The condition if properties.get('type') == 'nerve' in pg_import.py only checks for features explicitly marked as type nerve. This misses nerve terms identified in node-types by mapknowledge but not used as centrelines.
For example in ilxtr:neuron-type-keast-4 in human male and female maps the following node-types appear:
'node-types': [
['ILX:0793228', []],
['ILX:0793559', []],
['UBERON:0018675', []]
]
These are correctly recorded in path_node_types but ILX:0793228 is not included in feature_types since it is not a centreline. As a result NERVE_TYPE is missing.
This issue does not appear in rat-flatmap where ILX:0793228 is used as a centreline and therefore included.
Proposed fix is to extend the logic to also consider node-types when collecting NERVE_TYPE terms.
The condition
if properties.get('type') == 'nerve'in pg_import.py only checks for features explicitly marked as type nerve. This misses nerve terms identified in node-types by mapknowledge but not used as centrelines.For example in ilxtr:neuron-type-keast-4 in human male and female maps the following node-types appear:
These are correctly recorded in
path_node_typesbutILX:0793228is not included infeature_typessince it is not a centreline. As a resultNERVE_TYPEis missing.This issue does not appear in
rat-flatmapwhereILX:0793228is used as a centreline and therefore included.Proposed fix is to extend the logic to also consider node-types when collecting NERVE_TYPE terms.