From 85317a2bae506cccd20faa60ed8c10735733bae2 Mon Sep 17 00:00:00 2001 From: Philippe Rocca-Serra Date: Fri, 26 Jul 2024 14:49:28 +0100 Subject: [PATCH 01/10] Update stato.md adding publications adding usage examples --- ontology/stato.md | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/ontology/stato.md b/ontology/stato.md index e95f33ad6..2a90ffb63 100644 --- a/ontology/stato.md +++ b/ontology/stato.md @@ -18,10 +18,40 @@ license: preferredPrefix: STATO products: - id: stato.owl +publications: +- id: https://doi.org/10.1038/s41597-019-0286-0 + title: 'Experiment design driven FAIRification of omics data matrices, an exemplar.' +- id: https://doi.org/10.1038/s41597-020-0409-7 + title: 'Semantic concept schema of the linear mixed model of experimental observations' repository: https://github.com/ISA-tools/stato tags: - statistics tracker: https://github.com/ISA-tools/stato/issues +usages: +- description: an R/Bioconductor package, named struct (Statistics in R using Class-based Templates), which defines a suite of class-based templates that allows users to develop and implement highly standardized and readable statistical analysis workflows. Struct integrates with the STATistics Ontology to ensure consistent reporting and maximizes semantic interoperability + publications: + - id: https://doi.org/10.1101/2021.10.10.463703 + title: 'struct: an R/Bioconductor-based framework for standardized metabolomics data analysis and beyond' + type: annotation + user: https://bioconductor.org/packages/release/bioc/html/struct.html +- description: Scientific Evidence Code System (SEVCO) on the FEvIR platform. The FEvIR Platform includes many Builder Tools to create FHIR® Resources without requiring expertise in FHIR® or JSON, and Converter Tools to convert structured data to FHIR® Resources + publications: + - id: https://doi.org/10.1016/j.jbi.2021.103685 + title: 'Making science computable: Developing code systems for statistics, study design, and risk of bias' + type: annotation + user: https://fevir.net/resources/CodeSystem/27270#STATO:0000039 +- description: PSI-MS CV + publications: + - id: https://doi.org/10.1093/database/bat009 + title: 'The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.' + type: annotation + user: https://github.com/HUPO-PSI/psi-ms-CV +- description: OBCS + publications: + - id: https://doi.org/10.1186/s13326-016-0100-2 + title: 'The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis' + type: annotation + user: https://github.com/obcs/obcs activity_status: active --- From 9aa88d3d14dbdbec7ec1a46f325d3005bbc5a603 Mon Sep 17 00:00:00 2001 From: Philippe Rocca-Serra Date: Fri, 26 Jul 2024 15:00:55 +0100 Subject: [PATCH 02/10] Update stato.md typos . formatting fix --- ontology/stato.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ontology/stato.md b/ontology/stato.md index 2a90ffb63..b8008ca47 100644 --- a/ontology/stato.md +++ b/ontology/stato.md @@ -20,7 +20,7 @@ products: - id: stato.owl publications: - id: https://doi.org/10.1038/s41597-019-0286-0 - title: 'Experiment design driven FAIRification of omics data matrices, an exemplar.' + title: 'Experiment design driven FAIRification of omics data matrices, an exemplar' - id: https://doi.org/10.1038/s41597-020-0409-7 title: 'Semantic concept schema of the linear mixed model of experimental observations' repository: https://github.com/ISA-tools/stato @@ -34,7 +34,7 @@ usages: title: 'struct: an R/Bioconductor-based framework for standardized metabolomics data analysis and beyond' type: annotation user: https://bioconductor.org/packages/release/bioc/html/struct.html -- description: Scientific Evidence Code System (SEVCO) on the FEvIR platform. The FEvIR Platform includes many Builder Tools to create FHIR® Resources without requiring expertise in FHIR® or JSON, and Converter Tools to convert structured data to FHIR® Resources +- description: Scientific Evidence Code System (SEVCO) on the FEvIR platform. The FEvIR Platform includes many Builder Tools to create FHIR Resources without requiring expertise in FHIR or JSON, and Converter Tools to convert structured data to FHIR Resources publications: - id: https://doi.org/10.1016/j.jbi.2021.103685 title: 'Making science computable: Developing code systems for statistics, study design, and risk of bias' From 7e74319f82b1a5f9181ad12b40d68c92c9c4d15b Mon Sep 17 00:00:00 2001 From: Philippe Rocca-Serra Date: Fri, 26 Jul 2024 15:37:21 +0100 Subject: [PATCH 03/10] running tox linting command, no errors reported --- ontology/stato.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/ontology/stato.md b/ontology/stato.md index b8008ca47..eae6793d4 100644 --- a/ontology/stato.md +++ b/ontology/stato.md @@ -20,15 +20,15 @@ products: - id: stato.owl publications: - id: https://doi.org/10.1038/s41597-019-0286-0 - title: 'Experiment design driven FAIRification of omics data matrices, an exemplar' + title: Experiment design driven FAIRification of omics data matrices, an exemplar - id: https://doi.org/10.1038/s41597-020-0409-7 - title: 'Semantic concept schema of the linear mixed model of experimental observations' + title: Semantic concept schema of the linear mixed model of experimental observations repository: https://github.com/ISA-tools/stato tags: - statistics tracker: https://github.com/ISA-tools/stato/issues usages: -- description: an R/Bioconductor package, named struct (Statistics in R using Class-based Templates), which defines a suite of class-based templates that allows users to develop and implement highly standardized and readable statistical analysis workflows. Struct integrates with the STATistics Ontology to ensure consistent reporting and maximizes semantic interoperability +- description: struct (Statistics in R using Class-based Templates), Struct integrates with the STATistics Ontology to ensure consistent reporting and maximizes semantic interoperability publications: - id: https://doi.org/10.1101/2021.10.10.463703 title: 'struct: an R/Bioconductor-based framework for standardized metabolomics data analysis and beyond' @@ -43,13 +43,13 @@ usages: - description: PSI-MS CV publications: - id: https://doi.org/10.1093/database/bat009 - title: 'The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.' + title: The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. type: annotation user: https://github.com/HUPO-PSI/psi-ms-CV - description: OBCS publications: - id: https://doi.org/10.1186/s13326-016-0100-2 - title: 'The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis' + title: The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis type: annotation user: https://github.com/obcs/obcs activity_status: active From 7a4ea683d311498e3c9ff87226e1a465cb1a235c Mon Sep 17 00:00:00 2001 From: Philippe Rocca-Serra Date: Mon, 19 Aug 2024 14:15:03 +0100 Subject: [PATCH 04/10] Update stato.md --- ontology/stato.md | 6 ------ 1 file changed, 6 deletions(-) diff --git a/ontology/stato.md b/ontology/stato.md index eae6793d4..4cffda9ee 100644 --- a/ontology/stato.md +++ b/ontology/stato.md @@ -40,12 +40,6 @@ usages: title: 'Making science computable: Developing code systems for statistics, study design, and risk of bias' type: annotation user: https://fevir.net/resources/CodeSystem/27270#STATO:0000039 -- description: PSI-MS CV - publications: - - id: https://doi.org/10.1093/database/bat009 - title: The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. - type: annotation - user: https://github.com/HUPO-PSI/psi-ms-CV - description: OBCS publications: - id: https://doi.org/10.1186/s13326-016-0100-2 From 15c9c4e0d147092b9d497e5cef9064e5c80de40f Mon Sep 17 00:00:00 2001 From: Philippe Rocca-Serra Date: Tue, 3 Sep 2024 19:43:40 +0100 Subject: [PATCH 05/10] Update ontology/stato.md Co-authored-by: Deepak --- ontology/stato.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ontology/stato.md b/ontology/stato.md index 4cffda9ee..8f97af153 100644 --- a/ontology/stato.md +++ b/ontology/stato.md @@ -19,7 +19,7 @@ preferredPrefix: STATO products: - id: stato.owl publications: -- id: https://doi.org/10.1038/s41597-019-0286-0 +- id: https://pubmed.ncbi.nlm.nih.gov/31831744 title: Experiment design driven FAIRification of omics data matrices, an exemplar - id: https://doi.org/10.1038/s41597-020-0409-7 title: Semantic concept schema of the linear mixed model of experimental observations From 8dad7b83a4ed024d415c63e15cf0f779a99bb887 Mon Sep 17 00:00:00 2001 From: Philippe Rocca-Serra Date: Tue, 3 Sep 2024 19:43:48 +0100 Subject: [PATCH 06/10] Update ontology/stato.md Co-authored-by: Deepak --- ontology/stato.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ontology/stato.md b/ontology/stato.md index 8f97af153..39aa4cc38 100644 --- a/ontology/stato.md +++ b/ontology/stato.md @@ -36,7 +36,7 @@ usages: user: https://bioconductor.org/packages/release/bioc/html/struct.html - description: Scientific Evidence Code System (SEVCO) on the FEvIR platform. The FEvIR Platform includes many Builder Tools to create FHIR Resources without requiring expertise in FHIR or JSON, and Converter Tools to convert structured data to FHIR Resources publications: - - id: https://doi.org/10.1016/j.jbi.2021.103685 + - id: https://pubmed.ncbi.nlm.nih.gov/33486066 title: 'Making science computable: Developing code systems for statistics, study design, and risk of bias' type: annotation user: https://fevir.net/resources/CodeSystem/27270#STATO:0000039 From 5f95eb9d9219547eafc391a9c888817f3f39137e Mon Sep 17 00:00:00 2001 From: Philippe Rocca-Serra Date: Tue, 3 Sep 2024 19:48:21 +0100 Subject: [PATCH 07/10] Update ontology/stato.md --- ontology/stato.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ontology/stato.md b/ontology/stato.md index 39aa4cc38..b65ace118 100644 --- a/ontology/stato.md +++ b/ontology/stato.md @@ -30,7 +30,7 @@ tracker: https://github.com/ISA-tools/stato/issues usages: - description: struct (Statistics in R using Class-based Templates), Struct integrates with the STATistics Ontology to ensure consistent reporting and maximizes semantic interoperability publications: - - id: https://doi.org/10.1101/2021.10.10.463703 + - id: https://pubmed.ncbi.nlm.nih.gov/33325493 title: 'struct: an R/Bioconductor-based framework for standardized metabolomics data analysis and beyond' type: annotation user: https://bioconductor.org/packages/release/bioc/html/struct.html From ffedaa2bdd88f056f6d698b18651d73d90808203 Mon Sep 17 00:00:00 2001 From: Philippe Rocca-Serra Date: Tue, 3 Sep 2024 19:50:45 +0100 Subject: [PATCH 08/10] Update ontology/stato.md --- ontology/stato.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ontology/stato.md b/ontology/stato.md index b65ace118..6d772135c 100644 --- a/ontology/stato.md +++ b/ontology/stato.md @@ -42,7 +42,7 @@ usages: user: https://fevir.net/resources/CodeSystem/27270#STATO:0000039 - description: OBCS publications: - - id: https://doi.org/10.1186/s13326-016-0100-2 + - id: https://pubmed.ncbi.nlm.nih.gov/27627881 title: The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis type: annotation user: https://github.com/obcs/obcs From 8876df8cf12b405e4f045aedeb11bc458f01b4f7 Mon Sep 17 00:00:00 2001 From: Philippe Rocca-Serra Date: Tue, 3 Sep 2024 19:53:53 +0100 Subject: [PATCH 09/10] Update ontology/stato.md --- ontology/stato.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ontology/stato.md b/ontology/stato.md index 6d772135c..2f727d177 100644 --- a/ontology/stato.md +++ b/ontology/stato.md @@ -21,7 +21,7 @@ products: publications: - id: https://pubmed.ncbi.nlm.nih.gov/31831744 title: Experiment design driven FAIRification of omics data matrices, an exemplar -- id: https://doi.org/10.1038/s41597-020-0409-7 +- id: https://pubmed.ncbi.nlm.nih.gov/32109232 title: Semantic concept schema of the linear mixed model of experimental observations repository: https://github.com/ISA-tools/stato tags: From bdd4ddecf73ca0d6c9cc2403dbc4ed65751575c2 Mon Sep 17 00:00:00 2001 From: Deepak Date: Thu, 12 Sep 2024 15:09:32 +0200 Subject: [PATCH 10/10] Fix PMID links --- ontology/stato.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/ontology/stato.md b/ontology/stato.md index 2f727d177..c38a5bd6d 100644 --- a/ontology/stato.md +++ b/ontology/stato.md @@ -19,9 +19,9 @@ preferredPrefix: STATO products: - id: stato.owl publications: -- id: https://pubmed.ncbi.nlm.nih.gov/31831744 +- id: https://www.ncbi.nlm.nih.gov/pubmed/31831744 title: Experiment design driven FAIRification of omics data matrices, an exemplar -- id: https://pubmed.ncbi.nlm.nih.gov/32109232 +- id: https://www.ncbi.nlm.nih.gov/pubmed/32109232 title: Semantic concept schema of the linear mixed model of experimental observations repository: https://github.com/ISA-tools/stato tags: @@ -30,19 +30,19 @@ tracker: https://github.com/ISA-tools/stato/issues usages: - description: struct (Statistics in R using Class-based Templates), Struct integrates with the STATistics Ontology to ensure consistent reporting and maximizes semantic interoperability publications: - - id: https://pubmed.ncbi.nlm.nih.gov/33325493 + - id: https://www.ncbi.nlm.nih.gov/pubmed/33325493 title: 'struct: an R/Bioconductor-based framework for standardized metabolomics data analysis and beyond' type: annotation user: https://bioconductor.org/packages/release/bioc/html/struct.html - description: Scientific Evidence Code System (SEVCO) on the FEvIR platform. The FEvIR Platform includes many Builder Tools to create FHIR Resources without requiring expertise in FHIR or JSON, and Converter Tools to convert structured data to FHIR Resources publications: - - id: https://pubmed.ncbi.nlm.nih.gov/33486066 + - id: https://www.ncbi.nlm.nih.gov/pubmed/33486066 title: 'Making science computable: Developing code systems for statistics, study design, and risk of bias' type: annotation user: https://fevir.net/resources/CodeSystem/27270#STATO:0000039 - description: OBCS publications: - - id: https://pubmed.ncbi.nlm.nih.gov/27627881 + - id: https://www.ncbi.nlm.nih.gov/pubmed/27627881 title: The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis type: annotation user: https://github.com/obcs/obcs