Define Cypher queries for finding new terms.

[ubyndr]

Copied from https://github.com/cellannotation/CAS-LinkML/issues/5 which is created by @dosumis

Query 1: Find leaf node CL terms with nested cell sets underneath

Cypher query for leaf nodes:

MATCH p=(c:Class:Cell)<-[:composed_primarily_of]-(s1)<-[:subcluster_of*..]-(s2) where not (c)<-[:SUBCLASSOF]-() return p

Example results from Sikemma:

Misses some potentially interesting cases where CL term is not leaf node.

However, without the leaf node clause, most datasets will return too much to review.

Query to find General term used for specific class.

e.g. T-Cell here:

Candidate query:

MATCH p=(c:Class:Cell)<-[:composed_primarily_of]-(s1:Cluster) where (c)<-[:SUBCLASSOF]-() and not (s1)<-[:subcluster_of]-() return p

Looks promising - and at least in this case it returns a set of relatively easy to assess results

c.label	s1.label	More specific term needed*	CL term to use	Notes
serous secreting cell	SMG serous (nasal)	Y		SMG = submucosal gland. We have no nasal SMG serous term.
tracheobronchial goblet cell	Goblet (subsegmental)	?		Need to check if could be more precise
tracheobronchial serous cell	SMG serous (bronchial)	n	serous secreting cell of bronchus submucosal gland
bronchial goblet cell	Goblet (bronchial)	n
CD4-positive, alpha-beta T cell	CD4 T cells	n
mucus secreting cell	SMG mucous	n	mucus secreting cell of bronchus submucosal gland
ciliated columnar cell of tracheobronchial tree	Multiciliated (non-nasal)	n
dendritic cell	Migratory DCs	y
lung macrophage	Interstitial Mph perivascular	y	"perivascular macrophage" is currently brain specific! We also have lung interstitial macrophage
plasmacytoid dendritic cell	Plasmacytoid DCs	n
smooth muscle cell	SM activated stress response	y?
epithelial cell of alveolus of lung	AT0	Y
fibroblast	Subpleural fibroblasts	Y
tracheobronchial smooth muscle cell	Smooth muscle	N
epithelial cell of lower respiratory tract	pre-TB secretory	Y		TB = tracheobronchial
CD8-positive, alpha-beta T cell	CD8 T cells	N
T cell	T cells proliferating	N
conventional dendritic cell	DC1	N
brush cell of trachebronchial tree	Tuft	N

*quick assessment - may not be 100% acurate

[dosumis]

CC @AvolaAmg