From 7a7bd84996110b043e9a85b8258476b7d9d5d9f0 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Tue, 20 Feb 2018 14:01:13 -0800 Subject: [PATCH 1/3] Update ann-config.yaml Clarified semantics of regulates closure and adding a proposed new closure for getting 'regulates only'; i.e. following is_a and regulates (and -/+), with at least one regulates hop in there. We will want to expose this on amigo, and also via APIs, see https://github.com/biolink/biolink-api/issues/138 cc @selewis --- metadata/ann-config.yaml | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/metadata/ann-config.yaml b/metadata/ann-config.yaml index 51911518a..56a1e52c6 100644 --- a/metadata/ann-config.yaml +++ b/metadata/ann-config.yaml @@ -133,13 +133,26 @@ fields: property: [] searchable: true - id: regulates_closure - description: "Annotations for this term or its children (over regulates)." + description: "Annotations for this term or its children (over regulates, including isa/part-of)." display_name: GO class type: string cardinality: multi property: [] - id: regulates_closure_label - description: "Annotations for this term or its children (over regulates)." + description: "Annotations for this term or its children (over regulates, including isa/part-of)." + display_name: GO class + type: string + cardinality: multi + property: [] + searchable: true + - id: regulates_strict_closure + description: "Annotations for this term or its children (over regulates but not part-of)." + display_name: GO class + type: string + cardinality: multi + property: [] + - id: regulates_strict_closure_label + description: "Annotations for this term or its children (over regulates not not part-of)." display_name: GO class type: string cardinality: multi From 99d82f451321393495aa8bbdd5428ea3cf10e7fe Mon Sep 17 00:00:00 2001 From: kltm Date: Tue, 20 Feb 2018 14:52:12 -0800 Subject: [PATCH 2/3] Update ann-config.yaml "not not" -> "but not" and commas --- metadata/ann-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/metadata/ann-config.yaml b/metadata/ann-config.yaml index 56a1e52c6..3c7bff6d4 100644 --- a/metadata/ann-config.yaml +++ b/metadata/ann-config.yaml @@ -146,13 +146,13 @@ fields: property: [] searchable: true - id: regulates_strict_closure - description: "Annotations for this term or its children (over regulates but not part-of)." + description: "Annotations for this term or its children (over regulates, but not part-of)." display_name: GO class type: string cardinality: multi property: [] - id: regulates_strict_closure_label - description: "Annotations for this term or its children (over regulates not not part-of)." + description: "Annotations for this term or its children (over regulates, but not part-of)." display_name: GO class type: string cardinality: multi From aeb9b176ec8de7e72c922b19431e8953590e4b73 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 5 Mar 2018 10:51:23 -0800 Subject: [PATCH 3/3] Update ann-config.yaml --- metadata/ann-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/metadata/ann-config.yaml b/metadata/ann-config.yaml index 3c7bff6d4..a4859084c 100644 --- a/metadata/ann-config.yaml +++ b/metadata/ann-config.yaml @@ -120,7 +120,7 @@ fields: property: [] searchable: true - id: isa_partof_closure - description: "Annotations for this term or its children (over is_a/part_of)." + description: "Annotations for this term or its children (over is_a/part_of). When used to query bioentities, this corresponds to 'involved in' in RO" display_name: Involved in type: string cardinality: multi @@ -133,7 +133,7 @@ fields: property: [] searchable: true - id: regulates_closure - description: "Annotations for this term or its children (over regulates, including isa/part-of)." + description: "Annotations for this term or its children (over regulates, including isa/part-of). Note the field name is potentially confusing, as it includes cases where there are no actual regulates edges. When used to query bioentities, this corresponds to 'acts upstream of or within'" display_name: GO class type: string cardinality: multi @@ -146,7 +146,7 @@ fields: property: [] searchable: true - id: regulates_strict_closure - description: "Annotations for this term or its children (over regulates, but not part-of)." + description: "Annotations for this term or its children (over regulates, but not part-of). When used to query bioentities, this corresponds to 'involved in regulation of'" display_name: GO class type: string cardinality: multi