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Questions tagged [europepmc]

9 questions
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restful pagination using python elementree xml parser and loop

working on an app https://share.streamlit.io/carrlucy/hsl_oa/main that recurses the europmc database looking for open data and the restful api that is provided includes a "nextcursormark" field so that queries can do pagination... i'm stumbling with…
alibama
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Formatting JSON GET results in Python

I am trying to get Covid-19 JSON data from Europe Pubmed Central. The JSON results returned by Europe PMC server looks like this. My initial code querying the server looks like this: import requests import json mydata =…
Alex Maina
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Bulk download Europe PMC Metadata

I am trying to download entire metadata from Europe PMC dataset. I am able to download the metadata through rest api provided by the site. But the constraint is the volume of the data and because of that I am facing some performance…
Santosh Kadge
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Modifying a GET request for full-text retrival in R

I am using the R package europepmc (https://cran.r-project.org/web/packages/europepmc/europepmc.pdf) and the function epmc_ftxt for obtaining the full texts of some articles given their PMC ID. However for many articles I keep getting the following…
Francesca Longhin
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Bulk Data from Europe PMC annotation api

i have a pmc.txt file which contains atleast 20k pmc ids, and the api will only take i think 1000 request each time. i have written the code for one id, but i'm not able to do for the whole file, below is my main code. Please help. if __name__ ==…
Arvind
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I'm trying to get bulk data from Europe PMC annotations api in python

my code is if name == 'main': json_data=requests.get("https://www.ebi.ac.uk/europepmc/annotations_api/annotationsByArticleIds?articleIds=PMC%3A4771370§ion=Abstract&provider=Europe%20PMC&format=JSON").content r=json.loads(json_data) df =…
Arvind
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Parsing of PMCID table row to column form

dput(t1) structure(list(PMCID = c("PMC7809753", "PMC7809753", "PMC7809753", "PMC7809753", "PMC7809753", "PMC7790830", "PMC7790830", "PMC7790830", "PMC7790830", "PMC7790830"), table = c("Table 1", "Table 1", "Table 1", "Table 1", "Table 1", "Table…
PesKchan
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Use Node.js to consume Europe PMC SOAP web service

Any example of using JavaScript in the Node.js environment to consume the Europe PMC SOAP web service?
Yuci
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Transforms Europe PMC RESTful "search" responses to source/external-id lists

I would like to use Europe PMC RESTful API to transforms "search" responses to source/external-id lists, with one-line per record text. Any suggestions / examples (in JavaScript)?
Yuci
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