#11583 inconsistent parents for uracil:cation transporter vs transport

[Valerie Wood]

uracil transmembrane transport has
pyrimidine-containing compound transport in its ancestry, but not
nucleobase-containing compound transport

uracil:cation symporter activity
GO:0015932 nucleobase-containing compound transmembrane transporter activity
via
GO:0005350 pyrimidine nucleobase transmembrane transporter activity
GO:0015205 nucleobase transmembrane transporter activity

Could the "nucleobase-containing compound transport" term be added or removed as approproate.

Thanks

v

[Tanya Berardini]

This has to do with which CHEBI terms we have used for mapping the GO terms.

CHEBI:pyrimidines (aka pyrimidine-containing compound)
CHEBI:pyrimidine
CHEBI:pyrimidine nucleobase
CHEBI:pyrimidine nucleoside
CHEBI:pyrimidine nucleotide

Looking in ChEBI, it appears that not all pyrimidine-containing compounds (CHEBI:pyrimidines) are nucleobase-containing compounds (CHEBI:nucleobase-containing molecular entity) because not all pyrimidine-containing compounds are nucleobases.

I'll have to review the mappings more closely. I suspect there are some terms that need remapping and that the remapping will resolve the conflicting links.

[Tanya Berardini]

I think I've found the problem:

nucleobase-containing molecular entity (CHEBI:61120) has functional parent nucleobase (CHEBI:18282) (instead of is_a)

so nucleobase transport (parent of uracil transmembrane transport) is not a child of nucleobase-containing compound transport

In contrast,

pyrimidines (CHEBI:39447) which we are using in mapping pyrimidine-containing compound is an is_a parent of pyrimidine nucleobase

This translates into pyrimidine nucleobase TM transporter activity being an is_a child of pyrimidine-containing compound TM transporter activity.

Solution? Will consult with other GO eds.

[Tanya Berardini]

I added a new term, 'pyrimidine nucleobase transmembrane transport' GO:1904082 that allows uracil transmembrane transport to go up to nucleobase transport through pyrimidine nucleobase TM transport.

Modified relations for term GO:1903791 with label: uracil transmembrane transport

id: GO:1903791
is_a: GO:0015857 {is_inferred="true"} ! uracil transport
is_a: GO:1904082 {is_inferred="true"} ! pyrimidine nucleobase transmembrane transport
intersection_of: GO:0055085 ! transmembrane transport
intersection_of: transports_or_maintains_localization_of CHEBI:17568 ! uracil
relationship: transports_or_maintains_localization_of CHEBI:17568 {is_inferred="true"} ! uracil

Still to discuss what to do with the issues arising from has functional parent relationship in ChEBI.

[Tanya Berardini]

Will delete the relationship between nucleobase transport and nucleobase-containing compound transport after discussion with other GO eds.

[Tanya Berardini]

It was this link that needed deletion:

nucleobase transmembrane transporter activity
-is_a: GO:0015932 ! nucleobase-containing compound transmembrane transporter activity

The link in the BP branch was not present.

[Tanya Berardini]

replaced with
+is_a: GO:0022891 ! substrate-specific transmembrane transporter activity