Introduction

This page lists some useful PubMed queries

Find sequences published in a journal

We can find all sequences linked to a speciifc journal. This is useful if the journal is not indexed by PubMed. For example, to find all sequences linked to the journal Cladistics, use this query.

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&term=Cladistics[jour]&retmax=5000

Find PubMed id from DOI

Given a DOI we can see whether Pubmed has the corresponding paper using a simple term search. For example,

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=10.1073/pnas.0605858103

looks for the DOI doi:10.1073/pnas.0605858103. The resulting XML includes the PubMed identifier 17079492.

<?xml version="1.0"?>
<!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD eSearchResult, 11 May 2002//EN" 
"http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd">
<eSearchResult>
	<Count>1</Count>
	<RetMax>1</RetMax>
	<RetStart>0</RetStart>
	<IdList>
		<Id>17079492</Id>
	</IdList>
	<TranslationSet>
	</TranslationSet>
	<TranslationStack>
		<TermSet>
			<Term>10.1073/pnas.0605858103[All Fields]</Term>
			<Field>All Fields</Field>
			<Count>1</Count>
			<Explode>Y</Explode>
		</TermSet>
		<OP>GROUP</OP>
	</TranslationStack>
	<QueryTranslation>10.1073/pnas.0605858103[All Fields]</QueryTranslation>
</eSearchResult>

Find URL for article

Papers in Pubmed without a DOI may have a URL link to the online version. For example pmid:12655139 is linked to a paper by the URL http://joi.jlc.jst.go.jp/JST.JSTAGE/ggs/78.71. This URL is obtained by this query

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?&dbfrom=pubmed&id=12655139&cmd=prlinks