mapping-commons/lmha-obo-mappings

very drafy first pass

Not much time to document this, sorry...

• See: mappings
  • cl
  • uberon
  • no mappings

All mappings are in SSSOM format

They are generated automatically using rdf_matcher, but using existing xrefs as priors. These have high confidence, as the assumption is that previously curated xrefs are high quality, but the prior weightings can be altered

E.g

subject_id	subject_label	subject_category	predicate_id	object_id	object_label	object_category	match_type	subject_source	object_source	mapping_tool	confidence	subject_match_field	object_match_field	match_string	comment
LMHA:00090	basophil	Respiratory_System	owl:equivalentClass	CL:0000767	basophil	cell	Lexical	LMHA	CL	rdf_matcher	0.9783866146851686	oio:hasDbXref	dc:identifier	CL:0000767	.
LMHA:00179	granulocyte	Respiratory_System	owl:equivalentClass	CL:0000094	granulocyte	cell	Lexical	LMHA	CL	rdf_matcher	0.9784559180850925	oio:hasDbXref	dc:identifier	CL:0000094	.

If there is a match using something like a synonym or shared xref then this will get lower confidence:

subject_id	subject_label	subject_category	predicate_id	object_id	object_label	object_category	match_type	subject_source	object_source	mapping_tool	confidence	subject_match_field	object_match_field	match_string	comment
LMHA:00183	hyaline cartilage	general_tissue_structures	owl:equivalentClass	UBERON:0001994	hyaline cartilage tissue	uberon	Lexical	LMHA	UBERON	rdf_matcher	0.4482245494091784	rdfs:label	oio:hasExactSynonym	hyaline cartilage	.

Note I deliberately included all candidate mappings, e.g. there are 3 matches for LMHA:00150

subject_id	subject_label	subject_category	predicate_id	object_id	object_label	object_category	match_type	subject_source	object_source	mapping_tool	confidence	subject_match_field	object_match_field	match_string	comment
LMHA:00150	dendritic cell	Cell	owl:equivalentClass	CL:0000451	dendritic cell	cell	Lexical	LMHA	CL	rdf_matcher	0.4827360284687321	rdfs:label	rdfs:label	dendritic cell	.
LMHA:00150	dendritic cell	Cell	owl:equivalentClass	CL:0001056	dendritic cell, human	cell	Lexical	LMHA	CL	rdf_matcher	0.16884322574902352	rdfs:label	oio:hasBroadSynonym	dendritic cell	.
LMHA:00150	dendritic cell	Cell	owl:equivalentClass	CL:0000738	leukocyte	cell	Lexical	LMHA	CL	rdf_matcher	0.9577300291303523	oio:hasDbXref	dc:identifier	CL:0000738	.

• The lowest match to 'human dendritic cell' has a confidence of ~0.16, and this one is too specific (although arguably this is the correct one since LMHA is human, however, CL does not consistent populate human-specific groupings, so it is better to map to the same level of generality)
• the middle match (confidence 0.48) is the correct one
• interestingly the "best" match (confidence 0.96) is to leukocyte. This is clearly incorrect. But it highlights the fact that there is an incorrect curated xref in the LMHA ontology, and we should downweight these

It would be possible for me to do something more advanced to filter and better prioritize these but for now I think it is informative and transparent to show all candidate mappings to give curators a sense of the issues

unmapped LMHA terms

ones for which neither xref nor lexical match found:

• no mappings

This is being used to gapfill: #1

TODO

• make a useful report that shows which mappings are likely yet not present in source LMHA (trivial)
• configuring mapping weights
• run boomer