21 May 2016

Playing with the @ORCID_Org / @ncbi_pubmed graph. My notebook.

"ORCID provides a persistent digital identifier that distinguishes you from every other researcher and, through integration in key research workflows such as manuscript and grant submission, supports automated linkages between you and your professional activities ensuring that your work is recognized. "
I've recently discovered that pubmed now integrates ORCID identfiers.

And there are several minor problems, I found some articles where the ORCID id is malformed or where different people use the same ORCID-ID:







You can download the papers containing some orcid Identifiers using the entrez query http://www.ncbi.nlm.nih.gov/pubmed/?term=orcid[AUID].
I've used one of my tools pubmeddump to download the articles asXML and I wrote PubmedOrcidGraph to extract the author's orcid.
<?xml version="1.0" encoding="UTF-8"?>
<PubmedArticleSet>
  <!--Generated with PubmedOrcidGraph https://github.com/lindenb/jvarkit/wiki/PubmedOrcidGraph - Pierre Lindenbaum.-->
  <PubmedArticle pmid="27197243" doi="10.1101/gr.199760.115">
    <year>2016</year>
    <journal>Genome Res.</journal>
    <title>Improved definition of the mouse transcriptome via targeted RNA sequencing.</title>
    <Author orcid="0000-0002-4078-7413">
      <foreName>Giovanni</foreName>
      <lastName>Bussotti</lastName>
      <initials>G</initials>
      <affiliation>EMBL, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom;</affiliation>
    </Author>
    <Author orcid="0000-0002-4449-1863">
      <foreName>Tommaso</foreName>
      <lastName>Leonardi</lastName>
      <initials>T</initials>
      <affiliation>EMBL, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom;</affiliation>
    </Author>
    <Author orcid="0000-0002-6090-3100">
      <foreName>Anton J</foreName>
      <lastName>Enright</lastName>
      <initials>AJ</initials>
      <affiliation>EMBL, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom;</affiliation>
    </Author>
  </PubmedArticle>
  <PubmedArticle pmid="27197225" doi="10.1101/gr.204479.116">
    <year>2016</year>
    <journal>Genome Res.</journal>
(...)
Now, I want to insert those data into a sqlite3 database. I use the XSLT stylesheet below to convert the XML into some SQL statement.
<?xml version="1.0"?>
<xsl:stylesheet
 xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
 version="1.0"
    xmlns:xalan="http://xml.apache.org/xalan"
    xmlns:str="xalan://com.github.lindenb.xslt.strings.Strings"
    exclude-result-prefixes="xalan str"
 >
<xsl:output method="text"/>
<xsl:variable name="q">'</xsl:variable>

<xsl:template match="/">
create table author(orcid text unique,name text,affiliation text);
create table collab(orcid1 text,orcid2 text,unique(orcid1,orcid2));
begin transaction;
<xsl:apply-templates select="PubmedArticleSet/PubmedArticle"/>
commit;
</xsl:template>

<xsl:template match="PubmedArticle">
<xsl:for-each select="Author">
<xsl:variable name="o1" select="@orcid"/>insert or ignore into author(orcid,name,affiliation) values ('<xsl:value-of select="$o1"/>','<xsl:value-of select="translate(concat(lastName,' ',foreName),$q,' ')"/>','<xsl:value-of select="translate(affiliation,$q,' ')"/>');
<xsl:for-each select="following-sibling::Author">insert or ignore into collab(orcid1,orcid2) values(<xsl:variable name="o2" select="@orcid"/>
<xsl:choose>
 <xsl:when test="str:strcmp( $o1 , $o2) < 0">'<xsl:value-of select='$o1'/>','<xsl:value-of select='$o2'/>'</xsl:when>
 <xsl:otherwise>'<xsl:value-of select='$o2'/>','<xsl:value-of select='$o1'/>'</xsl:otherwise>
</xsl:choose>);
</xsl:for-each>
</xsl:for-each>
</xsl:template>
</xsl:stylesheet>

This stylesheet contains an extension 'strmcp' for the xslt processor xalan to compare two XML strings
This extension is just used to always be sure that the field "orcid1" in the table "collab" is always lower than "orcid2" to avoid duplicates pairs.
./src/xslt-sandbox/xalan/dist/xalan -XSL orcid2sqlite.xsl -IN orcid.xml

create table author(orcid text unique,name text,affiliation text);
create table collab(orcid1 text,orcid2 text,unique(orcid1,orcid2));
begin transaction;
insert or ignore into author(orcid,name,affiliation) values ('0000-0002-4078-7413','Bussotti Giovanni','EMBL, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom;');
insert or ignore into collab(orcid1,orcid2) values('0000-0002-4078-7413','0000-0002-4449-1863');
insert or ignore into collab(orcid1,orcid2) values('0000-0002-4078-7413','0000-0002-6090-3100');
insert or ignore into author(orcid,name,affiliation) values ('0000-0002-4449-1863','Leonardi Tommaso','EMBL, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom;');
insert or ignore into collab(orcid1,orcid2) values('0000-0002-4449-1863','0000-0002-6090-3100');
insert or ignore into author(orcid,name,affiliation) values ('0000-0002-6090-3100','Enright Anton J','EMBL, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom;');
(...)
and those sql statetements are loaded into sqlite3:
./src/xslt-sandbox/xalan/dist/xalan -XSL orcid2sqlite.xsl -IN orcid.xml |\
 sqlite3 orcid.sqlite

The next step is to produce a gexf+xml file to play with the orcid graph in gephi.
I use the following bash script to convert the sqlite3 database to gexf+xml.
DB=orcid.sqlite

cat << EOF
<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.2draft" xmlns:viz="http://www.gexf.net/1.1draft/viz" version="1.2">
<meta>
<creator>Pierre Lindenbaum</creator>
<description>Orcid Graph</description>
</meta>
<graph defaultedgetype="undirected" mode="static">

<attributes class="node">
<attribute type="string" title="affiliation" id="0"/>
</attributes>
<nodes>
EOF

sqlite3 -separator ' ' -noheader  ${DB} 'select orcid,name,affiliation from author' |\
 sed  -e 's/&/&/g' -e "s/</\</g" -e "s/>/\>/g" -e "s/'/\'/g"  -e 's/"/\"/g' |\
 awk -F ' ' '{printf("<node id=\"%s\" label=\"%s\"><attvalue for=\"0\" value=\"%s\"/></node>\n",$1,$2,$3);}'

echo "</nodes><edges>"
sqlite3 -separator ' ' -noheader  ${DB} 'select orcid1,orcid2 from collab' |\
 awk -F ' ' '{printf("<edge source=\"%s\" target=\"%s\"/>\n",$1,$2);}'
echo "</edges></graph></gexf>"



The output is saved and then loaded into gephi.






That's it,

Pierre
at

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