[Obo-phenotype-commits] [phenotype-ontologies] r411 committed - new

[<phe...@go...>]

Revision: 411
Author:   cmungall
Date:     Mon Nov 25 02:30:58 2013 UTC
Log:      new
http://code.google.com/p/phenotype-ontologies/source/detail?r=411

Added:
  /trunk/analysis
  /trunk/analysis/Makefile
  /trunk/analysis/sim.properties

=======================================
--- /dev/null
+++ /trunk/analysis/Makefile	Mon Nov 25 02:30:58 2013 UTC
@@ -0,0 +1,26 @@
+OBO = http://purl.obolibrary.org/obo
+UPHENO = $(OBO)/upheno
+ONT = ../src/ontology/
+DATA = ../data
+MM = $(DATA)/Mus_musculus
+DR = $(DATA)/Danio_rerio
+MM_G2P = $(MM)/Mm-gene-to-phenotype-BF.txt
+MM_G2L = $(MM)/Mm-gene-labels.txt
+DR_G2P = $(DR)/Dr-gene-to-phenotype-BF.txt
+DR_G2L = $(DR)/Dr-gene-labels.txt
+
+TRIGGERS = $(ONT)/mp.owl $(ONT)/hp.owl $(MM_G2P)
+
+USECAT = --catalog-xml $(ONT)/catalog-v001.xml
+
+Dr-gene-to-Dr-gene-sim.out:
+	OWLTOOLS_MEMORY=12G owltools  $(USECAT) $(UPHENO)/vertebrate.owl   
--load-labels $(DR_G2L) --load-instances $(DR_G2P) --fsim-basic -p  
sim.properties --set minimumMaxIC 3.0 --set minimumSimJ 0.25 --set  
compare "ZFIN,ZFIN" -o $@
+
+Mm-gene-to-Mm-gene-sim.out:
+	OWLTOOLS_MEMORY=12G owltools  $(USECAT) $(UPHENO)/vertebrate.owl   
--load-labels $(MM_G2L) --load-instances $(MM_G2P) --fsim-basic -p  
sim.properties --set minimumMaxIC 3.0 --set minimumSimJ 0.25 --set  
compare "MGI,MGI" -o $@
+
+Dr-gene-to-disease-sim.out:
+	owltools  $(USECAT) $(UPHENO)/vertebrate.owl  --load-labels $(DR_G2L)  
--load-instances $(DR_G2P) --fsim-basic -p sim.properties --set  
minimumMaxIC 3.0 --set minimumSimJ 0.6 --set compare "OMIM,ZFIN" -o $@
+
+
+
=======================================
--- /dev/null
+++ /trunk/analysis/sim.properties	Mon Nov 25 02:30:58 2013 UTC
@@ -0,0 +1,7 @@
+minimumMaxIC = 0.0
+minimumSimJ = 0.7
+minimumAsymSimJ = 0.5
+thresholdAsymSimJ = 0.9
+topN = 100
+compare = MP,HP
+scoringMetrics = JACCARD