Merge pull request #228 from FlyBase/release_2024-04-25

release files 2024-04-25

flybase_controlled_vocabulary.obo

@@ -1,7 +1,7 @@
 
 format-version: 1.2
-data-version: 2024-02-23
-date: 23:02:2024 09:20
+data-version: 2024-04-25
+date: 25:04:2024 15:03
 subsetdef: camcur "camcur"
 subsetdef: common_tool_use "Terms to summarize typical use of a gene from one organism that is introduced into another organism primarily for use an experimental tool, rather than to study the function of the gene"
 subsetdef: do_not_annotate "Term not to be used for direct annotation"
@@ -3430,77 +3430,91 @@ 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
@@ -8667,17 +8681,19 @@ is_a: FBcv:0005039 ! light-regulated activity regulation tag
 
 [Term]
 id: FBcv:0005042
-name: gene product degradation tag
+name: degradation tag
 namespace: experimental_tool_descriptor
 def: "Sequence that forms part of the gene product encoded by a transgenic locus or modified endogenous locus and which results in the tagged gene product being targeted for degradation." [FBC:GM]
-is_a: FBcv:0005001 ! experimental tool descriptor
+synonym: "gene product degradation tag" EXACT []
+is_a: FBcv:0007068 ! gene product degradation tool
 
 [Term]
 id: FBcv:0005043
-name: cell cycle-regulated gene product degradation tag
+name: cell cycle-regulated degradation tag
 namespace: experimental_tool_descriptor
 def: "Sequence that forms part of the gene product encoded by a transgenic locus or modified endogenous locus and which results in the tagged gene product being targeted for degradation, where this property can be regulated by the cell cycle." [FBC:GM]
-is_a: FBcv:0009016 ! conditional gene product degradation tag
+synonym: "cell cycle-regulated gene product degradation tag" EXACT []
+is_a: FBcv:0009016 ! conditional degradation tag
 
 [Term]
 id: FBcv:0005044
@@ -8969,11 +8985,12 @@ is_a: FBcv:0005081 ! engineered regulatory region
 
 [Term]
 id: FBcv:0005083
-name: small molecule-regulated gene product degradation tag
+name: small molecule-regulated degradation tag
 namespace: experimental_tool_descriptor
 def: "Sequence that forms part of the gene product encoded by a transgenic locus or modified endogenous locus and which results in the tagged gene product being targeted for degradation, where this property can be regulated by a small molecule." [FBC:GM]
 synonym: "small molecule-dependent gene product degradation tag" EXACT []
-is_a: FBcv:0009016 ! conditional gene product degradation tag
+synonym: "small molecule-regulated gene product degradation tag" EXACT []
+is_a: FBcv:0009016 ! conditional degradation tag
 
 [Term]
 id: FBcv:0006000
@@ -9286,6 +9303,13 @@ namespace: experimental_tool_descriptor
 def: "Sequence that has a property that allows specific binding to another macromolecule, where this property can be regulated by binding to a small molecule, such as an ion or ligand." [FBC:GM]
 is_a: FBcv:0007030 ! conditional specific binding tool
 
+[Term]
+id: FBcv:0007034
+name: signaling pathway group
+namespace: group_descriptor
+def: "Genes whose products act in a specified signal transduction pathway." [FBC:SM]
+is_a: FBcv:0003017 ! pathway group
+
 [Term]
 id: FBcv:0007035
 name: meganuclease
@@ -9384,10 +9408,11 @@ is_a: FBcv:0007045 ! RNA engineering tool
 
 [Term]
 id: FBcv:0007047
-name: light-regulated gene product degradation tag
+name: light-regulated degradation tag
 namespace: experimental_tool_descriptor
 def: "Sequence that forms part of the gene product encoded by a transgenic locus or modified endogenous locus and which results in the tagged gene product being targeted for degradation, where this property can be regulated by irradiation with a pulse of light." [FBC:GM]
-is_a: FBcv:0009016 ! conditional gene product degradation tag
+synonym: "light-regulated gene product degradation tag" EXACT []
+is_a: FBcv:0009016 ! conditional degradation tag
 
 [Term]
 id: FBcv:0007048
@@ -9522,6 +9547,36 @@ namespace: experimental_tool_descriptor
 def: "Transactivator ('driver') that forms part of a binary expression system and whose activity is regulated by irradiation with a pulse of light. A binary expression system requires a transactivator ('driver') that binds to a specific DNA sequence ('regulatory region' or 'effector'). A driver encoded by one transgenic locus or modified endogenous locus is used to drive expression of a downstream 'responder' or 'reporter' encoded by another transgenic locus or modified endogenous locus, by fusing the regulatory region sequence to which the driver binds upstream of the responder sequence. The temporal and spatial expression pattern of the responder thus depends on the regulatory elements used to drive expression of the driver. Use of a light-regulated driver permits further refinement of this expression pattern." [FBC:GM]
 is_a: FBcv:0005064 ! binary expression system - conditional driver
 
+[Term]
+id: FBcv:0007065
+name: metabolic pathway group
+namespace: group_descriptor
+def: "Genes whose products act in a specified metabolic pathway." [FBC:SM]
+is_a: FBcv:0003017 ! pathway group
+
+[Term]
+id: FBcv:0007066
+name: chemical labeling reporter
+namespace: experimental_tool_descriptor
+def: "Sequence that forms all or part of the protein product encoded by a transgenic locus or modified endogenous locus and that encodes an enzyme whose activity results in covalent tagging of the protein product with a small molecule whose properties (typically fluorescence) can be used to detect the presence of that protein product." [FBC:GM]
+subset: common_tool_use
+is_a: FBcv:0005005 ! reporter enzyme
+
+[Term]
+id: FBcv:0007067
+name: bioluminescence reporter
+namespace: experimental_tool_descriptor
+def: "Sequence that forms all or part of the protein product encoded by a transgenic locus or modified endogenous locus and that encodes an enzyme whose activity results in bioluminescence, which can be used to detect the presence of that protein product." [FBC:GM]
+is_a: FBcv:0005005 ! reporter enzyme
+
+[Term]
+id: FBcv:0007068
+name: gene product degradation tool
+namespace: experimental_tool_descriptor
+def: "Sequence that forms all or part of the gene product encoded by a transgenic locus or modified endogenous locus and which can be used to target a gene product for degradation in a defined manner." [FBC:GM]
+comment: Degradation tool may or may not be fused directly to the degradation target.
+is_a: FBcv:0005001 ! experimental tool descriptor
+
 [Term]
 id: FBcv:0007500
 name: abnormal anesthesia-resistant memory
@@ -10101,10 +10156,11 @@ is_a: FBcv:0003164 ! biosample method
 
 [Term]
 id: FBcv:0009016
-name: conditional gene product degradation tag
+name: conditional degradation tag
 namespace: experimental_tool_descriptor
 def: "Sequence that forms part of the gene product encoded by a transgenic locus or modified endogenous locus and which results in the tagged gene product being targeted for degradation, where this property can be regulated in response to a particular stimulus." [FBC:GM]
-is_a: FBcv:0005042 ! gene product degradation tag
+synonym: "conditional gene product degradation tag" EXACT []
+is_a: FBcv:0005042 ! degradation tag
 
 [Term]
 id: FBcv:0009017