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Questions tagged [pubmed]

PubMed is a free online database accessing the MEDLINE database of references and abstracts on life sciences and bio-medical topics. Tag pubmed can be used for web based database querying problems.

Wiki:

PubMed is a free online database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine ( NLM ) at the National Institutes of Health ( NIH ) maintains the database as part of the Entrez system of information retrieval.

MEDLINE online access to the MEDLARS computerized database had been primarily through institutional facilities like medical libraries. PubMed, first ushered in the era of private, free, and home-computerized MEDLINE searching. The PubMed system is offered free to the public.

Usage:

The can be used for web based programming related problems to access data from pubmed databases and other querying problems. Please avoid theoretical questions for usage of pubmed website.

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How to use the PubMed API to search for an article with an exact title?

I'm trying to use the PubMed API to search for articles with an exact title. As an example, I want to search for the title The cost-effectiveness of mirtazapine versus paroxetine in treating people with depression in primary care I want up to 1000…
Richard
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How do I download all the abstract datas from the pubmed data ncbi

I want to download all the pubmed data abstracts. Does anyone know how I can easily download all of the pubmed article abstracts? I got the source of the data : ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/af/12/ Is there anyway to download all these tar…
Soundarya Thiagarajan
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How to search PubMed or other databases using R

I have recently been using the excellent rplos package, which makes it very easy to search through papers hosted on the Public Library of Science (PLOS) API. I've hit a snag, in that the API itself seems to have some missing information - a major…
lukeholman
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Is there a way with biopython to obtain the full abstract from a pubmed article?

I currently have the following code which queries pubmed: from Bio import Entrez Entrez.email = "kuharrw@hiram.edu" # Always tell NCBI who you are handle = Entrez.esearch(db="pubmed", term="bacteria") record = Entrez.read(handle) list =…
Ryan Raten Kuhar
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Downloading all full-text articles in PMC and PubMed databases

According to one of the answered questions by NCBI Help Desk , we cannot "bulk-download" PubMed Central. However, can I use "NCBI E-utilities" to download all full-text papers in PMC database using Efetch or at least find all corresponding PMCids…
s.22217330
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Issue with parsing publication data from PubMed with Entrez

I am trying to use Entrez to import publication data into a database. The search part works fine, but when I try to parse: from Bio import Entrez def create_publication(pmid): handle = Entrez.efetch("pubmed", id=pmid, retmode="xml") …
apiljic
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How can I extract the abstract from efetch (Biopython, Entrez)?

I am new to python and would like to extract abstracts from pubmed using the entrez system from the bio package. I got the esearch to give me my UIDs (stored in my_list_ges) and I can also download an entry using efetch. Now, however, the result is…
MaxS
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Is there any way to get abstracts for a given list of pubmed ids?

I have list of pmids i want to get abstracts for both of them in a single url hit pmids=[17284678,9997] abstract_dict={} url = https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi? …
pat
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Full Text PDFs for PubMed Articles

While working on a project I need to download and process full text articles for PubMed abstracts, is there any implemented code or tool that allows the user to input a set of PubMed ids and downloads the free full text articles for the same. Any…
Shreyas Karnik
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Sort pubmed searches from rentrez by relevance

I'm searching PubMed using the rentrez package in R and would like to get the results sorted by relevance. Currently they are sorted by publication date. library(rentrez) query = 'regression to the mean[TITL]' entrez_search =…
agbarnett
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Sort options for Pubmed eutils esearch?

I am using BioPython to query the Pubmed database through the eutils API. The esearch endpoint has a sort option, but the API documentation doesn't list all of the options for this…
adamc
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Download all pubmed abstracts

Does anyone know how I can easily download all of the pubmed article abstracts? I am working on a text mining project. The closest one I can find can download one abstract at a time given an pmid, but that would be too slow for my purpose since I'd…
leontp587
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pyparsing one query format to another one

I am at a loss. I have been trying to get this to work for days now. But I am not getting anywhere with this, so I figured I'd consult you guys here and see if someone is able to help me! I am using pyparsing in an attempt to parse one query format…
Wurzelgogerer
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Slow first call to C# web service

I am trying to access the PubMed web services as provided here: http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/DOC/esoap_help.html I wrote code in java to access the web service and the return times were on the order of less than 1 second. I…
chi-hawk
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Get full paper content from PubMed via API and list of IDs

I'm hoping to query the PubMed API based on a list of paper IDs and return the title, abstract and content. So far I have been able to do the first three things doing the following: from metapub import PubMedFetcher pmids = [2020202, 1745076,…
msa
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