RDF-XML and BIOPAX is broken

[Matthew Hindle]

Hi,
We are trying to use the RDF-XML or BIOPAX representations of
IntAct. Both are reporting the following server error (below) when we
follow the Download link after selecting these formats.

500 Internal Server Error. Sorry!

Also, is there any chance that these formats could be made available
on the ftp site (per-species).

Many Thanks,
Matthew Hindle

--
Matthew M. Hindle
Bioinformatics Scientist
Department of Computer Science and Applied Statistics
University of New Brunswick, Canada
http://ca.linkedin.com/pub/matthew-hindle/24/1b7/960

[Bruno Aranda]

Hi Mathew.

On 25 November 2011 18:42, Matthew Hindle <matthew...@gmail.com> wrote:

Hi,
  We are trying to use the RDF-XML or BIOPAX representations of
IntAct. Both are reporting the following server error (below) when we
follow the Download link after selecting these formats.

500 Internal Server Error. Sorry!

I can reproduce and we are investigating the problem. Will get back to you when fixed...

The BioPAX from the web site is a direct conversion from the results tables, displaying binary interaction data that may have been expanded. This means that it may be less complete that the PSIMI-XML from the FTP, which contains a closer representation of the information we have in the database, not expanding interactions (hence there are n-nary interactions) and more detailed information.

Also, is there any chance that these formats could be made available
on the ftp site (per-species).

We are going to take this request into consideration. However, if you are using Java there exists a library already that can do the conversion for you. You can obtain this library with Maven:

<dependencies>
   <dependency>
       <groupId>psidev.psi.mi</groupId>
       <artifactId>psi25-xml-rdf</artifactId>
       <version>1.7.10-SNAPSHOT</version>
  </dependency>
  ...
</dependencies>

<repositories>
        <repository>
            <id>intact.nexus</id>
            <name>IntAct Nexus</name>
            <url>http://www.ebi.ac.uk/intact/maven/nexus/content/groups/public/</url>
        </repository>
</repositories>

And use it like this:

PsimiRdfConverter converter = new PsimiRdfConverter();
converter.convert(is, RdfFormat.BIOPAX_L3, System.out);
 
Let us know if this helps,

Bruno

[Bruno Aranda]

Hi Mathew,

The 500 error in the IntAct site should now be fixed and not appear when exporting to RDF formats.

Cheers,

Bruno