Retreive associated DOI from PDB

Question

[Joe]

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

Answer 1

[emmahe]

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'])

[Joe]

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

Answer 2

[Pierre Lindenbaum]

use ncbi eseach to get the NCBI structure id associated to your pdb acn E.g: 2M5E

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=structure&term=%222M5E%22[PDB%20Accession]

use elink to get the pubmed associated to this structure id:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=structure&db=pubmed&id=121620

result:

• https://www.ncbi.nlm.nih.gov/pubmed/28343066
• https://www.ncbi.nlm.nih.gov/pubmed/21439835

[Joe]

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

[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

[Pierre Lindenbaum]

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

[Joe]

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

[Pierre Lindenbaum]

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

Answer 3

[GenoMax]

See the example 2 for PDB API here.