EFO-OBA mapping (antibody measurement)

[ar-ibrahim]

• will map terms from oba-efo-unreviewed.dosdp.tsv
• filtered by attribute_label: antibody

subject_id	subject_label	match_type	quality	quality_label	attribute	attribute_label
EFO:0005200	antiphospholipid antibody measurement	Lexical	PATO:0000001	quality	GO:0042571	antibody
EFO:0600074	anti-human polyomavirus 6 antibody measurement	Lexical	PATO:0000001	quality	GO:0042571	antibody
EFO:0009273	anti-epstein barr virus antibody measurement	Lexical	PATO:0000001	quality	GO:0042571	antibody
EFO:0010150	anti-anoctamin 2 antibody measurement	Lexical	PATO:0000001	quality	GO:0042571	antibody
EFO:0010087	anti-meningococcal c serum bactericidal antibody measurement	Lexical	PATO:0000001	quality	GO:0042571	antibody
EFO:0009896	anti-thyroglobulin antibody measurement	Lexical	PATO:0000001	quality	GO:0042571	antibody
EFO:0004556	antibody measurement	Lexical	PATO:0000001	quality	GO:0042571	antibody
EFO:0005666	thyroid peroxidase antibody measurement	Lexical	PATO:0000001	quality	GO:0042571	antibody
EFO:0004733	anti-cyclic citrullinated peptide antibody measurement	Lexical	PATO:0000001	quality	GO:0042571	antibody
EFO:0600073	anti-wu polyomavirus antibody measurement	Lexical	PATO:0000001	quality	GO:0042571	antibody
EFO:0005949	antinuclear antibody measurement	Lexical	PATO:0000001	quality	GO:0042571	antibody
EFO:0009273	anti-ebv antibody measurement	Lexical	PATO:0000001	quality	GO:0042571	antibody

[ar-ibrahim]

• I broadly mapped these antibody terms to OBA:VT0002460 blood immunoglobulin amount with the exception of EFO:0004556 antibody measurement (skos:closeMatch).

Queries:
@rays22 @matentzn

• Wanted to know why blood immunoglobulin amount OBA:VT0002460 is a subclass of cellular component attribute and not blood protein amount OBA:VT0005416.

• Also blood immunoglobulin amount is in the entity_attribute.tsv file and not the entity_attribute_location.tsv file.

[rays22]

• broadly mapped these antibody terms to OBA:VT0002460 blood immunoglobulin amount with the exception of EFO:0004556 antibody measurement (skos:closeMatch).

We regard these 'measurement' terms as actually being traits/attributes, therefore I would use skos:exactMatch for the EFO:0004556 - OBA:VT0002460 pair.

Queries: @rays22 @matentzn

• Wanted to know why blood immunoglobulin amount OBA:VT0002460 is a subclass of cellular component attribute and not blood protein amount OBA:VT0005416.

• Also blood immunoglobulin amount is in the entity_attribute.tsv file and not the entity_attribute_location.tsv file.

Good catch. OBA:VT0002460 should be defined indeed in the entity_attribute_location table with 'blood' or 'serum' as the location.