ntr: chromosome regions at SO:nnn

[mah11]

For some improvements to logical definitions in FYPO, we'd like to request some CC terms for chromosome regions:

id: GO:new1 name: rDNA replication pause site heterochromatin def: "A region of heterochromatin associated with sites in rDNA repeats where replication forks pause." intersection_of: GO:0098687 ! chromosomal region intersection_of: coincident_with SO:0001914 PMID:25417108

id: GO:new2 (modeled on GO:0034507) name: chromosome, centromeric inner repeat region namespace: cellular_component def: "The portion of the centromeric region of a chromosome that contains the inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:0001798] synonym: "chromosome, centric outer repeat region" RELATED [] intersection_of: GO:0098687 ! chromosomal region intersection_of: coincident_with SO:0001798 ! regional_centromere_inner_repeat_region relationship: part_of GO:0000775 ! chromosome, centromeric region PMID:21437270

The PMIDs above are the ones where we found the phenotypes that would be logically defined using the GO:new terms. That's the best I have on hand to associate with the GO terms, although for GO:new2 @ValWood may know of a suitable paper or review.

also see https://github.com/obophenotype/upheno/issues/556

[ValWood]

I'm not sure about this.

I seem to remember that a while ago we decided only to include the functionally distinct regions in GO, and not the fine grained sequence regions which could be sO terms

a) The central core (which is where the kinetochore forms) GO:0061638 CENP-A containing chromatin The specialized chromatin located the centromeric core region or the entire centromeric region in organisms with point centromeres, which is enriched for CENP-A-containing nucleosomes. This chromatin forms a 3-dimensional structure which provides a platform for kinetochore assembly and microtubule attachment. PMID:20206496 PMID:22729156

b) the "pericentric regions" which from heterochromatin and is represented by GO:0005721 pericentric heterochromatin Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3. PMID:12019236 PMID:20206496 PMID:22729156

although I am confused that we still have terms like GO:0034507 chromosome, centromeric outer repeat region

[ValWood]

I can't find the ticket though! I thought I did this with @ukemi a year or two ago...

[mah11]

Well, if these GO terms go obsolete (or aren't added in the first place) then some FYPO terms lose their current logical definitions. We (@matentzn, @dosumis, and I) may be able to craft a different pattern for them, or they could just do without. But I did promise Nico I would open this ticket ;)

[ukemi]

We discussed this on the ontology call yesterday and the group seemed ok with it.

[ValWood]

OK< but they still seem to me to be sequence regions rather than cellular components. I would have defined these logically with SO.

[dosumis]

The use case is for refering to location in chromatin in some chromosomal region defined SO sequence:

GO has a pattern for making the link to SO - originating in a request from Midori. e.g. see

We could potentially post-compose the entity in phenotype terms, but it would be much simpler for us if GO could add the term.

[ukemi]

Requested terms in the SO import. #18423

[ukemi]

@balhoff, is ontobot configured to run on SO imports?

[balhoff]

It wasn't for some reason, but now it is: #18428

[ukemi]

Thanks! There is more than just what I added there, but it looks ok. Will merge once the checks pass and then finish up on this ticket.