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svn path=/bioperl-network/branches/branch-1-6/; revision=16219
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commit 86df7393e067adfa865ec8aa494841839eb1c400 1 parent dcd19da
cjfields authored
20 BioPerl-network.pm
View
@@ -0,0 +1,20 @@
+package BioPerl::Run;
+
+use strict;
+
+# At some future point, when we break the current core into more maintainable
+# bits, this will have a direct VERSION number, but for now we will be using
+# the root version for everything
+use Bio::Root::Version;
+
+our $VERSION = '1.006900';
+eval $VERSION;
+
+1;
+
+__END__
+
+=head1 NAME
+
+BioPerl-Network - BioPerl classes for parsing and analyzing protein-protein
+interaction data
4 Changes
View
@@ -3,6 +3,10 @@ Revision history for bioperl-network.
Full details of changes between all versions are available online at:
http://www.bioperl.org/wiki/Change_log
+1.6.0
+-----
+Minor updates and documentation fixes
+
1.5.2
-----
First named release: released with bioperl-1.5.2 developer branch release
8 lib/Bio/Network/Edge.pm
View
@@ -43,11 +43,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
9 lib/Bio/Network/IO.pm
View
@@ -62,11 +62,11 @@ Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
@@ -112,6 +112,7 @@ use vars qw(%DBNAMES);
-threshold => a confidence score for the interaction, optional
-source => optional database name (e.g. "intact")
-verbose => optional, set to 1 to get commentary
+
=cut
sub new {
8 lib/Bio/Network/IO/dip_tab.pm
View
@@ -71,11 +71,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
26 lib/Bio/Network/IO/psi/intact.pm
View
@@ -39,11 +39,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
@@ -72,15 +72,15 @@ use Bio::Annotation::Collection;
@EXPORT = qw(&);
-=head2
-
- Name :
- Purpose :
- Arguments :
- Returns :
- Usage :
-
-=cut
+#=head2
+#
+# Name :
+# Purpose :
+# Arguments :
+# Returns :
+# Usage :
+#
+#=cut
1;
210 lib/Bio/Network/IO/psi10.pm
View
@@ -28,14 +28,29 @@ This module parses version 1.0 of PSI MI.
The following databases provide their data as PSI MI XML:
-BIND L<http://www.bind.ca>
-DIP L<http://dip.doe-mbi.ucla.edu/>
-HPRD L<http://www.hprd.org>
-IntAct L<http://www.ebi.ac.uk/intact>
-MINT L<http://cbm.bio.uniroma2.it/mint/>
+=over 3
-Each of these databases will call PSI format by some different name. For
-example, PSI MI from DIP comes in files with the suffix "mif".
+=item *
+
+DIP L<http://dip.doe-mbi.ucla.edu/>
+
+=item *
+
+HPRD L<http://www.hprd.org>
+
+=item *
+
+IntAct L<http://www.ebi.ac.uk/intact>
+
+=item *
+
+MINT L<http://cbm.bio.uniroma2.it/mint/>
+
+=back
+
+Each of these databases will call PSI format by some different name.
+for example, PSI MI from DIP comes in files with the suffix "mif"
+whereas PSI MI from IntAct or MINT has the "xml" suffix.
Documentation for PSI XML can be found at L<http://www.psidev.info>.
@@ -68,71 +83,106 @@ B<interactor> (entrySet/entry/interactorList/interactor). The following are
subclasses of B<interactor> whose values are accessible through the Node
object.
-=head2 interactor/names/shortLabel
+=over 3
+
+=item *
+
+interactor/names/shortLabel
-Annotation::SimpleValue
+L<Bio::Annotation::SimpleValue|Bio::Annotation::SimpleValue>
-=head2 interactor/names/fullName
+=item *
-Annotation::SimpleValue
+interactor/names/fullName
-=head2 interactor/xref/primaryRef
+L<Bio::Annotation::SimpleValue|Bio::Annotation::SimpleValue>
-Annotation::DBLink
+=item *
-=head2 interactor/xref/secondaryRef
+interactor/xref/primaryRef
-Annotation::DBLink
+L<Bio::Annotation::DBLink|Bio::Annotation::DBLink>
-Bio::Species object
+=item *
-=head2 interactor/organism/names/alias
+interactor/xref/secondaryRef
-Bio::Species object
+L<Bio::Annotation::DBLink|Bio::Annotation::DBLink>
-=head2 interactor/organism/names/fullName
+L<Bio::Species|Bio::Species> object
-Bio::Species object
+=item *
-=head2 interactor/organism/names/shortLabel
+interactor/organism/names/alias
-Bio::Species object
+L<Bio::Species|Bio::Species> object
+
+=item *
+
+interactor/organism/names/fullName
+
+L<Bio::Species|Bio::Species> object
+
+=item *
+
+interactor/organism/names/shortLabel
+
+L<Bio::Species|Bio::Species> object
+
+=back
=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
+=over 3
+
+=item *
+
+interactor/names/alias
+
+L<Bio::Annotation::SimpleValue|Bio::Annotation::SimpleValue>
+
+=item *
-Annotation::SimpleValue
+interactor/sequence
-=head2 interactor/sequence
+=item *
-=head2 interactor/interactorType/names
+interactor/interactorType/names
Controlled vocabulary maintained by PSI MI
L<http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI>.
Example: "protein".
-OntologyTerm
+L<Bio::Annotation::OntologyTerm|Bio::Annotation::OntologyTerm>
-=head2 interactor/interactorType/xref
+=item *
-Annotation::DBLink
+interactor/interactorType/xref
-=head2 interactor/organism/cellType
+L<Bio::Annotation::DBLink|Bio::Annotation::DBLink>
-Annotation::OntologyTerm
+=item *
-=head2 interactor/organism/compartment
+interactor/organism/cellType
-Annotation::OntologyTerm
+L<Bio::Annotation::OntologyTerm|Bio::Annotation::OntologyTerm>
-=head2 interactor/organism/tissue
+=item *
-Annotation::OntologyTerm
+interactor/organism/compartment
+L<Bio::Annotation::OntologyTerm|Bio::Annotation::OntologyTerm>
+
+=item *
+
+interactor/organism/tissue
+
+L<Bio::Annotation::OntologyTerm|Bio::Annotation::OntologyTerm>
+
+=back
=head1 INTERACTION DATA
@@ -142,70 +192,100 @@ The Interaction object is roughly equivalent to the PSI MI B<interaction>
subclasses of B<interaction> and B<experimentDescription> whose values are
NOT yet accessible through the Interaction object.
-=head2 interaction/xref/primaryRef
+=over 3
+
+=item *
+
+interaction/xref/primaryRef
+
+L<Bio::Annotation::DBLink|Bio::Annotation::DBLink>
+
+=item *
+
+interaction/xref/secondaryRef
+
+L<Bio::Annotation::DBLink|Bio::Annotation::DBLink>
+
+=item *
-Annotation::DBLink
+interaction/organism/names/shortLabel
-=head2 interaction/xref/secondaryRef
+L<Bio::Species|Bio::Species> object
-Annotation::DBLink
+=item *
-=head2 interaction/organism/names/shortLabel
+interaction/organism/names/alias
-Bio::Species object
+L<Bio::Species|Bio::Species> object
-=head2 interaction/organism/names/alias
+=item *
-Bio::Species object
+interaction/organism/names/fullName
-=head2 interaction/organism/names/fullName
+L<Bio::Species|Bio::Species> object
-Bio::Species object
+=item *
-=head2 interaction/modelled
+interaction/modelled
-Annotation::SimpleValue
+L<Bio::Annotation::SimpleValue|Bio::Annotation::SimpleValue>
-=head2 interaction/intraMolecular
+=item *
-Annotation::SimpleValue
+interaction/intraMolecular
-=head2 interaction/negative
+L<Bio::Annotation::SimpleValue|Bio::Annotation::SimpleValue>
-Annotation::SimpleValue
+=item *
-=head2 interaction/interactionType
+interaction/negative
+
+L<Bio::Annotation::SimpleValue|Bio::Annotation::SimpleValue>
+
+=item *
+
+interaction/interactionType
Controlled vocabulary maintained by PSI MI
L<http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI>.
Example: "phosphorylation reaction".
-OntologyTerm
+L<Bio::Annotation::OntologyTerm|Bio::Annotation::OntologyTerm>
+
+=item *
+
+interaction/confidenceList
+
+L<Bio::Annotation::SimpleValue|Bio::Annotation::SimpleValue>
-=head2 interaction/confidenceList
+=item *
-Annotation::SimpleValue
+experimentDescription/confidenceList
-=head2 experimentDescription/confidenceList
+L<Bio::Annotation::SimpleValue|Bio::Annotation::SimpleValue>
-Annotation::SimpleValue
+=item *
-=head2 experimentDescription/interactionDetectionMethod
+experimentDescription/interactionDetectionMethod
Controlled vocabulary maintained by PSI MI
L<http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI>.
Example: "two hybrid array".
-Annotation::OntologyTerm
+L<Bio::Annotation::OntologyTerm|Bio::Annotation::OntologyTerm>
-=head2 featureElementType/featureType
+=item *
+
+featureElementType/featureType
Controlled vocabulary maintained by PSI MI
L<http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI>.
The featureType includes data on post-translational modification.
Example: "phospho-histidine".
-Annotation::OntologyTerm
+L<Bio::Annotation::OntologyTerm|Bio::Annotation::OntologyTerm>
+
+=back
=head1 FEEDBACK
@@ -219,11 +299,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
204 lib/Bio/Network/IO/psi25.pm
View
@@ -28,10 +28,25 @@ networks. This module parses version 2.5 of PSI MI.
The following databases provide their data as PSI MI XML:
-DIP L<http://dip.doe-mbi.ucla.edu/>
-HPRD L<http://www.hprd.org>
-IntAct L<http://www.ebi.ac.uk/intact>
-MINT L<http://cbm.bio.uniroma2.it/mint/>
+=over 3
+
+=item *
+
+DIP L<http://dip.doe-mbi.ucla.edu/>
+
+=item *
+
+HPRD L<http://www.hprd.org>
+
+=item *
+
+IntAct L<http://www.ebi.ac.uk/intact>
+
+=item *
+
+MINT L<http://cbm.bio.uniroma2.it/mint/>
+
+=back
Each of these databases will call PSI format by some different name.
for example, PSI MI from DIP comes in files with the suffix "mif"
@@ -69,71 +84,106 @@ B<interactor> (entrySet/entry/interactorList/interactor). The following are
subclasses of B<interactor> whose values are accessible through the Node
object.
-=head2 interactor/names/shortLabel
+=over 3
+
+=item *
+
+interactor/names/shortLabel
-Annotation::SimpleValue
+L<Bio::Annotation::SimpleValue|Bio::Annotation::SimpleValue>
-=head2 interactor/names/fullName
+=item *
-Annotation::SimpleValue
+interactor/names/fullName
-=head2 interactor/xref/primaryRef
+L<Bio::Annotation::SimpleValue|Bio::Annotation::SimpleValue>
-Annotation::DBLink
+=item *
-=head2 interactor/xref/secondaryRef
+interactor/xref/primaryRef
-Annotation::DBLink
+L<Bio::Annotation::DBLink|Bio::Annotation::DBLink>
-Bio::Species object
+=item *
-=head2 interactor/organism/names/alias
+interactor/xref/secondaryRef
-Bio::Species object
+L<Bio::Annotation::DBLink|Bio::Annotation::DBLink>
-=head2 interactor/organism/names/fullName
+L<Bio::Species|Bio::Species> object
-Bio::Species object
+=item *
-=head2 interactor/organism/names/shortLabel
+interactor/organism/names/alias
-Bio::Species object
+L<Bio::Species|Bio::Species> object
+
+=item *
+
+interactor/organism/names/fullName
+
+L<Bio::Species|Bio::Species> object
+
+=item *
+
+interactor/organism/names/shortLabel
+
+L<Bio::Species|Bio::Species> object
+
+=back
=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
+=over 3
+
+=item *
+
+interactor/names/alias
+
+L<Bio::Annotation::SimpleValue|Bio::Annotation::SimpleValue>
+
+=item *
-Annotation::SimpleValue
+interactor/sequence
-=head2 interactor/sequence
+=item *
-=head2 interactor/interactorType/names
+interactor/interactorType/names
Controlled vocabulary maintained by PSI MI
L<http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI>.
Example: "protein".
-OntologyTerm
+L<Bio::Annotation::OntologyTerm|Bio::Annotation::OntologyTerm>
-=head2 interactor/interactorType/xref
+=item *
-Annotation::DBLink
+interactor/interactorType/xref
-=head2 interactor/organism/cellType
+L<Bio::Annotation::DBLink|Bio::Annotation::DBLink>
-Annotation::OntologyTerm
+=item *
-=head2 interactor/organism/compartment
+interactor/organism/cellType
-Annotation::OntologyTerm
+L<Bio::Annotation::OntologyTerm|Bio::Annotation::OntologyTerm>
-=head2 interactor/organism/tissue
+=item *
-Annotation::OntologyTerm
+interactor/organism/compartment
+L<Bio::Annotation::OntologyTerm|Bio::Annotation::OntologyTerm>
+
+=item *
+
+interactor/organism/tissue
+
+L<Bio::Annotation::OntologyTerm|Bio::Annotation::OntologyTerm>
+
+=back
=head1 INTERACTION DATA
@@ -143,70 +193,100 @@ The Interaction object is roughly equivalent to the PSI MI B<interaction>
subclasses of B<interaction> and B<experimentDescription> whose values are
NOT yet accessible through the Interaction object.
-=head2 interaction/xref/primaryRef
+=over 3
+
+=item *
+
+interaction/xref/primaryRef
+
+L<Bio::Annotation::DBLink|Bio::Annotation::DBLink>
+
+=item *
+
+interaction/xref/secondaryRef
+
+L<Bio::Annotation::DBLink|Bio::Annotation::DBLink>
+
+=item *
-Annotation::DBLink
+interaction/organism/names/shortLabel
-=head2 interaction/xref/secondaryRef
+L<Bio::Species|Bio::Species> object
-Annotation::DBLink
+=item *
-=head2 interaction/organism/names/shortLabel
+interaction/organism/names/alias
-Bio::Species object
+L<Bio::Species|Bio::Species> object
-=head2 interaction/organism/names/alias
+=item *
-Bio::Species object
+interaction/organism/names/fullName
-=head2 interaction/organism/names/fullName
+L<Bio::Species|Bio::Species> object
-Bio::Species object
+=item *
-=head2 interaction/modelled
+interaction/modelled
-Annotation::SimpleValue
+L<Bio::Annotation::SimpleValue|Bio::Annotation::SimpleValue>
-=head2 interaction/intraMolecular
+=item *
-Annotation::SimpleValue
+interaction/intraMolecular
-=head2 interaction/negative
+L<Bio::Annotation::SimpleValue|Bio::Annotation::SimpleValue>
-Annotation::SimpleValue
+=item *
-=head2 interaction/interactionType
+interaction/negative
+
+L<Bio::Annotation::SimpleValue|Bio::Annotation::SimpleValue>
+
+=item *
+
+interaction/interactionType
Controlled vocabulary maintained by PSI MI
L<http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI>.
Example: "phosphorylation reaction".
-OntologyTerm
+L<Bio::Annotation::OntologyTerm|Bio::Annotation::OntologyTerm>
+
+=item *
+
+interaction/confidenceList
+
+L<Bio::Annotation::SimpleValue|Bio::Annotation::SimpleValue>
-=head2 interaction/confidenceList
+=item *
-Annotation::SimpleValue
+experimentDescription/confidenceList
-=head2 experimentDescription/confidenceList
+L<Bio::Annotation::SimpleValue|Bio::Annotation::SimpleValue>
-Annotation::SimpleValue
+=item *
-=head2 experimentDescription/interactionDetectionMethod
+experimentDescription/interactionDetectionMethod
Controlled vocabulary maintained by PSI MI
L<http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI>.
Example: "two hybrid array".
-Annotation::OntologyTerm
+L<Bio::Annotation::OntologyTerm|Bio::Annotation::OntologyTerm>
-=head2 featureElementType/featureType
+=item *
+
+featureElementType/featureType
Controlled vocabulary maintained by PSI MI
L<http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI>.
The featureType includes data on post-translational modification.
Example: "phospho-histidine".
-Annotation::OntologyTerm
+L<Bio::Annotation::OntologyTerm|Bio::Annotation::OntologyTerm>
+
+=back
=head1 FEEDBACK
@@ -220,11 +300,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
8 lib/Bio/Network/Interaction.pm
View
@@ -45,11 +45,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
8 lib/Bio/Network/Node.pm
View
@@ -43,11 +43,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
9 lib/Bio/Network/ProteinNet.pm
View
@@ -319,11 +319,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
@@ -951,6 +951,7 @@ sub unconnected_nodes {
the graph if deleted.
Notes : This method is currently broken due to bugs in Graph v. .69
and later
+
=cut
sub articulation_points {
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