OBA should only use PATO fillers from the attribute slim

[matentzn]

I am working on a QC check that ensures that all PATO fillers picked in OBA are drawn from the attribute slim.

https://api.triplydb.com/s/DKDWJ55uL

These are the current violations:

pato_class	pato_class_label	ct_oba_classes
http://purl.obolibrary.org/obo/PATO_0000001	quality	7881
http://purl.obolibrary.org/obo/PATO_0001236	process quality	476
http://purl.obolibrary.org/obo/PATO_0000068	qualitative	1079
http://purl.obolibrary.org/obo/PATO_0001241	physical object quality	5217
http://purl.obolibrary.org/obo/PATO_0001291	electromagnetic (EM) radiation quality	51
http://purl.obolibrary.org/obo/PATO_0001291	obsolete electromagnetic (EM) radiation quality	51
http://purl.obolibrary.org/obo/PATO_0050000	rate of occurence	7
http://purl.obolibrary.org/obo/PATO_0002182	molecular quality	14
http://purl.obolibrary.org/obo/PATO_0001995	organismal quality	31
http://purl.obolibrary.org/obo/PATO_0001396	cellular quality	4
http://purl.obolibrary.org/obo/PATO_0070044	anatomical structure quality	4
http://purl.obolibrary.org/obo/PATO_0000186	behavioral quality	10
http://purl.obolibrary.org/obo/PATO_0002266	3-D shape	57
http://purl.obolibrary.org/obo/PATO_0001599	rotated	10
http://purl.obolibrary.org/obo/PATO_0000440	regular spatial pattern	10
http://purl.obolibrary.org/obo/PATO_0000614	oriented	10
http://purl.obolibrary.org/obo/PATO_0001434	reproductive quality	7
http://purl.obolibrary.org/obo/PATO_0000502	delayed	1
http://purl.obolibrary.org/obo/PATO_0001005	latency	1
http://purl.obolibrary.org/obo/PATO_0000318	blue	1
http://purl.obolibrary.org/obo/PATO_0000952	brown	1
http://purl.obolibrary.org/obo/PATO_0002261	located in	2
http://purl.obolibrary.org/obo/PATO_0001629	aggregated	2
http://purl.obolibrary.org/obo/PATO_0000330	irregular spatial pattern	2
http://purl.obolibrary.org/obo/PATO_0002036	axial to	1
http://purl.obolibrary.org/obo/PATO_0000383	female	1
http://purl.obolibrary.org/obo/PATO_0000384	male	1
http://purl.obolibrary.org/obo/PATO_0000402	branched	3
http://purl.obolibrary.org/obo/PATO_0001997	decreased amount	1
http://purl.obolibrary.org/obo/PATO_0000467	present	1
http://purl.obolibrary.org/obo/PATO_0002045	dendritic	3
http://purl.obolibrary.org/obo/PATO_0002301	decreased quality	1
http://purl.obolibrary.org/obo/PATO_0002107	peripheral	2
http://purl.obolibrary.org/obo/PATO_0001514	delaminated	1

EDIT: I should say that the query generating this list is looking for subsumption in ubergraph, so PATO class used may be a child of one of the indicated terms here (i.e. qualititative may not actually be used)

@ar-ibrahim can you work with @rays22 to review these by adding a column that states:

1. Wether the use of a class should be known exception (quality, process quality - are these attributes perhaps or not? Check with @dosumis)
2. Whether the use of a class constitutes a qualitative value (blue, rotated) or effect (decreased quality?) and should therefore be obsoleted
3. Whether PATO is simply missing the "attribute slim" tag (latency, located in? weird one)

This requires some deep thinking on what an attribute is. I hope you will have fun doing this!

[matentzn]

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix RO: <http://purl.obolibrary.org/obo/RO_>
prefix HP: <http://purl.obolibrary.org/obo/HP_>
prefix OBA: <http://purl.obolibrary.org/obo/OBA_>
prefix PATO: <http://purl.obolibrary.org/obo/PATO_>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix oio: <http://www.geneontology.org/formats/oboInOwl#>
prefix def: <http://purl.obolibrary.org/obo/IAO_0000115>
prefix owl: <http://www.w3.org/2002/07/owl#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

# Get all classes related to diseases that 
SELECT DISTINCT ?pato_class WHERE
{
  
  ?oba_class rdfs:subClassOf OBA:0000001 .
  ?oba_class rdfs:subClassOf ?pato_class .
  ?pato_class rdfs:subClassOf PATO:0000001 .
  
  FILTER NOT EXISTS {
  	?pato_class oio:inSubset <http://purl.obolibrary.org/obo/pato#attribute_slim> .
  }
  
  # Which ones are included here depends of the outcome of this ticket
  #FILTER (?pato_class NOT IN (PATO:0000001, PATO:0001241, PATO:0000068, PATO:0001236, PATO:0001291, PATO:0001291, PATO:0050000, PATO:0000186, PATO:0001599, PATO:0001995, PATO:0002182, PATO:0000440, PATO:0002266, PATO:0000402, PATO:0001997, PATO:0000318, PATO:0000952, PATO:0000467, PATO:0000502, PATO:0001514, PATO:0001629, PATO:0000330, PATO:0002107, PATO:0000383, PATO:0000384, PATO:0001005, PATO:0002036, PATO:0002045, PATO:0002261, PATO:0001396, PATO:0000614, PATO:0001434, PATO:0002301, PATO:0070044))
    
  ?oba_class rdfs:label ?oba_class_label .
  ?pato_class rdfs:label ?pato_class_label .

  FILTER(STRSTARTS(STR(?oba_class), "http://purl.obolibrary.org/obo/OBA_"))
   FILTER(STRSTARTS(STR(?pato_class), "http://purl.obolibrary.org/obo/PATO_"))
}