Score of 2

1 answer

106 views

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 ...

Score of 0

0 answers

150 views

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 ...

Score of 0

1 answer

153 views

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 &...

Score of 0

1 answer

313 views

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:...

Score of -1

1 answer

205 views

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 ...

Score of 0

0 answers

382 views

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 ...

Score of 1

3 answers

1440 views

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 ...