cmungall

#!/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.*

cmungall

#!/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++) {

cmungall

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()

cmungall

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

cmungall

============================== 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).

cmungall

# 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

cmungall

README is empty

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

cmungall

SciLink

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

cmungall

## Type Definitions (contract)

type Drug {
  id: ID!
  name: String!
  drugInteractions: [DrugInteraction]
  drugTargets: [DrugTarger]
}

type DrugTarget {