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Edits to query gating for regions #76

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Merged
Clare72 merged 4 commits into from
Jul 14, 2026
Merged

Edits to query gating for regions #76

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84c9a36
change partsof query to use Class, Anatomy NOT Cell
Clare72 Jul 14, 2026
06a7ebe
Merge branch 'main' into query-gating
Clare72 Jul 14, 2026
ebc3f56
improve parent selection for query inheritance
Clare72 Jul 14, 2026
0055b09
use Cell instead of Neuron to gate region queries
Clare72 Jul 14, 2026
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111 changes: 72 additions & 39 deletions src/vfbquery/vfb_queries.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1052,31 +1052,32 @@ def term_info_parse_object(results, short_form):
q = NeuronNeuronConnectivityQuery_to_schema(termInfo["Name"], {"short_form": vfbTerm.term.core.short_form})
queries.append(q)

# NeuronsPartHere query - for Class+Anatomy terms (synaptic neuropils, etc.)
# Matches XMI criteria: Class + Synaptic_neuropil, or other anatomical regions
# Excluded for neuron classes: "neurons with some part in <a neuron>" is not a meaningful query
if contains_all_tags(termInfo["SuperTypes"], ["Class"]) and "Neuron" not in termInfo["SuperTypes"] and (
# NeuronsPartHere query - for anatomical regions (neuropils, ganglia, etc.)
# Gate: Class + (Synaptic_neuropil OR Anatomy), but NOT Cell.
# Excluded for cell classes (neurons, glia, neuroblasts): "neurons with some
# part in <a cell>" is not a meaningful query. Cell subsumes Neuron.
if contains_all_tags(termInfo["SuperTypes"], ["Class"]) and "Cell" not in termInfo["SuperTypes"] and (
"Synaptic_neuropil" in termInfo["SuperTypes"] or
"Anatomy" in termInfo["SuperTypes"]
):
q = NeuronsPartHere_to_schema(termInfo["Name"], {"short_form": vfbTerm.term.core.short_form})
queries.append(q)

# NeuronsSynaptic query - for synaptic neuropils and visual systems
# Matches XMI criteria: Class + (Synaptic_neuropil OR Visual_system OR Synaptic_neuropil_domain)
if contains_all_tags(termInfo["SuperTypes"], ["Class"]) and "Neuron" not in termInfo["SuperTypes"] and "Nervous_system" in termInfo["SuperTypes"]:
# NeuronsSynaptic query - for neural regions (neuropils, ganglia, visual system, etc.)
# Gate: Class + Nervous_system, but NOT Cell (excludes neurons, glia, neuroblasts).
if contains_all_tags(termInfo["SuperTypes"], ["Class"]) and "Cell" not in termInfo["SuperTypes"] and "Nervous_system" in termInfo["SuperTypes"]:
q = NeuronsSynaptic_to_schema(termInfo["Name"], {"short_form": vfbTerm.term.core.short_form})
queries.append(q)

# NeuronsPresynapticHere query - for synaptic neuropils and visual systems
# Matches XMI criteria: Class + (Synaptic_neuropil OR Visual_system OR Synaptic_neuropil_domain)
if contains_all_tags(termInfo["SuperTypes"], ["Class"]) and "Neuron" not in termInfo["SuperTypes"] and "Nervous_system" in termInfo["SuperTypes"]:
# NeuronsPresynapticHere query - for neural regions (neuropils, ganglia, visual system, etc.)
# Gate: Class + Nervous_system, but NOT Cell (excludes neurons, glia, neuroblasts).
if contains_all_tags(termInfo["SuperTypes"], ["Class"]) and "Cell" not in termInfo["SuperTypes"] and "Nervous_system" in termInfo["SuperTypes"]:
q = NeuronsPresynapticHere_to_schema(termInfo["Name"], {"short_form": vfbTerm.term.core.short_form})
queries.append(q)

# NeuronsPostsynapticHere query - for synaptic neuropils and visual systems
# Matches XMI criteria: Class + (Synaptic_neuropil OR Visual_system OR Synaptic_neuropil_domain)
if contains_all_tags(termInfo["SuperTypes"], ["Class"]) and "Neuron" not in termInfo["SuperTypes"] and "Nervous_system" in termInfo["SuperTypes"]:
# NeuronsPostsynapticHere query - for neural regions (neuropils, ganglia, visual system, etc.)
# Gate: Class + Nervous_system, but NOT Cell (excludes neurons, glia, neuroblasts).
if contains_all_tags(termInfo["SuperTypes"], ["Class"]) and "Cell" not in termInfo["SuperTypes"] and "Nervous_system" in termInfo["SuperTypes"]:
q = NeuronsPostsynapticHere_to_schema(termInfo["Name"], {"short_form": vfbTerm.term.core.short_form})
queries.append(q)

Expand All @@ -1086,11 +1087,18 @@ def term_info_parse_object(results, short_form):
q = ComponentsOf_to_schema(termInfo["Name"], {"short_form": vfbTerm.term.core.short_form})
queries.append(q)

# PartsOf query - for any Class except neuron classes
# Matches XMI criteria: Class (any)
# Excluded for neuron classes: anatomical sub-parts of a neuron type are not modelled
# in the ontology in a way that makes this query useful at the class level.
if contains_all_tags(termInfo["SuperTypes"], ["Class"]) and "Neuron" not in termInfo["SuperTypes"]:
# PartsOf query - for anatomical classes that are not individual cells
# Gate: Class + Anatomy, but NOT Cell.
# - Anatomy: "part of" is only meaningful for anatomical structures; it
# excludes non-anatomy classes (genes, features, GO process terms,
# deprecated/stage classes, and data-less expression patterns lacking
# the Anatomy tag).
# - NOT Cell: excludes individual cell types (neurons, glia, neuroblasts),
# whose anatomical sub-parts are not modelled usefully at the class
# level. Cell subsumes Neuron, so this also keeps neuron classes out.
# Retains neuropils, tracts/nerves, clones, ganglia, whole regions, and
# imaged expression patterns/splits (all Anatomy, not Cell).
if contains_all_tags(termInfo["SuperTypes"], ["Class", "Anatomy"]) and "Cell" not in termInfo["SuperTypes"]:
q = PartsOf_to_schema(termInfo["Name"], {"short_form": vfbTerm.term.core.short_form})
queries.append(q)

Expand Down Expand Up @@ -1135,10 +1143,10 @@ def term_info_parse_object(results, short_form):
q = LineageClonesIn_to_schema(termInfo["Name"], {"short_form": vfbTerm.term.core.short_form})
queries.append(q)

# ImagesNeurons query - for synaptic neuropils
# Matches XMI criteria: Class + (Synaptic_neuropil OR Synaptic_neuropil_domain)
# ImagesNeurons query - for anatomical regions (mirrors NeuronsPartHere)
# Gate: Class + (Synaptic_neuropil OR Anatomy), but NOT Cell.
# Returns individual neuron images (instances) rather than neuron classes
if contains_all_tags(termInfo["SuperTypes"], ["Class"]) and "Neuron" not in termInfo["SuperTypes"] and (
if contains_all_tags(termInfo["SuperTypes"], ["Class"]) and "Cell" not in termInfo["SuperTypes"] and (
"Synaptic_neuropil" in termInfo["SuperTypes"] or
"Anatomy" in termInfo["SuperTypes"]
):
Expand Down Expand Up @@ -1357,12 +1365,29 @@ def term_info_parse_object(results, short_form):
)
instance_super_types = termInfo["SuperTypes"] or []
if termInfo["IsIndividual"] and any(t in instance_super_types for t in inherit_instance_types):
# Legacy anchored on the first parent Class (classVariable = parents[0]).
inherit_parent = next(
(p for p in (vfbTerm.parents or []) if p.types and "Class" in p.types),
None,
)
if inherit_parent is not None:
# Choose the parent class(es) that best represent the instance's
# inherited type. Exclude the generic preferred_root (e.g.
# 'anatomical entity'): it is a direct parent of many instances but
# would anchor broad queries like "Subclasses of anatomical entity"
# on the instance. Among the remaining direct Class parents, keep
# those whose type set overlaps inherit_instance_types the most (the
# "closest match"); ties are all kept so an instance typed by several
# equally-specific classes inherits each class's queries, anchored on
# that class. Every gated instance has such a parent in the data, so
# best_overlap is >= 1 (best_overlap == 0 -> inherit nothing, since no
# parent is a valid target for the facet-specific queries).
inherit_set = set(inherit_instance_types)
candidates = [
p for p in (vfbTerm.parents or [])
if p.types and "Class" in p.types and "preferred_root" not in p.types
]
best_overlap = max((len(set(p.types) & inherit_set) for p in candidates), default=0)
inherit_parents = [
p for p in candidates
if best_overlap > 0 and len(set(p.types) & inherit_set) == best_overlap
]
seen = set()
for inherit_parent in inherit_parents:
p_types = set(inherit_parent.types or [])
p_ref = {"short_form": inherit_parent.short_form}
p_label = inherit_parent.label if inherit_parent.label else inherit_parent.short_form
Expand All @@ -1371,11 +1396,11 @@ def term_info_parse_object(results, short_form):
# own menu above so an instance shows exactly what its class shows.
inheritable_class_queries = (
(ListAllAvailableImages_to_schema, lambda p: {"Class", "Anatomy"} <= p),
(NeuronsPartHere_to_schema, lambda p: "Class" in p and "Neuron" not in p and ("Synaptic_neuropil" in p or "Anatomy" in p)),
(NeuronsSynaptic_to_schema, lambda p: "Class" in p and ("Synaptic_neuropil" in p or "Visual_system" in p or "Synaptic_neuropil_domain" in p)),
(NeuronsPresynapticHere_to_schema, lambda p: "Class" in p and ("Synaptic_neuropil" in p or "Visual_system" in p or "Synaptic_neuropil_domain" in p)),
(NeuronsPostsynapticHere_to_schema, lambda p: "Class" in p and ("Synaptic_neuropil" in p or "Visual_system" in p or "Synaptic_neuropil_domain" in p)),
(ImagesNeurons_to_schema, lambda p: "Class" in p and ("Synaptic_neuropil" in p or "Synaptic_neuropil_domain" in p)),
(NeuronsPartHere_to_schema, lambda p: "Class" in p and "Cell" not in p and ("Synaptic_neuropil" in p or "Anatomy" in p)),
(NeuronsSynaptic_to_schema, lambda p: "Class" in p and "Cell" not in p and "Nervous_system" in p),
(NeuronsPresynapticHere_to_schema, lambda p: "Class" in p and "Cell" not in p and "Nervous_system" in p),
(NeuronsPostsynapticHere_to_schema, lambda p: "Class" in p and "Cell" not in p and "Nervous_system" in p),
(ImagesNeurons_to_schema, lambda p: "Class" in p and "Cell" not in p and ("Synaptic_neuropil" in p or "Anatomy" in p)),
(TractsNervesInnervatingHere_to_schema, lambda p: "Class" in p and ("Synaptic_neuropil" in p or "Synaptic_neuropil_domain" in p)),
(LineageClonesIn_to_schema, lambda p: "Class" in p and ("Synaptic_neuropil" in p or "Synaptic_neuropil_domain" in p)),
(NeuronClassesFasciculatingHere_to_schema, lambda p: "Class" in p and "Neuron_projection_bundle" in p),
Expand All @@ -1388,12 +1413,16 @@ def term_info_parse_object(results, short_form):
(TargetNeurons_to_schema, lambda p: {"Class", "Split"} <= p),
(DownstreamClassConnectivity_to_schema, lambda p: {"Class", "Neuron"} <= p),
(UpstreamClassConnectivity_to_schema, lambda p: {"Class", "Neuron"} <= p),
(PartsOf_to_schema, lambda p: "Class" in p and "Neuron" not in p),
(PartsOf_to_schema, lambda p: {"Class", "Anatomy"} <= p and "Cell" not in p),
(SubclassesOf_to_schema, lambda p: "Class" in p),
)
for schema_fn, predicate in inheritable_class_queries:
if predicate(p_types):
queries.append(schema_fn(p_label, p_ref))
q = schema_fn(p_label, p_ref)
key = (q.query, inherit_parent.short_form)
if key not in seen:
seen.add(key)
queries.append(q)

# Add Publications to the termInfo object
if vfbTerm.pubs and len(vfbTerm.pubs) > 0:
Expand Down Expand Up @@ -1778,18 +1807,22 @@ def PartsOf_to_schema(name, take_default):
"""
Schema for PartsOf query.
Finds parts of the specified anatomical class.

Matching criteria from XMI:
- Class (any)


Matching criteria:
- Class + Anatomy, but NOT Cell (gated in term_info_parse_object).

Note: `takes` can only express positive facets (Class + Anatomy); the
"NOT Cell" exclusion lives in the Python gate, since the $and/$or grammar
has no negation operator.

Query chain: Owlery part_of query → process → SOLR
OWL query: "part_of some $ID"
"""
query = "PartsOf"
label = f"Parts of {name}"
function = "get_parts_of"
takes = {
"short_form": {"$and": ["Class"]},
"short_form": {"$and": ["Class", "Anatomy"]},
"default": take_default,
}
preview = 5
Expand Down
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