add method to curate oligomerization states / subunit composition/ documentation

[ValWood]

Document oligomerizatio curation here:
document this here
https://github.com/pombase/curation/wiki/Working-with-contig-files

This is all I can find in
https://docs.google.com/document/d/1M4zca0WRPv0nUOHIIcq2gleQ4ENi0gGnPxvbthSx1HE/edit?tab=t.0#heading=h.mm5ckaol7w0i

Oligomerization states
/controlled_curation="term=subunit composition, homooligomeric; cv=subunit_composition; db_xref=PMID:17208257; date=20080417"
/controlled_curation="term=subunit composition, homomeric(2); cv=subunit_composition; db_xref=PMID:11884628; date=20051017"

(replace the info in the curation catalog with a link to the wiki docs)

[kimrutherford]

could you query for all examples of "subunit composition" plus extensions so that we can write new docs.

How's this?:

subunit_composition.tsv.txt

[ValWood]

This is what we have:

18 monomeric
68 homomeric(2)
3 homomeric(3)
10 homomeric(4)
1 homomeric(5)
1 homomeric(6)
2 homomeric(8)
10 heteromeric(10)
2 heteromeric(12)
46 heteromeric(2)
6 heteromeric(3)
6 heteromeric(4)
3 heteromeric(6)
2 heteromeric(8)

fixes

• 1 homomeric(16) This looked odd the paper says 9-40 subunits, -> remove

• 1 dimeric -> change to homomeric(2)

• 1 homodimeric -> change to homomeric(2)

• 2 homomeric(1) ????? -> should these be monomeric?
  SPCC297.04c
  SPAC227.13c

• 1 homomeric(2), RING domain-dependent -> dependency from root term

• 1 pentameric -> change to homomeric(5)

• 1 tetrameric(1) -> homomeric(4)

• 1 homotetrameric -> homomeric(4)

• 4 homooligomeric -> need to find number of subunits if possible
  SPAC2G11.08c homooligomeric homooligomeric PMID:10816558
  SPAC30D11.10 homooligomeric homooligomeric PMID:17208257
  SPBC119.14 homooligomeric homooligomeric PMID:17208257
  SPCC4B3.15 homooligomeric homooligomeric PMID:15572668

• 1 homooligomeric in h- cells -> can in h- cells be an extension (we have a PB term for that) (or remove?)
  SPAC11H11.04 homooligomeric in h- cells homooligomeric in h- cells PMID:15659165

• 4 oligomeric -> need to find number of subunits if possible
  SPBC26H8.10
  SPAC458.07
  SPBC776.02c
  SPCC1672.08c

Extensions have been used to be to describe different oligomerization states at different locations
SPAC25G10.07c homomeric(2) [located_in] kinetochore PMID:26258632
SPAC25G10.07c homomeric(4) homomeric(4) [located_in] mitotic spindle pole body PMID:26258632

PROPOSED DOCUMENTATION

Oligomerization states are described in the Artemic contig files, using the following qualifier:

/controlled_curation="term=subunit composition, qualifier; cv=subunit_composition; annotation_extension=located_in(GO:0044732) db_xref=PMID:17208257; date=20080417"

Allowed qualifiers for subunit composition are
monomeric, homomeric(n), or heteromeric(n) where n = number of subunits

The "annotation extension" "located_in" can be used to describe the different locations of complexes with specific compositions

CC @PCarme

[PCarme]

The "annotation extension" "located_in" can be used to describe the different locations of complexes with specific compositions

We could also use the "during" extension to capture compositions that are observed in specific cell cycle phase or stress response for example. I encountered such a case in a recent community curation, with a tetramerisation that is observed only in spores

[ValWood]

Yes go ahead and use, I'll add that as an extension option.