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Add year to cxgn time ontology #6100

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ac335dd
Add year to cxgn time ontology
ktmeaton May 8, 2026
2055101
update expected trait count for brapi phenotyping test
ktmeaton May 12, 2026
4a2e663
fix ontology definition and raise time root to 5000
ktmeaton May 19, 2026
44e9b49
update conf to have new time in years ontology root
ktmeaton May 19, 2026
708f016
add time in years to composable cvs
ktmeaton May 19, 2026
be88e1d
update compose trait to use new time in years accession
ktmeaton May 19, 2026
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99 changes: 99 additions & 0 deletions db/00205/AddTimeOntologyYear.pm
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@@ -0,0 +1,99 @@
#!/usr/bin/env perl

=head1 NAME

AddTimeOntologyYear.pm

=head1 SYNOPSIS

mx-run AddTimeOntologyYear [options] [-F]

this is a subclass of L<CXGN::Metadata::Dbpatch>
see the perldoc of parent class for more details.

=head1 DESCRIPTION

This patch:
- Adds new cvterm for time ontology: year

=head1 AUTHOR

Katherine Eaton

=head1 COPYRIGHT & LICENSE

Copyright 2026 University of Alberta

This program is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.

=cut

package AddTimeOntologyYear;

use Moose;
use Bio::Chado::Schema;
use SGN::Model::Cvterm;
extends 'CXGN::Metadata::Dbpatch';

has '+description' => ( default => <<'' );
Adds new cvterm for time ontology age in years: year 1-100.

sub patch {
my $self=shift;

print STDOUT "Executing the patch:\n " . $self->name . ".\n\nDescription:\n ". $self->description . ".\n\nExecuted by:\n " . $self->username . " .";

print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";

print STDOUT "\nExecuting the SQL commands.\n";
my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );

print STDERR "INSERTING CV TERMS...\n";
my $is_a_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'is_a', 'relationship')->cvterm_id();
my $time_ontology_rs = $schema->resultset("Cv::Cvterm")->find({name => "Time"});

# Create the root cvterm
# next available dbxref accession in time ontology is '0000481'
# but this accession is already used in other databases that have
# non-standardized time units. So we jump ahead to 5000.
my $dbxref_accession = 5000;
my $time_in_years_rs = $schema->resultset("Cv::Cvterm")->create_with({
name => "time in years",
cv => 'cxgn_time_ontology',
db => 'TIME',
dbxref => sprintf("%07d", $dbxref_accession)
});
# Manually add definition after creation
$time_in_years_rs->update( { definition => "Time in years" } ) ;

# Link root cvterm to the time ontology
$schema->resultset("Cv::CvtermRelationship")->find_or_create({
subject_id => $time_in_years_rs->cvterm_id(),
type_id => $is_a_cvterm_id,
object_id => $time_ontology_rs->cvterm_id()
});

# Create years 1 through 100
foreach my $year (1..100) {
$dbxref_accession += 1;
my $year_rs = $schema->resultset("Cv::Cvterm")->create_with({
name => "year $year",
cv => 'cxgn_time_ontology',
db => 'TIME',
dbxref => sprintf("%07d", $dbxref_accession)
});
# link to time in years root cvterm
$schema->resultset("Cv::CvtermRelationship")->find_or_create({
subject_id => $year_rs->cvterm_id(),
type_id => $is_a_cvterm_id,
object_id => $time_in_years_rs->cvterm_id()
});
}

print "You're done!\n";
}

####
1; #
####
3 changes: 3 additions & 0 deletions js/source/legacy/CXGN/ComposeTrait.js
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Expand Up @@ -40,6 +40,7 @@ function get_component_ids () {
if (jQuery("#experiment_treatment_select").val()) { component_ids.push(jQuery("#experiment_treatment_select").val()); }
if (jQuery("#tod_select").val()) { component_ids.push(jQuery("#tod_select").val()); }
if (jQuery("#toy_select").val()) { component_ids.push(jQuery("#toy_select").val()); }
if (jQuery("#tiy_select").val()) { component_ids.push(jQuery("#tiy_select").val()); }
if (jQuery("#gen_select").val()) { component_ids.push(jQuery("#gen_select").val()); }
if (jQuery("#evt_select").val()) { component_ids.push(jQuery("#evt_select").val()); }
if (jQuery("#meta_select").val()) { component_ids.push(jQuery("#meta_select").val()); }
Expand All @@ -62,6 +63,7 @@ function retrieve_matching_traits (component_ids) {
}
ids["tod_ids"] = jQuery("#tod_select").val();
ids["toy_ids"] = jQuery("#toy_select").val();
ids["tiy_ids"] = jQuery("#tiy_select").val();
ids["gen_ids"] = jQuery("#gen_select").val();
ids["evt_ids"] = jQuery("#evt_select").val();
ids["meta_ids"] = jQuery("#meta_select").val();
Expand All @@ -76,6 +78,7 @@ jQuery.ajax( {
'trait_ids': ids["trait_ids"],
'tod_ids': ids["tod_ids"],
'toy_ids': ids["toy_ids"],
'tiy_ids': ids["tiy_ids"],
'gen_ids': ids["gen_ids"],
'evt_ids': ids["evt_ids"],
'meta_ids': ids["meta_ids"],
Expand Down
4 changes: 3 additions & 1 deletion lib/SGN/Controller/AJAX/Onto.pm
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Expand Up @@ -362,11 +362,12 @@ sub get_traits_from_component_categories: Path('/ajax/onto/get_traits_from_compo
my @trait_ids = $c->req->param("trait_ids[]");
my @tod_ids = $c->req->param("tod_ids[]");
my @toy_ids = $c->req->param("toy_ids[]");
my @tiy_ids = $c->req->param("tiy_ids[]");
my @gen_ids = $c->req->param("gen_ids[]");
my @evt_ids = $c->req->param("evt_ids[]");
my @meta_ids = $c->req->param("meta_ids[]");

print STDERR "Obj ids are @object_ids\n Attr ids are @attribute_ids\n Method ids are @method_ids\n unit ids are @unit_ids\n trait ids are @trait_ids\n tod ids are @tod_ids\n toy ids are @toy_ids\n gen ids are @gen_ids\n evt ids are @evt_ids\n metadata ids are @meta_ids\n";
print STDERR "Obj ids are @object_ids\n Attr ids are @attribute_ids\n Method ids are @method_ids\n unit ids are @unit_ids\n trait ids are @trait_ids\n tod ids are @tod_ids\n toy ids are @toy_ids\n tiy ids are @tiy_ids\n gen ids are @gen_ids\n evt ids are @evt_ids\n metadata ids are @meta_ids\n";
my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');

my $traits = SGN::Model::Cvterm->get_traits_from_component_categories($schema, \@allowed_composed_cvs, $composable_cvterm_delimiter, $composable_cvterm_format, {
Expand All @@ -377,6 +378,7 @@ sub get_traits_from_component_categories: Path('/ajax/onto/get_traits_from_compo
trait => \@trait_ids,
tod => \@tod_ids,
toy => \@toy_ids,
tiy => \@tiy_ids,
gen => \@gen_ids,
evt => \@evt_ids,
meta => \@meta_ids,
Expand Down
2 changes: 2 additions & 0 deletions lib/SGN/Controller/Ontology.pm
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Expand Up @@ -119,6 +119,7 @@ sub compose_trait : Path('/tools/compose_trait') :Args(0) {
$c->stash->{composable_cvs_allowed_combinations} = $c->config->{composable_cvs_allowed_combinations};
$c->stash->{composable_tod_root_cvterm} = $c->config->{composable_tod_root_cvterm};
$c->stash->{composable_toy_root_cvterm} = $c->config->{composable_toy_root_cvterm};
$c->stash->{composable_tiy_root_cvterm} = $c->config->{composable_tiy_root_cvterm};
$c->stash->{composable_gen_root_cvterm} = $c->config->{composable_gen_root_cvterm};
$c->stash->{composable_evt_root_cvterm} = $c->config->{composable_evt_root_cvterm};
$c->stash->{composable_meta_root_cvterm} = $c->config->{composable_meta_root_cvterm};
Expand Down Expand Up @@ -205,6 +206,7 @@ sub compose_treatment : Path('/tools/compose_treatment') :Args(0) {
$c->stash->{composable_cvs_allowed_combinations} = $c->config->{composable_cvs_allowed_combinations};
$c->stash->{composable_tod_root_cvterm} = $c->config->{composable_tod_root_cvterm};
$c->stash->{composable_toy_root_cvterm} = $c->config->{composable_toy_root_cvterm};
$c->stash->{composable_tiy_root_cvterm} = $c->config->{composable_tiy_root_cvterm};
$c->stash->{composable_gen_root_cvterm} = $c->config->{composable_gen_root_cvterm};
$c->stash->{composable_evt_root_cvterm} = $c->config->{composable_evt_root_cvterm};
$c->stash->{composable_meta_root_cvterm} = $c->config->{composable_meta_root_cvterm};
Expand Down
26 changes: 21 additions & 5 deletions mason/ontology/compose_trait.mas
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Expand Up @@ -11,6 +11,7 @@ $composable_cvs => undef
$composable_cvs_allowed_combinations => undef
$composable_tod_root_cvterm => undef
$composable_toy_root_cvterm => undef
$composable_tiy_root_cvterm => undef
$composable_gen_root_cvterm => undef
$composable_evt_root_cvterm => undef
$composable_meta_root_cvterm => undef
Expand Down Expand Up @@ -115,6 +116,14 @@ $composable_meta_root_cvterm => undef
<button class="btn btn-default btn-sm" id="toy_select_all" name="toy_select_all"/>Select All</button>
<button class="btn btn-default btn-sm" id="toy_select_clear" name="toy_select_clear"/>Clear</button>
</div>
<div id="tiy_div" class="col-md-6" style="display: none;">
<label for="tiy_select_div" class="control-label">Time in Years</label>
<p class="help-block"><small><i>Optional</i> Pick the year in which the new trait is measured</small></p>
<input type="text" id="tiy_search" class="form-control input-sm" placeholder="Search year...">
<div id="tiy_select_div"></div><br>
<button class="btn btn-default btn-sm" id="tiy_select_all" name="tiy_select_all"/>Select All</button>
<button class="btn btn-default btn-sm" id="tiy_select_clear" name="tiy_select_clear"/>Clear</button>
</div>
<div id="gen_div" class="col-md-6" style="display: none;">
<label for="gen_select_div" class="control-label">Generation</label>
<p class="help-block"><small><i>Optional</i> Pick the generation on which the new trait is measured</small></p>
Expand Down Expand Up @@ -249,7 +258,7 @@ name = name.replace('_root_select', '');
get_select_box('trait_components', name +'_select_div', { 'id' : name +'_select', 'name': name +'_select', 'multiple': 'true', 'cv_id': cv_id, 'size':'10' });
});

jQuery(document).on('change','#object_select, #attribute_select, #method_select, #unit_select, #trait_select, #tod_select, #toy_select, #gen_select, #evt_select, #meta_select', function() { // retrieve matching traits each time component selection changes
jQuery(document).on('change','#object_select, #attribute_select, #method_select, #unit_select, #trait_select, #tod_select, #toy_select, #tiy_select, #gen_select, #evt_select, #meta_select', function() { // retrieve matching traits each time component selection changes
if (jQuery(this).attr('name') == 'trait_select') {
//console.log("trait select changed");
//clearAllOptions(document.getElementById('object_select'));
Expand All @@ -264,15 +273,15 @@ jQuery(document).on('change','#object_select, #attribute_select, #method_select,
display_matching_traits();
});

jQuery('#object_select_all, #attribute_select_all, #method_select_all, #unit_select_all, #trait_select_all, #tod_select_all, #toy_select_all, #gen_select_all, #evt_select_all, #meta_select_all').click( // select all data in a panel
jQuery('#object_select_all, #attribute_select_all, #method_select_all, #unit_select_all, #trait_select_all, #tod_select_all, #toy_select_all, #tiy_select_all, #gen_select_all, #evt_select_all, #meta_select_all').click( // select all data in a panel
function() {
var name = jQuery(this).attr('name');
var select_id = name.substring(0, name.length - 4);
selectAllOptions(document.getElementById(select_id));
display_matching_traits();
});

jQuery('#object_select_clear, #attribute_select_clear, #method_select_clear, #unit_select_clear, #trait_select_clear, #gen_select_clear, #tod_select_clear, #toy_select_clear, #evt_select_clear, #meta_select_clear').click( // clear all selections in a panel
jQuery('#object_select_clear, #attribute_select_clear, #method_select_clear, #unit_select_clear, #trait_select_clear, #gen_select_clear, #tod_select_clear, #toy_select_clear, #tiy_select_clear, #evt_select_clear, #meta_select_clear').click( // clear all selections in a panel
function() {
var name = jQuery(this).attr('name');
var select_id = name.substring(0, name.length - 6);
Expand Down Expand Up @@ -348,6 +357,7 @@ function create_multi_selects(allowed_names) {
jQuery('#compose_trait').prop('disabled', true);
jQuery('#tod_div').hide();
jQuery('#toy_div').hide();
jQuery('#tiy_div').hide();
jQuery('#gen_div').hide();
jQuery('#evt_div').hide();
jQuery('#object_div').hide();
Expand All @@ -358,6 +368,7 @@ function create_multi_selects(allowed_names) {
jQuery('#meta_div').hide();
jQuery('#tod_select').val([]);
jQuery('#toy_select').val([]);
jQuery('#tiy_select').val([]);
jQuery('#gen_select').val([]);
jQuery('#evt_select').val([]);
jQuery('#object_select').val([]);
Expand Down Expand Up @@ -388,9 +399,10 @@ function create_multi_selects(allowed_names) {
jQuery('#method_div').show();
break;
case "time":
jQuery("#tod_div,#toy_div,#gen_div","evt_div","meta_div").show();
jQuery("#tod_div,#toy_div,#tiy_div,#gen_div","evt_div","meta_div").show();
get_select_box('ontology_children', 'tod_select_div', { 'selectbox_id' : 'tod_select', 'selectbox_name': 'tod_select', 'multiple': 'true', 'parent_node_cvterm': '<% $composable_tod_root_cvterm %>', 'rel_cvterm': 'is_a', 'rel_cv': 'relationship' });
get_select_box('ontology_children', 'toy_select_div', { 'selectbox_id' : 'toy_select', 'selectbox_name': 'toy_select', 'multiple': 'true', 'parent_node_cvterm': '<% $composable_toy_root_cvterm %>', 'rel_cvterm': 'is_a', 'rel_cv': 'relationship' });
get_select_box('ontology_children', 'tiy_select_div', { 'selectbox_id' : 'tiy_select', 'selectbox_name': 'tiy_select', 'multiple': 'true', 'parent_node_cvterm': '<% $composable_tiy_root_cvterm %>', 'rel_cvterm': 'is_a', 'rel_cv': 'relationship' });
get_select_box('ontology_children', 'gen_select_div', { 'selectbox_id' : 'gen_select', 'selectbox_name': 'gen_select', 'multiple': 'true', 'parent_node_cvterm': '<% $composable_gen_root_cvterm %>', 'rel_cvterm': 'is_a', 'rel_cv': 'relationship' });
get_select_box('ontology_children', 'evt_select_div', { 'selectbox_id' : 'evt_select', 'selectbox_name': 'evt_select', 'multiple': 'true', 'parent_node_cvterm': '<% $composable_evt_root_cvterm %>', 'rel_cvterm': 'is_a', 'rel_cv': 'relationship' });
get_select_box('ontology_children', 'meta_select_div', { 'selectbox_id' : 'meta_select', 'selectbox_name': 'meta_select', 'multiple': 'true', 'parent_node_cvterm': '<% $composable_meta_root_cvterm %>', 'rel_cvterm': 'is_a', 'rel_cv': 'relationship' });
Expand All @@ -403,6 +415,10 @@ function create_multi_selects(allowed_names) {
jQuery("#toy_div").show();
get_select_box('ontology_children', 'toy_select_div', { 'selectbox_id' : 'toy_select', 'selectbox_name': 'toy_select', 'multiple': 'true', 'parent_node_cvterm': '<% $composable_toy_root_cvterm %>', 'rel_cvterm': 'is_a', 'rel_cv': 'relationship' });
break;
case "tiy":
jQuery("#tiy_div").show();
get_select_box('ontology_children', 'tiy_select_div', { 'selectbox_id' : 'tiy_select', 'selectbox_name': 'tiy_select', 'multiple': 'true', 'parent_node_cvterm': '<% $composable_tiy_root_cvterm %>', 'rel_cvterm': 'is_a', 'rel_cv': 'relationship' });
break;
case "gen":
jQuery("#gen_div").show();
get_select_box('ontology_children', 'gen_select_div', { 'selectbox_id' : 'gen_select', 'selectbox_name': 'gen_select', 'multiple': 'true', 'parent_node_cvterm': '<% $composable_gen_root_cvterm %>', 'rel_cvterm': 'is_a', 'rel_cv': 'relationship' });
Expand Down Expand Up @@ -436,7 +452,7 @@ jQuery(document).ready(function() {
});

jQuery(document).ready(function () {
const searchable = ['trait', 'toy'];
const searchable = ['trait', 'toy', 'tiy'];

searchable.forEach(function (prefix) {
const searchSelector = '#' + prefix + '_search';
Expand Down
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