From 39738c7abb8b839f71d38d570f7a92e7683e6e78 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Wed, 11 Jun 2025 13:01:04 -0500 Subject: [PATCH 1/6] change original subject/object to plural, multivalued --- biolink-model.yaml | 22 ++++++++++++++-------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/biolink-model.yaml b/biolink-model.yaml index c44520da00..23c41ae6a1 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -5360,17 +5360,23 @@ slots: in_subset: - translator_minimal - original subject: + original subjects: is_a: association slot description: >- - used to hold the original subject of a relation (or predicate) that an external knowledge - source uses before transformation to match the biolink-model specification. + used to hold the original subject(s) of a relation (or predicate) that an external knowledge + source uses before transformation to match the biolink-model specification or Translator + node normalization. + multivalued: true + domain: association - original object: + original objects: is_a: association slot description: >- - used to hold the original object of a relation (or predicate) that an external knowledge - source uses before transformation to match the biolink-model specification. + used to hold the original object(s) of a relation (or predicate) that an external knowledge + source uses before transformation to match the biolink-model specification or Translator + node normalization. + multivalued: true + domain: association original predicate: aliases: ['original relation', 'relation'] @@ -9438,9 +9444,9 @@ classes: - knowledge level - agent type - timepoint - - original subject + - original subjects - original predicate - - original object + - original objects # denormalized fields - subject category - object category From 916d7b025047d32a16db7fa567a0dae43c73e8e9 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Wed, 28 May 2025 19:22:35 -0500 Subject: [PATCH 2/6] add sources: edge property used in TRAPI --- biolink-model.yaml | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/biolink-model.yaml b/biolink-model.yaml index 23c41ae6a1..24a09cd940 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -6016,6 +6016,25 @@ slots: multivalued: true range: publication + sources: + aliases: ['source retrieval provenance'] + description: >- + A set of RetrievalSources, which traces where the statement expressed in an + Association came from. For example, the provenance of a Gene-Chemical Edge + might be traced through the Translator Resource that provided it (e.g. MolePro) + to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to + the resource that originally created/curated it (e.g. ClinicalTrials.org). + comments: >- + Note that source retrieval provenance concerns the mechanical retrieval and + transformation of data between web accessible information systems. It does not + trace the source of knowledge back to specific publications or data sets. And + it is not concerned with the reasoning, inference or analysis activities that + generate knowledge in the first place (this is instead covered by 'knowledge + level' and 'agent type' properties). + is_a: association slot + multivalued: true + range: retrieval source + associated environmental context: is_a: association slot description: >- From 4e58714c3f8b566da23a6c8110f338e42ce4310d Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Wed, 28 May 2025 19:31:12 -0500 Subject: [PATCH 3/6] minor edits to existing properties of retrieval source --- biolink-model.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/biolink-model.yaml b/biolink-model.yaml index 24a09cd940..8f2ee5376c 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -745,6 +745,7 @@ slots: an Edge provided by the ARAGORN ARA can expressing knowledge it retrieved from both the automat-mychem-info and molepro KPs, which both provided it with records of this single fact. + multivalued: true domain: retrieval source range: uriorcurie @@ -7027,13 +7028,13 @@ classes: resource role: required: true description: >- - The role of the InformationResource in the retrieval of the - knowledge expressed in an Edge, or data used to generate this knowledge. + The role of the InformationResource in the retrieval of the + knowledge expressed in an Edge, or data used to generate this knowledge. upstream resource ids: description: >- - The InformationResources that served as a source for the - InformationResource that served as a source for the knowledge - expressed in an Edge, or data used to generate this knowledge. + A list of upstream InformationResources from which the resource + being described directly retrieved a record of the knowledge + expressed in the Edge, or data used to generate this knowledge. ## Top Level Abstractions of Material & Process Entities From 600cb4b110e6e214377e68781c3f8a34631ed4e9 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Wed, 28 May 2025 19:40:03 -0500 Subject: [PATCH 4/6] add source record urls to RetrievalSource: to align with TRAPI --- biolink-model.yaml | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/biolink-model.yaml b/biolink-model.yaml index 8f2ee5376c..4a693028ca 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -749,6 +749,17 @@ slots: domain: retrieval source range: uriorcurie + source record urls: + is_a: node property + description: >- + A URL linking to a specific web page or document provided by the + source, that contains a record of the knowledge expressed in the + Edge. If the knowledge is contained in more than one web page on + an Information Resource's site, urls MAY be provided for each. + multivalued: true + domain: retrieval source + range: uriorcurie + description: aliases: ['definition'] range: narrative text @@ -7018,6 +7029,7 @@ classes: - resource id - resource role - upstream resource ids + - source record urls - xref slot_usage: resource id: @@ -7035,6 +7047,11 @@ classes: A list of upstream InformationResources from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. + source record urls: + description: >- + One or more URLs that link to a specific web page or document provided by + the InformationResource, that contains a record of the knowledge expressed + in the Edge. ## Top Level Abstractions of Material & Process Entities From aa48308273e76c90a89cfd0205009060387f538c Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Wed, 28 May 2025 22:15:13 -0500 Subject: [PATCH 5/6] add sources to Association slots (aka edge properties) --- biolink-model.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/biolink-model.yaml b/biolink-model.yaml index 4a693028ca..e6ccfd7b7b 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -9474,6 +9474,7 @@ classes: - qualifier - qualifiers # deprecated - publications + - sources - has evidence - knowledge source - primary knowledge source From 3adaf64c1559d875ff060ae10826dacac829e430 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Tue, 24 Jun 2025 11:48:52 -0700 Subject: [PATCH 6/6] shorten lines with 'line too long' warnings --- biolink-model.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/biolink-model.yaml b/biolink-model.yaml index e6ccfd7b7b..c29a16120e 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -1255,13 +1255,15 @@ slots: affinity: description: >- - The numerical value describing the strength of an affinity between two entities. For instance, if a chemical inhibits a protein with a pIC50 of 8.6, the affinity is 8.6. Used in conjunction with the affinity parameter slot. + The numerical value describing the strength of an affinity between two entities. For instance, if a chemical inhibits a protein with a pIC50 of 8.6, + the affinity is 8.6. Used in conjunction with the affinity parameter slot. is_a: association slot range: float affinity parameter: description: >- - The type of parameter describing the strength of an affinity between two entities. For instance, if a chemical inhibits a protein with a pIC50 of 8.6, the affinity parameter is pIC50. Used in conjunction with the affinity slot. + The type of parameter describing the strength of an affinity between two entities. For instance, if a chemical inhibits a protein with a pIC50 of 8.6, + the affinity parameter is pIC50. Used in conjunction with the affinity slot. is_a: association slot range: AffinityParameterEnum