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ParseReactomeBioPAX.pm
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ParseReactomeBioPAX.pm
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# Copyright SRA International
#
# Distributed under the OSI-approved BSD 3-Clause License.
# See http://ncip.github.com/pathway-interaction-database/LICENSE.txt for details.
package ParseReactomeBioPAX;
require Exporter;
@ISA = qw(Exporter);
#@EXPORT = qw(
# CreateIsA
# CreateLabelSort
#);
use strict;
use XML::Parser;
use PWLabel;
use Pathway;
use IdMap;
use constant REACTOME_SOURCE_ID => 7;
use constant REACTOME_SOURCE_NAME => "Reactome";
#### global unique numeric ids
#### to be used for pathways, interactions, molecules, ptms
my ($next_id, $next_pathway_id, $next_interaction_id, $next_molecule_id,
$next_ptm_id);
my (%final_id);
my (%rdf_id2id, %id2rdf_id);
#### global lv, pw
my ($lv, $pw, $idm);
my (@elem_stack, @attr_stack, %char_value, %id_def);
my ($unification_db, $unification_id);
my ($xref_db, $xref_id);
my (@components, @pathway_components, @step_interactions, @next_steps);
my (%id2type, %id2xref, %reaction2participant, %complex2component,
%network2component,
%catalysis2controller, %catalysis2controlled,
%catalysis2direction, %catalysis2control_type,
%r_catalysis,
%id2name, %id2short_name, %id2synonym,
%participant2stoichiometry, %participant2cellular_location,
%participant2physical_entity,
%participant2db_id, ## populated from COMMENT's: internal Reactome DB_ID
%edge2participant,
%sequence_participant2feature, %sequence_feature2type,
%feature2location, %feature2residue,
%unification, %relationship, %publication,
%site2position, %site2position_status, %interval2begin, %interval2end);
my (%uniprot2entrez_gene);
my ($pathway2reaction);
### Shiva's mapping of our terms to CHEBI
# Acetylation: MOD:00394; acetyl group (CHEBI:22190)
# Biotinylation: MOD:00126; biotin (CHEBI:15956)??
# Dephosphoryaltion
# Farnesyaltion: MOD:00437; farnesyl group (CHEBI:24017)
# Glysoaminoglycan: MOD:00224????; glycosaminoglycans (CHEBI:18085)
# Geranylgeranylation: MOD:00441; geranylgeranyl group (CHEBI:24231)
# Glycosylation: MOD:00693; glycosyl glycosides (CHEBI:24407)???
# Methylation: MOD:00599; methyl group (CHEBI:32875)
# Myristoylation: MOD:00438; myristoyl group (CHEBI:25456)
# Oxidation: MOD:00412;
# Palmitoylation: MOD:00440; palmitoyl group (CHEBI:25839)
# Phosphorylation: MOD:00696; phosphate group (CHEBI:32958)??
# poly (ADP-ribosyl)ation: CHEBI:16960
# Sumoylation
# Ubiquitination
### Reactome mapping to ChEBI
# _1_4_alpha_D_glucosyl_n_group : ChEBI_15444
# L_selenocysteinyl_group : ChEBI_30003
# palmitoyl_group : ChEBI_25839
# phosphate_group : ChEBI_35780
# carboxyl_group : ChEBI_23025
# glycogen_group : ChEBI_28087
# myristoyl_group : ChEBI_25456
# acetyl_group : ChEBI_22190
# hydroxyl_group : ChEBI_24706
# half_cystyl_group : ChEBI_30770
# methyl_group : ChEBI_25251
my %translate_location;
my %reactome_feature_types = (
"_1_4_alpha_D_glucosyl_n_group" => "_1_4_alpha_D_glucosyl_n_group", ## not PID standard
"_1_6__alpha_glucosyl__1_4_alpha_D_glucosyl_n_group" => "_1_6__alpha_glucosyl__1_4_alpha_D_glucosyl_n_group", ## not PID standard
"acetyl_group" => "acetylation",
"acyl_GPI_group" => "acyl_GPI_group", ## not PID standard
"carboxyl_group" => "carboxyl_group", ## not PID standard
"glycogen_group" => "glycogen_group", ## not PID standard
"GPI_anchor_group" => "GPI_anchor_group", ## not PID standard
"half_cystyl_group" => "half_cystyl_group", ## not PID standard
"hydroxyl_group" => "hydroxyl_group", ## not PID standard
"L_selenocysteinyl_group" => "L_selenocysteinyl_group", ## not PID standard
"limit_dextrin_group" => "limit_dextrin_group", ## not PID standard
"methyl_group" => "methyl_group", ## not PID standard
"myristoyl_group" => "myristoylation",
"oligo__1_4_alpha_D_glucosyl__group" => "oligo__1_4_alpha_D_glucosyl__group", ## not PID standard
"Orthophosphate__ChEBI_18367_1" => "Orthophosphate__ChEBI_18367_1", ## not PID standard
"palmitoyl_group" => "palmitoylation",
"Pantetheine_4__phosphate__ChEBI_16858_" => "Pantetheine_4__phosphate__ChEBI_16858_", ## not PID standard
# Shiva: may be ok to map to phosphorylation if we allow unspecified
# amino acids
# "phosphate_group" => "phosphate_group"
"phosphate_group" => "phosphorylation"
);
my %residue_type = (
"L-Threonine [ChEBI:6308]" => "T",
"L-Serine [ChEBI:6301]" => "S",
"L-Tyrosine [ChEBI:17895]" => "Y",
"Glycine [ChEBI:15428]" => "G",
"L-Aspartate [ChEBI:17053]" => "D",
"L-Cysteine [ChEBI:17561]" => "C",
"L-Glutamate [ChEBI:16015]" => "E",
"asparagino group" => "X"
##Per Shiva: [aspartate + glutamine + ATP <=> asparagine + glutamate + AMP + pyrophosphate]
);
my $p;
######################################################################
sub MaxValue {
my $max = 0;
for my $v (@_) {
if ($v > $max) {
$max = $v;
}
}
return $max;
}
######################################################################
sub InferConnections {
my ($self) = @_;
my (%pid2abstraction);
my $pathway_type =
$lv->StringToLabelValue("process-type", "pathway");
for my $atom (@{ $pw->Atoms() }) {
if ($pw->AtomType($atom) eq $pathway_type) {
if (defined $pw->AbstractionId($atom)) {
$pid2abstraction{$pw->AbstractionId($atom)}{$atom} = 1;
#print STDERR "added pathway " . $pw->AbstractionId($atom) . ", atom $atom\n";
} else {
print STDERR "no abstraction defined for atom $atom of pathway type\n";
}
}
}
my $agent_type =
$lv->StringToLabelValue("edge-type", "agent");
my $inhibitor_type =
$lv->StringToLabelValue("edge-type", "inhibitor");
my $input_type =
$lv->StringToLabelValue("edge-type", "input");
my $output_type =
$lv->StringToLabelValue("edge-type", "output");
my $pathway_type =
$lv->StringToLabelValue("process-type", "pathway");
my (%mi2e, %m_p_e, %parent, %children, %siblings, %already_added);
for my $atom (@{ $pw->Atoms() }) {
my @pids = @{ $pw->AtomPathway($atom) };
if ($pw->AtomType($atom) eq "$pathway_type") {
for my $pid (@pids) {
$children{$pid}{$pw->AbstractionId($atom)} = 1;
$parent{$pw->AbstractionId($atom)}{$pid} = 1;
}
}
for my $edge (@{ $pw->Edges($atom) }) {
my $edgetype = $pw->EdgeType($atom, $edge);
my $molinstid = $pw->MolInstId($atom, $edge);
## need to save this so that we can recover the full PTM info
## for the instance
if (! defined $mi2e{$molinstid}) {
$mi2e{$molinstid} = "$atom,$edge";
}
for my $pid (@pids) {
$m_p_e{$molinstid}{$pid}{$edgetype} = 1;
}
}
}
for my $pid (keys %children) {
my @pids = keys %{ $children{$pid} };
for (my $i = 0; $i < @pids - 1; $i++) {
for (my $j = $i+1; $j < @pids; $j++) {
$siblings{$pids[$i]}{$pids[$j]} = 1;
$siblings{$pids[$j]}{$pids[$i]} = 1;
}
}
}
my $more = 1;
while ($more) {
$more = 0;
for my $molinstid (keys %m_p_e) {
my ($a,$e) = split(",", $mi2e{$molinstid});
my @pids = keys %{ $m_p_e{$molinstid} };
#print STDERR "pids = ". scalar(@pids) . "\n";
my %hits;
for (my $i = 0; $i < @pids - 1; $i++) {
for (my $j = $i+1; $j < @pids; $j++) {
if (defined $siblings{$pids[$i]}{$pids[$j]}) {
$hits{$pids[$i]}++;
$hits{$pids[$j]}++;
} elsif (defined $parent{$pids[$i]}{$pids[$j]}) {
$hits{$pids[$i]}++;
} elsif (defined $parent{$pids[$j]}{$pids[$i]}) {
$hits{$pids[$j]}++;
}
}
}
@pids = keys %hits;
#print STDERR "hits = ". scalar(@pids) . "\n";
if (@pids > 1) {
for my $pid (@pids) {
#print STDERR "looking at pid $pid\n";
if (! defined $pid2abstraction{$pid}) {
print STDERR "no abstraction defined for pathway $pid\n";
next;
}
for my $abstraction (keys %{ $pid2abstraction{$pid} }) {
#print STDERR "looking at abstraction $abstraction\n";
my $next_edge = MaxValue(@{ $pw->Edges($abstraction) });
for my $edgetype (keys %{ $m_p_e{$molinstid}{$pid} }) {
if (! defined $already_added{"$molinstid,$abstraction,$edgetype"}) {
$already_added{"$molinstid,$abstraction,$edgetype"} = 1;
for my $parent (keys %{ $parent{$pid} }) {
$m_p_e{$molinstid}{$parent}{$edgetype} = 1
}
$next_edge++;
$pw->AddEdge($abstraction,
$next_edge, $edgetype, $pw->EdgeMol($a, $e));
#print STDERR "adding edge $next_edge, edgetype $edgetype to $abstraction\n";
for my $lvid (@{ $pw->MolLabel($a, $e) }) {
$pw->AddMolLabel($abstraction, $next_edge, $lvid);
}
for my $ptm (@{ $pw->EdgePTM($a, $e) }) {
my ($protein_id, $position, $amino_acid,
$modification_label_value,
$modification_label_name) = @{ $ptm };
$pw->AddEdgePTM($abstraction,
$next_edge, $protein_id, $position, $amino_acid,
$modification_label_value, $modification_label_name);
}
$more++;
}
}
}
}
}
}
}
}
######################################################################
sub DumpXrefs {
for my $x (keys %id2xref) {
for my $y (keys %{ $id2xref{$x} }) {
print "$x : $y\n";
}
}
}
######################################################################
sub Close {
my ($relation) = @_;
my %copy;
for my $x (keys %{ $relation }) {
for my $y (keys %{ $$relation{$x} }) {
$copy{$x}{$y} = 1;
}
}
my $more = 1;
while ($more) {
$more = 0;
for my $x (keys %copy) {
for my $y (keys %{ $copy{$x} }) {
if (defined $copy{$y}) {
for my $z (keys %{ $copy{$y} }) {
if (!defined $copy{$x}{$z}) {
$copy{$x}{$z} = 1;
$more++;
}
}
}
}
}
}
return \%copy;
}
######################################################################
sub CollapseCatalysis {
for my $c (keys %catalysis2controlled) {
my $controlled = $catalysis2controlled{$c};
if ($id2type{$catalysis2controlled{$c}} eq "bp:catalysis") {
$r_catalysis{$catalysis2controlled{$c}} = $c;
# print STDERR "found catalysis $c that controls a " .
# "$id2type{$catalysis2controlled{$c}}\n";
}
}
for my $c (keys %catalysis2controlled) {
my $controller = $catalysis2controller{$c};
my $controlled = $catalysis2controlled{$c};
my $control_type = $catalysis2control_type{$c};
my $direction = $catalysis2direction{$c}; ##!!!!!!! huh
if ($id2type{$catalysis2controlled{$c}} eq "bp:biochemicalReaction") {
$reaction2participant{$controlled}{$control_type}{$controller} = 1;
for my $xref (keys %{ $id2xref{$c} }) {
if (defined $publication{$xref}) {
$id2xref{$controlled}{$xref} = 1;
# print STDERR "transferred $xref from $c to $controlled\n";
}
}
}
if (defined $r_catalysis{$c}) {
my $c1 = $c;
my $level = 2;
while (defined $r_catalysis{$c1}) {
$c1 = $r_catalysis{$c1};
my $controller1 = $catalysis2controller{$c1};
my $controlled1 = $catalysis2controlled{$c1};
my $control_type1 = $catalysis2control_type{$c1} . "_$level";
my $direction1 = $catalysis2direction{$c1}; ##!!!!!!! huh
$reaction2participant{$controlled}{$control_type1}{$controller1} = 1;
$level++;
for my $xref1 (keys %{ $id2xref{$c1} }) {
if (defined $publication{$xref1}) {
$id2xref{$controlled}{$xref1} = 1;
# print STDERR "transferred $xref1 from $c1 to $controlled\n";
}
}
}
}
}
}
######################################################################
sub GetRootsAndLeaves {
my ($relation) = @_;
## close the whole relation
my $copy = Close($relation);
## find roots in the relation
my %roots;
for my $x (keys %{ $relation }) {
$roots{$x} = 1;
}
for my $x (keys %{ $relation }) {
for my $y (keys %{ $$relation{$x} }) {
if (defined $roots{$y}) {
$roots{$y} = 0;
}
}
}
## remove from the closed relation anything that involves something
## that is both not a root and not a leaf
for my $x (keys %roots) {
if ($roots{$x} == 0) {
delete $$copy{$x};
}
}
for my $x (keys %{ $copy }) {
for my $y (keys %{ $$copy{$x}}) {
if (defined $roots{$y}) {
delete $$copy{$x}{$y};
}
}
}
return $copy;
}
######################################################################
sub dump {
my ($self, $fh) = @_;
for my $id (keys %id2type) {
print $fh "#type\t$id\t$id2type{$id}\n";
}
for my $id (keys %id2xref) {
for my $xref (keys %{ $id2xref{$id} }) {
if (defined $unification{$xref}) {
if (defined $unification{$xref}{UniProt}) {
print $fh "#xref\t$id\tUniProt\t$unification{$xref}{UniProt}\n";
}
}
}
}
for my $reaction (keys %reaction2participant) {
for my $role (keys %{ $reaction2participant{$reaction} }) {
for my $participant (keys %{ $reaction2participant{$reaction}{$role}}) {
print $fh "#participant\t$reaction\t$role\t$participant\n";
}
}
}
for my $complex (keys %complex2component) {
for my $component (keys %{ $complex2component{$complex} }) {
print $fh "#complex_component\t$complex\t$component\n";
}
}
for my $network (keys %network2component) {
for my $component (keys %{ $network2component{$network} }) {
# we'll skip this in favor of the pathway2interaction
# print "#network_component\t$network\t$component\n";
}
}
for my $pathway (keys %{ $pathway2reaction }) {
for my $interaction (keys %{ $$pathway2reaction{$pathway} }) {
print $fh "#pathway_interaction\t$pathway\t$interaction\n";
}
}
}
######################################################################
sub DeleteSpontaneousInteractions {
my $transcription_type =
$lv->StringToLabelValue("process-type", "transcription");
my $reaction_type =
$lv->StringToLabelValue("process-type", "reaction");
my $modification_type =
$lv->StringToLabelValue("process-type", "modification");
my $translocation_type =
$lv->StringToLabelValue("process-type", "translocation");
my $pathway_type =
$lv->StringToLabelValue("process-type", "pathway");
my %of_interest = (
$transcription_type => 1,
$reaction_type => 1,
$modification_type => 1,
$translocation_type => 1
);
my $agent_type =
$lv->StringToLabelValue("edge-type", "agent");
my $inhibitor_type =
$lv->StringToLabelValue("edge-type", "inhibitor");
my $input_type =
$lv->StringToLabelValue("edge-type", "input");
my %incoming = (
$agent_type => 1,
$inhibitor_type => 1,
$input_type => 1
);
my (%pathway2atom, %atom2pathway);
my (%pathway2abstraction);
for my $atom (@{ $pw->Atoms() }) {
my $atomtype = $pw->AtomType($atom);
for my $pid (@{ $pw->AtomPathway($atom) }) {
$pathway2atom{$pid}{$atom} = 1;
$atom2pathway{$atom}{$pid} = 1;
}
if ($atomtype eq $pathway_type) {
if (defined $pw->AbstractionId($atom)) {
$pathway2abstraction{$pw->AbstractionId($atom)}{$atom} = 1;
}
}
}
my %kill;
for my $atom (@{ $pw->Atoms() }) {
my $atomtype = $pw->AtomType($atom);
if (defined $of_interest{$atomtype}) {
my $incoming = 0;
for my $edge (@{ $pw->Edges($atom) }) {
if (defined $incoming{$pw->EdgeType($atom, $edge)}) {
$incoming++;
last;
}
}
if (@{ $pw->AtomCondition($atom) } > 0) {
$incoming++;
}
if (! $incoming) {
print STDERR "#deleting_spontaneous_interaction\t$atom\n";
$pw->PruneAtoms([ $atom ], {});
$kill{$atom} = 1;
}
}
}
## now we have to propagate kills
my %fresh_kill_atom;
my %kill_pathway;
my %p2a_count;
for my $pid (keys %pathway2atom) {
$p2a_count{$pid} = scalar(keys %{ $pathway2atom{$pid} });
}
for my $atom (keys %kill) {
$fresh_kill_atom{$atom} = 1;
}
my $more = 1;
while ($more) {
$more = 0;
undef %kill;
for my $atom (keys %fresh_kill_atom) {
$kill{$atom} = 1;
}
undef %fresh_kill_atom;
for my $atom (keys %kill) {
for my $pid (keys %{ $atom2pathway{$atom} }) {
$p2a_count{$pid}--;
if ($p2a_count{$pid} == 0) { ## that is, it just became == 0
$kill_pathway{$pid} = 1;
for my $abs (keys %{ $pathway2abstraction{$pid} }) {
$fresh_kill_atom{$abs} = 1;
$more++;
}
}
}
}
for my $atom (keys %fresh_kill_atom) {
$pw->PruneAtoms([ $atom ], {});
print STDERR "#deleting_dangling_abstraction\t$atom\n";
}
}
for my $pid (keys %kill_pathway) {
print STDERR "#deleting_empty_pathway\t$pid\n";
delete $pw->{pathway2source}{$pid};
delete $pw->{pathway}{$pid};
delete $pw->{pathwayreference}{$pid};
delete $pw->{pathwayreviewer}{$pid};
delete $pw->{pathwaycurator}{$pid};
}
}
######################################################################
sub DoGraphStuff {
my ($self) = @_;
$pathway2reaction = GetRootsAndLeaves(\%network2component);
CollapseCatalysis();
if (defined $self->{uniprot_f}) {
DoUniProt($self->{uniprot_f});
}
FinishComplexes();
FinishMols();
FinishInteractions();
FinishPathways();
PropagateWholeProteinIDs();
DeleteSpontaneousInteractions();
# for my $i (keys %id2rdf_id) {
# print STDERR "#PID-to-Reactome\t$i\t$id2rdf_id{$i}\n";
# }
}
######################################################################
sub DoUniProt {
my ($f) = @_;
my ($uniprot, $entrez_gene);
open(UNI, $f) or die "cannot open $f";
while (<UNI>) {
chop;
($uniprot, $entrez_gene) = split /\t/;
$uniprot2entrez_gene{$uniprot}{$entrez_gene} = 1;
}
close UNI;
}
######################################################################
sub FlattenPathwaySteps {
my $more = 1;
while ($more) {
$more = 0;
my %add;
my %remove;
for my $p (keys %network2component) {
for my $q (keys %{ $network2component{$p} }) {
if ($id2type{$q} eq "bp:pathwayStep") {
$more++;
for my $r (keys %{ $network2component{$q} }) {
$add{$p}{$r} = 1;
$remove{$q}{$r} = 1;
}
$remove{$p}{$q} = 1;
}
}
}
for my $q (keys %remove) {
for my $r (keys %{ $remove{$q} }) {
delete $network2component{$q}{$r};
}
}
for my $p (keys %add) {
for my $r (keys %{ $add{$p} }) {
$network2component{$p}{$r} = 1;
}
}
}
for my $p (keys %network2component) {
if ($id2type{$p} eq "bp:pathwayStep") {
delete $network2component{$p};
}
}
## delete remaining pathways that do not have components
my $more = 1;
while ($more) {
$more = 0;
my %kill;
for my $x (keys %network2component) {
for my $y (keys %{ $network2component{$x}}) {
if ($id2type{$x} eq "bp:pathway") {
if (! defined $network2component{$y} &&
$id2type{$y} eq "bp:pathway") {
$more++;
$kill{$x}{$y} = 1;
}
}
}
}
if ($more) {
for my $x (keys %kill) {
for my $y (keys %{ $kill{$x} }) {
delete $network2component{$x}{$y};
#print STDERR "deleting $x, $y\n";
}
}
for my $x (keys %network2component) {
if (keys %{ $network2component{$x} } == 0) {
#print STDERR "deleting $x\n";
delete $network2component{$x};
}
}
}
}
}
######################################################################
sub FinishPathways {
FlattenPathwaySteps();
## May 30, 2007: we should add another type of flattening. If p is pathway
## that is not a top-level pathway and if p contains only ONE component c
## (where c is either interaction or pathway), then raise c to be a component
## of parent(p) and delete p.
for my $pathway (keys %id2type) {
if ($id2type{$pathway} ne "bp:pathway") {
next;
}
my $pathway_id = FinalId("pathway", LookUp($pathway));
$pw->AddPathwayId($pathway_id);
$pw->AddPathwaySource($pathway_id, REACTOME_SOURCE_ID);
$pw->SetPathwayExId($pathway_id, $pathway);
$pw->SetPathwayOrg($pathway_id, "Hs");
$pw->SetIsSubnet($pathway_id, 0); ## initially, set everything to not-subnet
for my $name (keys %{ $id2name{$pathway} }) {
$pw->SetPathwayName($pathway_id, $name);
last; ##### take only one name
}
for my $xref (keys %{ $id2xref{$pathway} }) {
if (defined $publication{$xref}{"Pubmed"}) {
$pw->AddPathwayReferences($pathway_id, $publication{$xref}{"Pubmed"});
}
}
}
for my $pathway (keys %network2component) {
for my $pway_component (keys %{ $network2component{$pathway} }) {
if ($id2type{$pway_component} eq "bp:pathway") {
if (defined $network2component{$pway_component}) {
$pw->SetIsSubnet(FinalId("pathway", LookUp($pway_component)), 1);
} else {
print STDERR "#empty_subnet\t$pway_component\n";
}
}
}
}
for my $pathway (keys %network2component) {
my $pathway_id = FinalId("pathway", LookUp($pathway));
for my $pway_component (keys %{ $network2component{$pathway} }) {
my $pway_component_id = FinalId("interaction", LookUp($pway_component));
if ($id2type{$pway_component} eq "bp:pathway") {
$pw->AddAtom($pway_component_id,
$lv->StringToLabelValue("process-type", "pathway"));
$pw->AddAtomSource($pway_component_id, REACTOME_SOURCE_ID);
my $abstracted_p = FinalId("pathway", LookUp($pway_component));
$pw->AddAbstraction($pway_component_id, $abstracted_p,
$pw->PathwayName($abstracted_p),
$pw->PathwayExId($abstracted_p));
}
$pw->AddAtomPathway($pway_component_id, $pathway_id);
}
}
}
######################################################################
sub FinishMols {
for my $id (keys %id2type) {
my $id_type = $id2type{$id};
if ($id_type eq "bp:protein" || $id_type eq "bp:rna") {
if (defined $id2xref{$id}) {
for my $xref (keys %{ $id2xref{$id} }) {
if (defined $unification{$xref}{UniProt}) {
my $uniprot = $unification{$xref}{UniProt};
$pw->AddMolExId(FinalId("molecule", LookUp($id)), "UP", $uniprot);
}
}
}
}
if ($id_type eq "bp:smallMolecule") {
if (defined $id2xref{$id}) {
for my $xref (keys %{ $id2xref{$id} }) {
if (defined $unification{$xref}{ChEBI}) {
my $chebi = $unification{$xref}{ChEBI};
$pw->AddMolExId(FinalId("molecule", LookUp($id)), "CH", $chebi);
}
}
}
}
if ($id_type eq "bp:protein" || $id_type eq "bp:rna" ||
$id_type eq "bp:complex" || $id_type eq "bp:smallMolecule" ||
$id_type eq "bp:physicalEntity") {
my (@preferred);
for my $name (
keys %{ $id2short_name{$id} },
keys %{ $id2name{$id} },
keys %{ $id2synonym{$id} }
) {
## lose the cellular location part of the name
if ($name =~ / *\[[^\]]+\]$/) {
print STDERR "dropping cellular location part of $name\n";
$name =~ s/ *\[[^\]]+\]$//;
}
if (length($name) <= 200) {
push @preferred, $name;
} else {
print STDERR "dropping name with length > 200: $name\n";
}
}
if (@preferred) {
for my $name (@preferred) {
$pw->AddMolName(FinalId("molecule", LookUp($id)), "AS", $name);
}
} else {
print STDERR "no name for $id\n";
}
}
}
AddHUGOSymbols();
}
######################################################################
sub PropagateWholeProteinIDs {
for my $mol (@{ $pw->Mols() }) {
my @parts = @{ $pw->MolPart($mol) };
if (@parts) {
my @ups;
my $hash = $pw->MolExId($mol);
my $name = $pw->PickMolName($mol);
if (defined $$hash{"UP"}) {
@ups = keys %{ $$hash{"UP"} };
for my $part (@parts) {
my $part_hash = $pw->MolExId($part);
if (! defined $$part_hash{"UP"}) {
for my $up (@ups) {
$pw->AddMolExId($part, "UP", $up);
}
}
my $name_hash = $pw->MolName($part);
if (keys %{ $name_hash } == 0) {
my $bounds = $pw->PartBounds($part);
$bounds =~ s/,/_/;
$pw->AddMolName($part, "PF", join("_", $name, "subunit",
$bounds));
}
}
}
}
}
}
######################################################################
sub DoFeatures {
my ($what, $container_id, $sequence_id, $participant, $mol) = @_;
## container_id is interaction or complex
## sequence_id is edge_id or component_id
my $physical_entity = $participant2physical_entity{$participant};
for my $feature (keys %{ $sequence_participant2feature{$participant} }) {
my $feature_type = $sequence_feature2type{$feature};
if ($feature_type =~ /^LengthFeature/) {
## make a subunit
my $fl = $feature2location{$feature};
my $begin_site = $interval2begin{$fl};
my $end_site = $interval2end{$fl};
my $begin_pos = $site2position{$begin_site};
my $end_pos = $site2position{$end_site};
my $whole = $mol; ## they don't distinguish
my $part = FinalId("molecule", LookUp(join("_",
$mol, "subunit", $begin_pos, $end_pos)));
## can't hurt to add it more than once, right?
$pw->AddMol($part, $lv->BasicMolTypeCode("PR"));
$pw->AddMolPart($part, $whole, $begin_pos, $end_pos);
## now replace the whole with the part
$mol = $part;
} else {
my ($modification_label_name, $modification_label_value);
my ($protein, $position, $amino_acid);
$protein = "";
$position = "0";
$amino_acid = "X";
## try to nail down the protein
for my $xref (keys %{ $id2xref{$physical_entity} }) {
if (defined $unification{$xref}{UniProt}) {
$protein = $unification{$xref}{UniProt};
last;
}
}
## try to nail down the residue
if (defined $feature2residue{$feature}) {
my $residue = $feature2residue{$feature};
if (defined $residue_type{$residue}) {
$amino_acid = $residue_type{$residue};
}
}
## try to nail down the position
if (defined $feature2location{$feature}) {
my $site = $feature2location{$feature};
if (defined $site2position{$site}) {
$position = $site2position{$site};
}
}
if (defined $reactome_feature_types{$feature_type}) {
$modification_label_name = $reactome_feature_types{$feature_type};
}
if (!defined $modification_label_name ||
$modification_label_name eq "") {
print STDERR "unknown_feature_type\t$feature_type for feature $feature\n";
$modification_label_name = "ptm";
}
$modification_label_value = $lv->StringToLabelValue("ptm",
$modification_label_name);
if ($what eq "edge") {
$pw->AddEdgePTM($container_id, $sequence_id, $protein,
$position, $amino_acid,
$modification_label_value, $modification_label_name);
} elsif ($what eq "component") {
$pw->AddComponentPTM($container_id, $sequence_id, $protein,
$position, $amino_acid,
$modification_label_value, $modification_label_name);
} else {
print STDERR "DoFeatures: bad 'what' = $what\n";
}
}
}
return $mol;
}
######################################################################
sub FinishComplexes {
## Reactome components do not have location
for my $complex (keys %complex2component) {
my $complex_id = FinalId("molecule", LookUp($complex));
my $comp;
for my $component (keys %{ $complex2component{$complex} }) {
my $stoichiometry;
if (defined $participant2stoichiometry{$component}) {
$stoichiometry = $participant2stoichiometry{$component};
} else {
$stoichiometry = 1;
}
if ($stoichiometry > 8) {
print STDERR "reducing stoichiometry from $stoichiometry to 2 for " .
" component $component of complex $complex\n";
$stoichiometry = 2;
}
while ($stoichiometry) {
$comp++;
$stoichiometry--;
my $component_mol = FinalId("molecule",
LookUp($participant2physical_entity{$component}));
$component_mol = DoFeatures("component", $complex_id, $comp,
$component, $component_mol);
$pw->AddComponent($complex_id, $comp, $component_mol);
}
}
}
}
######################################################################
sub CheckInteractionType {
my ($id) = @_;
## check atoms if modification type to see if they should actually
## be declared to be transloactions
my $atomtype_lvid = $pw->AtomType($id);
my ($dummy, $atomtype) = $lv->LabelValueToString($atomtype_lvid);
if ($atomtype ne "modification") {
return;
}
my $translocation_type =
$lv->StringToLabelValue("process-type", "translocation");
my (%mol2edge, %mol2type, %activity_labels, %ptms, %location_labels);
my (@inputs, @outputs, %components, %edge2type, %no_match);
my ($pr_in, $cx_in, $pr_out, $cx_out);
for my $edge (@{ $pw->Edges($id) }) {
my ($dummy, $edgetype) =
$lv->LabelValueToString($pw->EdgeType($id, $edge));
$edge2type{$edge} = $edgetype;
if ($edgetype eq "input") {
push @inputs, $edge;
} elsif ($edgetype eq "output") {
push @outputs, $edge;
}
my $mol = $pw->EdgeMol($id, $edge);
$mol2edge{$mol}{$edge} = 1;
my ($dummy, $moltype) =
$lv->LabelValueToString($pw->MolType($mol));
$mol2type{$mol} = $moltype;
## are we doing anything with these components ???
## Not now, but they could be used to test for state changes
## within complexes
if ($moltype eq "complex") {
for my $comp (@{ $pw->Components($mol) }) {
push @{ $components{$edge} }, $pw->ComponentMol($mol, $comp);
}
}
if ($moltype eq "protein") {
if ($edgetype eq "input") {
$pr_in++;
} elsif ($edgetype eq "output") {
$pr_out++;
}
} elsif ($moltype eq "complex") {
if ($edgetype eq "input") {
$cx_in++;
} elsif ($edgetype eq "output") {
$cx_out++;
}
}
for my $lvid (@{ $pw->MolLabel($id, $edge) }) {
my ($label, $value) = $lv->LabelValueToString($lvid);
if ($label eq "activity-state") {
$activity_labels{$edge}{$lvid} = 1;
} elsif ($label eq "location") {
$location_labels{$edge}{$lvid} = 1;
}
my $ptms = $pw->EdgePTM($id, $edge);
if (@{ $ptms }) {
$ptms{$edge} = Pathway::NormalPTMString($ptms);
}
}