Marker sets don't wire up to clusters

[dosumis]

This may be a CellMark pipeline issue (lookup of cell set IRIs not working?)

Lots of marker sets loaded:

But - none of these are cell sets

*(No idea what the Class+Individual entities are...)

Some examples of the individuals:

From the names of marker sets - it looks like these Individuals should be cell sets:

Example - I think this one:

Should link up to one of these:

(I think from HLCA)

On top of this - it looks like marker sets don't have genes(!):

[ubyndr]

Based on some digging, I discovered that in 2025 several IDs in the CellMark repo became outdated, so we should update them.

The node on the right-hand side now uses the IRI http://example.org/7d1acf27-32b8-59e8-897c-4430648680b5. In 2024 backups these were represented as CellSets, but that changed in 2025.

ugurb@ada:~/csv_imports$ grep -l "7d1acf27-32b8-59e8-897c-4430648680b5" *_csv_imports/nodes_*.csv
01042025_csv_imports/nodes_Individual.csv
06022025_csv_imports/nodes_Individual.csv
08012025_csv_imports/nodes_Individual.csv
11122024_csv_imports/nodes_Cell_cluster.csv
11122024_csv_imports/nodes_Individual.csv
12122024_csv_imports/nodes_Cell_cluster.csv
12122024_csv_imports/nodes_Individual.csv
13042025_csv_imports/nodes_Individual.csv
27022025_csv_imports/nodes_Individual.csv
29012025_csv_imports/nodes_Individual.csv

I'll make a proper CellMark release. cc @hkir-dev

[ubyndr]

I attempted a CellMark release with updated IDs, but that wasn’t the problem—none of the IDs in Clusters.tsv have changed.

[ubyndr]

Related with Cellular-Semantics/CellMark#42