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Update handling of NCBI Taxonomy ranks in ComparaTree #1104

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Merged
merged 6 commits into from
Oct 28, 2025
Merged

Update handling of NCBI Taxonomy ranks in ComparaTree #1104

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fc4ece4
Update NCBI Taxonomy rank order in ComparaTree
twalsh-ebi Sep 3, 2025
57d0259
Treat taxa of rank clade as having no rank
twalsh-ebi Sep 3, 2025
c59a04d
Take next most basal rank for unranked taxon
twalsh-ebi Sep 3, 2025
52bfcd9
Prevent infinite loop when fetching closest hierarchical rank
twalsh-ebi Sep 3, 2025
30b9b4c
Add comment on NCBI Taxonomy depth cutoff
twalsh-ebi Oct 1, 2025
d349ef9
Add clarifying note about rank order in ComparaTree
twalsh-ebi Oct 6, 2025
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88 changes: 81 additions & 7 deletions modules/EnsEMBL/Web/Component/Gene/ComparaTree.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -488,7 +488,71 @@ sub collapsed_nodes {
}
} elsif ($action =~ /rank_(\w+)/) {
my $asked_rank = $1;
my @rank_order = qw(subspecies species subgenus genus subfamily family superfamily parvorder infraorder suborder order superorder infraclass subclass class superclass subphylum phylum superphylum subkingdom kingdom superkingdom);

# Rank order info as described in
# Schoch et al. (2020) NCBI Taxonomy: a comprehensive update on curation, resources and tools.
# <https://europepmc.org/article/MED/32761142>,
# with some updates based on NCBI Insights (2024-06-04) Upcoming changes to NCBI Taxonomy classifications.
# <https://ncbiinsights.ncbi.nlm.nih.gov/2024/06/04/changes-ncbi-taxonomy-classifications/>
# and NCBI Insights (2025-04-25) NCBI Taxonomy updates to virus classification.
# <https://ncbiinsights.ncbi.nlm.nih.gov/2025/04/25/ncbi-taxonomy-updates-virus-classification-april-2025/>.
# Note that a handful of taxonomic lineages have ranks inconsistent with this ordering
# (e.g. taxon 200324 of rank 'forma specialis' has parent taxon 860303 of rank 'varietas').
# As of release 116, all such cases are below the species level, and species is the lowest taxonomic
# rank in the collapse-by-rank dropdown, so these inconsistencies should not be an issue in practice.
my @rank_order = (
'isolate',
'strain',
'serotype',
'biotype',
'genotype',
'serogroup',
'pathogroup',
'forma',
'subvariety',
'varietas',
'form',
'morph',
'subspecies',
'forma specialis',
'special form',
'species',
'species subgroup',
'species group',
'subseries',
'series',
'subsection',
'section',
'subgenus',
'genus',
'subtribe',
'tribe',
'subfamily',
'family',
'superfamily',
'parvorder',
'infraorder',
'suborder',
'order',
'superorder',
'subcohort',
'cohort',
'infraclass',
'subclass',
'class',
'superclass',
'infraphylum',
'subphylum',
'phylum',
'superphylum',
'subkingdom',
'kingdom',
'domain',
'realm',
'cellular root',
'acellular root',
);

my %rank_pos = map {$rank_order[$_] => $_} 0..(scalar(@rank_order)-1);
my @nodes_to_check = ($tree);
while (@nodes_to_check) {
Expand All @@ -497,15 +561,25 @@ sub collapsed_nodes {
next unless $internal_node->species_tree_node;
my $taxon = $internal_node->species_tree_node->taxon;
my $this_rank = $taxon->rank;
if ($this_rank eq 'no rank') {
# We traverse the taxonomy upwards until we find a rank, and get
# the rank just below instead
while ($this_rank eq 'no rank') {
# Rank 'clade' is assigned to recognised groups without a formal rank.
# See Schoch et al. (2020) NCBI Taxonomy: a comprehensive update on curation, resources and tools.
# <https://europepmc.org/article/MED/32761142>.
if ($this_rank eq 'no rank' || $this_rank eq 'clade') {
# We traverse the taxonomy upwards until we find a rank
my $i = 0;
# We short-circuit the traversal if the number of steps exceeds the depth cutoff.
# This cutoff must be greater than the maximum depth of the NCBI Taxonomy (~40),
# with some headroom so we don't short-circuit a genuine lineage of unranked taxa.
# The Hardy–Ramanujan number (1729) was chosen because it is a very interesting
# number that happens to satisfy these criteria.
my $depth_cutoff = 1729;
do {
$taxon = $taxon->parent;
last unless $taxon;
$this_rank = $taxon->rank;
}
$this_rank = $rank_pos{$this_rank}-1;
$i += 1;
} while (($this_rank eq 'no rank' || $this_rank eq 'clade') && $i < $depth_cutoff);
$this_rank = $rank_pos{$this_rank};
#warn sprintf("Mapped 'no rank' %s to %s\n", $internal_node->species_tree_node->taxon->name, $rank_order[$this_rank]);
} else {
$this_rank = $rank_pos{$this_rank};
Expand Down