Chris Mungall cmungall

Bold Hypothesis: GO BPs can be cleanly separated into cellular processes and larger processes formed from assemblages of these. Any process should be diagrammable. If the diagram is expressed using cell parts and molecules, it is cellular. If the diagram is expressed using cells or tissues it is at a larger level of organization.

Additionally, we may have grouping classes which can abstract over both branches, in terms of some objective or phenotype. Examples are: growth (to increase the size of the organism or a part), immune system

README is empty

	fmt,num,diffsize,iteration
	owl,1,250481,1
	ofn,1,15,1
	obo,1,2,1
	ttl,1,245804,1
	omn,1,22,1
	owl,2,249967,1
	ofn,2,12,1
	obo,2,8,1
	ttl,2,245001,1

	library(ggplot2)

	the.data <- read.table( header=TRUE, sep=",", "foo.OUT")
	ggplot(the.data, aes( x = numAxiomsDeleted, y = diffsize, shape = fmt, label = fmt, group = fmt ) ) +
	scale_shape_discrete(solid=T, legend=T) +
	scale_y_log10() +
	scale_x_log10() +
	geom_point(aes(colour = fmt)) +
	geom_smooth()

	#!/usr/bin/perl
	my $f = shift @ARGV;

	runcmd("save-in-all-formats.sh $f");

	our $N=16;
	our $ITERATIONS=10;

	for (my $iter=1; $iter<= $ITERATIONS; $iter++) {

	#!/bin/sh
	if [ -e catalog-v001.xml ]
	then
	X='--use-catalog'
	else
	X=""
	fi
	F=$1;
	owltools $X $1 -o $F.owl -o -f ofn $F.ofn -o -f omn $F.omn -o -f ttl $F.ttl -o -f obo --no-check $F.obo
	du -sh $F.*

	# see thea/benchmarks directory
	TIME THEA CARO 0.0697942
	MEM THEA CARO 1.885792
	TIME THEA CL 1.38948
	MEM THEA CL 8.553492
	TIME THEA FBbt 19.0624
	MEM THEA FBbt 38.238024
	TIME THEA GO 411.418
	MEM THEA GO 381.50792
	TIME THEA SO 3.1424

	============================== Prover9 ===============================
	Prover9 (32) version 2008-11A, November 2008.
	Process 8186 was started by cjm on skerryvore,
	Wed Aug 5 13:44:32 2009
	The command was "prover9".
	============================== end of head ===========================

	============================== INPUT =================================

	formulas(sos).