Pubmed API: What are systemID and publicID?

The Matlab script I'd written in April 2016 to interface with the Pubmed API to automatically extract a bunch of gene info is no longer working. Something about needing both a SystemID and PublicID. Any ideas?

Simplified version of the code:

baseSearchURL = ['http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed'];

gene = 'pten';

termOptTOTAL = ['&term=', gene]; 

searchURL = [baseSearchURL,termOptTOTAL];

Full error message:

[Fatal Error] esearch.fcgi?db=pubmed&term=pten:1:50: White spaces are required between publicId and systemId.

Error using xmlread (line 97)

Java exception occurred:

org.xml.sax.SAXParseException; systemId: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=pten; lineNumber:

1; columnNumber: 50; White spaces are required between publicId and systemId.

at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)

at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)

at javax.xml.parsers.DocumentBuilder.parse(Unknown Source)

Answer 1

[Star Strider]

I use PubMed frequently, but not to do what you’re doing. When I plugged ‘http://eutils.ncbi.nlm.nih.gov/entrez/eutils/’ into the URL bar, I got ‘Page has moved here’ and was vectored to Entrez Programming Utilities Help. You might see if that page has the information you need.

Answer 2

[Robert Snoeberger]

It is possible to avoid XML by using webread and setting the retmode parameter to 'json'. JSON is easier to work with because webread will parse it and give you a struct.

Example:

>> result = webread('http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi','db','pubmed','term','pten','retmode','json')

result = 

    struct with fields:

             header: [1×1 struct]
      esearchresult: [1×1 struct]

>>

You can find some information about the retmode parameter in [1].

1. https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch