Fix 'conjugation' branch

[pgaudet]

• GO:0000746 conjugation: obsolete: unnecessary and confusing grouping term
• rehouse and redefine:

• GO:0000747 'conjugation with cellular fusion'
• GO:0000748 'conjugation with mutual genetic exchange'
• GO:0009291 'unidirectional conjugation'
• GO:0000762 pheromone-induced unidirectional conjugation

• Also need to obsolete

• GO:0046999 regulation of conjugation: 2 EXP dicty (fusion of cells of opposite mating types)
• • GO:0031135 negative regulation of conjugation 0 annotations
• • GO:0031136 positive regulation of conjugation 0 annotations

[pgaudet]

This addresses a remaining issue in #21459

[pgaudet]

Dear all,

The proposal has been made to obsolete

• GO:0046999 regulation of conjugation:
• GO:0031135 negative regulation of conjugation 0 annotations
• GO:0031136 positive regulation of conjugation 0 annotations

The reason for obsoletion is that 'conjugation' is a confusing grouping term, has been used inconsistently and so will be obsoleted. There are 2 EXP annotations to GO:0046999 by dictyBase. There are no mappings, these terms are not present in any subsets.

You can comment on the ticket:

#22916

Thanks, Pascale

[pgaudet]

Dear all,

The proposal has been made to obsolete 'GO:0000762 pheromone-induced unidirectional conjugation'. The reason for obsoletion is that this term is a child of a term that describes bacterial conjugation but is defined as a eukaryote conjugation (ie it refers to different mating types). There are no references, no annotations, no mappings, this term is not in any subset.

You can comment on the ticket: #22916

Thanks, Pascale

[pgaudet]

• conjugation with mutual genetic exchange: add def xref: PMID:2244414
• unidirectional conjugation: remove is_a conjugation

[pgaudet]

In fact I found some references for 'GO:0000762 pheromone-induced unidirectional conjugation', so I'll add these and edit the definition to "The process of unidirectional (polarized) transfer of genetic information involving direct cellular contact between a donor and recipient cell; the contact is followed by the formation of a cellular bridge that physically connects the cells; some or all of the chromosome(s) of the donor cell is transferred into the recipient cell; unidirectional conjugation occurs between cells of different mating types." (ie remove 'male/female' in favor of donor/recipient)

[pgaudet]

Dear all,

The proposal has been made to obsolete

• GO:0000746 conjugation - 0 annotations
• GO:0000767 cell morphogenesis involved in conjugation 1 EXP by SGD (consider the child term: GO:0000753
  cell morphogenesis involved in conjugation with cellular fusion)
• GO:0000771 agglutination involved in conjugation - 0 annotations

The reason for obsoletion is that this term represents an unnecessary and confusing grouping class, as it is defined as "The union or introduction of genetic information from compatible mating types that results in a genetically different individual", but this is not the case for all existing children. Children have been rehoused and redefined (see comments in the ticket).

There are no mappings, these terms are not present in any subsets.

You can comment on the ticket: #22916

Thanks, Pascale

[pgaudet]

• GO:0071835 mating pheromone secretion involved in regulation of conjugation > change label to 'mating pheromone secretion involved in regulation of conjugation with cellular fusion'

[pgaudet]

• GO:0071832 peptide pheromone export involved in regulation of conjugation -> 0 annotations; merge into GO:0071835 mating pheromone secretion involved in regulation of conjugation with cellular fusion
• GO:0071833 peptide pheromone export involved in positive regulation of conjugation -> 0 annotations; merge into GO:0071631 mating pheromone secretion involved in positive regulation of conjugation with cellular fusion

[pgaudet]

In fact there were mappings to conjugation:

• goslim_aspergillus -> change mapping to GO:0000747 conjugation with cellular fusion
• goslim_yeast -> change mapping to GO:0000747 conjugation with cellular fusion
• goslim_candida -> change mapping to GO:0000747 conjugation with cellular fusion
• goslim_pir -> change mapping to GO:0000747 conjugation with cellular fusion (fungal)
  AND GO:0009291 unidirectional conjugation (bacterial)

@marekskrzypek @srengel @nataled let me know if you want to do something different

[pgaudet]

@Antonialock There is a KW mapping to conjugation, KW-0184

I dont think this can be remapped, as the KW describes both yeast and bacterial conjugation.

[Antonialock]

@pgaudet I removed the mapping and suggested the KW is used in a rule instead.

[pgaudet]

Further changes during discussion in multiorg group
@dsiegele @mgiglio99 @genegodbold @nsuvarnaiari

[pgaudet]

add synonym: "bacterial conjugation" RELATED

[pgaudet]

GO:0000762 pheromone-induced unidirectional conjugation
Change def:
-def: "Unidirectional transfer of genetic information in response to a pheromone." [GOC:elh, PMID:17360276, PMID:27021562, PMID:31191478]
+def: "Unidirectional transfer of genetic information triggered by to a pheromone signal.