The 'existing gene product degradation tag' (FBcv:0005042) term is for tools that are used as a tag i.e. the tool is fused ('tagged') to some other gene product of interest, and results in the degradation of that tagged gene product (this is in the definition of FBcv:0005042 which says "which results in the tagged gene product being targeted for degradation").
However, there are degradation tools that do not act as tags, instead they cause degradation of another gene product. An example is deGradFP ) - which binds to GFP-tagged proteins (because of the VHH(GFP4) sequence in the deGradFP) and results in degradation of the GFP-tagged protein.
The changes in this ticket address this issue.
1. A new 'parent' term:
id: FBcv:NEW
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]
is_a: FBcv:0005001 ! experimental tool descriptor
This new term is so can cope with cases like deGradFP where the degradation tool is not a tag fused directly to the gene being targeted for degradation - that is why the definition is vague and says 'which can be used to target a gene product for degradation'
2. Change of name for 'existing gene product degradation tag' (FBcv:0005042) term and its children (so that they are more easily distinguishable from the above new term, and shorter, so better on the web)
a. changes for FBcv:0005042
id: FBcv:0005042
name: gene product degradation tag
change to:
name: degradation tag
The 'existing gene product degradation tag' (FBcv:0005042) term is for tools that are used as a tag i.e. the tool is fused ('tagged') to some other gene product of interest, and results in the degradation of that tagged gene product (this is in the definition of FBcv:0005042 which says "which results in the tagged gene product being targeted for degradation").
However, there are degradation tools that do not act as tags, instead they cause degradation of another gene product. An example is deGradFP ) - which binds to GFP-tagged proteins (because of the VHH(GFP4) sequence in the deGradFP) and results in degradation of the GFP-tagged protein.
The changes in this ticket address this issue.
1. A new 'parent' term:
id: FBcv:NEW 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] is_a: FBcv:0005001 ! experimental tool descriptor
This new term is so can cope with cases like deGradFP where the degradation tool is not a tag fused directly to the gene being targeted for degradation - that is why the definition is vague and says 'which can be used to target a gene product for degradation'
2. Change of name for 'existing gene product degradation tag' (FBcv:0005042) term and its children (so that they are more easily distinguishable from the above new term, and shorter, so better on the web)
a. changes for FBcv:0005042
id: FBcv:0005042 name: gene product degradation tag change to: name: degradation tag
is_a: FBcv:0005001 ! experimental tool descriptor change to: is_a: FBcv:NEW ! gene product degradation tool
b. changes for child terms under FBcv:0005042
id: FBcv:0009016 name: conditional gene product degradation tag change to: name: conditional degradation tag
id: FBcv:0005043 name: cell cycle-regulated gene product degradation tag change to: name: cell cycle-regulated degradation tag
id: FBcv:0007047 name: light-regulated gene product degradation tag change to: name: light-regulated degradation tag
id: FBcv:0005083 name: small molecule-regulated gene product degradation tag change to: name: small molecule-regulated degradation tag
am also attaching a ppt file that shows change to tree in picture form degradation_tool_v2.pptx