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changeset 8:00a5ede354a0

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Uploaded
author jorrit
date Tue, 26 Feb 2013 17:45:58 -0500
parents 9d9a06b511ff
children aebf24eea338
files README fetch_ontology.xml ontologizer.xml test-data/ontologizer/test.gaf test-data/ontologizer/test.gset test-data/ontologizer/test.obo test-data/ontologizer/test.output tool_dependencies.xml
diffstat 7 files changed, 485 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/README	Tue Feb 19 18:16:12 2013 -0500
+++ b/README	Tue Feb 26 17:45:58 2013 -0500
@@ -20,6 +20,9 @@
 
 http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/go-db-perl/scripts/go-find-enriched-terms.pl?view=log
 
+--- Gene Associations ---
+svn --ignore-externals co svn://ext.geneontology.org/trunk/gene-associations gene-associations
+
 --- AmiGO related ---
 
 for AmiGO Manual 
--- a/fetch_ontology.xml	Tue Feb 19 18:16:12 2013 -0500
+++ b/fetch_ontology.xml	Tue Feb 26 17:45:58 2013 -0500
@@ -13,7 +13,7 @@
   <tests>
     <test>
      <param name="ont" value="ECO" />
-     <output name="output" file="output.eco.obo.contains" compare="contains"/>
+     <output name="output" file="output.eco.obo.contains"/>
     </test>
   </tests>
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ontologizer.xml	Tue Feb 26 17:45:58 2013 -0500
@@ -0,0 +1,35 @@
+<tool id="ontologizer" name="ontologizer" version="0.0.14">
+  <description>from http://compbio.charite.de/contao/</description>
+  <requirements>
+    <requirement type="package" version="0.0.1">ontologizer</requirement>
+  </requirements>
+  <command>java -Xmx2G -jar $ONTOLOGIZER_JAR --go $go --association $gaf --population $pop --studyset $study --dot 0.05 > $output</command>
+  <inputs>
+    <param name="go" format="obo" label="Gene ontology" />
+    <param name="gaf" format="gaf" label="Gene association file" />
+    <param name="pop" format="text" label="population gene set" />
+    <param name="study" format="text" label="study gene set" />
+  </inputs>
+  <outputs>
+    <!-- need to figure out how to handle multiple outputs -->
+    <data format="text" name="output" />
+  </outputs>
+  <tests>
+    <!-- see http://wiki.galaxyproject.org/Admin/Tools/Writing%20Tests -->
+    <test>
+     <param name="go" file="ontologizer/test.obo" />
+     <param name="gaf" file="ontologizer/test.gaf" />
+     <param name="pop" file="ontologizer/test.gs" />
+     <param name="study" file="ontologizer/test.gs" />
+     <output name="output" file="test.output"/>
+    </test>
+  </tests>
+
+
+  <help>
+    see http://compbio.charite.de/contao/index.php/ontologizer2.html
+  </help>
+
+</tool>
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ontologizer/test.gaf	Tue Feb 26 17:45:58 2013 -0500
@@ -0,0 +1,50 @@
+!gaf-version: 2.0
+!FOR TEST PURPOSES ONLY
+UniProtKB	C9J0V6	GIGYF2		GO:0048009	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000027475	P	PERQ amino acid-rich with GYF domain-containing protein 2	C9J0V6_HUMAN|GIGYF2	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	C9J1A6	GIGYF2		GO:0048009	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000027475	P	PERQ amino acid-rich with GYF domain-containing protein 2	C9J1A6_HUMAN|GIGYF2	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	C9JH18	GIGYF2		GO:0048009	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000027475	P	PERQ amino acid-rich with GYF domain-containing protein 2	C9JH18_HUMAN|GIGYF2	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	C9JHT0	GIGYF2		GO:0048009	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000027475	P	PERQ amino acid-rich with GYF domain-containing protein 2	C9JHT0_HUMAN|GIGYF2	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	C9JPV7	GIGYF2		GO:0048009	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000027475	P	PERQ amino acid-rich with GYF domain-containing protein 2	C9JPV7_HUMAN|GIGYF2	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	C9JRZ2	GIGYF2		GO:0048009	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000027475	P	PERQ amino acid-rich with GYF domain-containing protein 2	C9JRZ2_HUMAN|GIGYF2	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	C9JXQ0	GIGYF2		GO:0048009	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000027475	P	PERQ amino acid-rich with GYF domain-containing protein 2	C9JXQ0_HUMAN|GIGYF2	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	C9JZC0	GIGYF2		GO:0048009	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000027475	P	PERQ amino acid-rich with GYF domain-containing protein 2	C9JZC0_HUMAN|GIGYF2	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	D6RG33	FGF10		GO:0008589	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000022246	P	Fibroblast growth factor 10	D6RG33_HUMAN|FGF10	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	E5RGI8	PIK3R1		GO:0048009	GO_REF:0000019	IEA	Ensembl:ENSRNOP00000060575	P	Phosphatidylinositol 3-kinase regulatory subunit alpha	E5RGI8_HUMAN|PIK3R1	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	E5RHI0	PIK3R1		GO:0048009	GO_REF:0000019	IEA	Ensembl:ENSRNOP00000060575	P	Phosphatidylinositol 3-kinase regulatory subunit alpha	E5RHI0_HUMAN|PIK3R1	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	E5RJY0	PIK3R1		GO:0048009	GO_REF:0000019	IEA	Ensembl:ENSRNOP00000060575	P	Phosphatidylinositol 3-kinase regulatory subunit alpha	E5RJY0_HUMAN|PIK3R1	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	E7ER02	EIF2AK3		GO:0048009	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000034093	P	Eukaryotic translation initiation factor 2-alpha kinase 3	E7ER02_HUMAN|EIF2AK3	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	E7EX19	PIK3R1		GO:0048009	GO_REF:0000019	IEA	Ensembl:ENSRNOP00000060575	P	Phosphatidylinositol 3-kinase regulatory subunit alpha	E7EX19_HUMAN|PIK3R1	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	H3BPF5	RPGRIP1L		GO:0008589	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000042702	P	Protein fantom	H3BPF5_HUMAN|RPGRIP1L	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	I3L2P2	RPGRIP1L		GO:0008589	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000042702	P	Protein fantom	I3L2P2_HUMAN|RPGRIP1L	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	O15520	FGF10		GO:0008589	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000022246	P	Fibroblast growth factor 10	FGF10_HUMAN|FGF10	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	O75420	GIGYF1		GO:0048009	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000031727	P	PERQ amino acid-rich with GYF domain-containing protein 1	PERQ1_HUMAN|GIGYF1|PP3360|CDS2|PERQ1	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	P05019	IGF1		GO:0048009	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000056668	P	Insulin-like growth factor I	IGF1_HUMAN|IGF1|IBP1	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	P08069	IGF1R		GO:0048009	PMID:7679099	IDA		P	Insulin-like growth factor 1 receptor	IGF1R_HUMAN|IGF1R	protein	taxon:9606	20051129	UniProtKB		
+UniProtKB	P08151	GLI1		GO:0008589	PMID:11238441	TAS		P	Zinc finger protein GLI1	GLI1_HUMAN|GLI|GLI1	protein	taxon:9606	20040506	UniProtKB		
+UniProtKB	P10070	GLI2		GO:0008589	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000054837	P	Zinc finger protein GLI2	GLI2_HUMAN|THP|GLI2	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	P10912	GHR		GO:0048009	PMID:7565946	IMP		P	Growth hormone receptor	GHR_HUMAN|GHR	protein	taxon:9606	20081205	BHF-UCL		
+UniProtKB	P11717	IGF2R		GO:0048009	PMID:10799489	TAS		P	Cation-independent mannose-6-phosphate receptor	MPRI_HUMAN|IGF2R|MPRI	protein	taxon:9606	20130105	GOC		
+UniProtKB	P21802	FGFR2		GO:0008589	GO_REF:0000024	ISS	UniProtKB:P21803	P	Fibroblast growth factor receptor 2	FGFR2_HUMAN|BEK|FGFR2|KGFR|KSAM	protein	taxon:9606	20101105	UniProtKB		
+UniProtKB	P27986	PIK3R1		GO:0048009	PMID:7541045	IPI	UniProtKB:P08069	P	Phosphatidylinositol 3-kinase regulatory subunit alpha	P85A_HUMAN|PIK3R1|GRB1	protein	taxon:9606	20051207	UniProtKB		
+UniProtKB	P27986	PIK3R1		GO:0048009	PMID:7782332	IDA		P	Phosphatidylinositol 3-kinase regulatory subunit alpha	P85A_HUMAN|PIK3R1|GRB1	protein	taxon:9606	20081209	BHF-UCL		
+UniProtKB	P31749	AKT1		GO:0048009	PMID:8978681	IMP		P	RAC-alpha serine/threonine-protein kinase	AKT1_HUMAN|AKT1|PKB|RAC	protein	taxon:9606	20060109	UniProtKB		
+UniProtKB	P32243	OTX2		GO:0008589	PMID:15705863	TAS		P	Homeobox protein OTX2	OTX2_HUMAN|OTX2	protein	taxon:9606	20050607	UniProtKB		
+UniProtKB	P35568	IRS1		GO:0048009	PMID:7541045	IPI	UniProtKB:P08069	P	Insulin receptor substrate 1	IRS1_HUMAN|IRS1	protein	taxon:9606	20051129	UniProtKB		
+UniProtKB	P49815	TSC2		GO:0048009	GO_REF:0000024	ISS	UniProtKB:Q61037	P	Tuberin	TSC2_HUMAN|TSC4|TSC2	protein	taxon:9606	20080314	UniProtKB		
+UniProtKB	P49815	TSC2		GO:0048009	GO_REF:0000033	IBA	PANTHER:PTN000006943	P	Tuberin	TSC2_HUMAN|TSC4|TSC2	protein	taxon:9606	20110614	RefGenome		
+UniProtKB	P54826	GAS1		GO:0008589	GO_REF:0000024	ISS	UniProtKB:Q01721	P	Growth arrest-specific protein 1	GAS1_HUMAN|GAS1	protein	taxon:9606	20111117	UniProtKB		
+UniProtKB	Q13322	GRB10		GO:0048009	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000091011	P	Growth factor receptor-bound protein 10	GRB10_HUMAN|GRB10|GRBIR|KIAA0207	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	Q13635	PTCH1		GO:0008589	GO_REF:0000024	ISS	UniProtKB:Q61115	P	Protein patched homolog 1	PTC1_HUMAN|PTCH|PTCH1	protein	taxon:9606	20060508	UniProtKB		
+UniProtKB	Q15915	ZIC1		GO:0008589	GO_REF:0000024	ISS	UniProtKB:P46684	P	Zinc finger protein ZIC 1	ZIC1_HUMAN|ZIC|ZIC1|ZNF201	protein	taxon:9606	20041006	UniProtKB		
+UniProtKB	Q1PSW9	GLI2		GO:0008589	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000054837	P	GLI2 transcription factor	Q1PSW9_HUMAN|GLI2	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	Q2MV58	TCTN1		GO:0008589	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000107367	P	Tectonic-1	TECT1_HUMAN|TECT1|TCTN1|UNQ9369/PRO34160	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	Q4AC94	C2CD3		GO:0008589	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000062637	P	C2 domain-containing protein 3	C2CD3_HUMAN|C2CD3	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	Q68CZ1	RPGRIP1L		GO:0008589	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000042702	P	Protein fantom	FTM_HUMAN|RPGRIP1L|FTM|KIAA1005|NPHP8	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	Q6Y7W6	GIGYF2		GO:0048009	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000027475	P	PERQ amino acid-rich with GYF domain-containing protein 2	PERQ2_HUMAN|KIAA0642|GIGYF2|PERQ2|TNRC15	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	Q92793	CREBBP		GO:0008589	PMID:11001584	TAS		P	CREB-binding protein	CBP_HUMAN|CREBBP|CBP	protein	taxon:9606	20111117	BHF-UCL		
+UniProtKB	Q9BT04	FUZ		GO:0008589	GO_REF:0000024	ISS	UniProtKB:Q3UYI6	P	Protein fuzzy homolog	FUZZY_HUMAN|FUZ|FY	protein	taxon:9606	20110413	UniProtKB		
+UniProtKB	Q9NQ66	PLCB1		GO:0048009	GO_REF:0000024	ISS	UniProtKB:Q9Z1B3	P	1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1	PLCB1_HUMAN|KIAA0581|PLCB1	protein	taxon:9606	20110304	BHF-UCL		
+UniProtKB	Q9NZJ5	EIF2AK3		GO:0048009	GO_REF:0000024	ISS	UniProtKB:Q9Z2B5	P	Eukaryotic translation initiation factor 2-alpha kinase 3	E2AK3_HUMAN|EIF2AK3|PEK|PERK	protein	taxon:9606	20080924	UniProtKB		
+UniProtKB	Q9NZV1	CRIM1		GO:0048009	PMID:10642437	TAS		P	Cysteine-rich motor neuron 1 protein	CRIM1_HUMAN|S52|UNQ1886/PRO4330|CRIM1	protein	taxon:9606	20130105	GOC		
+UniProtKB	Q9ULC3	RAB23		GO:0008589	GO_REF:0000019	IEA	Ensembl:ENSMUSP00000085625	P	Ras-related protein Rab-23	RAB23_HUMAN|HSPC137|RAB23	protein	taxon:9606	20130105	ENSEMBL		
+UniProtKB	Q9ULD6	INTU		GO:0008589	GO_REF:0000024	ISS	UniProtKB:Q059U7	P	Protein inturned	INTU_HUMAN|KIAA1284|INTU|PDZD6|PDZK6	protein	taxon:9606	20120127	UniProtKB		
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ontologizer/test.gset	Tue Feb 26 17:45:58 2013 -0500
@@ -0,0 +1,18 @@
+*reference_set: test
+*expected_enriched_term:GO:0048009 ! insulin-like growth factor receptor signaling pathway
+*item_id_type: symbol
+###
+AKT1
+CRIM1
+EIF2AK3
+GHR
+GIGYF1
+GIGYF2
+GRB10
+IGF1
+IGF1R
+IGF2R
+IRS1
+PIK3R1
+PLCB1
+TSC2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ontologizer/test.obo	Tue Feb 26 17:45:58 2013 -0500
@@ -0,0 +1,356 @@
+format-version: 1.2
+ontology: go
+subsetdef: Cross-product_review "Involved_in"
+subsetdef: goslim_aspergillus "Aspergillus GO slim"
+subsetdef: goslim_candida "Candida GO slim"
+subsetdef: goslim_generic "Generic GO slim"
+subsetdef: goslim_metagenomics "Metagenomics GO slim"
+subsetdef: goslim_pir "PIR GO slim"
+subsetdef: goslim_plant "Plant GO slim"
+subsetdef: goslim_pombe "Fission yeast GO slim"
+subsetdef: goslim_yeast "Yeast GO slim"
+subsetdef: gosubset_prok "Prokaryotic GO subset"
+subsetdef: high_level_annotation_qc "High-level terms not to be used for direct annotation"
+subsetdef: mf_needs_review "Catalytic activity terms in need of attention"
+subsetdef: termgenie_unvetted "Terms created by TermGenie that do not follow a template and require additional vetting by editors"
+subsetdef: virus_checked "Viral overhaul terms"
+synonymtypedef: systematic_synonym "Systematic synonym" EXACT
+
+[Term]
+id: GO:0007154
+name: cell communication
+namespace: biological_process
+def: "Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:mah]
+subset: goslim_metagenomics  ! Metagenomics GO slim
+subset: goslim_pir  ! PIR GO slim
+subset: goslim_plant  ! Plant GO slim
+subset: gosubset_prok  ! Prokaryotic GO subset
+xref: Wikipedia:Cell_signaling
+is_a: GO:0044763  ! single-organism cellular process
+
+[Term]
+id: GO:0007165
+name: signal transduction
+namespace: biological_process
+alt_id: GO:0023033
+def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11]
+comment: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.
+subset: goslim_aspergillus  ! Aspergillus GO slim
+subset: goslim_candida  ! Candida GO slim
+subset: goslim_generic  ! Generic GO slim
+subset: goslim_metagenomics  ! Metagenomics GO slim
+subset: goslim_plant  ! Plant GO slim
+subset: gosubset_prok  ! Prokaryotic GO subset
+synonym: "signaling cascade" NARROW []
+synonym: "signaling pathway" RELATED []
+synonym: "signalling cascade" NARROW []
+synonym: "signalling pathway" RELATED [GOC:mah]
+xref: Reactome:REACT_100624
+xref: Reactome:REACT_102354
+xref: Reactome:REACT_112130
+xref: Reactome:REACT_112549
+xref: Reactome:REACT_113151
+xref: Reactome:REACT_113601
+xref: Reactome:REACT_113964
+xref: Reactome:REACT_114657
+xref: Reactome:REACT_114690
+xref: Reactome:REACT_114820
+xref: Reactome:REACT_114910
+xref: Reactome:REACT_115037
+xref: Reactome:REACT_115147
+xref: Reactome:REACT_12478
+xref: Reactome:REACT_31232
+xref: Reactome:REACT_78535
+xref: Reactome:REACT_89740
+xref: Reactome:REACT_93680
+xref: Reactome:REACT_98872
+xref: Wikipedia:Signal_transduction
+is_a: GO:0050794  ! regulation of cellular process
+is_a: GO:0051716  ! cellular response to stimulus
+relationship: part_of GO:0007154 ! cell communication
+relationship: part_of GO:0044700 ! single organism signaling
+
+[Term]
+id: GO:0007166
+name: cell surface receptor signaling pathway
+namespace: biological_process
+def: "A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:mah, GOC:pr, GOC:signaling]
+subset: gosubset_prok  ! Prokaryotic GO subset
+synonym: "cell surface receptor linked signal transduction" EXACT []
+synonym: "cell surface receptor linked signaling pathway" EXACT [GOC:bf]
+synonym: "cell surface receptor linked signalling pathway" EXACT [GOC:mah]
+xref: Reactome:REACT_6290
+is_a: GO:0007165  ! signal transduction
+
+[Term]
+id: GO:0007167
+name: enzyme linked receptor protein signaling pathway
+namespace: biological_process
+def: "Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell, where the receptor possesses catalytic activity or is closely associated with an enzyme such as a protein kinase, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, ISBN:0185316194]
+synonym: "enzyme linked receptor protein signalling pathway" EXACT []
+is_a: GO:0007166  ! cell surface receptor signaling pathway
+
+[Term]
+id: GO:0007169
+name: transmembrane receptor protein tyrosine kinase signaling pathway
+namespace: biological_process
+def: "A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:ceb, GOC:signaling]
+synonym: "transmembrane receptor protein tyrosine kinase signalling pathway" EXACT []
+xref: Reactome:REACT_101238
+xref: Reactome:REACT_104074
+xref: Reactome:REACT_106114
+xref: Reactome:REACT_106720
+xref: Reactome:REACT_108494
+xref: Reactome:REACT_11064
+xref: Reactome:REACT_29786
+xref: Reactome:REACT_82296
+xref: Reactome:REACT_90767
+xref: Reactome:REACT_97816
+is_a: GO:0007167  ! enzyme linked receptor protein signaling pathway
+
+[Term]
+id: GO:0007224
+name: smoothened signaling pathway
+namespace: biological_process
+def: "A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened." [GOC:mah, PMID:15205520]
+synonym: "Shh signaling pathway" RELATED [GOC:dph]
+synonym: "Sonic hedgehog signaling pathway" NARROW [GOC:dph]
+synonym: "hedgehog signaling pathway" EXACT []
+synonym: "hh signaling pathway" NARROW []
+synonym: "hh signalling pathway" NARROW []
+synonym: "smoothened signalling pathway" EXACT []
+xref: Wikipedia:Hedgehog_signaling_pathway
+is_a: GO:0007166  ! cell surface receptor signaling pathway
+
+[Term]
+id: GO:0008150
+name: biological_process
+namespace: biological_process
+alt_id: GO:0000004
+alt_id: GO:0007582
+def: "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [GOC:go_curators, GOC:isa_complete]
+comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
+subset: goslim_aspergillus  ! Aspergillus GO slim
+subset: goslim_candida  ! Candida GO slim
+subset: goslim_generic  ! Generic GO slim
+subset: goslim_metagenomics  ! Metagenomics GO slim
+subset: goslim_pir  ! PIR GO slim
+subset: goslim_plant  ! Plant GO slim
+subset: goslim_pombe  ! Fission yeast GO slim
+subset: goslim_yeast  ! Yeast GO slim
+subset: gosubset_prok  ! Prokaryotic GO subset
+synonym: "biological process" EXACT []
+synonym: "biological process unknown" NARROW []
+synonym: "physiological process" EXACT []
+xref: Wikipedia:Biological_process
+
+[Term]
+id: GO:0008589
+name: regulation of smoothened signaling pathway
+namespace: biological_process
+alt_id: GO:0007226
+alt_id: GO:0043109
+def: "Any process that modulates the frequency, rate or extent of smoothened signaling." [GOC:go_curators]
+synonym: "regulation of hedgehog signaling pathway" EXACT [GOC:bf, GOC:ecd]
+synonym: "regulation of hh signaling pathway" EXACT [GOC:bf, GOC:ecd]
+synonym: "regulation of smoothened activity" RELATED []
+synonym: "regulation of smoothened by patched" RELATED []
+synonym: "regulation of smoothened receptor activity by patched" RELATED []
+synonym: "regulation of smoothened signalling pathway" EXACT []
+is_a: GO:0009966  ! regulation of signal transduction
+relationship: regulates GO:0007224 ! smoothened signaling pathway
+intersection_of: GO:0065007  ! biological regulation
+intersection_of: regulates GO:0007224 ! smoothened signaling pathway
+
+[Term]
+id: GO:0009966
+name: regulation of signal transduction
+namespace: biological_process
+alt_id: GO:0035466
+def: "Any process that modulates the frequency, rate or extent of signal transduction." [GOC:sm]
+subset: gosubset_prok  ! Prokaryotic GO subset
+synonym: "regulation of signaling pathway" RELATED []
+synonym: "regulation of signalling pathway" RELATED [GOC:mah]
+is_a: GO:0010646  ! regulation of cell communication
+is_a: GO:0023051  ! regulation of signaling
+is_a: GO:0048583  ! regulation of response to stimulus
+relationship: regulates GO:0007165 ! signal transduction
+intersection_of: GO:0065007  ! biological regulation
+intersection_of: regulates GO:0007165 ! signal transduction
+
+[Term]
+id: GO:0009987
+name: cellular process
+namespace: biological_process
+alt_id: GO:0008151
+alt_id: GO:0050875
+def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete]
+subset: goslim_pir  ! PIR GO slim
+subset: goslim_plant  ! Plant GO slim
+subset: gosubset_prok  ! Prokaryotic GO subset
+synonym: "cell growth and/or maintenance" NARROW []
+synonym: "cell physiology" EXACT []
+synonym: "cellular physiological process" EXACT []
+is_a: GO:0008150  ! biological_process
+
+[Term]
+id: GO:0010646
+name: regulation of cell communication
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:dph, GOC:tb]
+is_a: GO:0050794  ! regulation of cellular process
+relationship: regulates GO:0007154 ! cell communication
+intersection_of: GO:0065007  ! biological regulation
+intersection_of: regulates GO:0007154 ! cell communication
+
+[Term]
+id: GO:0023051
+name: regulation of signaling
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of a signaling process." [GOC:mtg_signal]
+synonym: "regulation of signaling process" RELATED [GOC:bf]
+synonym: "regulation of signalling process" RELATED [GOC:mah]
+is_a: GO:0050789  ! regulation of biological process
+relationship: regulates GO:0044700 ! single organism signaling
+intersection_of: GO:0065007  ! biological regulation
+intersection_of: regulates GO:0023052 ! signaling
+
+[Term]
+id: GO:0023052
+name: signaling
+namespace: biological_process
+alt_id: GO:0023046
+def: "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered." [GOC:mtg_signal, GOC:mtg_signaling_feb11, GOC:signaling]
+comment: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.
+subset: goslim_pombe  ! Fission yeast GO slim
+subset: goslim_yeast  ! Yeast GO slim
+synonym: "biological signaling" EXACT []
+synonym: "signaling process" EXACT []
+synonym: "signalling" EXACT []
+synonym: "signalling process" RELATED [GOC:mah]
+is_a: GO:0008150  ! biological_process
+
+[Term]
+id: GO:0044699
+name: single-organism process
+namespace: biological_process
+def: "A biological process that involves only one organism." [GOC:jl]
+synonym: "single organism process" EXACT []
+is_a: GO:0008150  ! biological_process
+
+[Term]
+id: GO:0044700
+name: single organism signaling
+namespace: biological_process
+def: "A signaling process occurring within a single organism." [GOC:jl]
+is_a: GO:0023052  ! signaling
+is_a: GO:0044699  ! single-organism process
+
+[Term]
+id: GO:0044763
+name: single-organism cellular process
+namespace: biological_process
+def: "Any process that is carried out at the cellular level, occurring within a single organism." [GOC:jl]
+is_a: GO:0009987  ! cellular process
+is_a: GO:0044699  ! single-organism process
+
+[Term]
+id: GO:0048009
+name: insulin-like growth factor receptor signaling pathway
+namespace: biological_process
+def: "The series of molecular signals generated as a consequence of the insulin-like growth factor receptor binding to one of its physiological ligands." [GOC:ceb]
+synonym: "IGF receptor signaling pathway" EXACT []
+synonym: "IGF receptor signalling pathway" EXACT []
+is_a: GO:0007169  ! transmembrane receptor protein tyrosine kinase signaling pathway
+
+[Term]
+id: GO:0048583
+name: regulation of response to stimulus
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." [GOC:jid]
+comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC.
+subset: gosubset_prok  ! Prokaryotic GO subset
+subset: high_level_annotation_qc  ! High-level terms not to be used for direct annotation
+is_a: GO:0050789  ! regulation of biological process
+relationship: regulates GO:0050896 ! response to stimulus
+intersection_of: GO:0065007  ! biological regulation
+intersection_of: regulates GO:0050896 ! response to stimulus
+
+[Term]
+id: GO:0050789
+name: regulation of biological process
+namespace: biological_process
+alt_id: GO:0050791
+def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators]
+subset: goslim_aspergillus  ! Aspergillus GO slim
+subset: goslim_candida  ! Candida GO slim
+subset: gosubset_prok  ! Prokaryotic GO subset
+synonym: "regulation of physiological process" EXACT []
+is_a: GO:0065007  ! biological regulation
+relationship: regulates GO:0008150 ! biological_process
+intersection_of: GO:0065007  ! biological regulation
+intersection_of: regulates GO:0008150 ! biological_process
+
+[Term]
+id: GO:0050794
+name: regulation of cellular process
+namespace: biological_process
+alt_id: GO:0051244
+def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators]
+subset: gosubset_prok  ! Prokaryotic GO subset
+synonym: "regulation of cellular physiological process" EXACT []
+is_a: GO:0050789  ! regulation of biological process
+relationship: regulates GO:0009987 ! cellular process
+intersection_of: GO:0065007  ! biological regulation
+intersection_of: regulates GO:0009987 ! cellular process
+
+[Term]
+id: GO:0050896
+name: response to stimulus
+namespace: biological_process
+alt_id: GO:0051869
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf]
+comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC.
+subset: goslim_pir  ! PIR GO slim
+subset: gosubset_prok  ! Prokaryotic GO subset
+subset: high_level_annotation_qc  ! High-level terms not to be used for direct annotation
+synonym: "physiological response to stimulus" EXACT []
+is_a: GO:0008150  ! biological_process
+
+[Term]
+id: GO:0051716
+name: cellular response to stimulus
+namespace: biological_process
+def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell." [GOC:bf, GOC:jl]
+comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC.
+subset: gosubset_prok  ! Prokaryotic GO subset
+subset: high_level_annotation_qc  ! High-level terms not to be used for direct annotation
+is_a: GO:0044763  ! single-organism cellular process
+is_a: GO:0050896  ! response to stimulus
+
+[Term]
+id: GO:0065007
+name: biological regulation
+namespace: biological_process
+def: "Any process that modulates a measurable attribute of any biological process, quality or function." [GOC:dph, GOC:isa_complete, GOC:mah, GOC:pr, GOC:vw]
+subset: goslim_pir  ! PIR GO slim
+subset: gosubset_prok  ! Prokaryotic GO subset
+synonym: "regulation" BROAD []
+is_a: GO:0008150  ! biological_process
+
+[Typedef]
+id: part_of
+name: part_of
+namespace: gene_ontology
+is_transitive: true
+xref: BFO:0000050
+xref: OBO_REL:part_of
+
+[Typedef]
+id: regulates
+name: regulates
+namespace: gene_ontology
+xref: RO:0002211
+transitive_over: part_of  ! part_of
+
+
--- a/tool_dependencies.xml	Tue Feb 19 18:16:12 2013 -0500
+++ b/tool_dependencies.xml	Tue Feb 26 17:45:58 2013 -0500
@@ -1,20 +1,37 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <package name="ontologizer" version="0.0.1">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">curl http://compbio.charite.de/contao/index.php/cmdlineOntologizer.html?file=tl_files/ontologizer/cmdline/Ontologizer.jar > ontologizer.jar</action>
+                <action type="move_directory_files">
+                    <source_directory>./</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="ONTOLOGIZER_JAR">$INSTALL_DIR/ontologizer.jar</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            ontologizer requires java and curl to be installed.
+        </readme>
+    </package>
     <package name="obo-scripts" version="1.0.12">
         <install version="1.0">
             <actions>
                 <action type="shell_command">git clone http://github.com/cmungall/obo-scripts</action>
-		<action type="move_directory_files">
+                <action type="move_directory_files">
                     <source_directory>./</source_directory>
                     <destination_directory>$INSTALL_DIR</destination_directory>
                 </action>
-		<action type="set_environment">
+                <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                 </action>
             </actions>
         </install>
         <readme>
-		obo_scripts require perl to be installed.
-        </readme>
-    </package>
+          obo_scripts require perl to be installed.
+      </readme>
+  </package>
 </tool_dependency>