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============================== 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). |
# 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 |
#!/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.* |
#!/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++) { |
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() |
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 |
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
https://docs.google.com/document/d/136NBEwqi0Jwon4h23m0BfDMMIn_TBx06o1pPXNz8HXk/edit
This API wraps a number of different more modular APIs and database engines or analysis services. The idea is that the API implementation will do the right thing - for example, using Solr for searches but injecting results with fast in-memory traversal of ontology graphs.
When starting up, configure with:
- PURL of tbox
- BOLT connector metadata for neo4j
## Type Definitions (contract) | |
type Drug { | |
id: ID! | |
name: String! | |
drugInteractions: [DrugInteraction] | |
drugTargets: [DrugTarger] | |
} | |
type DrugTarget { |