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Questions tagged [pubmed-api]

14 questions
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1 answer

Rismed R package fails to run EUtilsGet function

I'm using the Rismed package to make s search query for the word "hsv". search_topic_hsv <- "HSV" search_query_hsv <- EUtilsSummary(search_topic_hsv, retmax= 27000, mindate= 1970, maxdate= 2022) summary(search_query_hsv) #returns to…
Başak Uysal
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Biopython elink citation search function does not take a list and returns non separated results

I am trying to extract the citation network of a list of papers from pubmed using Biopython Entrez.elink. I was able to submit a list of PMIDs when using efetch but elink only lets me query multiple PMIDs when I use elink(db…
Mnemonic
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1 answer

Extracting pubmed abstracts in r retrieves each abstract in multiple rows (more rows in abstracts that in pubmed ID)

I am trying to extract pubmed abstracts and their titles to place them in a dataframe. will the help of members stackoverflow, I was able to write the code below, which works. The issue now is that the number of rows in the abstracts variable is…
Bahi8482
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1 answer

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 additional filters such as species My code: import…
kaotech
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1 answer

NotXMLError: Failed to parse the XML data

I'm trying to use the Entrez module from Biopython to retrive full text articles from PubMed Central. This is my code to do the same. import urllib3 import json import requests from Bio import Entrez from Bio.Entrez import efetch,…
AnonymousMe
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1 answer

Getting data from PUBMED database passing multiple keywords at a time

I am trying to pass a keywords list to PubMed to get the papers that contain any of those words. I am trying the following code and it produces around 744 papers that are much less than that of the actual number of papers. def…
JAMSHAID
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1 answer

Pubmed API returns less results than web interface

I'm trying to access Pubmed results via R using their API, but I consistently get fewer results than what the same query achieves when used with the web interface. By digging in the output I noticed that the problem lays in a different query…
Bakaburg
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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 the command $ export NCBI_API_KEY=xxxx But I keep…
TraPS-VarI
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How to search full text free and last 5 years data in pubmed API?

I am using below API : https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmode=json&sort=relevance&term=breast%20cancer and i want use full text free and last 5 years data filter in query string
SURENDER SINGH
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Parsing multiple elements with multiple tags from XML file - edited request

I have accessed descriptions of publications from PubMed using their e-utilities using Python. There are many characteristics of each article that I want to extract for each article/author combination the "Id", "Author", "Title" and "DOI"to put into…
Gregg Lund
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Is there a way to keep connection warm for API?

I am using PubMed api and the first request is quite slow. When performing a simple curl request such as curl -X GET "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" it takes around 7s. So I made an experiment and when using python…
purple_lolakos
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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 published dates/gaps between them. Would there be a…
mickmars51
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Fetching multiple pubmed abstract using r (httr)

This is continuation for the same task I am trying to perform from this question. Working with pubmed api in R (httr) to retrieve abstracts using the answer below, I am able to find the pubmed IDs for the abstracts of interest. Now, I am trying to…
Bahi8482
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Working with pubmed api in R (httr) to retrieve abstracts

I am trying to work directly with the pubmed api from R using httr. There are excellent packages available such as RISmed and easypubmed but for this particular task, I need to interact directly with the api. Using this set of instructions…
Bahi8482
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