From 4f29154c95ea557ca86518986b538309df15945f Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Mon, 24 Jun 2024 11:45:18 +0100 Subject: [PATCH 1/7] Add conditional RNA-guided nuclease terms. Add `conditional RNA-guided nuclease` and `small molecule-regulated RNA-guided nuclease` experimental tools. closes #237 --- src/ontology/fbcv-edit.obo | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/src/ontology/fbcv-edit.obo b/src/ontology/fbcv-edit.obo index cb91afd..f0d7490 100644 --- a/src/ontology/fbcv-edit.obo +++ b/src/ontology/fbcv-edit.obo @@ -9253,6 +9253,24 @@ is_a: FBcv:0009036 ! conditional protease target site property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 property_value: http://purl.org/dc/terms/date "2024-05-29T10:13:50Z" xsd:dateTime +[Term] +id: FBcv:0009038 +name: conditional RNA-guided nuclease +namespace: experimental_tool_descriptor +def: "An enzyme that catalyzes hydrolysis of DNA in a site-specific manner, where the specificity is determined by a guide RNA that contains sequence complementary to the DNA sequence of interest (rather than being an inherent property of the nuclease itself) and where the nuclease activity can be regulated in response to a particular stimulus." [FBC:GM] +is_a: FBcv:0005078 ! RNA-guided nuclease +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2024-06-24T10:42:33Z" xsd:dateTime + +[Term] +id: FBcv:0009039 +name: small molecule-regulated RNA-guided nuclease +namespace: experimental_tool_descriptor +def: "An enzyme that catalyzes hydrolysis of DNA in a site-specific manner, where the specificity is determined by a guide RNA that contains sequence complementary to the DNA sequence of interest (rather than being an inherent property of the nuclease itself) and where the nuclease activity can be regulated by binding to a small molecule, such as an ion or ligand." [FBC:GM] +is_a: FBcv:0009038 ! conditional RNA-guided nuclease +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2024-06-24T10:44:12Z" xsd:dateTime + [Term] id: FBcv:0010000 name: obsolete living stock From acd147bc455fcc59f24bbfba9c66db2cdd2ec7e3 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Mon, 24 Jun 2024 12:01:13 +0100 Subject: [PATCH 2/7] Add protein splicing tag terms. Add the following new experimental tool descriptors (under `gene product engineering tool`): * protein splicing tag * conditional protein splicing tag * small molecule-regulated protein splicing tag closes #238 --- src/ontology/fbcv-edit.obo | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/src/ontology/fbcv-edit.obo b/src/ontology/fbcv-edit.obo index f0d7490..ead4fb6 100644 --- a/src/ontology/fbcv-edit.obo +++ b/src/ontology/fbcv-edit.obo @@ -9271,6 +9271,33 @@ is_a: FBcv:0009038 ! conditional RNA-guided nuclease property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 property_value: http://purl.org/dc/terms/date "2024-06-24T10:44:12Z" xsd:dateTime +[Term] +id: FBcv:0009040 +name: protein splicing tag +namespace: experimental_tool_descriptor +def: "Sequence that forms part of the protein product encoded by a transgenic locus or modified endogenous locus and which results in the tagged gene product undergoing protein splicing." [FBC:GM] +is_a: FBcv:0009022 ! gene product engineering tool +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2024-06-24T10:47:32Z" xsd:dateTime + +[Term] +id: FBcv:0009041 +name: conditional protein splicing tag +namespace: experimental_tool_descriptor +def: "Sequence that forms part of the protein product encoded by a transgenic locus or modified endogenous locus and which results in the tagged gene product undergoing protein splicing, where this process can be regulated in response to a particular stimulus." [FBC:GM] +is_a: FBcv:0009040 ! protein splicing tag +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2024-06-24T10:48:27Z" xsd:dateTime + +[Term] +id: FBcv:0009042 +name: small molecule-regulated protein splicing tag +namespace: experimental_tool_descriptor +def: "Sequence that forms part of the protein product encoded by a transgenic locus or modified endogenous locus and which results in the tagged gene product undergoing protein splicing, where this process can be regulated by binding to a small molecule, such as an ion or ligand." [FBC:GM] +is_a: FBcv:0009041 ! conditional protein splicing tag +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2024-06-24T10:49:38Z" xsd:dateTime + [Term] id: FBcv:0010000 name: obsolete living stock From df3096d0017c25b7b93509b2809c3df7c22b51f1 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Mon, 24 Jun 2024 12:09:06 +0100 Subject: [PATCH 3/7] Add 'cell death inhibition tool'. Add new experimental tool descriptor `cell death inhibition tool`. Also add new generic parent `cell viability regulation tool`, and re-classify the existing `cell ablation tool` under it. closes #239 --- src/ontology/fbcv-edit.obo | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/src/ontology/fbcv-edit.obo b/src/ontology/fbcv-edit.obo index ead4fb6..928de74 100644 --- a/src/ontology/fbcv-edit.obo +++ b/src/ontology/fbcv-edit.obo @@ -8362,7 +8362,7 @@ name: cell ablation 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 that confers a specific property used to ablate a specific cell or anatomical structure." [FBC:GM] subset: common_tool_use -is_a: FBcv:0005001 ! experimental tool descriptor +is_a: FBcv:0009043 ! cell viability regulation tool property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-1373-1705 property_value: http://purl.org/dc/terms/date "2019-06-25T10:53:21Z" xsd:dateTime @@ -9298,6 +9298,24 @@ is_a: FBcv:0009041 ! conditional protein splicing tag property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 property_value: http://purl.org/dc/terms/date "2024-06-24T10:49:38Z" xsd:dateTime +[Term] +id: FBcv:0009043 +name: cell viability regulation 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 that confers a specific property used to regulate the viability of a specific cell or anatomical structure." [FBC:GM] +is_a: FBcv:0005001 ! experimental tool descriptor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2024-06-24T11:04:56Z" xsd:dateTime + +[Term] +id: FBcv:0009044 +name: cell death inhibition 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 that confers a specific property used to inhibit cell death in a specific cell or anatomical structure." [FBC:GM] +is_a: FBcv:0009043 ! cell viability regulation tool +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2024-06-24T11:06:20Z" xsd:dateTime + [Term] id: FBcv:0010000 name: obsolete living stock From 8077af8bd9c7f0ae97a862e465c214bf0e288bd2 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Mon, 24 Jun 2024 12:17:50 +0100 Subject: [PATCH 4/7] Add grouping terms under 'split system component'. Add grouping terms under 'split system component' to mimic the hierarchy of terms used overall by experimental tool descriptors. Specifically, we add: * split genome engineering tool * split gene product engineering tool * split gene product detection tool * split protein detection tool * split cell viability regulation tool closes #240 --- src/ontology/fbcv-edit.obo | 45 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/src/ontology/fbcv-edit.obo b/src/ontology/fbcv-edit.obo index 928de74..e361255 100644 --- a/src/ontology/fbcv-edit.obo +++ b/src/ontology/fbcv-edit.obo @@ -9316,6 +9316,51 @@ is_a: FBcv:0009043 ! cell viability regulation tool property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 property_value: http://purl.org/dc/terms/date "2024-06-24T11:06:20Z" xsd:dateTime +[Term] +id: FBcv:0009045 +name: split genome engineering tool +namespace: experimental_tool_descriptor +def: "Non-functional fragment of a genome engineering tool. A functional genome engineering tool can be reconstituted when complementary split genome engineering tool fragments are brought together in vivo, for example by fusing the fragments to peptides that physically interact." [FBC:GM] +is_a: FBcv:0005051 ! split system component +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2024-06-24T11:11:57Z" xsd:dateTime + +[Term] +id: FBcv:0009046 +name: split gene product engineering tool +namespace: experimental_tool_descriptor +def: "Non-functional fragment of a gene product engineering tool. A functional gene product engineering tool can be reconstituted when complementary split gene product engineering tool fragments are brought together in vivo, for example by fusing the fragments to peptides that physically interact." [FBC:GM] +is_a: FBcv:0005051 ! split system component +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2024-06-24T11:13:39Z" xsd:dateTime + +[Term] +id: FBcv:0009047 +name: split gene product detection tool +namespace: experimental_tool_descriptor +def: "Non-functional fragment of a gene product detection tool. A functional gene product detection tool can be reconstituted when complementary split gene product detection tool fragments are brought together in vivo, for example by fusing the fragments to peptides that physically interact." [FBC:GM] +is_a: FBcv:0005051 ! split system component +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2024-06-24T11:14:32Z" xsd:dateTime + +[Term] +id: FBcv:0009048 +name: split protein detection tool +namespace: experimental_tool_descriptor +def: "Non-functional fragment of a protein detection tool. A functional protein detection tool can be reconstituted when complementary split protein detection tool fragments are brought together in vivo, for example by fusing the fragments to peptides that physically interact." [FBC:GM] +is_a: FBcv:0009047 ! split gene product detection tool +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2024-06-24T11:15:29Z" xsd:dateTime + +[Term] +id: FBcv:0009049 +name: split cell viability regulation tool +namespace: experimental_tool_descriptor +def: "Non-functional fragment of a cell viability regulation tool. A functional cell viability regulation tool can be reconstituted when complementary split cell viability regulation tool fragments are brought together in vivo, for example by fusing the fragments to peptides that physically interact." [FBC:GM] +is_a: FBcv:0005051 ! split system component +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2024-06-24T11:16:29Z" xsd:dateTime + [Term] id: FBcv:0010000 name: obsolete living stock From 6db6b2f9aeb8a0ca5a81d2ebcad3fd9da56b17b2 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Mon, 24 Jun 2024 12:24:21 +0100 Subject: [PATCH 5/7] Re-classify existing split system component terms. Now that we have new grouping terms under `split system component`, we re-classify pre-existing terms for split tools under the newly created grouping terms. closes #243 --- src/ontology/fbcv-edit.obo | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/ontology/fbcv-edit.obo b/src/ontology/fbcv-edit.obo index e361255..10c3b89 100644 --- a/src/ontology/fbcv-edit.obo +++ b/src/ontology/fbcv-edit.obo @@ -7929,7 +7929,7 @@ id: FBcv:0005052 name: split fluorescent protein namespace: experimental_tool_descriptor def: "Non-fluorescent fragment of a fluorescent protein. A functional fluorophore can be reconstituted if a split fluorescent protein fragment is expressed with a complementary split fluorescent protein fragment and the fragments are brought together in vivo, permitting the study of biological interactions. Protein-protein interactions can be studied using the bimolecular fluorescence complementation (BiFC) technique, where a fluorescent protein is reconstituted if the two complementary split fluorescent protein fragments are fused to interacting proteins or protein domains that bring the split halves together into the same macromolecular complex. Associations between closely apposed cells can be studied if the two complementary split fluorescent protein fragments are tethered to the surface of these cells, for example to study connectivity in the nervous system using the GFP Reconstitution Across Synaptic Partners (GRASP) technique." [FBC:GM, PMID:11983170, PMID:18255029] -is_a: FBcv:0005051 ! split system component +is_a: FBcv:0009048 ! split protein detection tool property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-0027-0858 property_value: http://purl.org/dc/terms/date "2017-06-28T11:41:27Z" xsd:dateTime @@ -7938,7 +7938,7 @@ id: FBcv:0005053 name: split reporter enzyme 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 a catalytically inactive fragment of an enzyme whose activity can be used to detect the presence of that protein product when complementary split reporter enzyme fragments are brought together in vivo. Fragments may be brought together when fused to peptides that physically interact, permitting the study of protein-protein interactions." [FBC:GM, http://orcid.org/0000-0002-1373-1705, PMID:9237989] -is_a: FBcv:0005051 ! split system component +is_a: FBcv:0009048 ! split protein detection tool property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-0027-0858 property_value: http://purl.org/dc/terms/date "2017-06-28T11:41:27Z" xsd:dateTime @@ -8501,7 +8501,7 @@ id: FBcv:0007028 name: split recombinase namespace: experimental_tool_descriptor def: "Catalytically inactive fragment of a recombinase. A functional recombinase can be reconstituted when complementary split recombinase fragments are brought together in vivo, for example by fusing the fragments to peptides that physically interact." [FBC:GM] -is_a: FBcv:0005051 ! split system component +is_a: FBcv:0009045 ! split genome engineering tool property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-1373-1705 property_value: http://purl.org/dc/terms/date "2019-06-26T07:55:34Z" xsd:dateTime @@ -9195,7 +9195,7 @@ id: FBcv:0009031 name: split protease namespace: experimental_tool_descriptor def: "Catalytically inactive fragment of a protease. A functional protease can be reconstituted when complementary split protease fragments are brought together in vivo, for example by fusing the fragments to peptides that physically interact." [FBC:GM] -is_a: FBcv:0005051 ! split system component +is_a: FBcv:0009046 ! split gene product engineering tool property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 property_value: http://purl.org/dc/terms/date "2024-05-03T13:12:34Z" xsd:dateTime @@ -9231,7 +9231,7 @@ id: FBcv:0009035 name: split cell ablation tool namespace: experimental_tool_descriptor def: "Non-functional fragment of a cell ablation tool. A functional cell ablation tool can be reconstituted when complementary split cell ablation tool fragments are brought together in vivo, for example by fusing the fragments to peptides that physically interact." [FBC:GM] -is_a: FBcv:0005051 ! split system component +is_a: FBcv:0009049 ! split cell viability regulation tool property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 property_value: http://purl.org/dc/terms/date "2024-05-29T10:09:01Z" xsd:dateTime From 9ad0ddb1e44f85e8a060a89c42ee59ebd481cd6e Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Mon, 24 Jun 2024 12:36:35 +0100 Subject: [PATCH 6/7] Add 'split RNA-guided nuclease' terms. Add `small molecule-regulated split RNA-guided nuclease` (will be needed to annotate RDX constructs in FBrf0245398). The term is inserted at the bottom of a hierarchy of split component terms that mimic similar terms for non-split experimental tools. closes #242 --- src/ontology/fbcv-edit.obo | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/src/ontology/fbcv-edit.obo b/src/ontology/fbcv-edit.obo index 10c3b89..e209ed2 100644 --- a/src/ontology/fbcv-edit.obo +++ b/src/ontology/fbcv-edit.obo @@ -9361,6 +9361,42 @@ is_a: FBcv:0005051 ! split system component property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 property_value: http://purl.org/dc/terms/date "2024-06-24T11:16:29Z" xsd:dateTime +[Term] +id: FBcv:0009050 +name: split nuclease +namespace: experimental_tool_descriptor +def: "Non-functional fragment of a nuclease. A functional nuclease can be reconstituted when complementary split nuclease fragments are brought together in vivo, for example by fusing the fragments to peptides that physically interact." [FBC:GM] +is_a: FBcv:0009045 ! split genome engineering tool +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2024-06-24T11:30:43Z" xsd:dateTime + +[Term] +id: FBcv:0009051 +name: split RNA-guided nuclease +namespace: experimental_tool_descriptor +def: "Non-functional fragment of an RNA-guided nuclease. A functional RNA-guided nuclease can be reconstituted when complementary split RNA-guided nuclease fragments are brought together in vivo, for example by fusing the fragments to peptides that physically interact." [FBC:GM] +is_a: FBcv:0009050 ! split nuclease +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2024-06-24T11:31:36Z" xsd:dateTime + +[Term] +id: FBcv:0009052 +name: conditional split RNA-guided nuclease +namespace: experimental_tool_descriptor +def: "Non-functional fragment of an RNA-guided nuclease that can be used to reconstitute a functional RNA-guided nuclease when brought together in vivo with a complementary split RNA-guided nuclease fragment, where the process that brings the complementary fragments together can be regulated in response to a particular stimulus." [FBC:GM] +is_a: FBcv:0009051 ! split RNA-guided nuclease +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2024-06-24T11:33:51Z" xsd:dateTime + +[Term] +id: FBcv:0009053 +name: small molecule-regulated split RNA-guided nuclease +namespace: experimental_tool_descriptor +def: "Non-functional fragment of an RNA-guided nuclease that can be used to reconstitute a functional RNA-guided nuclease when brought together in vivo with a complementary split RNA-guided nuclease fragment, where the process that brings the complementary fragments together can be regulated by binding to a small molecule, such as an ion or ligand." [FBC:GM] +is_a: FBcv:0009052 ! conditional split RNA-guided nuclease +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2024-06-24T11:35:10Z" xsd:dateTime + [Term] id: FBcv:0010000 name: obsolete living stock From c2185fa1ba3beedea847a613d8cffd207f000716 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Mon, 24 Jun 2024 12:46:38 +0100 Subject: [PATCH 7/7] Add 'split protein splicing tag'. Add new term `split protein splicing tag` (will be needed to annotate the CfaC and CfaN split inteins used in FBrf0259289) under `split gene product engineering tool`. We also amend the definition of `split system component` to remove the bit stating that the reconstituted functional tool "would normally be encoded by a single gene product", as it is not true for inteins. closes #241 --- src/ontology/fbcv-edit.obo | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/src/ontology/fbcv-edit.obo b/src/ontology/fbcv-edit.obo index e209ed2..db59622 100644 --- a/src/ontology/fbcv-edit.obo +++ b/src/ontology/fbcv-edit.obo @@ -7919,7 +7919,7 @@ property_value: http://purl.org/dc/terms/date "2017-06-28T11:41:27Z" xsd:dateTim id: FBcv:0005051 name: split system component namespace: experimental_tool_descriptor -def: "Component that forms part of a 'split system'. A split system component corresponds to a non-functional fragment of a functional experimental tool that would normally be encoded by a single gene product. When combined with another appropriate split system component in vivo, a functional experimental tool is produced. The fragments of a split system can be brought together in vivo in a number of different ways; for example, by fusing fragments to peptides that physically interact in vivo." [FBC:GM] +def: "Component that forms part of a 'split system'. A split system component corresponds to a non-functional fragment of a functional experimental tool. When combined with another appropriate split system component in vivo, a functional experimental tool is produced. The fragments of a split system can be brought together in vivo in a number of different ways; for example, by fusing fragments to peptides that physically interact in vivo." [FBC:GM] is_a: FBcv:0005001 ! experimental tool descriptor property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-0027-0858 property_value: http://purl.org/dc/terms/date "2017-06-28T11:41:27Z" xsd:dateTime @@ -9397,6 +9397,15 @@ is_a: FBcv:0009052 ! conditional split RNA-guided nuclease property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 property_value: http://purl.org/dc/terms/date "2024-06-24T11:35:10Z" xsd:dateTime +[Term] +id: FBcv:0009054 +name: split protein splicing tag +namespace: experimental_tool_descriptor +def: "Sequence that forms part of the protein product encoded by a transgenic locus or modified endogenous locus and that can catalyze protein splicing when brought together with a complementary split protein splicing tag in vivo. Typically used to join two separate protein sequences by trans-splicing; in this case the two separate protein sequences are each initially tagged with one half of a pair of complementary split protein splicing tags. Alternatively, if both halves of a pair of complementary split protein splicing tags are used to tag each end of a single protein sequence, they can be used to generate a cyclized protein molecule." [FBC:GM] +is_a: FBcv:0009046 ! split gene product engineering tool +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2024-06-24T11:44:00Z" xsd:dateTime + [Term] id: FBcv:0010000 name: obsolete living stock