---
name: "Bio::Graph::IO::psi_xml"
section: "3pm"
platform: "linux"
package: "bioperl"
version: "1.5.2.102-3"
release: "Debian 5.0 (Lenny)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Graph::IO::psi_xml"
---

# Bio::Graph::IO::psi\_xml(3pm)

Bio::Graph::IO::psi\_xml - access and manipulate PSI XML graphs Do not use this module directly, use Bio::Graph::IO, for example:

```
  my $graph_io = Bio::Graph::IO->new(-format => 'psi_xml',
                                     -file   => 'data.xml');
```

PSI XML is a format to describe protein-protein interactions and  interaction networks. The following databases support PSI XML: \<http://www.bind.ca\> \<http://dip.doe-mbi.ucla.edu/\> \<http://www.hprd.org\> \<http://www.ebi.ac.uk/intact\> \<http://cbm.bio.uniroma2.it/mint/\> Notes on PSI XML from various databases can be found in the Bioperl Wiki at \<http://bioperl.org/wiki/Module:Bio::Graph::IO::psi\_xml\> Documentation for PSI XML can be found at \<http://psidev.sourceforge.net\>. The naming system is analagous to the SeqIO system, although usually *next\_network()* will be called only once per file.\
 **next\_network**

```
 name       : next_network
 purpose    : to construct a protein interaction graph from xml data
 usage      : my $gr = $io->next_network();
 arguments  : void
 returns    : A Bio::Graph::ProteinGraph object
```

**\_proteinInteractor**

```
 name      : _proteinInteractor
 purpose   : parses protein information into Bio::Seq::RichSeq objects
 returns   : void
 usage     : internally called by next_network(),
 arguments : none.
```

**add\_edge**

```
 name     : _addEdge
 purpose  : adds a new edge to a graph
 usage    : do not call, called by next_network
 returns  : void
```