Looking for an expert ?

Yesterday, Andrew Su asked on Biostar: "Given a gene, what is the best automated method to identify the world experts? ".

Here is my solution:

• First for a given gene name, we use NCBI-ESearch to find its Gene-Id in NCBI Gene
• The Gene record is then downloaded as XML using NCBI-EFetch
• XPATH is used to retrieve all the articles in pubmed about this gene and identified by the XML tags <PubMedId>
• Each article is downloaded from pubmed. The element <Affiliation> is extracted from the record; sometimes this tag contains the the main contact's email. The authors are also extracted and we count the number of times each author was found. I tried to solve the problem of ambiguity for the names of the authors by looking at the name, surname and initials. If an author's name was contained in the e-mail, it was affected to him
• At the end, all the authors are sorted in function of the number of times they were seen and the most prolific author is printed out.

Source code

	/**
	* Author: Pierre Lindenbaum PhD
	* WWW: http://plindenbaum.blogspot.com
	* Motivation:
	* Given a gene, identify the world experts
	* http://biostar.stackexchange.com/questions/4296
	*/
	import java.net.URLEncoder;
	import java.text.Collator;
	import java.util.ArrayList;
	import java.util.Collections;
	import java.util.Comparator;
	import java.util.HashSet;
	import java.util.List;
	import java.util.Locale;
	import java.util.Set;
	import java.util.TreeSet;
	import java.util.logging.Level;
	import java.util.logging.Logger;
	import javax.xml.parsers.DocumentBuilder;
	import javax.xml.parsers.DocumentBuilderFactory;
	import javax.xml.stream.XMLOutputFactory;
	import javax.xml.stream.XMLStreamWriter;
	import javax.xml.xpath.XPath;
	import javax.xml.xpath.XPathConstants;
	import javax.xml.xpath.XPathFactory;
	import org.w3c.dom.Document;
	import org.w3c.dom.Node;
	import org.w3c.dom.NodeList;
	public class BioStar4296
	{
	private Logger LOG=Logger.getLogger(BioStar4296.class.getName());
	private String organism="Homo Sapiens";
	private DocumentBuilder docBuilder;
	private XPath xpath;
	private Collator collator;
	static class Author
	{
	String suffix="";
	String firstName="";
	String lastName="";
	String initials="";
	Set<String> mails=new HashSet<String>();
	Set<Integer> pmids=new TreeSet<Integer>();
	int factor=1;
	Set<String> affilitations=new HashSet<String>();
	@Override
	public int hashCode() {
	final int prime = 31;
	int result = 1;
	result = prime * result
	+ ((firstName == null) ? 0 : firstName.hashCode());
	result = prime * result
	+ ((lastName == null) ? 0 : lastName.hashCode());
	return result;
	}
	@Override
	public boolean equals(Object obj) {
	if (this == obj)
	return true;
	if (obj == null)
	return false;
	if (getClass() != obj.getClass())
	return false;
	Author other = (Author) obj;
	if (firstName == null) {
	if (other.firstName != null)
	return false;
	} else if (!firstName.equals(other.firstName))
	return false;
	if (lastName == null) {
	if (other.lastName != null)
	return false;
	} else if (!lastName.equals(other.lastName))
	return false;
	return true;
	}
	@Override
	public String toString() {
	return firstName+" "+lastName+" lab:"+this.affilitations+" mails:"+this.mails;
	}
	void write(XMLStreamWriter w)
	throws Exception
	{
	w.writeStartElement("Person");
	w.writeCharacters("\n");
	w.writeStartElement("firstName");
	w.writeCharacters(firstName);
	w.writeEndElement();
	w.writeCharacters("\n");
	w.writeStartElement("lastName");
	w.writeCharacters(lastName);
	w.writeEndElement();
	w.writeCharacters("\n");
	for(Integer s:pmids)
	{
	w.writeStartElement("pmid");
	w.writeCharacters(String.valueOf(s));
	w.writeEndElement();
	w.writeCharacters("\n");
	}
	for(String s:mails)
	{
	w.writeStartElement("mail");
	w.writeCharacters(s);
	w.writeEndElement();
	w.writeCharacters("\n");
	}
	for(String s:affilitations)
	{
	w.writeStartElement("affilitation");
	w.writeCharacters(s);
	w.writeEndElement();
	w.writeCharacters("\n");
	}
	w.writeEndElement();
	w.writeCharacters("\n");
	}
	}
	private BioStar4296() throws Exception
	{
	LOG.setLevel(Level.OFF);
	DocumentBuilderFactory f=DocumentBuilderFactory.newInstance();
	f.setNamespaceAware(false);
	f.setCoalescing(true);
	f.setIgnoringComments(true);
	f.setIgnoringElementContentWhitespace(true);
	f.setValidating(false);
	this.docBuilder=f.newDocumentBuilder();
	XPathFactory factory=XPathFactory.newInstance();
	this.xpath=factory.newXPath();
	this.collator= Collator.getInstance(Locale.FRENCH);
	this.collator.setStrength(Collator.PRIMARY);
	}
	private int search(XMLStreamWriter w,String geneName)
	throws Exception
	{
	w.writeCharacters("\n");
	w.writeStartElement("gene");
	w.writeAttribute("name", geneName);
	String url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term="+
	URLEncoder.encode(geneName+"[PREF] \""+this.organism+"\"[ORGN]", "UTF-8");
	LOG.info(url);
	Document dom=this.docBuilder.parse(url);
	NodeList list=(NodeList)this.xpath.evaluate(
	"/eSearchResult/IdList/Id",
	dom,XPathConstants.NODESET);
	if(list.getLength()==0)
	{
	w.writeComment("Cannot find any entry for "+geneName);
	w.writeEndElement();
	return -1;
	}
	else if(list.getLength()!=1)
	{
	w.writeComment("Ambigous name "+geneName);
	w.writeEndElement();
	return -1;
	}
	String geneId= list.item(0).getTextContent();
	LOG.info("GeneId:"+geneId);
	w.writeAttribute("geneId", geneId);
	url="http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id="+
	geneId+
	"&rettype=text&retmode=xml";
	LOG.info(url);
	dom=this.docBuilder.parse(url);
	list=(NodeList)this.xpath.evaluate(
	"//PubMedId",
	dom,XPathConstants.NODESET);
	if(list.getLength()==0)
	{
	w.writeComment("No pubmed for "+geneName);
	w.writeEndElement();
	return -1;
	}
	List<Author> authors=new ArrayList<Author>();
	Set<Integer> pmidSet=new TreeSet<Integer>();
	for(int articleIdx=0;articleIdx< list.getLength();++articleIdx)
	{
	String pmid= list.item(articleIdx).getTextContent();
	LOG.info("PMID:"+pmid);
	pmidSet.add(Integer.parseInt(pmid));
	}
	w.writeAttribute("count-pmids",String.valueOf(pmidSet.size()));
	w.writeCharacters("\n");
	for(Integer pmid: pmidSet)
	{
	LOG.info("PMID:"+pmid);
	url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id="+pmid+"&retmode=xml";
	LOG.info("url:"+url);
	dom=this.docBuilder.parse(url);
	Node n=(Node)this.xpath.evaluate("//Affiliation", dom,XPathConstants.NODE);
	if(n==null) continue;
	String affiliation=n.getTextContent();
	String adressFragments[]=affiliation.split("[ \t\\:\\<,\\>\\(\\)]");
	LOG.info("affiliation:"+affiliation);
	NodeList authorList=(NodeList)this.xpath.evaluate(
	"//AuthorList/Author",
	dom,XPathConstants.NODESET);
	LOG.info("Authors:"+authorList.getLength());
	if(authorList.getLength()==0) continue;
	for(int j=0;j< authorList.getLength();++j)
	{
	boolean collective=false;
	Author author=new Author();
	for(Node c1=authorList.item(j).getFirstChild();c1!=null;c1=c1.getNextSibling())
	{
	if(c1.getNodeType()!=Node.ELEMENT_NODE) continue;
	String tag=c1.getNodeName();
	String content= c1.getTextContent();
	if(tag.equals("LastName"))
	{
	author.lastName= content;
	}
	else if(tag.equals("FirstName") || tag.equals("ForeName"))
	{
	author.firstName= content;
	}
	else if(tag.equals("Initials"))
	{
	author.initials= content;
	}
	else if(tag.equals("CollectiveName"))
	{
	collective=true;
	break;
	}
	else if(tag.equals("Suffix"))
	{
	author.suffix= content;
	}
	}
	if(collective) continue;
	LOG.info("Make New Author:"+author);
	int k=0;
	for(k=0;k< authors.size();++k)
	{
	Author p=authors.get(k);
	if( !p.firstName.isEmpty() &&
	this.collator.compare(p.firstName,author.firstName)==0 &&
	this.collator.compare(p.lastName,author.lastName)==0)
	{
	LOG.info("Same: "+p+" "+author);
	author=p;
	break;
	}
	}
	if(k==authors.size())
	{
	k=0;
	for(k=0;k< authors.size();++k)
	{
	Author p=authors.get(k);
	if(
	(
	(!author.initials.isEmpty() && p.firstName.toLowerCase().startsWith(author.initials.toLowerCase())) ||
	(!p.initials.isEmpty() && author.firstName.toLowerCase().startsWith(p.initials) )||
	this.collator.compare(p.initials,author.initials)==0 )&&
	this.collator.compare(p.lastName,author.lastName)==0)
	{
	LOG.info("Same: "+p+" "+author);
	if(p.firstName.length()< author.firstName.length())
	{
	p.firstName=author.firstName;
	}
	author=p;
	break;
	}
	}
	}
	if(k==authors.size())
	{
	LOG.info("Adding: "+author);
	authors.add(author);
	}
	author.factor*=j;
	author.affilitations.add(affiliation);
	author.pmids.add(pmid);
	if(affiliation.indexOf('@')!=-1)
	{
	for(String mail: adressFragments)
	{
	mail.replaceAll("\\{\\}", "");
	if(mail.endsWith(".")) mail= mail.substring(0,mail.length()-1);
	int index=mail.indexOf('@');
	if(index==-1) continue;
	String mailPrefix=mail.substring(0,index).toLowerCase();
	if(mailPrefix.contains(author.lastName.toLowerCase()) ||
	collator.compare(mailPrefix, author.lastName)==0)
	{
	LOG.info("Adding: "+mail+" to "+author);
	author.mails.add(mail.toLowerCase());
	}
	else if( author.firstName.length()>1 &&
	(mailPrefix.contains( author.firstName.toLowerCase()) ||
	collator.compare(mailPrefix, author.firstName)==0))
	{
	LOG.info("Adding: "+mail+" to "+author);
	author.mails.add(mail.toLowerCase());
	}
	}
	}
	}
	}
	if(authors.isEmpty())
	{
	w.writeComment("No Author found");
	w.writeEndElement();
	return -1;
	}
	Collections.sort(authors,new Comparator<Author>()
	{
	@Override
	public int compare(Author o1, Author o2)
	{
	int i= o2.pmids.size()-o1.pmids.size();
	if(i!=0) return i;
	i= o2.factor-o1.factor;//later is more interesting ? not sure...
	return i;
	}
	});
	authors.get(0).write(w);
	w.writeEndElement();
	return 0;
	}
	public static void main(String[] args)
	{
	try {
	BioStar4296 app= new BioStar4296();
	int optind=0;
	while(optind<args.length)
	{
	if(args[optind].equals("-h"))
	{
	System.err.println("Pierre Lindenbaum");
	System.err.println("Options:");
	System.err.println(" -o <organism> ["+app.organism+"]");
	System.err.println(" -v show logs");
	return;
	}
	else if(args[optind].equals("-o"))
	{
	app.organism=args[++optind];
	}
	else if(args[optind].equals("-v"))
	{
	app.LOG.setLevel(Level.ALL);
	}
	else if(args[optind].equals("--"))
	{
	optind++;
	break;
	}
	else if(args[optind].startsWith("-"))
	{
	System.err.println("Unnown option: "+args[optind]);
	return;
	}
	else
	{
	break;
	}
	++optind;
	}
	if(optind==args.length)
	{
	System.err.println("Gene Name missing");
	}
	else
	{
	XMLOutputFactory xmlfactory= XMLOutputFactory.newInstance();
	XMLStreamWriter w= xmlfactory.createXMLStreamWriter(System.out,"UTF-8");
	w.writeStartDocument("UTF-8","1.0");
	w.writeCharacters("\n");
	w.writeStartElement("experts");
	w.writeCharacters("\n");
	while(optind < args.length)
	{
	app.search(w,args[optind]);
	optind++;
	w.writeCharacters("\n");
	}
	w.writeEndElement();
	w.writeEndDocument();
	w.flush();
	}
	} catch (Exception e)
	{
	e.printStackTrace();
	}
	}
	}

view raw BioStar4296.java hosted with ❤ by GitHub

Compilation

javac BioStar4296.java

Test

java BioStar4296 ZC3H7B eif4G1 PRNP

<?xml version="1.0" encoding="UTF-8"?>
<experts>
<gene name="ZC3H7B" geneId="23264" count-pmids="13">
<Person>
<firstName>Sumio</firstName>
<lastName>Sugano</lastName>
<pmid>8125298</pmid>
<pmid>9373149</pmid>
<pmid>14702039</pmid>
<affilitation>International and Interdisciplinary Studies, The University of Tokyo, Japan.</affilitation>
<affilitation>Institute of Medical Science, University of Tokyo, Japan.</affilitation>
<affilitation>Helix Research Institute, 1532-3 Yana, Kisarazu, Chiba 292-0812, Japan.</affilitation>
</Person>
</gene>
<gene name="eif4G1" geneId="1981" count-pmids="106">
<Person>
<firstName>Nahum</firstName>
<lastName>Sonenberg</lastName>
<pmid>7651417</pmid>
<pmid>7935836</pmid>
<pmid>8449919</pmid>
(...)
<affilitation>Department of Biochemistry and McGill Cancer Center, McGill University, Montreal, H3G 1Y6, Quebec, Canada.</affilitation>
<affilitation>Department of Biochemistry, McGill University, Montreal, Quebec, Canada.</affilitation>
<affilitation>Laboratories of Molecular Biophysics, The Rockefeller University, New York, New York 10021, USA.</affilitation>
(...)
</Person>
</gene>
<gene name="PRNP" geneId="5621" count-pmids="429">
<Person>
<firstName>John</firstName>
<lastName>Collinge</lastName>
<pmid>1352724</pmid>
<pmid>1677164</pmid>
<pmid>2159587</pmid>
<pmid>20583301</pmid>
(...)
<mail>j.collinge@ic.ac.uk</mail>
<affilitation>Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.</affilitation>
<affilitation>MRC Prion Unit and Department of Neurogenetics, Imperial College School of Medicine at St. Mary's, London, United Kingdom. J.Collinge@ic.ac.uk</affilitation>
<affilitation>Division of Neuroscience (Neurophysiology), Medical School, University of Birmingham, Edgbaston, Birmingham, UK. sratte@pitt.edu</affilitation>
(...)
</Person>
</gene>
</experts>

about this result

• ZC3H7B the result is wrong. In Dr Sugano's article (3 articles) ZC3H7B was present in among a large set of other genes used in his studies. The expert would be Dr D. Poncet, my former thesis advisor but he 'only' wrote two articles about this protein.
• Eif4G1: I know Dr Sonenberg is the expert. His email wasn't found.
• PRNP Collinge seems to be the expert. Dr Collinge's e-mail was detected.

That's it,

Pierre