This issue is to make the FBcv terms for 'gene product engineering' type tools better arranged in the tree and more complete.
current tree:
experimental tool descriptor
RNA engineering tool
RNA-guided ribonuclease
gene product cleavage tag
protein cleavage tag
small molecule-regulated protein cleavage tag
new proposed tree:
experimental tool descriptor
gene product engineering tool
RNA engineering tool
RNA-guided ribonuclease
protease
gene product cleavage tag
protein cleavage tag
small molecule-regulated protein cleavage tag
protease target site
(note, I am not proposing to make a 'protein engineering tool' at the same level as 'RNA engineering tool' as 'protein engineering' in the literature has a different meaning from the intended use here (in the literature its used for the rational design and directed evolution of proteins in vitro with the intent of getting new properties/functions), but here the 'engineering' is used in the sense that the tool is expected to change the gene product in a defined manner (e.g. by cutting at a specific protease target site) so that it can be predicted what the sequence of the changed gene product will be.)
1. new parent term
[Term]
id: FBcv:NEW
name: gene product engineering tool
namespace: experimental_tool_descriptor
def: "Sequence that forms all or part of a transgenic locus or modified endogenous locus and which can be used to modify a gene product of interest in a defined manner." [FBC:GM]
is_a: FBcv:0005001 ! experimental tool descriptor
2. change of immediate parent for two existing terms
(The GO term corresponding to protease is 'peptidase activity' (GO:0008233) - it has the exact synonym 'protease activity' and the definition "Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. [ GOC : jl https://www.worldcat.org/search?q=bn%3A0815332181 ] " so kind of used the same phrasing in the definition. I don't know whether the GO term can be referred to as the source of the FBcv term definition in place of the [FBC:GM]
[Term]
id: FBcv:NEW
name: protease target site
namespace: experimental_tool_descriptor
def: "A recognition site for a protease, an enzyme that catalyzes hydrolysis of a peptide bond." [FBC:GM]
is_a: FBcv:0005057 ! protein cleavage tag
This issue is to make the FBcv terms for 'gene product engineering' type tools better arranged in the tree and more complete.
current tree:
new proposed tree:
(note, I am not proposing to make a 'protein engineering tool' at the same level as 'RNA engineering tool' as 'protein engineering' in the literature has a different meaning from the intended use here (in the literature its used for the rational design and directed evolution of proteins in vitro with the intent of getting new properties/functions), but here the 'engineering' is used in the sense that the tool is expected to change the gene product in a defined manner (e.g. by cutting at a specific protease target site) so that it can be predicted what the sequence of the changed gene product will be.)
1. new parent term
[Term] id: FBcv:NEW name: gene product engineering tool namespace: experimental_tool_descriptor def: "Sequence that forms all or part of a transgenic locus or modified endogenous locus and which can be used to modify a gene product of interest in a defined manner." [FBC:GM] is_a: FBcv:0005001 ! experimental tool descriptor
2. change of immediate parent for two existing terms
[Term] id: FBcv:0007045 name: RNA engineering tool
change: is_a: FBcv:0005001 ! experimental tool descriptor to: is_a: FBcv:NEW ! gene product engineering tool
id: FBcv:0005056 name: gene product cleavage tag
change: is_a: FBcv:0005001 ! experimental tool descriptor to: is_a: FBcv:NEW ! gene product engineering tool
3. new terms for protease and protease target site.
[Term] id: FBcv:NEW name: protease namespace: experimental_tool_descriptor def: "An enzyme that catalyzes hydrolysis of a peptide bond." [FBC:GM] subset: common_tool_use synonym: "peptidase" EXACT [FBC:GM] is_a: FBcv:NEW ! gene product engineering tool
(The GO term corresponding to protease is 'peptidase activity' (GO:0008233) - it has the exact synonym 'protease activity' and the definition "Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. [ GOC : jl https://www.worldcat.org/search?q=bn%3A0815332181 ] " so kind of used the same phrasing in the definition. I don't know whether the GO term can be referred to as the source of the FBcv term definition in place of the [FBC:GM]
[Term] id: FBcv:NEW name: protease target site namespace: experimental_tool_descriptor def: "A recognition site for a protease, an enzyme that catalyzes hydrolysis of a peptide bond." [FBC:GM] is_a: FBcv:0005057 ! protein cleavage tag