about Java Access of Complete PubMed IDs or Titles Attached to One Entry

Question

[taojincs]

Is there any way to access ALL the publications in java attached to one swissprot entry?

I know how to use the method List<citation> citation = current.getCitationsNew(). I can get the titles of these publications too. However, the list of publications is not complete. For example, https://www.uniprot.org/uniprot/P0AD86/publications, publication 7 and 8 will not be included in the output.

I checked the documentations carefully: ttps://www.ebi.ac.uk/uniprot/japi/javadoc/uk/ac/ebi/kraken/interfaces/uniprot/UniProtEntry.html https://www.ebi.ac.uk/uniprot/japi/usage.html https://www.ebi.ac.uk/uniprot/japi/javadoc/uk/ac/ebi/uniprot/dataservice/query/class-use/Query.html#uk.ac.ebi.uniprot.dataservice.client.uniprot

I didn't find other useful functions from API. The only way I came up with is to use URL to access the source html page and parse the title out. I prefer not to do this as it is not stable and might not work in the future.

Is there any way to get the complete list of publication PubMed IDs or titles of one protein entry in java using existing API?

Thank you.

Answer 1

[Pierre Lindenbaum]

here is a basic code using xpath:

$ javac Biostar376339.java 
$ java Biostar376339 
287010 Regulation of the threonine operon: tandem threonine and isoleucine codons in the control region and translational control of transcription termination.
6277952 Initiation, pausing, and termination of transcription in the threonine operon regulatory region of Escherichia coli.
2410621 Identification and characterization of mutants affecting transcription termination at the threonine operon attenuator.
7610040 Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes.
9278503 The complete genome sequence of Escherichia coli K-12.
16738553 Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110.

I'm using xpath but for something more complete/beautiful you'de better use XSLT.

	import java.net.*;
	import java.util.*;
	import java.io.*;
	import org.w3c.dom.*;
	import javax.xml.xpath.*;
	import javax.xml.parsers.*;
	public class Biostar376339 {
	public static void main(final String args[]) {
	try {
	String urlstr="https://www.uniprot.org/uniprot/P0AD86.xml";
	DocumentBuilderFactory factory =DocumentBuilderFactory.newInstance();
	factory.setNamespaceAware(true);
	DocumentBuilder builder = factory.newDocumentBuilder();
	Document dom = builder.parse(urlstr);
	XPathFactory xpathfactory = XPathFactory.newInstance();
	XPath xpath = xpathfactory.newXPath();
	XPathExpression expr = xpath.compile("//*[local-name()='dbReference' and @type='PubMed']/@id");
	XPathExpression expr2 = xpath.compile("/PubmedArticleSet/PubmedArticle/MedlineCitation/Article/ArticleTitle");
	NodeList nodes = (NodeList)expr.evaluate(dom, XPathConstants.NODESET);
	for (int i = 0; i < nodes.getLength(); i++) {
	final String pmid=nodes.item(i).getNodeValue();
	Document dom2 = builder.parse("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=xml&db=pubmed&id="+pmid);
	System.out.println(pmid+" "+expr2.evaluate(dom2, XPathConstants.STRING));
	}
	}
	catch(Exception err) {
	err.printStackTrace();
	}
	}
	}

view raw Biostar376339.java hosted with ❤ by GitHub

Answer 2

[Elisabeth Gasteiger]

I am not familiar with the EBI java API, but I may be able to shed some light on the reason why publications 7 and 8 of P0AD86 are not included:

https://www.uniprot.org/uniprot/P0AD86/publications lists 8 publications, the first 6 of which have been curated by a biocurator and are actually listed in the database record (as you can see in text, xml or rdf formats): e.g. text: https://www.uniprot.org/uniprot/P0AD86.txt

The remainder of the publications have been computationally mapped: https://www.uniprot.org/uniprot/P0AD86/publications?query=&fil=Mapped

You can obtain their PubMed IDs with this query:

https://www.uniprot.org/citations/?query=mappedin:(id:P0AD86)

and download them with

https://www.uniprot.org/citations/?query=mappedin:(id:P0AD86)&format=list The latter can be used programmatically (REST), and no specific parsing is required (tab-separated, excel, xml/rdf formats are also available).

Similarly, all citations (those in the entry AND the mapped ones) can be obtained with the query

https://www.uniprot.org/citations/?query=mappedin:(id:P0AD86)+or+citedin:(id:P0AD86)&sort=score (use format={tab|list|rdf} for programmatic use).