The PerlCyc and JavaCyc APIs

1. The PerlCyc and JavaCyc APIs

2. 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

3. 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…

4. GFP functions (require knowledge of Pathway Tools schema): get_slot_values get_class_all_instances put_slot_values Pathway Tools functions (described at http://bioinformatics.ai.sri.com/ptools/ptools-fns.html): genes_of_reaction find_indexed_frame pathways_of_gene transport_p getSlotValues getClassAllInstances putSlotValues genesOfReaction findIndexedFrame pathwaysOfGene transportP Examples of PerlCyc, JavaCyc Functions

5. 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”); }

6. 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";

7. 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"; } }

8. 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; } }

9. 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();

10. 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); } } } }