From 675934dd43bebd607f4e63251a027a43a9135e96 Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Thu, 9 May 2024 16:11:06 -0400 Subject: [PATCH 1/6] Update README.md Removed a new line genontology/noctua-standard-annotations#14 --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index 39878ac..c50af18 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,6 @@ Using RDF Shapes to define the schema of Gene Ontology Causal Activity Models - # Schema See [shapes/go-cam-shapes.shex](shapes/go-cam-shapes.shex) From 7a87fd5d2199aa04142de4e90ab5261816423a50 Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Thu, 9 May 2024 16:20:18 -0400 Subject: [PATCH 2/6] Update go-cam-shapes.shex Added an extra line --- shapes/go-cam-shapes.shex | 1 + 1 file changed, 1 insertion(+) diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex index 0737686..dc5684b 100644 --- a/shapes/go-cam-shapes.shex +++ b/shapes/go-cam-shapes.shex @@ -129,6 +129,7 @@ PREFIX results_in_growth_of: PREFIX results_in_movement_of: PREFIX results_in_remodeling_of: + { a [owl:Ontology] + ; contributor: xsd:string +; #TODO would be better as an IRI From 3734d2e0f1d6adee71911c57dc98e989680f8a39 Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Fri, 10 May 2024 17:01:49 -0400 Subject: [PATCH 3/6] Update go-cam-shapes.shex Adding // true; comment to constrain relations' use for standard annotations --- shapes/go-cam-shapes.shex | 37 ++++++++++++++++++++----------------- 1 file changed, 20 insertions(+), 17 deletions(-) diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex index dc5684b..82bc851 100644 --- a/shapes/go-cam-shapes.shex +++ b/shapes/go-cam-shapes.shex @@ -408,32 +408,32 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a ( @ OR @ ) {1}; - enabled_by: ( @ OR @ ) *; + enabled_by: ( @ OR @ ) *; // true; part_of: @ *; - has_part: @ *; + has_part: @ *; // true; occurs_in: @ {0,1}; has_output: ( @ OR @ ) *; has_input: ( @ OR @ ) *; has_primary_input: ( @ OR @ ) *; has_primary_output: ( @ OR @ ) *; - directly_provides_input_for: ( @ OR @ ) *; + directly_provides_input_for: ( @ OR @ ) *; // true; regulates: ( @ OR @ ) *; negatively_regulates: ( @ OR @ ) *; positively_regulates: ( @ OR @ ) *; directly_regulates: ( @ OR @ ) *; directly_negatively_regulates: ( @ OR @ ) *; directly_positively_regulates: ( @ OR @ ) *; - indirectly_regulates: ( @ OR @) *; - indirectly_positively_regulates: ( @ OR @ ) *; - indirectly_negatively_regulates: ( @ OR @ ) *; - constitutively_upstream_of: ( @ OR @ ) *; - removes_input_for: ( @ OR @ ) *; - has_small_molecule_regulator: @ *; - has_small_molecule_activator: @ *; - has_small_molecule_inhibitor: @ *; - causally_upstream_of_or_within: ( @ OR @ OR @ ) *; - causally_upstream_of_or_within_negative_effect: @ *; - causally_upstream_of_or_within_positive_effect: @ *; + indirectly_regulates: ( @ OR @) *; // true; + indirectly_positively_regulates: ( @ OR @ ) *; // true; + indirectly_negatively_regulates: ( @ OR @ ) *; // true; + constitutively_upstream_of: ( @ OR @ ) *; // true; + removes_input_for: ( @ OR @ ) *; // true; + has_small_molecule_regulator: @ *; // true; + has_small_molecule_activator: @ *; // true; + has_small_molecule_inhibitor: @ *; // true; + causally_upstream_of_or_within: ( @ OR @ OR @ ) *; // true; + causally_upstream_of_or_within_negative_effect: @ *; // true; + causally_upstream_of_or_within_positive_effect: @ *; // true; causally_upstream_of: ( @ OR @ OR @ ) *; causally_upstream_of_negative_effect: ( @ OR @ OR @ ) *; causally_upstream_of_positive_effect: ( @ OR @ OR @ ) *; @@ -524,11 +524,14 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a @; - located_in: @ {0,1}; - is_active_in: @ OR @ {0,1}; - has_part: ( @ OR @) *; + located_in: @ {0,1}; // true; + is_active_in: @ OR @ {0,1}; // true; + part_of: @ {0,1}; + adjacent_to: @ *; + overlaps: @ *; existence_overlaps: ( @ OR @ OR @ ) *; existence_starts_and_ends_during: ( @ OR @ OR @ ) *; + has_part: ( @ OR @) *; // true; } // rdfs:comment "a protein complex" IRI @ AND EXTRA rdfs:subClassOf { From 967a11e0ae6737a6afe61f48a981ee721bdff966 Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Fri, 10 May 2024 17:18:28 -0400 Subject: [PATCH 4/6] Update go-cam-shapes.shex Trying again with adding extensions rules. Spaces vs tabs? From f54cfdbf622cc98f6029264cff3a56e45ed695a1 Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Mon, 13 May 2024 12:31:43 -0400 Subject: [PATCH 5/6] Update go-cam-shapes.shex Removing extra semi-colon --- shapes/go-cam-shapes.shex | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex index 82bc851..e9690ec 100644 --- a/shapes/go-cam-shapes.shex +++ b/shapes/go-cam-shapes.shex @@ -408,32 +408,32 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a ( @ OR @ ) {1}; - enabled_by: ( @ OR @ ) *; // true; + enabled_by: ( @ OR @ ) * // true; part_of: @ *; - has_part: @ *; // true; + has_part: @ * // true; occurs_in: @ {0,1}; has_output: ( @ OR @ ) *; has_input: ( @ OR @ ) *; has_primary_input: ( @ OR @ ) *; has_primary_output: ( @ OR @ ) *; - directly_provides_input_for: ( @ OR @ ) *; // true; + directly_provides_input_for: ( @ OR @ ) * // true; regulates: ( @ OR @ ) *; negatively_regulates: ( @ OR @ ) *; positively_regulates: ( @ OR @ ) *; directly_regulates: ( @ OR @ ) *; directly_negatively_regulates: ( @ OR @ ) *; directly_positively_regulates: ( @ OR @ ) *; - indirectly_regulates: ( @ OR @) *; // true; - indirectly_positively_regulates: ( @ OR @ ) *; // true; - indirectly_negatively_regulates: ( @ OR @ ) *; // true; - constitutively_upstream_of: ( @ OR @ ) *; // true; - removes_input_for: ( @ OR @ ) *; // true; - has_small_molecule_regulator: @ *; // true; - has_small_molecule_activator: @ *; // true; - has_small_molecule_inhibitor: @ *; // true; - causally_upstream_of_or_within: ( @ OR @ OR @ ) *; // true; - causally_upstream_of_or_within_negative_effect: @ *; // true; - causally_upstream_of_or_within_positive_effect: @ *; // true; + indirectly_regulates: ( @ OR @) * // true; + indirectly_positively_regulates: ( @ OR @ ) * // true; + indirectly_negatively_regulates: ( @ OR @ ) * // true; + constitutively_upstream_of: ( @ OR @ ) * // true; + removes_input_for: ( @ OR @ ) * // true; + has_small_molecule_regulator: @ * // true; + has_small_molecule_activator: @ * // true; + has_small_molecule_inhibitor: @ * // true; + causally_upstream_of_or_within: ( @ OR @ OR @ ) * // true; + causally_upstream_of_or_within_negative_effect: @ * // true; + causally_upstream_of_or_within_positive_effect: @ * // true; causally_upstream_of: ( @ OR @ OR @ ) *; causally_upstream_of_negative_effect: ( @ OR @ OR @ ) *; causally_upstream_of_positive_effect: ( @ OR @ OR @ ) *; @@ -524,14 +524,14 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a @; - located_in: @ {0,1}; // true; - is_active_in: @ OR @ {0,1}; // true; + located_in: @ {0,1} // true; + is_active_in: @ OR @ {0,1} // true; part_of: @ {0,1}; adjacent_to: @ *; overlaps: @ *; existence_overlaps: ( @ OR @ OR @ ) *; existence_starts_and_ends_during: ( @ OR @ OR @ ) *; - has_part: ( @ OR @) *; // true; + has_part: ( @ OR @) * // true; } // rdfs:comment "a protein complex" IRI @ AND EXTRA rdfs:subClassOf { From 5db4d993b252527d1014d8d4336b8fe8ed192874 Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Tue, 4 Jun 2024 09:26:56 -0400 Subject: [PATCH 6/6] Update go-cam-shapes.shex --- shapes/go-cam-shapes.shex | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex index e9690ec..dd61728 100644 --- a/shapes/go-cam-shapes.shex +++ b/shapes/go-cam-shapes.shex @@ -417,12 +417,12 @@ PREFIX results_in_remodeling_of: has_primary_input: ( @ OR @ ) *; has_primary_output: ( @ OR @ ) *; directly_provides_input_for: ( @ OR @ ) * // true; - regulates: ( @ OR @ ) *; - negatively_regulates: ( @ OR @ ) *; - positively_regulates: ( @ OR @ ) *; - directly_regulates: ( @ OR @ ) *; - directly_negatively_regulates: ( @ OR @ ) *; - directly_positively_regulates: ( @ OR @ ) *; + regulates: ( @ OR @ ) * // true; + negatively_regulates: ( @ OR @ ) * // true; + positively_regulates: ( @ OR @ ) * // true; + directly_regulates: ( @ OR @ ) * // true; + directly_negatively_regulates: ( @ OR @ ) * // true; + directly_positively_regulates: ( @ OR @ ) * // true; indirectly_regulates: ( @ OR @) * // true; indirectly_positively_regulates: ( @ OR @ ) * // true; indirectly_negatively_regulates: ( @ OR @ ) * // true; @@ -434,9 +434,9 @@ PREFIX results_in_remodeling_of: causally_upstream_of_or_within: ( @ OR @ OR @ ) * // true; causally_upstream_of_or_within_negative_effect: @ * // true; causally_upstream_of_or_within_positive_effect: @ * // true; - causally_upstream_of: ( @ OR @ OR @ ) *; - causally_upstream_of_negative_effect: ( @ OR @ OR @ ) *; - causally_upstream_of_positive_effect: ( @ OR @ OR @ ) *; + causally_upstream_of: ( @ OR @ OR @ ) * // true; + causally_upstream_of_negative_effect: ( @ OR @ OR @ ) * // true; + causally_upstream_of_positive_effect: ( @ OR @ OR @ ) * // true; happens_during: ( @ OR @ OR @ ) *; } // rdfs:comment "A molecular function"