Potential Missing Data in Pathway Nodes Despite Listed Connectivity

[akhuoa]

It looks like there may be missing data in the nodes field for some pathways in the flatmap data, even though the corresponding features are listed in the connectivity. This was observed while testing "Human Male" data on the devel server.

For example, the pathway ilxtr:sparc-nlp/liver/121 includes the liver (UBERON:0002107) in its connectivity and also includes the related feature ID 1121 in its nodes. However, another pathway, ilxtr:sparc-nlp/liver/109, also lists liver in its connectivity, but does not include feature ID 1121 in its nodes.

Furthermore, in the node-paths object:

"1121": [
  "ilxtr:sparc-nlp/liver/112",
  "ilxtr:sparc-nlp/liver/121",
  "ilxtr:sparc-nlp/liver/119",
  "ilxtr:sparc-nlp/liver/125",
  "ilxtr:sparc-nlp/liver/110",
  "ilxtr:sparc-nlp/liver/123"
],

ilxtr:sparc-nlp/liver/109 is missing from the list, despite having the same connectivity feature.

Liver is just one example, but this issue may affect other pathways as well. Based on previous discussions with Yuda, this could be due to the recent addition of connectivity data in the Maps. Opening this issue to confirm whether this is a case of missing data or expected behaviour.

[dbrnz]

@napakalas I see from the nodes that make up the ilxtr:sparc-nlp/liver/109 path, that it terminates in ILX:0795010 (parasympathetic ganglia of the liver). This feature though doesn't appear to be on the map yet mapmaker has terminated the path in the liver without including it in the node-paths for the liver. In fact there appear to be a quite a few other ilxtr:sparc-nlp/liver/ paths like this (e.g. 114, 111, 122, 124, 127...?) -- are you able to provide some insights??

[napakalas]

The terminals of those paths, including ILX:0795010, are aliases for the liver. That’s why the renderings are terminated at the liver. I have checked the ./pathways folder and found that the paths passing through centrelines are missing complete nodes; they only list the additional nodes that the centrelines pass through. These additional nodes may or may not be part of the actual paths. For example, if a path includes the vagus nerve but not the inferior vagus X or superior vagus X ganglia, these ganglia can still appear because the selected segment of the vagus nerve passes through them.