Mercurial > repos > erick-antezana > onto-toolkit
changeset 1:d2d26d330236
v 0.2: tools added for OPPL-galaxy
| author | easr |
|---|---|
| date | Wed, 11 Apr 2012 10:33:41 +0200 |
| parents | 4484575e4186 |
| children | 77c75bf3fbe6 |
| files | onto-toolkit/INSTALL onto-toolkit/README onto-toolkit/datatypes_conf.xml onto-toolkit/suite_config.xml onto-toolkit/tool_conf.xml onto-toolkit/tools/ontology/get_parent_terms_by_relationship_type.pl onto-toolkit/tools/ontology/get_parent_terms_by_relationship_type.xml onto-toolkit/tools/ontology/get_terms_by_relationship_type.pl onto-toolkit/tools/ontology/get_terms_by_relationship_type.xml |
| diffstat | 9 files changed, 442 insertions(+), 21 deletions(-) [+] |
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--- 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 @@ <section name="OBO Ontology manipulation" id="ONTO-ToolKit"> <tool file="ontology/get_ancestor_terms.xml"/> - <tool file="ontology/get_parent_terms.xml"/> + <tool file="ontology/get_child_terms.xml"/> <tool file="ontology/get_descendent_terms.xml"/> - <tool file="ontology/get_child_terms.xml"/> + <tool file="ontology/get_intersection_ontology_from.xml"/> + <tool file="ontology/get_list_intersection_from.xml"/> + <tool file="ontology/get_parent_terms_by_relationship_type.xml"/> + <tool file="ontology/get_parent_terms.xml"/> + <tool file="ontology/get_relationship_types.xml"/> + <tool file="ontology/get_subontology_from.xml"/> + <tool file="ontology/get_terms_by_relationship_type.xml"/> + <tool file="ontology/obo2owl.xml" /> + <tool file="ontology/obo2rdf.xml" /> + <tool file="ontology/obo2tran.xml" /> <tool file="ontology/term_id_vs_term_def.xml"/> <tool file="ontology/term_id_vs_term_name.xml"/> - <tool file="ontology/get_relationship_types.xml"/> - <tool file="ontology/obo2rdf.xml" /> - <tool file="ontology/obo2tran.xml" /> - <tool file="ontology/obo2owl.xml" /> </section> 4. Restart your Galaxy instance.
--- 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.
--- /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 @@ +<?xml version="1.0"?> +<datatypes> + <registration converters_path="lib/galaxy/datatypes/converters"> + <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/> + <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true"> + <converter file="bam_to_bai.xml" target_datatype="bai"/> + </datatype> + <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true"> + <converter file="bed_to_gff_converter.xml" target_datatype="gff"/> + <converter file="interval_to_coverage.xml" target_datatype="coverage"/> + <converter file="bed_to_interval_index_converter.xml" target_datatype="interval_index"/> + </datatype> + <datatype extension="binseq.zip" type="galaxy.datatypes.binary:Binseq" mimetype="application/zip" display_in_upload="true"/> + <datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true"> + <!-- no converters yet --> + </datatype> + <datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage" display_in_upload="true"> + <indexer file="coverage.xml" /> + </datatype> + <datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/> + <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/> + <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream"/> + <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true"> + <converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/> + </datatype> + <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true"/> + <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"/> + <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"/> + <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true"> + <converter file="gff_to_bed_converter.xml" target_datatype="bed"/> + </datatype> + <datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true"/> + <datatype extension="gif" type="galaxy.datatypes.images:Image" mimetype="image/gif"/> + <datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/> + <datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/> + <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true"> + <converter file="interval_to_bed_converter.xml" target_datatype="bed"/> + <indexer file="interval_awk.xml" /> + </datatype> + <datatype extension="jpg" type="galaxy.datatypes.images:Image" mimetype="image/jpeg"/> + <datatype extension="laj" type="galaxy.datatypes.images:Laj"/> + <datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true"/> + <datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true"> + <converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/> + <converter file="maf_to_interval_converter.xml" target_datatype="interval"/> + </datatype> + <datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/> + <datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/> + <datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/> + <datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/> + <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/> + <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"/> + <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/> + <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/> + <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/> + <datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" display_in_upload="true"/> + <datatype extension="txtseq.zip" type="galaxy.datatypes.data:Txtseq" mimetype="application/zip" display_in_upload="true"/> + <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true"> + <converter file="wiggle_to_array_tree_converter.xml" target_datatype="array_tree"/> + <converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/> + </datatype> + <datatype extension="array_tree" type="galaxy.datatypes.data:Data" /> + <datatype extension="interval_index" type="galaxy.datatypes.data:Data" /> + <!-- Start EMBOSS tools --> + <datatype extension="acedb" type="galaxy.datatypes.data:Text"/> + <datatype extension="asn1" type="galaxy.datatypes.data:Text"/> + <datatype extension="btwisted" type="galaxy.datatypes.data:Text"/> + <datatype extension="cai" type="galaxy.datatypes.data:Text"/> + <datatype extension="charge" type="galaxy.datatypes.data:Text"/> + <datatype extension="checktrans" type="galaxy.datatypes.data:Text"/> + <datatype extension="chips" type="galaxy.datatypes.data:Text"/> + <datatype extension="clustal" type="galaxy.datatypes.data:Text"/> + <datatype extension="codata" type="galaxy.datatypes.data:Text"/> + <datatype extension="codcmp" type="galaxy.datatypes.data:Text"/> + <datatype extension="coderet" type="galaxy.datatypes.data:Text"/> + <datatype extension="compseq" type="galaxy.datatypes.data:Text"/> + <datatype extension="cpgplot" type="galaxy.datatypes.data:Text"/> + <datatype extension="cpgreport" type="galaxy.datatypes.data:Text"/> + <datatype extension="cusp" type="galaxy.datatypes.data:Text"/> + <datatype extension="cut" type="galaxy.datatypes.data:Text"/> + <datatype extension="dan" type="galaxy.datatypes.data:Text"/> + <datatype extension="dbmotif" type="galaxy.datatypes.data:Text"/> + <datatype extension="diffseq" type="galaxy.datatypes.data:Text"/> + <datatype extension="digest" type="galaxy.datatypes.data:Text"/> + <datatype extension="dreg" type="galaxy.datatypes.data:Text"/> + <datatype extension="einverted" type="galaxy.datatypes.data:Text"/> + <datatype extension="embl" type="galaxy.datatypes.data:Text"/> + <datatype extension="epestfind" type="galaxy.datatypes.data:Text"/> + <datatype extension="equicktandem" type="galaxy.datatypes.data:Text"/> + <datatype extension="est2genome" type="galaxy.datatypes.data:Text"/> + <datatype extension="etandem" type="galaxy.datatypes.data:Text"/> + <datatype extension="excel" type="galaxy.datatypes.data:Text"/> + <datatype extension="feattable" type="galaxy.datatypes.data:Text"/> + <datatype extension="fitch" type="galaxy.datatypes.data:Text"/> + <datatype extension="freak" type="galaxy.datatypes.data:Text"/> + <datatype extension="fuzznuc" type="galaxy.datatypes.data:Text"/> + <datatype extension="fuzzpro" type="galaxy.datatypes.data:Text"/> + <datatype extension="fuzztran" type="galaxy.datatypes.data:Text"/> + <datatype extension="garnier" type="galaxy.datatypes.data:Text"/> + <datatype extension="gcg" type="galaxy.datatypes.data:Text"/> + <datatype extension="geecee" type="galaxy.datatypes.data:Text"/> + <datatype extension="genbank" type="galaxy.datatypes.data:Text"/> + <datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text"/> + <datatype extension="hennig86" type="galaxy.datatypes.data:Text"/> + <datatype extension="hmoment" type="galaxy.datatypes.data:Text"/> + <datatype extension="ig" type="galaxy.datatypes.data:Text"/> + <datatype extension="isochore" type="galaxy.datatypes.data:Text"/> + <datatype extension="jackknifer" type="galaxy.datatypes.data:Text"/> + <datatype extension="jackknifernon" type="galaxy.datatypes.data:Text"/> + <datatype extension="markx10" type="galaxy.datatypes.data:Text"/> + <datatype extension="markx1" type="galaxy.datatypes.data:Text"/> + <datatype extension="markx0" type="galaxy.datatypes.data:Text"/> + <datatype extension="markx3" type="galaxy.datatypes.data:Text"/> + <datatype extension="markx2" type="galaxy.datatypes.data:Text"/> + <datatype extension="match" type="galaxy.datatypes.data:Text"/> + <datatype extension="mega" type="galaxy.datatypes.data:Text"/> + <datatype extension="meganon" type="galaxy.datatypes.data:Text"/> + <datatype extension="motif" type="galaxy.datatypes.data:Text"/> + <datatype extension="msf" type="galaxy.datatypes.data:Text"/> + <datatype extension="nametable" type="galaxy.datatypes.data:Text"/> + <datatype extension="ncbi" type="galaxy.datatypes.data:Text"/> + <datatype extension="needle" type="galaxy.datatypes.data:Text"/> + <datatype extension="newcpgreport" type="galaxy.datatypes.data:Text"/> + <datatype extension="newcpgseek" type="galaxy.datatypes.data:Text"/> + <datatype extension="nexus" type="galaxy.datatypes.data:Text"/> + <datatype extension="nexusnon" type="galaxy.datatypes.data:Text"/> + <datatype extension="noreturn" type="galaxy.datatypes.data:Text"/> + <datatype extension="pair" type="galaxy.datatypes.data:Text"/> + <datatype extension="palindrome" type="galaxy.datatypes.data:Text"/> + <datatype extension="pepcoil" type="galaxy.datatypes.data:Text"/> + <datatype extension="pepinfo" type="galaxy.datatypes.data:Text"/> + <datatype extension="pepstats" type="galaxy.datatypes.data:Text"/> + <datatype extension="phylip" type="galaxy.datatypes.data:Text"/> + <datatype extension="phylipnon" type="galaxy.datatypes.data:Text"/> + <datatype extension="pir" type="galaxy.datatypes.data:Text"/> + <datatype extension="polydot" type="galaxy.datatypes.data:Text"/> + <datatype extension="preg" type="galaxy.datatypes.data:Text"/> + <datatype extension="prettyseq" type="galaxy.datatypes.data:Text"/> + <datatype extension="primersearch" type="galaxy.datatypes.data:Text"/> + <datatype extension="regions" type="galaxy.datatypes.data:Text"/> + <datatype extension="score" type="galaxy.datatypes.data:Text"/> + <datatype extension="selex" type="galaxy.datatypes.data:Text"/> + <datatype extension="seqtable" type="galaxy.datatypes.data:Text"/> + <datatype extension="showfeat" type="galaxy.datatypes.data:Text"/> + <datatype extension="showorf" type="galaxy.datatypes.data:Text"/> + <datatype extension="simple" type="galaxy.datatypes.data:Text"/> + <datatype extension="sixpack" type="galaxy.datatypes.data:Text"/> + <datatype extension="srs" type="galaxy.datatypes.data:Text"/> + <datatype extension="srspair" type="galaxy.datatypes.data:Text"/> + <datatype extension="staden" type="galaxy.datatypes.data:Text"/> + <datatype extension="strider" type="galaxy.datatypes.data:Text"/> + <datatype extension="supermatcher" type="galaxy.datatypes.data:Text"/> + <datatype extension="swiss" type="galaxy.datatypes.data:Text"/> + <datatype extension="syco" type="galaxy.datatypes.data:Text"/> + <datatype extension="table" type="galaxy.datatypes.data:Text"/> + <datatype extension="textsearch" type="galaxy.datatypes.data:Text"/> + <datatype extension="vectorstrip" type="galaxy.datatypes.data:Text"/> + <datatype extension="wobble" type="galaxy.datatypes.data:Text"/> + <datatype extension="wordcount" type="galaxy.datatypes.data:Text"/> + <datatype extension="tagseq" type="galaxy.datatypes.data:Text"/> + <!-- End EMBOSS tools --> + <!-- Start ONTO-PERL tools --> + <datatype extension="obo" type="galaxy.datatypes.data:Text"/> + <!-- End ONTO-PERL tools --> + <!-- Start RGenetics Datatypes --> + <datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/> + <!-- eigenstrat pedigree input file --> + <datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/> + <!-- eigenstrat pca output file for adjusted eigenQTL eg --> + <datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/> + <datatype extension="eset" type="galaxy.datatypes.genetics:Eset" display_in_upload="true" /> + <!-- fbat/pbat format pedigree (header row of marker names) --> + <datatype extension="fped" type="galaxy.datatypes.genetics:Fped" display_in_upload="true"/> + <!-- phenotype file - fbat format --> + <datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe" display_in_upload="true" mimetype="text/html"/> + <!-- genome graphs ucsc file - first col is always marker then numeric values to plot --> + <datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/> + <!-- part of linkage format pedigree --> + <datatype extension="lmap" type="galaxy.datatypes.genetics:Lmap" display_in_upload="true"/> + <datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/> + <!-- linkage format pedigree (separate .map file) --> + <datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true"> + <converter file="lped_to_fped_converter.xml" target_datatype="fped"/> + <converter file="lped_to_pbed_converter.xml" target_datatype="pbed"/> + </datatype> + <!-- plink compressed file - has bed extension unfortunately --> + <datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true"> + <converter file="pbed_to_lped_converter.xml" target_datatype="lped"/> + </datatype> + <datatype extension="pheno" type="galaxy.datatypes.genetics:Pheno"/> + <!-- phenotype file - plink format --> + <datatype extension="pphe" type="galaxy.datatypes.genetics:Pphe" display_in_upload="true" mimetype="text/html"/> + <datatype extension="rexpbase" type="galaxy.datatypes.genetics:RexpBase"/> + <datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/> + <datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest" display_in_upload="true"/> + <datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix" display_in_upload="true"/> + <datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/> + <!-- End RGenetics Datatypes --> + </registration> + <sniffers> + <!-- + The order in which Galaxy attempts to determine data types is + important because some formats are much more loosely defined + than others. The following list should be the most rigidly + defined format first, followed by next-most rigidly defined, + and so on. + --> + <sniffer type="galaxy.datatypes.binary:Bam"/> + <sniffer type="galaxy.datatypes.binary:Sff"/> + <sniffer type="galaxy.datatypes.xml:BlastXml"/> + <sniffer type="galaxy.datatypes.sequence:Maf"/> + <sniffer type="galaxy.datatypes.sequence:Lav"/> + <sniffer type="galaxy.datatypes.sequence:csFasta"/> + <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/> + <sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/> + <sniffer type="galaxy.datatypes.sequence:Fasta"/> + <sniffer type="galaxy.datatypes.sequence:Fastq"/> + <sniffer type="galaxy.datatypes.interval:Wiggle"/> + <sniffer type="galaxy.datatypes.images:Html"/> + <sniffer type="galaxy.datatypes.sequence:Axt"/> + <sniffer type="galaxy.datatypes.interval:Bed"/> + <sniffer type="galaxy.datatypes.interval:CustomTrack"/> + <sniffer type="galaxy.datatypes.interval:Gff"/> + <sniffer type="galaxy.datatypes.interval:Gff3"/> + <sniffer type="galaxy.datatypes.interval:Interval"/> + <sniffer type="galaxy.datatypes.tabular:Sam"/> + </sniffers> +</datatypes>
--- 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 @@ -<suite id="ONTO-ToolKit" name="Suite of OBO Ontology manipulation tools" version="0.1"> +<suite id="ONTO-ToolKit" name="Suite of OBO Ontology manipulation tools" version="0.2"> <description>This suite contains tools for managing ontologies that are represented in the OBO flat file format</description> <tool id="get_ancestor_terms" name="Get the ancestor terms of a given OBO term" version="1.22"> @@ -21,6 +21,10 @@ <description>Collects common OBO terms from a given set of list containing OBO terms</description> </tool> + <tool id="get_parent_terms_by_relationship_type" name="Get the terms of a given OBO term through a concrete relationship type" version="1.22"> + <description>Collects the terms from a given term in the given OBO ontology, filtered by a relationship type</description> + </tool> + <tool id="get_parent_terms" name="Get the parent terms of a given OBO term" version="1.22"> <description>Collects the parent terms from a given term in the given OBO ontology</description> </tool> @@ -33,6 +37,10 @@ <description>Extracts a subontology (in OBO format) of a given ontology having as root node the provided term ID</description> </tool> + <tool id="get_terms_by_relationship_type" name="Get the terms that are related by a concrete relationship type" version="1.22"> + <description>Collects the terms that are related by a concrete relationship type</description> + </tool> + <tool id="obo2owl" name="Convert OBO to OWL" version="1.22"> <description>Converts an OBO formatted ontology to OWL format</description> </tool>
--- 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 @@ </section> <section name="OBO Ontology manipulation" id="ONTO-ToolKit"> <tool file="ontology/get_ancestor_terms.xml"/> - <tool file="ontology/get_parent_terms.xml"/> + <tool file="ontology/get_child_terms.xml"/> <tool file="ontology/get_descendent_terms.xml"/> - <tool file="ontology/get_child_terms.xml"/> - <tool file="ontology/term_id_vs_term_def.xml"/> - <tool file="ontology/term_id_vs_term_name.xml"/> + <tool file="ontology/get_intersection_ontology_from.xml" /> + <tool file="ontology/get_list_intersection_from.xml" /> + <tool file="ontology/get_parent_terms_by_relationship_type.xml"/> + <tool file="ontology/get_parent_terms.xml"/> <tool file="ontology/get_relationship_types.xml"/> + <tool file="ontology/get_subontology_from.xml" /> + <tool file="ontology/get_terms_by_relationship_type.xml" /> <tool file="ontology/obo2rdf.xml" /> <tool file="ontology/obo2tran.xml" /> <tool file="ontology/obo2owl.xml" /> - <tool file="ontology/get_subontology_from.xml" /> - <tool file="ontology/get_list_intersection_from.xml" /> - <tool file="ontology/get_intersection_ontology_from.xml" /> + <tool file="ontology/term_id_vs_term_def.xml"/> + <tool file="ontology/term_id_vs_term_name.xml"/> </section> <section name="Send Data" id="send"> <tool file="data_destination/epigraph.xml" />
--- /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__ + + + + + +
--- /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 @@ +<tool id="get_parent_terms_by_relationship_type" name="Get the terms of a given OBO term through a concrete relationship type" version="1.22"> + <description>Collects the terms from a given term in the given OBO ontology, filtered by a relationship type</description> + <command interpreter="perl">/usr/bin/get_parent_terms_by_relationship_type.pl $input_ontology $term_id $rel_id > $output</command> + <inputs> + <param format="text" name="input_ontology" type="data" label="Source file"/> + <param name="term_id" type="text" size="30" value="" label="Term ID" /> + <param name="rel_id" type="text" size="30" value="" label="Rel ID" /> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <tests> + <test> + <param name="input" value="pre_cco.obo"/> + <param name="term_id" value="CCO:B0000073"/> + <param name="rel_id" value="participates_in"/> + <output name="out_file" file="ancestors_rel_filtered.txt"/> + </test> + </tests> + + <help> + +.. 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 + + </help> + +</tool> +
--- /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__
--- /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 @@ +<tool id="get_terms_by_relationship_type" name="Get the terms that are related by a concrete relationship type" version="1.22"> + <description>Collects the terms that are related by a concrete relationship type</description> + <command interpreter="perl">/usr/bin/get_terms_by_relationship_type.pl $input_ontology $rel_id > $output</command> + <inputs> + <param format="text" name="input_ontology" type="data" label="Source file"/> + <param name="rel_id" type="text" size="30" value="" label="Rel ID" /> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <tests> + <test> + <param name="input" value="pre_cco.obo"/> + <param name="rel_id" value="participates_in"/> + <output name="out_file" file="terms_rel_filtered.txt"/> + </test> + </tests> + + <help> + +.. 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 + + </help> + +</tool> \ No newline at end of file