabine is a place holder, mensur, for a noun of any kind

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