Add homology similarity scores

[shawntanzk]

Annotate 'in historical homology relation' with a custom AP homology_similarity_score based on https://github.com/AllenInstitute/MOp_taxonomies_ontology/blob/main/mouseMOp_CCN202002013/Mouse_CrossSpecies_Similarity.csv <- there is similar files for all 3 species.

[dosumis]

This should be transcriptomic_similarity_score. Homology (which is a statement about evolutionary history) is inferred from it.

[dosumis]

From AllenInstitute/MOp_taxonomies_ontology#16

• dist = the Euclidean distance between cluster centroids in an integrated human-marmoset-mouse space. Pairwise distances are calculated within classes (i.e. GABAergic mouse type vs. GABAergic human type)
• similarity = a reverse scaling of the dist metric (since greater distance between cluster centroids implies "less similar" types). Used on the heatmaps as this was more intuitive

If I understand correctly, this is relative to a specific clustering and is literally the distance between the centres of 2 clusters on a tSNE or UMAP.

For STATO, we could request a general:

transcriptomic similiarity score: A measure of the degree of similarity of the complete gene expression profile of two individual cells or of two groups of cells.

STATO includes plenty of specific terms that set a precedent for terms like this.

We might also request a more specific one that reflects the score we are recording.

General issue - how do we move from STATO classes to APs (or DPs?) for recording these values? Asking on OBO Foundry Slack.