bioinformatics toolbox: getpubmed.m does not return the expected number of records
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George on 17 Dec 2021
Commented: George on 18 Dec 2021
I'm running the 'getpubmed.m' script that is found in the bioinformatics toolbox. I'm using examples from the script.
Example1: out = getpubmed('breast+cancer+AND+BRCA1+AND+Clinical+Trial[PT]',...
According the script maxnum = 50; % NUMBEROFRECORDS default is 50
However, running the above script the number of records returned is nine (9).
Example2: out = getpubmed('OBP+insect',...
give the same result (output of 9 records)
Is there a way to tweak with the script and get the requisite number of records. Thanks in advance for any suggestions
Ive J on 18 Dec 2021
Edited: Ive J on 18 Dec 2021
getpubmed (and generally, most of the functions in Bioinformatics toolbox) are quite outdated and TMW for some reasons, does not put any effort in improving/expanding it's functionality.
You can write your own scripts using Eutils API, take a look at examples there.
x = webread('https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmode=json&retmax=20&sort=relevance&term=breast+cancer'); % retmax: max number of IDs to return
x.esearchresult.idlist % returned pumbed Ids
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