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Commit c0944d84 authored by Magali Ruffier's avatar Magali Ruffier
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when loading OBO files, add is_root flag to terms which are root within the... 

when loading OBO files, add is_root flag to terms which are root within the OBO file loaded and part of the ontology
add ontology information to relation and closure tables
a relation's ontology is the ontology from which the relation was loaded from
for example, a GO to GO relation is an EFO relation if it was loaded from the EFO obo file
parent e456bea9
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misc-scripts/ontology/scripts/add_subset_maps.pl
+ 2
− 0
View file @ c0944d84
......@@ -91,6 +91,8 @@ FROM ontology
ON (child_term.term_id = closure.child_term_id)
WHERE ontology.name = %s
AND FIND_IN_SET(%s, parent_term.subsets) > 0
AND parent_term.ontology_id = closure.ontology_id
AND child_term.ontology_id = closure.ontology_id
GROUP BY child_term.term_id, parent_term.term_id
);
......
misc-scripts/ontology/scripts/compute_closure.pl
+ 20
− 8
View file @ c0944d84
......@@ -67,16 +67,26 @@ $dbh->do('ALTER TABLE closure DISABLE KEYS');
$dbh->do(
q(
INSERT INTO closure
(child_term_id, parent_term_id, distance, subparent_term_id)
SELECT term_id, term_id, 0, NULL
(child_term_id, parent_term_id, distance, subparent_term_id, ontology_id)
SELECT term_id, term_id, 0, NULL, ontology_id
FROM term
) );
$dbh->do(
q(
INSERT INTO closure
(child_term_id, parent_term_id, distance, subparent_term_id)
SELECT DISTINCT child_term_id, parent_term_id, 1, child_term_id
INSERT IGNORE INTO closure
(child_term_id, parent_term_id, distance, subparent_term_id, ontology_id)
SELECT term_id, term_id, 0, NULL, r.ontology_id
FROM term t, relation r
WHERE term_id = child_term_id
AND t.ontology_id != r.ontology_id
) );
$dbh->do(
q(
INSERT IGNORE INTO closure
(child_term_id, parent_term_id, distance, subparent_term_id, ontology_id)
SELECT DISTINCT child_term_id, parent_term_id, 1, child_term_id, ontology_id
FROM relation r,
relation_type rt
WHERE rt.name IN (
......@@ -93,19 +103,21 @@ SELECT DISTINCT
child.child_term_id,
parent.parent_term_id,
child.distance + 1,
parent.child_term_id
parent.child_term_id,
child.ontology_id
FROM closure child
JOIN closure parent
ON (parent.child_term_id = child.parent_term_id)
WHERE child.distance = ?
AND parent.distance = 1
AND child.ontology_id = parent.ontology_id
) );
my $insert_sth = $dbh->prepare(
q(
REPLACE INTO closure
(child_term_id, parent_term_id, distance, subparent_term_id)
VALUES (?, ?, ?, ?)
(child_term_id, parent_term_id, distance, subparent_term_id, ontology_id)
VALUES (?, ?, ?, ?, ?)
) );
my ($oldsize) =
......
misc-scripts/ontology/scripts/load_OBO_file.pl
+ 50
− 21
View file @ c0944d84
......@@ -143,7 +143,7 @@ sub write_subset {
$lookup_sth->bind_param(1, $subset->{name}, SQL_VARCHAR);
$lookup_sth->execute();
($id) = $lookup_sth->fetchrow_array();
printf(STDERR "CLASH: SUBSET '%s' already exists in this database. Reusing ID %d\n", $subset->{name}, $id);
printf("CLASH: SUBSET '%s' already exists in this database. Reusing ID %d\n", $subset->{name}, $id);
}
$subset->{'id'} = $id;
......@@ -170,13 +170,13 @@ sub write_term {
$dbh->do("LOCK TABLES term WRITE, synonym WRITE");
my $statement = "INSERT IGNORE INTO term (ontology_id, subsets, accession, name, definition) VALUES (?,?,?,?,?)";
my $statement = "INSERT IGNORE INTO term (ontology_id, subsets, accession, name, definition, is_root) VALUES (?,?,?,?,?,?)";
my $syn_stmt = "INSERT INTO synonym (term_id, name) VALUES (?,?)";
my $existing_term_st = "SELECT term_id, ontology_id FROM term WHERE accession = ?";
my $update_stmt = "UPDATE term SET ontology_id = ?, subsets = ?, name = ?, definition = ? WHERE term_id = ?";
my $update_stmt = "UPDATE term SET ontology_id = ?, subsets = ?, name = ?, definition = ?, is_root = ? WHERE term_id = ?";
my $sth = $dbh->prepare($statement);
my $update_sth = $dbh->prepare($update_stmt);
......@@ -218,6 +218,7 @@ sub write_term {
$sth->bind_param(3, $term->{'accession'}, SQL_VARCHAR);
$sth->bind_param(4, 'UNKNOWN NAME', SQL_VARCHAR);
$sth->bind_param(5, 'UNKNOWN DEFINITION', SQL_VARCHAR);
$sth->bind_param(6, $term->{'is_root'}, SQL_INTEGER);
$sth->execute();
my $id = $dbh->last_insert_id(undef, undef, 'term', 'term_id');
$term->{'id'} = $id;
......@@ -238,6 +239,7 @@ sub write_term {
$update_sth->bind_param(3, $term->{'name'}, SQL_VARCHAR);
$update_sth->bind_param(4, $term->{'definition'}, SQL_VARCHAR);
$update_sth->bind_param(5, $existing_term_id, SQL_INTEGER);
$update_sth->bind_param(6, $term->{'is_root'}, SQL_INTEGER);
$update_sth->execute();
......@@ -251,6 +253,7 @@ sub write_term {
$sth->bind_param(3, $term->{'accession'}, SQL_VARCHAR);
$sth->bind_param(4, $term->{'name'}, SQL_VARCHAR);
$sth->bind_param(5, $term->{'definition'}, SQL_VARCHAR);
$sth->bind_param(6, $term->{'is_root'}, SQL_INTEGER);
$sth->execute();
my $id = $dbh->last_insert_id(undef, undef, 'term', 'term_id');
......@@ -258,7 +261,7 @@ sub write_term {
$existing_term_sth->execute($term->{'accession'});
my ($existing_term_id, $ontology_id) = $existing_term_sth->fetchrow_array;
$id = $existing_term_id;
printf(STDERR "DUPLICATION: TERM '%s' already exists in this database. Reusing ID %d\n", $term->{accession}, $existing_term_id);
printf("DUPLICATION: TERM '%s' already exists in this database. Reusing ID %d\n", $term->{accession}, $existing_term_id);
$reuse = 1;
}
$term->{'id'} = $id;
......@@ -268,7 +271,7 @@ sub write_term {
if($term->{synonyms} && @{$term->{synonyms}}) {
if($reuse) {
print STDERR "REUSE: SKIPPING SYNONYM writing as term already exists in this database\n";
print "REUSE: SKIPPING SYNONYM writing as term already exists in this database\n";
}
else {
foreach my $syn (@{$term->{'synonyms'}}) {
......@@ -344,17 +347,18 @@ sub write_relation_type {
#-----------------------------------------------------------------------
sub write_relation {
my ($dbh, $terms, $relation_types) = @_;
my ($dbh, $terms, $relation_types, $ontology, $namespaces) = @_;
print("Writing to 'relation' table...\n");
$dbh->do("LOCK TABLE relation WRITE");
my $statement = "INSERT IGNORE INTO relation " . "(child_term_id, parent_term_id, relation_type_id, intersection_of) " . "VALUES (?,?,?,?)";
my $statement = "INSERT IGNORE INTO relation " . "(child_term_id, parent_term_id, relation_type_id, intersection_of, ontology_id) " . "VALUES (?,?,?,?,?)";
my $sth = $dbh->prepare($statement);
my $count = 0;
my $ontology_id;
local $SIG{ALRM} = sub {
printf("\t%d entries, %d to go...\n", $count, scalar(keys(%{$terms})) - $count);
......@@ -365,6 +369,12 @@ sub write_relation {
foreach my $child_term (sort { $a->{'id'} <=> $b->{'id'} } values(%{$terms})) {
foreach my $relation_type (sort(keys(%{$child_term->{'parents'}}))) {
foreach my $parent_acc (sort(@{$child_term->{'parents'}{$relation_type}})) {
if ($namespaces->{$child_term->{'namespace'}}{'name'} eq $ontology) {
$ontology_id = $namespaces->{$child_term->{'namespace'}}{'id'};
} else {
$ontology_id = $namespaces->{$ontology}{'id'}
}
if (!defined($terms->{$parent_acc})) {
printf("WARNING: Parent accession '%s' does not exist!\n", $parent_acc);
}
......@@ -375,20 +385,27 @@ sub write_relation {
exit;
}
$sth->bind_param(1, $child_term->{'id'}, SQL_INTEGER);
$sth->bind_param(2, $terms->{$parent_acc}{'id'}, SQL_INTEGER);
$sth->bind_param(3, $relation_types->{$relation_type}{'id'}, SQL_INTEGER);
$sth->bind_param(4, 0, SQL_INTEGER);
$sth->bind_param(1, $child_term->{'id'}, SQL_INTEGER);
$sth->bind_param(2, $terms->{$parent_acc}{'id'}, SQL_INTEGER);
$sth->bind_param(3, $relation_types->{$relation_type}{'id'}, SQL_INTEGER);
$sth->bind_param(4, 0, SQL_INTEGER);
$sth->bind_param(5, $ontology_id, SQL_INTEGER);
$sth->execute();
if(! $dbh->last_insert_id(undef, undef, 'relation', 'relation_id')) {
printf "DUPLICATION: RELATION %s (child) %s %s (parent) has been repeated. Ignoring this insert\n", $child_term->{accession}, $relation_type, $parent_acc;
printf "DUPLICATION: RELATION %s (child) %s %s (parent) has been repeated. Ignoring this insert for ontology %s\n", $child_term->{accession}, $relation_type, $parent_acc, $ontology_id;
}
}
}
}
foreach my $relation_type (sort(keys(%{$child_term->{'intersection_of_parents'}}))) {
foreach my $parent_acc (sort(@{$child_term->{'intersection_of_parents'}{$relation_type}})) {
if ($namespaces->{$child_term->{'namespace'}}{'name'} eq $ontology) {
$ontology_id = $namespaces->{$child_term->{'namespace'}}{'id'};
} else {
$ontology_id = $namespaces->{$ontology}{'id'}
}
if (!defined($terms->{$parent_acc})) {
printf("WARNING: Parent accession '%s' does not exist!\n", $parent_acc);
}
......@@ -399,19 +416,21 @@ sub write_relation {
exit;
}
$sth->bind_param(1, $child_term->{'id'}, SQL_INTEGER);
$sth->bind_param(2, $terms->{$parent_acc}{'id'}, SQL_INTEGER);
$sth->bind_param(3, $relation_types->{$relation_type}{'id'}, SQL_INTEGER);
$sth->bind_param(4, 1, SQL_INTEGER);
$sth->bind_param(1, $child_term->{'id'}, SQL_INTEGER);
$sth->bind_param(2, $terms->{$parent_acc}{'id'}, SQL_INTEGER);
$sth->bind_param(3, $relation_types->{$relation_type}{'id'}, SQL_INTEGER);
$sth->bind_param(4, 1, SQL_INTEGER);
$sth->bind_param(5, $ontology_id, SQL_INTEGER);
$sth->execute();
if(! $dbh->last_insert_id(undef, undef, 'relation', 'relation_id')) {
printf "DUPLICATION: RELATION %s (child) %s %s (parent) has been repeated. Ignoring this insert\n", $child_term->{accession}, $relation_type, $parent_acc;
printf "DUPLICATION: RELATION %s (child) %s %s (parent) has been repeated for ontology %s. Ignoring this insert\n", $child_term->{accession}, $relation_type, $parent_acc, $ontology_id;
}
}
}
}
++$count;
} ## end foreach my $child_term ( sort...)
alarm(0);
$dbh->do("OPTIMIZE TABLE relation");
......@@ -492,7 +511,7 @@ my @returncode = `grep -i "default-namespace: efo" $obo_file_name`;
@returncode = `grep 'property_value: "hasDefaultNamespace" "EFO"' $obo_file_name` if scalar(@returncode) == 0;
my $returncode = @returncode;
if ($returncode > 0) {
printf STDERR "Detected an EFO file; performing post-processing\n";
printf "Detected an EFO file; performing post-processing\n";
my $new_obo_file_name = "${obo_file_name}.new";
open my $obo_fh, '<', $obo_file_name or die "Cannot open the file ${obo_file_name}: $!";
open my $new_obo_fh, '>', $new_obo_file_name or die "Cannot open target file ${new_obo_file_name}: $!";
......@@ -536,7 +555,7 @@ if ($returncode > 0) {
close($obo_fh);
close($new_obo_fh);
printf STDERR "Switching to loading the file %s which is a post-processed file\n", $new_obo_file_name;
printf "Switching to loading the file %s which is a post-processed file\n", $new_obo_file_name;
$obo_file_name = $new_obo_file_name;
}
......@@ -551,7 +570,7 @@ $ontology->default_namespace($efo_default_namespace) if $efo_default_namespace &
#Set date to today if one was not present
if(! $ontology->date()) {
print STDERR "No date found; generating one\n";
print "No date found; generating one\n";
my $date = strftime('%d:%m:%Y %H:%M', localtime());
$ontology->date($date);
}
......@@ -617,6 +636,7 @@ foreach my $t (@{$ontology->get_terms()}) {
if (!($t->is_obsolete())) {
my %term;
my $is_root = 1;
my @t_namespace = $t->namespace();
my $t_namespace_elm = @t_namespace;
......@@ -632,6 +652,15 @@ foreach my $t (@{$ontology->get_terms()}) {
$term{'name'} = $t->name();
$term{'definition'} = $t->def_as_string();
if ($t->idspace() ne $ontology_name) {
$is_root = 0;
} else {
if (scalar(@{ $ontology->get_parent_terms($t) }) > 0) {
$is_root = 0;
}
}
$term{'is_root'} = $is_root;
my $rels = $ontology->get_relationships_by_source_term($t);
foreach my $r (@{$rels}) {
......@@ -689,7 +718,7 @@ my $unknown_onto_id = write_ontology($dbh, \%namespaces);
write_subset($dbh, \%subsets);
write_term($dbh, \%terms, \%subsets, \%namespaces, $unknown_onto_id);
write_relation_type($dbh, \%relation_types);
write_relation($dbh, \%terms, \%relation_types);
write_relation($dbh, \%terms, \%relation_types, $ontology_name, \%namespaces);
print("Updating meta table...\n");
......
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