[Bioperl-guts-l] bioperl-network/Bio/Network/IO psi.pm,1.13,1.14

Brian Osborne bosborne at dev.open-bio.org
Sun Jan 21 17:43:32 EST 2007


Update of /home/repository/bioperl/bioperl-network/Bio/Network/IO
In directory dev.open-bio.org:/tmp/cvs-serv12295/Bio/Network/IO

Modified Files:
	psi.pm 
Log Message:
Update docs

Index: psi.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-network/Bio/Network/IO/psi.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** psi.pm	2 Oct 2006 23:30:08 -0000	1.13
--- psi.pm	21 Jan 2007 22:43:29 -0000	1.14
***************
*** 41,46 ****
  =head2 Version
  
! This module supports PSI MI version 2.5, described at
! L<http://psidev.sourceforge.net/mi/rel25/>.
  
  =head2 Notes
--- 41,47 ----
  =head2 Version
  
! This module supports a subset of the fields described in PSI MI version 2.5
! (L<http://psidev.sourceforge.net/mi/rel25/>). The NODE DATA section below
! describes which fields are currently parsed into ProteinNet networks.
  
  =head2 Notes
***************
*** 60,64 ****
  next_network() will be called only once per file.
  
! =head1 NODE DATA
  
  The Node (protein or protein complex) is roughly equivalent to the PSI MI 
--- 61,65 ----
  next_network() will be called only once per file.
  
! =head1 DATA IN THE NODE
  
  The Node (protein or protein complex) is roughly equivalent to the PSI MI 
***************
*** 71,98 ****
  Annotation::SimpleValue
  
- =head2 interactor/names/alias
- 
- Annotation::SimpleValue
- 
  =head2 interactor/names/fullName
  
  Annotation::SimpleValue
  
- =head2 interactor/sequence
- 
- Sequence object
- 
- =head2 interactor/interactorType/names
- 
- Controlled vocabulary maintained by PSI MI
- L<http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI>.
- Example: "protein".
- 
- OntologyTerm
- 
- =head2 interactor/interactorType/xref
- 
- Annotation::DBLink
- 
  =head2 interactor/xref/primaryRef
  
--- 72,79 ----
***************
*** 103,108 ****
  Annotation::DBLink
  
- =head2 interactor/organism/names/shortLabel
- 
  Bio::Species object
  
--- 84,87 ----
***************
*** 115,118 ****
--- 94,124 ----
  Bio::Species object
  
+ =head2 interactor/organism/names/shortLabel
+ 
+ Bio::Species object
+ 
+ =head1 DATA NOT YET AVAILABLE
+ 
+ The following are subclasses of B<interactor> whose values are currently not
+ accessible through the Node object.
+ 
+ =head2 interactor/names/alias
+ 
+ Annotation::SimpleValue
+ 
+ =head2 interactor/sequence
+ 
+ =head2 interactor/interactorType/names
+ 
+ Controlled vocabulary maintained by PSI MI
+ L<http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI>.
+ Example: "protein".
+ 
+ OntologyTerm
+ 
+ =head2 interactor/interactorType/xref
+ 
+ Annotation::DBLink
+ 
  =head2 interactor/organism/cellType
  
***************
*** 134,138 ****
  (entrySet/entry/experimentList/experimentDescription). The following are
  subclasses of B<interaction> and B<experimentDescription> whose values are 
! accessible through the Interaction object.
  
  =head2 interaction/xref/primaryRef
--- 140,144 ----
  (entrySet/entry/experimentList/experimentDescription). The following are
  subclasses of B<interaction> and B<experimentDescription> whose values are 
! NOT yet accessible through the Interaction object.
  
  =head2 interaction/xref/primaryRef
***************
*** 391,395 ****
  
  sub _addInteraction {
- 
  	my ($twig, $i) = @_;
  	my @ints = $i->first_child('participantList')->children;
--- 397,400 ----



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