Merge pull request #22953 from geneontology/issue-22916-2

changes to genetic transfer fixes #22916 fixes #22952

src/ontology/go-edit.obo

@@ -5543,7 +5543,7 @@ relationship: part_of GO:0000748 ! conjugation with mutual genetic exchange
 id: GO:0000762
 name: pheromone-induced unidirectional conjugation
 namespace: biological_process
-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." [GOC:elh, PMID:17360276, PMID:27021562, PMID:31191478]
 is_a: GO:0009291 ! unidirectional conjugation
 
 [Term]
@@ -88645,37 +88645,42 @@ intersection_of: part_of GO:0009294 ! DNA-mediated transformation
 id: GO:0009291
 name: unidirectional conjugation
 namespace: biological_process
-def: "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." [Wikipedia:Bacterial_conjugation]
+def: "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." [Wikipedia:Bacterial_conjugation]
 comment: Unidirectional conjugation is not a type of not sexual reproduction, since no exchange of gamete occurs and no generation of a new organism: instead an existing organism is transformed.
 subset: goslim_pir
+synonym: "bacterial conjugation" RELATED []
 xref: Wikipedia:Bacterial_conjugation
-is_a: GO:0009292 ! genetic transfer
+is_a: GO:0009292 ! horizontal gene transfer
 
 [Term]
 id: GO:0009292
-name: genetic transfer
+name: horizontal gene transfer
 namespace: biological_process
-def: "In the absence of a sexual life cycle, the process involved in the introduction of genetic information to create a genetically different individual." [GOC:clt]
-comment: GO:0009292 should not be used for annotation of phage lysogeny (integration of the bacteriophage nucleic acid into the host bacterium's genome).
+def: "The introduction of genetic information into a cell to create a genetically different individual, without production of new individuals." [PMID:26184597]
 subset: goslim_pir
 synonym: "genetic exchange" BROAD []
+synonym: "genetic transfer" EXACT []
+synonym: "lateral gene transfer" EXACT []
 is_a: GO:0009987 ! cellular process
+property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22952 xsd:anyURI
 
 [Term]
 id: GO:0009293
 name: transduction
 namespace: biological_process
-def: "A genetic transfer process in which genetic material is introduced into a bacterium by a bacteriophage or between bacterial or yeast cells mediated by a phage vector." [PMID:33597173]
+def: "A type of horizontal gene transfer in which genetic material is introduced into a cell mediated by a virus." [PMID:18265289, PMID:33597173]
+comment: This process occurs both in prokaryotes and in eukaryotes.
 xref: Wikipedia:Transduction_(genetics)
-is_a: GO:0009292 ! genetic transfer
+is_a: GO:0009292 ! horizontal gene transfer
+property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22952 xsd:anyURI
 
 [Term]
 id: GO:0009294
 name: DNA-mediated transformation
 namespace: biological_process
-def: "The direct uptake and incorporation of exogenous genetic material (DNA or RNA) into a cell from its surroundings through the cell membrane." [PMID:12706993, PMID:24509783, PMID:27826682]
+def: "The direct uptake and incorporation of exogenous genetic material (DNA or RNA) into a cell from its surroundings through the cell envelope." [PMID:12706993, PMID:24509783, PMID:27826682]
 synonym: "DNA mediated transformation" EXACT []
-is_a: GO:0009292 ! genetic transfer
+is_a: GO:0009292 ! horizontal gene transfer
 
 [Term]
 id: GO:0009295