From 0881025c7a5fba763b935c0eb656e2130073a38f Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Tue, 11 Jun 2024 11:43:30 -0700 Subject: [PATCH 1/5] Update foodon.md Updating usages --- ontology/foodon.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/ontology/foodon.md b/ontology/foodon.md index 09b42c225..eb477cd4e 100644 --- a/ontology/foodon.md +++ b/ontology/foodon.md @@ -38,6 +38,15 @@ tags: - food tracker: https://github.com/FoodOntology/foodon/issues/ activity_status: active +usages: +- user: https://fdc.nal.usda.gov/ + description: FoodData Central nutrition database web portal provided by USDA Agricultural Research Service +- user: https://www.fda.gov/food/whole-genome-sequencing-wgs-program/genometrakr-network + description: FDA GenomeTrackr surveillance program for reporting foodborne pathogen biosamples. +- user: https://foodperiodictable.org/ + description: Periodic Table Of Food Initiative database of food biosample nutrition analytics. +- user: https://wikifcd.wikibase.cloud/wiki/Main_Page + description: Wiki database consolidating over 30 global food composition databases. --- A broadly scoped ontology representing entities which bear a “food role”. It encompasses materials in natural ecosystems and food webs as well as human-centric categorization and handling of food. From a83bebb93ee648041e1c51e7a0ed2677352284bc Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Thu, 18 Jul 2024 23:43:12 -0700 Subject: [PATCH 2/5] Added links to example pages containing FoodOn IDs --- ontology/foodon.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/ontology/foodon.md b/ontology/foodon.md index eb477cd4e..58624f433 100644 --- a/ontology/foodon.md +++ b/ontology/foodon.md @@ -40,13 +40,13 @@ tracker: https://github.com/FoodOntology/foodon/issues/ activity_status: active usages: - user: https://fdc.nal.usda.gov/ - description: FoodData Central nutrition database web portal provided by USDA Agricultural Research Service + description: FoodData Central nutrition database web portal provided by USDA Agricultural Research Service. E.g. https://fdc.nal.usda.gov/fdc-app.html#/food-details/1750340/attributes - user: https://www.fda.gov/food/whole-genome-sequencing-wgs-program/genometrakr-network - description: FDA GenomeTrackr surveillance program for reporting foodborne pathogen biosamples. + description: FDA GenomeTrackr surveillance program for reporting foodborne pathogen biosamples. E.g. https://www.ncbi.nlm.nih.gov/biosample/SAMN03455272 - user: https://foodperiodictable.org/ - description: Periodic Table Of Food Initiative database of food biosample nutrition analytics. + description: Periodic Table Of Food Initiative database of food biosample nutrition analytics. E.g. https://ptfidiscover.markerlab.com/detail/food/GGB100329 - user: https://wikifcd.wikibase.cloud/wiki/Main_Page - description: Wiki database consolidating over 30 global food composition databases. + description: Wiki database consolidating over 30 global food composition databases. E.g. https://wikifcd.wikibase.cloud/wiki/Item:Q568877 --- A broadly scoped ontology representing entities which bear a “food role”. It encompasses materials in natural ecosystems and food webs as well as human-centric categorization and handling of food. From 8fd2e0d91282486a378bf8a1ac61b3ba22105c21 Mon Sep 17 00:00:00 2001 From: Deepak Date: Mon, 12 Aug 2024 16:10:01 +0200 Subject: [PATCH 3/5] Add description to usage examples --- ontology/foodon.md | 30 +++++++++++++++++++++--------- 1 file changed, 21 insertions(+), 9 deletions(-) diff --git a/ontology/foodon.md b/ontology/foodon.md index 58624f433..7a9550984 100644 --- a/ontology/foodon.md +++ b/ontology/foodon.md @@ -37,16 +37,28 @@ repository: https://github.com/FoodOntology/foodon tags: - food tracker: https://github.com/FoodOntology/foodon/issues/ -activity_status: active usages: -- user: https://fdc.nal.usda.gov/ - description: FoodData Central nutrition database web portal provided by USDA Agricultural Research Service. E.g. https://fdc.nal.usda.gov/fdc-app.html#/food-details/1750340/attributes -- user: https://www.fda.gov/food/whole-genome-sequencing-wgs-program/genometrakr-network - description: FDA GenomeTrackr surveillance program for reporting foodborne pathogen biosamples. E.g. https://www.ncbi.nlm.nih.gov/biosample/SAMN03455272 -- user: https://foodperiodictable.org/ - description: Periodic Table Of Food Initiative database of food biosample nutrition analytics. E.g. https://ptfidiscover.markerlab.com/detail/food/GGB100329 -- user: https://wikifcd.wikibase.cloud/wiki/Main_Page - description: Wiki database consolidating over 30 global food composition databases. E.g. https://wikifcd.wikibase.cloud/wiki/Item:Q568877 +- description: FoodData Central nutrition database web portal provided by USDA Agricultural Research Service. + examples: + - description: An entry for 'Apples, fuji, with skin, raw' from the FoodData Central nutrition database which is annotated with the term FOODON:00002862. + url: https://fdc.nal.usda.gov/fdc-app.html#/food-details/1750340/attributes + user: https://fdc.nal.usda.gov/ +- description: FDA GenomeTrackr surveillance program for reporting foodborne pathogen biosamples. + examples: + - description: An entry from NCBI Biosample that describes a *Samonella enterica* sample extracted from Chicken and annotated with the term FOODON:03411457. + url: https://www.ncbi.nlm.nih.gov/biosample/SAMN03455272 + user: https://www.fda.gov/food/whole-genome-sequencing-wgs-program/genometrakr-network +- description: Periodic Table Of Food Initiative database of food biosample nutrition analytics. + examples: + - description: + url: https://ptfidiscover.markerlab.com/detail/food/GGB100329 + user: https://foodperiodictable.org/ +- description: Wiki database consolidating over 30 global food composition databases. + examples: + - description: An entry from WikiFCD that describes Walnuts and is annotated with the term FOODON:03301364. + url: https://wikifcd.wikibase.cloud/wiki/Item:Q568877 + user: https://wikifcd.wikibase.cloud/wiki/Main_Page +activity_status: active --- A broadly scoped ontology representing entities which bear a “food role”. It encompasses materials in natural ecosystems and food webs as well as human-centric categorization and handling of food. From a787c7337a9dfbd0b4b3d584089399ca0feb0807 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 19 Aug 2024 13:22:05 -0700 Subject: [PATCH 4/5] Dropped PTFI DB example because of login Added a publication --- ontology/foodon.md | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/ontology/foodon.md b/ontology/foodon.md index 7a9550984..3354fcc5b 100644 --- a/ontology/foodon.md +++ b/ontology/foodon.md @@ -20,8 +20,8 @@ description: A broadly scoped ontology representing entities which bear a “foo domain: diet, metabolomics, and nutrition homepage: https://foodon.org/ license: - label: CC BY 3.0 - url: http://creativecommons.org/licenses/by/3.0/ + label: CC BY 4.0 + url: http://creativecommons.org/licenses/by/4.0/ preferredPrefix: FOODON products: - id: foodon.owl @@ -33,6 +33,8 @@ products: publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31304272 title: 'FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration' +- id: https://content.iospress.com/articles/semantic-web/sw223096 + title: Food process ontology requirements repository: https://github.com/FoodOntology/foodon tags: - food @@ -48,11 +50,6 @@ usages: - description: An entry from NCBI Biosample that describes a *Samonella enterica* sample extracted from Chicken and annotated with the term FOODON:03411457. url: https://www.ncbi.nlm.nih.gov/biosample/SAMN03455272 user: https://www.fda.gov/food/whole-genome-sequencing-wgs-program/genometrakr-network -- description: Periodic Table Of Food Initiative database of food biosample nutrition analytics. - examples: - - description: - url: https://ptfidiscover.markerlab.com/detail/food/GGB100329 - user: https://foodperiodictable.org/ - description: Wiki database consolidating over 30 global food composition databases. examples: - description: An entry from WikiFCD that describes Walnuts and is annotated with the term FOODON:03301364. From bc31c9e843bd427fd2dd7c56dd85045359133272 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 19 Aug 2024 13:29:25 -0700 Subject: [PATCH 5/5] removed non pubmed publication reference --- ontology/foodon.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/ontology/foodon.md b/ontology/foodon.md index 3354fcc5b..2a7b412b8 100644 --- a/ontology/foodon.md +++ b/ontology/foodon.md @@ -33,8 +33,6 @@ products: publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31304272 title: 'FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration' -- id: https://content.iospress.com/articles/semantic-web/sw223096 - title: Food process ontology requirements repository: https://github.com/FoodOntology/foodon tags: - food