The PerlCyc and JavaCyc APIs
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Architecture of the API server
 Works
on Unix (Solaris or Linux) only
 Start up Pathway Tools with the –api arg
 Pathway Tools listens on a Unix socket – perl
program communicates through this socket
 Supports both querying and editing PGDBs
 Must run perl or java program on the same
machine that runs Pathway Tools
 This is a security measure, as the API server has no built-in
security
 Can only handle one connection at a time
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Obtaining PerlCyc and JavaCyc
Download from
http://www.sgn.cornell.edu/downloads/
PerlCyc written and maintained by Lukas Mueller at
Boyce Thompson Institute for Plant Research.
JavaCyc written by Thomas Yan at Carnegie
Institute, maintained by Lukas Mueller.
Easy to extend…
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Examples of PerlCyc, JavaCyc
Functions
GFP
functions (require knowledge of Pathway Tools
schema):
 getSlotValues
 get_slot_values
 getClassAllInstances
 get_class_all_instances
 putSlotValues
 put_slot_values
Pathway Tools functions (described at
http://bioinformatics.ai.sri.com/ptools/ptools-fns.html):
 genes_of_reaction
 genesOfReaction
 find_indexed_frame
 findIndexedFrame
 pathways_of_gene
 pathwaysOfGene
 transport_p
 transportP
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Writing a PerlCyc or JavaCyc program



Create a PerlCyc, JavaCyc object:
perlcyc -> new (“ORGID”)
new Javacyc (“ORGID”)
Call PerlCyc, JavaCyc functions on this object:
my $cyc = perlcyc -> new (“ECOLI”);
my @pathways = $cyc -> all_pathways ();
Javacyc cyc = new Javacyc(“ECOLI”);
ArrayList pathways = cyc.allPathways ();
Functions return object IDs, not objects.
 Must connect to server again to retrieve attributes of an object.
foreach my $p (@pathways) {
print $cyc -> get_slot_value ($p, “COMMON-NAME”);}
for (int i=0; I < pathways.size(); i++) {
String pwy = (String) pathways.get(i);
System.out.println (cyc.getSlotValue (pwy, “COMMON-NAME”); }
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Sample PerlCyc Query
 Number
of proteins in E. coli
use perlcyc;
my $cyc = perlcyc -> new (“ECOLI”);
my @proteins = $cyc->
get_class_all_instances("|Proteins|");
my $protein_count = scalar(@proteins);
print "Protein count: $protein_count.\n";
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SRI International Bioinformatics
Sample PerlCyc Query
 Print
IDs of all proteins with molecular weight
between 10 and 20 kD and pI between 4 and 5.
use perlcyc;
my $cyc = perlcyc -> new (“ECOLI”);
foreach my $p ($cyc->get_class_all_instances("|Proteins|")) {
my $mw = $cyc->get_slot_value($p, "molecular-weight-kd");
my $pI = $cyc->get_slot_value($p, "pi");
if ($mw <= 20 && $mw >= 10 && $pI <= 5 && $pI >= 4) {
print "$p\n";
}
}
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SRI International Bioinformatics
Sample PerlCyc Query
 List
all the transcription factors in E. coli, and the
list of genes that each regulates:
use perlcyc;
my $cyc = perlcyc -> new (“ECOLI”);
foreach my $p ($cyc->get_class_all_instances("|Proteins|")) {
if ($cyc->transcription_factor_p($p)) {
my $name = $cyc->get_slot_value($p, "common-name");
my %genes = ();
foreach my $tu ($cyc->regulon_of_protein($p)) {
foreach my $g ($cyc->transcription_unit_genes($tu)) {
$genes{$g} = $cyc->get_slot_value($g, "common-name");
}
}
print "\n\n$name: ";
print join " ", values %genes;
}
}
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SRI International Bioinformatics
Sample Editing Using PerlCyc
 Add
a link from each gene to the corresponding
object in MY-DB (assume ID is same in both
cases)
use perlcyc;
my $cyc = perlcyc -> new (“HPY”);
my @genes = $cyc->get_class_all_instances (“|Genes|”);
foreach my $g (@genes) {
$cyc->add_slot_value ($g, “DBLINKS”, “(MY-DB \”$g\”)”);
}
$cyc->save_kb();
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Sample JavaCyc Query
 Find
all enzymes for which ATP is a regulator
import java.util.*;
public class JavacycSample {
public static void main(String[] args) {
Javacyc cyc = new Javacyc("ECOLI");
ArrayList regframes =
cyc.getClassAllInstances("|Regulation-of-Enzyme-Activity|");
for (int i = 0; i < regframes.size(); i++) {
String reg = (String)regframes.get(i);
boolean bool = cyc.memberSlotValueP(reg, “Regulator", "ATP");
if (bool) {
String enzrxn = cyc.getSlotValue (reg, “Regulated-Entity”);
String enzyme = cyc.getSlotValue (enzrxn, “Enzyme”);
System.out.println(enz); } } } }
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