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The-Sequence-Ontology / SO-Ontologies

Collect of SO Ontologies
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RTS1 synonyms attached to wrong term #350

Open mah11 opened 8 years ago

mah11 commented 8 years ago

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 commented 8 years ago

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]

keilbeck commented 8 years ago

ooops. Will definitely fix that.

mah11 commented 6 years ago

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

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

2. 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]

3. 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

4. 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 commented 6 years ago

< 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