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Retreive associated DOI from PDB

Does anyone know if it's possible (and if so how) to obtain a DOI number associated with a PDB ID, through a script - preferably in python.

The idea is this:

  1. Existing script trawls HMMs, returns a closest PDB ID match.
  2. Results of script in 1 are tabulated by my own script.
  3. For each PDB hit that's returned, I'd like to 'look up' the DOI of the paper responsible for depositing it, and append that DOI to the end of the line in the table.

Cheers

pdb python doi
• 2,636 views • link
updated by emmahe • emmahe • written by Joe Joe

3 answers

Check out the PDBe REST API: http://www.ebi.ac.uk/pdbe/api/doc/

Simple python example:

import requests

res = requests.get("https://www.ebi.ac.uk/pdbe/api/pdb/entry/publications/5m98")
data = res.json()

print(data["5m98"][0]['doi'])
• 0 views • link
written by emmahe • emmahe

Oh perfect, thanks very much! Python continues to amaze.

• 0 views • link
written by Joe Joe

Interesting, this was the approach a colleague suggested, I'll give it a go!

• 0 views • link
written by Joe Joe

Thanks Pierre, the following worked for me: 

esearch -db pubmed -query "4MIX" | esummary | xtract -pattern DocumentSummary -block ArticleId -sep "\t" -tab "\n" -element IdType,Value | grep doi | cut -f 2
• 0 views • link
written by Joe Joe

I'm surprised you didn't choose genomax2's answer

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

My experience with XML and web querying is pretty limited so chose the path of least resistance!

• 0 views • link
written by Joe Joe

using a xsltstylesheet:


<xsl:stylesheet xmlns:xsl="&lt;a href=" <a="" href="http://www.w3.org/1999/XSL/Transform" rel="nofollow">http://www.w3.org/1999/XSL/Transform" "="" rel="nofollow">http://www.w3.org/1999/XSL/Transform' version='1.0'>
<xsl:output method="text"/>
<xsl:template match="/">
<xsl:apply-templates select="dataset/record"/>
</xsl:template>
<xsl:template match="record">
    <xsl:variable name="acn" select="dimStructure.structureId/text()"/>
    <xsl:for-each select="dimStructure.doi">
        <xsl:value-of select="$acn"/>
        <xsl:text> </xsl:text>
        <xsl:value-of select="./text()"/>
        <xsl:text>
</xsl:text>
    </xsl:for-each>
</xsl:template>
</xsl:stylesheet>

execute:

curl -s  'http://www.rcsb.org/pdb/rest/customReport.xml?pdbids=1stp,2jef,1cdg&customReportColumns=structureId,doi&primaryOnly=1' |\
xsltproc stylesheet.xsl -

1STP null
2JEF 10.1074/jbc.M700656200
1CDG 10.1006/jmbi.1994.1168
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

See the example 2 for PDB API here.

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written by GenoMax GenoMax

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