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I'm using this "RISmed" library to do some query of my gene or protein of interest and the output comes with pubmed ID basically, but most of the times it consist of non-specific hits as well which are not my interest. As I can only see the pubmed ID I have to manually put those returned ID and search them in NCBI to see if the paper is of my interest or not.

Question: Is there a way to to return the abstract of the paper or summary sort of along with its pumed ID , which can be implemented in R?

If anyone can help it would be really great..

zx8754
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kcm
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1 Answers1

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Using the example from the manuals we need EUtilsGet function.

library(RISmed)

search_topic <- 'copd'
search_query <- EUtilsSummary(search_topic, retmax = 10,
                              mindate = 2012, maxdate = 2012)
summary(search_query)

# see the ids of our returned query
QueryId(search_query)

# get actual data from PubMed
records <- EUtilsGet(search_query)
class(records)

# store it
pubmed_data <- data.frame('Title' = ArticleTitle(records),
                          'Abstract' = AbstractText(records))
zx8754
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  • As i try to ask a new question i get this message "Im no longer allowed to ask question" but i did ask question about venn diagram from this forum itself. Can you tell me what shall i do or modify so that i can ask question? – kcm Jul 27 '20 at 07:59
  • @krushnachChandra Hard to guess, could be that you asked too many low quality posts - they were downvoted, closed, deleted, etc. Can be temporary automatic suspension. See related meta post - https://meta.stackoverflow.com/q/255583/680068 – zx8754 Jul 27 '20 at 08:02
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    "ould be that you asked too many low quality posts - they were downvoted, closed, deleted" in this forum the last question i asked in venn diagram related ..which you can check and no question as such....but thanks for the clarification i will wait – kcm Jul 27 '20 at 09:06
  • I would be really glad if you have a look at this https://stackoverflow.com/questions/63171300/parsing-column-and-splitting-it-into-tabular-form – kcm Jul 30 '20 at 12:38