199 questions
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108
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Why Entrez esearch doesn't provide all abstracts from PubMed?
I'm trying to fetch abstracts from PubMed using Entrez (Biopython). In the code, I collect the data with Entrez.esearch and Entrez.efetch, write it to the file and then get needed info to the ...
- 21 reputation score 21
Score of 1
1
vote
3 answers
3
answers
284 views
284
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Extracting a list from PubMed XML in R and adding to data frame/tibble
I am trying to extract a few bits of information from XML using R and then put them into a data frame to export as a csv. The XML is coming from PubMed records and I'm using the rentrez package to ...
- 11 reputation score 11
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1 answer
1
answer
78 views
78
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PubMed query: priority of operations using parenthesis leads to zero results
I am using the easyPubMed package in R, but I think this applies to PubMed generally, for example using the website interface (which is perhaps simpler for debugging since we know the R package is not ...
- 1,038 reputation score 1038
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150 views
150
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Extracting data from XML Pubmed articles
Im trying to write a python script that takes articles from de pubmed db, extracts information and creates a SQL database. The info I need from the articles is this one:
pmid
title
year
doi
...
- 1 reputation score 1
Score of 0
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1 answer
1
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154 views
154
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Rentrez pubmed search - order by descending publication date
Using the Rentrez package in R, I want to search a list of drugs and find the date of the earliest publication mentioning each. My strategy is as follows:
# Search for pubmed IDs for a drug
drug_name &...
- 446 reputation score 446
Score of 0
0
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1 answer
1
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314 views
314
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Searching Entrez based on paper title
I am trying to search NCBI's Entrez based on a title. Here are my GET requests's URL and parameters:
import requests
url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
# SEE:...
- 3,139 reputation score 3139
Score of 2
2
votes
1 answer
1
answer
542 views
542
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Downloading large chunks of Pubmed abstracts using easyPubMed in R
I am trying to download large chunks of abstracts via the easyPubMed package in R.
Here is my code:
out.A <- easyPubMed::batch_pubmed_download(pubmed_query_string = "ineichen bv",
...
- 21 reputation score 21
Score of 2
2
votes
1 answer
1
answer
641 views
641
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Is there a way to add filters such as article type ("only show meta-analyses") to a PubMed/Entrez esearch API search?
Thanks for taking the time to read this. I would like to know if it is possible to filter results from the PubMed API by e.g. article type (only show meta analysis/clinical trial/etc) or use the ...
- 33 reputation score 33
Score of -1
-1
votes
1 answer
1
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205 views
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pyPubmed API_Key not found?
I get this error. How to fix this?
$ pubmed advance-search [2023-05-29 11:08:50 Eutils validate_api_key WARNING MainThread:234] API_KEY not found! Use eutils with a api_key is a good idea!
I tried ...
- 19 reputation score 19
Score of 0
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1 answer
1
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159 views
159
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How do I get ISSNs and full journal names from a list of abbreviated journal names in R?
I have a list of research journals that I have extracted from iCite and pubmed, but they only give me the abbreviated journal names. How do I get the full names and ISSNs?
[1] Nat Commun ...
- 59 reputation score 59
Score of 0
0
votes
0 answers
0
answers
382 views
382
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Searching PubMed via python vs web
I am trying to search articles on PubMed. I was hoping to get the same articles when searching the website, test out the search terms and then use it via python code. I tried a few libraries but the ...
- 566 reputation score 566
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1 answer
1
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426 views
426
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Extracting author and affiliation from xml file retrieved using rentrez
I was following this post's code: https://quantixed.org/2021/04/04/ten-years-vs-the-spread-ii-calculating-publication-lag-times-in-r/ and was amazed at the ability to output received, accepted and ...
- 1 reputation score 1
Score of 2
2
votes
1 answer
1
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10976 views
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Why do I get a ChunkedEncodingError in Python when using requests module?
I try to query this API https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi
with these params ?db=mesh&id=68016019
So the whole URL is https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch....
- 83 reputation score 83
Score of 2
2
votes
1 answer
1
answer
572 views
572
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Using R to analyse pubmed articles. Trying to create wordcloud but also association with year of publication
MOST RECENT EDIT:
I have successfully created my required data frames containing pmid,year and abstract as columns from a literature search on pubmed. I then split this data frame into many separate ...
- 23 reputation score 23
Score of 1
1
vote
3 answers
3
answers
1441 views
1k
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Extracting PubMed central article to Python Dataframe
I'm working with PubMed central articles and need to create columns with 'pmc' id, 'title', 'abstract', 'full-text' and 'authors'.
I have worked with other similar questions and unable to apply on my ...
- 11 reputation score 11