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Published 20 hours ago • verified publisher icon The-Sequence-Ontology

RTS1 synonyms attached to wrong term

Open mah11 opened this issue 9 years ago • 4 comments

From PMID:12840005 it looks like these synonyms

synonym: "RTS1 barrier" EXACT []
synonym: "RTS1 element" EXACT []

should go with SO:0002021 mating_type_region_replication_fork_barrier, not SO:0001914 rDNA_replication_fork_barrier. Seems like it should be an easy fix.

thanks, m

mah11 avatar Apr 05 '16 15:04 mah11

I also just spotted that the SO:0002021 text definition just got copied over from SO:0001914, without the necessary text edits. It should be:

A DNA motif that is found in the mating type region of fission yeasts, and is a site of replication fork pausing. [PMID:17614787]

mah11 avatar Apr 06 '16 16:04 mah11

ooops. Will definitely fix that.

keilbeck avatar Apr 07 '16 15:04 keilbeck

Update: I've just learned of a second fork barrier in the pombe mating-type locus. So we could do this:

id: SO:0001914 name: rDNA_replication_fork_barrier REMOVE synonym: "RTS1 barrier" EXACT [] REMOVE synonym: "RTS1 element" EXACT []

id: SO:0002021 name: mating_type_region_replication_fork_barrier update def to: "A DNA motif that is found in the mating type region of fission yeasts, and is a site of replication fork pausing." [PMID:17614787, PMID:21423720]

SO:new1 name: RTS1_barrier def: "A mating type replication fork barrier that is located at the centromere-proximal side of the fission yeast mating type region and causes replication forks originating from the centromere-proximal side to pause, such that the mating type region is replicated unidirectionally." [PMID:21423720] synonym: "RTS1 barrier" EXACT [] synonym: "RTS1 element" EXACT [] is_a: SO:0002021 ! mating_type_region_replication_fork_barrier

SO:new2 name: MPS1_barrier def: "A mating type replication fork barrier that is located near the site of a strand-specific imprint at the fission yeast mating type locus and causes replication fork pausing that allows imprint formation." [PMID:21423720] synonym: "MPS1 barrier" EXACT [] synonym: "MPS1 element" EXACT [] is_a: SO:0002021 ! mating_type_region_replication_fork_barrier

mah11 avatar May 04 '18 13:05 mah11

< bump >

I'm now adding some phenotype ontology terms for effects on pausing at the two different mating type region fork barriers (in PMID:26201080), so it would be useful to have the requested new terms.

Let me know if you'd like this to move to a new ticket.

thanks, Midori

mah11 avatar Jun 27 '18 10:06 mah11