# HG changeset patch
# User easr
# Date 1334133221 -7200
# Node ID d2d26d330236dc2822b11ebe1de4e52ffb0dd0c2
# Parent 4484575e4186c6288aefce64a97deceae0ceabb9
v 0.2: tools added for OPPL-galaxy
diff -r 4484575e4186 -r d2d26d330236 onto-toolkit/INSTALL
--- a/onto-toolkit/INSTALL Tue Jun 07 17:51:45 2011 -0400
+++ b/onto-toolkit/INSTALL Wed Apr 11 10:33:41 2012 +0200
@@ -7,7 +7,7 @@
http://main.g2.bx.psu.edu/
-2. ONTO-PERL (version >= 1.18):
+2. ONTO-PERL (version >= 1.37):
http://search.cpan.org/dist/ONTO-PERL/
@@ -21,15 +21,20 @@
4. Restart your Galaxy instance.
diff -r 4484575e4186 -r d2d26d330236 onto-toolkit/README
--- a/onto-toolkit/README Tue Jun 07 17:51:45 2011 -0400
+++ b/onto-toolkit/README Wed Apr 11 10:33:41 2012 +0200
@@ -4,14 +4,22 @@
ONTO-Toolkit is a collection of Galaxy tools for managing ontologies
that are represented in the OBO flat file format (spec 1.2).
-Those tools are basically wrappers around the most commonly used tasks
+Those tools are basically wrappers around the most commonly used tools
provided by the ONTO-PERL suite.
See also:
- ONTO-PERL: An API supporting the development and analysis of bio-ontologies
- Antezana E, Egana M, De Baets B, Kuiper M, Mironov V.
- Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042
+ 1. ONTO-PERL: An API supporting the development and analysis of bio-ontologies
+ Antezana E, Egana M, De Baets B, Kuiper M, Mironov V.
+ Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042
+
+ 2. ONTO-Toolkit: A set of Galaxy tools to deal with OBO-formatted ontologies
+ Antezana E, Venkatesan A, Mungall C, Mironov V, Kuiper M.
+ BMC Bioinformatics 2010, 11(Suppl 12):S8 doi:10.1186/1471-2105-11-S12-S8
+
+ 3. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL.
+ Egana M, Fernandez-Breis JT, Antezana E.
+ Semantic Web Applications and Tools for Life Sciences (SWAT4LS), London, UK (2011)
For installing this collection of tools:
@@ -26,14 +34,23 @@
http://main.g2.bx.psu.edu/
-2. ONTO-PERL (version >= 1.18):
+2. ONTO-PERL (version >= 1.37):
http://search.cpan.org/dist/ONTO-PERL/
+CITING ONTO-Toolkit
+===================
+
+If you use ONTO-Toolkit in your work, you are kindly requested to cite:
+
+ ONTO-Toolkit: A set of Galaxy tools to deal with OBO-formatted ontologies
+ Antezana E, Venkatesan A, Mungall C, Mironov V, Kuiper M.
+ BMC Bioinformatics 2010, 11(Suppl 12):S8 doi:10.1186/1471-2105-11-S12-S8
+
COPYRIGHT AND LICENCE
=====================
-Copyright (c) 2010 Erick Antezana. All rights reserved.
+Copyright (c) 2010-2012 Erick Antezana. All rights reserved.
OONTO-Toolkit is free software; you can redistribute it and/or
modify it under the same terms as Perl itself.
diff -r 4484575e4186 -r d2d26d330236 onto-toolkit/datatypes_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/onto-toolkit/datatypes_conf.xml Wed Apr 11 10:33:41 2012 +0200
@@ -0,0 +1,231 @@
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diff -r 4484575e4186 -r d2d26d330236 onto-toolkit/suite_config.xml
--- a/onto-toolkit/suite_config.xml Tue Jun 07 17:51:45 2011 -0400
+++ b/onto-toolkit/suite_config.xml Wed Apr 11 10:33:41 2012 +0200
@@ -1,4 +1,4 @@
-
+
This suite contains tools for managing ontologies that are represented in the OBO flat file format
@@ -21,6 +21,10 @@
Collects common OBO terms from a given set of list containing OBO terms
+
+ Collects the terms from a given term in the given OBO ontology, filtered by a relationship type
+
+
Collects the parent terms from a given term in the given OBO ontology
@@ -33,6 +37,10 @@
Extracts a subontology (in OBO format) of a given ontology having as root node the provided term ID
+
+ Collects the terms that are related by a concrete relationship type
+
+
Converts an OBO formatted ontology to OWL format
diff -r 4484575e4186 -r d2d26d330236 onto-toolkit/tool_conf.xml
--- a/onto-toolkit/tool_conf.xml Tue Jun 07 17:51:45 2011 -0400
+++ b/onto-toolkit/tool_conf.xml Wed Apr 11 10:33:41 2012 +0200
@@ -25,18 +25,20 @@
diff -r 4484575e4186 -r d2d26d330236 onto-toolkit/tools/ontology/get_parent_terms_by_relationship_type.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/onto-toolkit/tools/ontology/get_parent_terms_by_relationship_type.pl Wed Apr 11 10:33:41 2012 +0200
@@ -0,0 +1,34 @@
+#!/usr/bin/perl
+
+eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
+ if 0; # not running under some shell
+
+
+use Carp;
+use strict;
+use warnings;
+
+use OBO::Parser::OBOParser;
+
+my $my_parser = OBO::Parser::OBOParser->new();
+my $ontology = $my_parser->work(shift(@ARGV));
+my $term_id = shift(@ARGV);
+my $rel_id = shift(@ARGV);
+
+my $target_term = $ontology->get_term_by_id($term_id);
+my @rels = @{$ontology->get_relationships_by_source_term($target_term, $rel_id)};
+
+foreach my $r (@rels) {
+ # print "rel: ", $r->id(), "\n";
+ print $r->head()->id();
+ # print "tail: ", $r->tail()->id(), "\n\n";
+}
+
+exit 0;
+__END__
+
+
+
+
+
+
diff -r 4484575e4186 -r d2d26d330236 onto-toolkit/tools/ontology/get_parent_terms_by_relationship_type.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/onto-toolkit/tools/ontology/get_parent_terms_by_relationship_type.xml Wed Apr 11 10:33:41 2012 +0200
@@ -0,0 +1,51 @@
+
+ Collects the terms from a given term in the given OBO ontology, filtered by a relationship type
+ /usr/bin/get_parent_terms_by_relationship_type.pl $input_ontology $term_id $rel_id > $output
+
+
+
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+.. class:: infomark
+
+Collects the terms (list of IDs) from a given term (existing ID) through a given relationship type in the given OBO ontology.
+**Example**
+
+id: A
+name: A
+A part_of B
+A part_of D
+A participates_in F
+
+Que me devuelva los padres de A along part_of, es decir B y D.
+
+If you ask for the parent terms of **A** along along part_of you will get::
+
+ B
+ D
+
+**More information**
+
+ ONTO-PERL: An API supporting the development and analysis of bio-ontologies
+ E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov
+ Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042
+
+
+
+
+
diff -r 4484575e4186 -r d2d26d330236 onto-toolkit/tools/ontology/get_terms_by_relationship_type.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/onto-toolkit/tools/ontology/get_terms_by_relationship_type.pl Wed Apr 11 10:33:41 2012 +0200
@@ -0,0 +1,28 @@
+#!/usr/bin/perl
+
+eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
+ if 0; # not running under some shell
+
+use Carp;
+use strict;
+use warnings;
+use Encode;
+
+use OBO::Parser::OBOParser;
+
+my $my_parser = OBO::Parser::OBOParser->new();
+my $ontology = $my_parser->work(shift(@ARGV));
+my $rel_type_name = shift(@ARGV);
+my @relationships = @{$ontology->get_relationships()};
+
+foreach my $r (@relationships) {
+ if($r->type() eq $rel_type_name){
+ print $r->tail()->id(), "\t";
+ print $r->type(),"\t";
+ print $r->head()->id(), "\n";
+ }
+}
+
+exit 0;
+
+__END__
diff -r 4484575e4186 -r d2d26d330236 onto-toolkit/tools/ontology/get_terms_by_relationship_type.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/onto-toolkit/tools/ontology/get_terms_by_relationship_type.xml Wed Apr 11 10:33:41 2012 +0200
@@ -0,0 +1,45 @@
+
+ Collects the terms that are related by a concrete relationship type
+ /usr/bin/get_terms_by_relationship_type.pl $input_ontology $rel_id > $output
+
+
+
+
+
+
+
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+.. class:: infomark
+
+Collects the terms that are related by a concrete relationship type (e.g. is_a)
+
+**Example**
+
+If you ask for terms related by the relationship type 'participates_in' you will get tab delimited records like::
+
+ PR:0000001 participates_in GO:0000023
+ PR:0000002 participates_in GO:0033224
+ PR:0000003 participates_in GO:0021109
+ PR:0000004 participates_in GO:0034099
+ ...
+ ...
+
+**More information**
+
+ ONTO-PERL: An API supporting the development and analysis of bio-ontologies
+ E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov
+ Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042
+
+
+
+
\ No newline at end of file