Merge pull request #223 from FlyBase/construct-obsoletions

Obsolete in vitro construct subclasses

src/ontology/fbcv-edit.obo

@@ -2493,77 +2493,91 @@ is_a: FBcv:0000452 ! origin of mutation
 
 [Term]
 id: FBcv:0000456
-name: in vitro construct - regulatory fusion
+name: obsolete in vitro construct - regulatory fusion
 namespace: origin_of_mutation
 def: "Sequence change introduced by using an in vitro construct that contains a fusion of the regulatory region of one gene on to the coding region of another. Examples in FlyBase include heat shock constructs, FRT flip out constructs and reporter genes." [FBC:DOS]
-comment: Notes on usage: Use this, rather than 'in vitro construct - deletion', for families of promoter deletions. Thus, a family of deletions of eve promoters driving Ecol\\\\lacZ will have regulatory fusion, but not deletion, as their mutagen.
+comment: This term has been obsoleted because the nature of an in vitro construct (e.g. 'regulatory fusion') is now captured in FlyBase using SO terms instead and the parent term (in vitro construct) is used to capture the origin_of_mutation information.
 synonym: "change induced by an in vitro construct - regulatory fusion" EXACT []
 synonym: "in vitro construct | regulatory fusion" RELATED []
-is_a: FBcv:0000455 ! in vitro construct
+is_obsolete: true
+consider: FBcv:0000455
 
 [Term]
 id: FBcv:0000457
-name: in vitro construct - coding region fusion
+name: obsolete in vitro construct - coding region fusion
 namespace: origin_of_mutation
 def: "Sequence change introduced by using an in vitro construct that contains a in-frame fusion of the open reading frames from two or more genes. In FlyBase, the resulting genes may be classified as fusion genes or tagged genes." [FBC:DOS]
+comment: This term has been obsoleted because the nature of an in vitro construct (e.g. 'coding region fusion') is now captured in FlyBase using SO terms instead and the parent term (in vitro construct) is used to capture the origin_of_mutation information.
 synonym: "change induced by an in vitro construct - coding region fusion" EXACT []
 synonym: "in vitro construct | coding region fusion" RELATED []
-is_a: FBcv:0000455 ! in vitro construct
+is_obsolete: true
+consider: FBcv:0000455
 
 [Term]
 id: FBcv:0000458
-name: in vitro construct - site directed mutagenesis
+name: obsolete in vitro construct - site directed mutagenesis
 namespace: origin_of_mutation
 def: "Mutation induced by an in vitro construct that uses site directed mutagenesis to target a particular region of the gene." [FBC:DOS]
+comment: This term has been obsoleted because the nature of an in vitro construct (e.g. 'site directed mutagenesis') is now captured in FlyBase using SO terms instead and the parent term (in vitro construct) is used to capture the origin_of_mutation information.
 synonym: "in vitro construct | site directed mutagenesis" RELATED []
 synonym: "mutation induced by an in vitro construct - site directed mutagenesis" EXACT []
-is_a: FBcv:0000455 ! in vitro construct
+is_obsolete: true
+consider: FBcv:0000455
 
 [Term]
 id: FBcv:0000459
-name: in vitro construct - deletion
+name: obsolete in vitro construct - deletion
 namespace: origin_of_mutation
 def: "Sequence change introduced by an in vitro construct generated by internal deletion of some genomic sequence or cDNA." [FBC:DOS]
+comment: This term has been obsoleted because the nature of an in vitro construct (e.g. 'deletion') is now captured in FlyBase using SO terms instead and the parent term (in vitro construct) is used to capture the origin_of_mutation information.
 synonym: "change induced by an in vitro construct - deletion" EXACT []
 synonym: "in vitro construct | deletion" RELATED []
-is_a: FBcv:0000455 ! in vitro construct
+is_obsolete: true
+consider: FBcv:0000455
 
 [Term]
 id: FBcv:0000460
-name: in vitro construct - genomic fragment
+name: obsolete in vitro construct - genomic fragment
 namespace: origin_of_mutation
 def: "Sequence change introduced by an in vitro construct containing a genomic fragment that partially or fully rescues loss of function mutations or deletions of the gene whose sequence it carries." [FBC:DOS]
-comment: Notes on usage: 1. This term is applicable whether or not rescue using the construct is complete. 2. When a smaller rescue fragment is derived from a larger, by deletion of one or both ends, the mutagen shall be 'in vitro construct | deletion', with the larger being stated as the progenitor allele.
+comment: This term has been obsoleted because the nature of an in vitro construct (e.g. 'genomic fragment') is now captured in FlyBase using SO terms instead and the parent term (in vitro construct) is used to capture the origin_of_mutation information.
 synonym: "change induced by an in vitro construct - genomic fragment" EXACT []
 synonym: "in vitro construct | genomic fragment" RELATED []
-is_a: FBcv:0000455 ! in vitro construct
+is_obsolete: true
+consider: FBcv:0000455
 
 [Term]
 id: FBcv:0000461
-name: in vitro construct - minigene
+name: obsolete in vitro construct - minigene
 namespace: origin_of_mutation
 def: "Sequence change introduced by an in vitro construct that contains the wild-type open reading frame of a gene (without introns), the expression of which is controlled by a wild-type promoter of the same gene. Such constructs are often generated by fusing a cDNA to a genomic region containing promoter sequences, or more rarely by deletion of introns and other non-essential sequences from a genomic region, leaving a wild type coding region and promoter intact." [FBC:DOS]
+comment: This term has been obsoleted because the nature of an in vitro construct (e.g. 'minigene') is now captured in FlyBase using SO terms instead and the parent term (in vitro construct) is used to capture the origin_of_mutation information.
 synonym: "change induced by an in vitro construct - minigene" EXACT []
 synonym: "in vitro construct | minigene" RELATED []
-is_a: FBcv:0000455 ! in vitro construct
+is_obsolete: true
+consider: FBcv:0000455
 
 [Term]
 id: FBcv:0000462
-name: in vitro construct - amino acid replacement
+name: obsolete in vitro construct - amino acid replacement
 namespace: origin_of_mutation
 def: "Sequence change introduced by an in vitro construct that uses site directed mutagenesis to target a particular region of the gene resulting in a change to the change to the amino acids sequence encodes.." [FBC:DOS]
+comment: This term has been obsoleted because the nature of an in vitro construct (e.g. 'amino acid replacement') is now captured in FlyBase using SO terms instead and the parent term (in vitro construct) is used to capture the origin_of_mutation information.
 synonym: "change induced by an in vitro construct - amino acid replacement" EXACT []
 synonym: "in vitro construct | amino acid replacement" RELATED []
-is_a: FBcv:0000458 ! in vitro construct - site directed mutagenesis
+is_obsolete: true
+consider: FBcv:0000455
 
 [Term]
 id: FBcv:0000463
-name: in vitro construct - RNAi
+name: obsolete in vitro construct - RNAi
 namespace: origin_of_mutation
 def: "Sequence change introduced by an in vitro construct designed to generate dsRNA for RNA interference (RNAi) experiments." [FBC:DOS]
+comment: This term has been obsoleted because the nature of an in vitro construct (e.g. 'RNAi') is now captured in FlyBase using SO terms instead and the parent term (in vitro construct) is used to capture the origin_of_mutation information.
 synonym: "change induced by an in vitro construct - RNAi" EXACT []
 synonym: "in vitro construct | RNAi" RELATED []
-is_a: FBcv:0000455 ! in vitro construct
+is_obsolete: true
+consider: FBcv:0000455
 
 [Term]
 id: FBcv:0000464