From b5b6e4f7679c5bb22d962b2b6b06d3ac746dde0a Mon Sep 17 00:00:00 2001 From: hrshdhgd Date: Thu, 7 Dec 2023 14:26:54 +0000 Subject: [PATCH 1/4] [create-pull-request] automated change --- src/bioregistry/data/bioregistry.json | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 795d30e6b..1d97bbc59 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -57900,6 +57900,20 @@ "MetaCyc" ] }, + "metacyc.pathway": { + "contributor": { + "github": "hrshdhgd", + "name": "Harshad Hegde", + "orcid": "0000-0002-2411-565X" + }, + "description": "MetaCyc is a database of non-redundant, experimentally elucidated metabolic pathways and enzymes. It also contains reactions, chemical compounds, and genes. It stores predominantly qualitative information rather than quantitative data, although it does contain some quantitative data such as enzyme kinetics data. “MetaCyc” is pronounced “met-a-sike”. It sounds like “encyclopedia”. A unique property of MetaCyc is that it is curated[[def]](http://www.biocyc.org/glossary.shtml?sid=biocyc14-3908554027#Curation) from the scientific experimental literature according to an extensive process [[4](https://metacyc.org/MetaCycUserGuide.shtml#TAG:__tex2page_sec_4)], such that: - 3,443​ ​ different organisms are represented, with the majority of pathways occurring in microorganisms and plants - 3,128​ ​ metabolic pathways are stored, with 18,819​ ​ enzymatic reactions and 76,283​ ​ associated literature citations - MetaCyc stores the full complement of reactions that have been assigned EC numbers by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology [(NC-IUBMB)](https://iubmb.org/about/committees/nomenclature-committee/) - MetaCyc stores thousands of additional enzyme-catalyzed reactions that have not yet been assigned an EC number", + "example": "12DICHLORETHDEG-PWY", + "github_request_issue": 1012, + "homepage": "https://metacyc.org", + "name": "Metabolic Encyclopedia for Pathway/Genome Databases", + "publications": [], + "repository": "bioregistry" + }, "metacyc.reaction": { "biocontext": { "prefix": "METACYC.REACTION" From a270b9b3c041382d7a4ad9b25752e108806069fc Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Thu, 7 Dec 2023 17:36:06 +0100 Subject: [PATCH 2/4] Update --- src/bioregistry/data/bioregistry.json | 22 +++++++++++++++++++--- 1 file changed, 19 insertions(+), 3 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 1d97bbc59..2a8be59ac 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -57906,13 +57906,29 @@ "name": "Harshad Hegde", "orcid": "0000-0002-2411-565X" }, - "description": "MetaCyc is a database of non-redundant, experimentally elucidated metabolic pathways and enzymes. It also contains reactions, chemical compounds, and genes. It stores predominantly qualitative information rather than quantitative data, although it does contain some quantitative data such as enzyme kinetics data. “MetaCyc” is pronounced “met-a-sike”. It sounds like “encyclopedia”. A unique property of MetaCyc is that it is curated[[def]](http://www.biocyc.org/glossary.shtml?sid=biocyc14-3908554027#Curation) from the scientific experimental literature according to an extensive process [[4](https://metacyc.org/MetaCycUserGuide.shtml#TAG:__tex2page_sec_4)], such that: - 3,443​ ​ different organisms are represented, with the majority of pathways occurring in microorganisms and plants - 3,128​ ​ metabolic pathways are stored, with 18,819​ ​ enzymatic reactions and 76,283​ ​ associated literature citations - MetaCyc stores the full complement of reactions that have been assigned EC numbers by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology [(NC-IUBMB)](https://iubmb.org/about/committees/nomenclature-committee/) - MetaCyc stores thousands of additional enzyme-catalyzed reactions that have not yet been assigned an EC number", + "description": "MetaCyc is a database of non-redundant, experimentally elucidated metabolic pathways and enzymes. It also contains reactions, chemical compounds, and genes. It stores predominantly qualitative information rather than quantitative data, although it does contain some quantitative data such as enzyme kinetics data.\n\nMetaCyc is [curated](http://www.biocyc.org/glossary.shtml?sid=biocyc14-3908554027#Curation) from the scientific experimental literature according to an [extensive process](https://metacyc.org/MetaCycUserGuide.shtml#TAG:__tex2page_sec_4)]. The majority of pathways occurring in it are from microorganisms and plants. MetaCyc stores thousands of additional enzyme-catalyzed reactions that have not yet been assigned an EC number", "example": "12DICHLORETHDEG-PWY", "github_request_issue": 1012, "homepage": "https://metacyc.org", "name": "Metabolic Encyclopedia for Pathway/Genome Databases", - "publications": [], - "repository": "bioregistry" + "publications": [ + { + "pubmed": "31586394" + }, + { + "pubmed": "23746312" + }, + { + "pubmed": "21523460" + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://metacyc.org/META/NEW-IMAGE?object=$1" }, "metacyc.reaction": { "biocontext": { From 130bcae763ebc906cceec30ddbd4fa2e9e73d4d6 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Thu, 7 Dec 2023 17:38:33 +0100 Subject: [PATCH 3/4] Add contact information --- src/bioregistry/data/bioregistry.json | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 2a8be59ac..fd9299d9d 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -57787,6 +57787,12 @@ "prefix": "MetaCyc", "uri_format": "http://translator.ncats.nih.gov/MetaCyc_$1" }, + "contact": { + "email": "pkarp@ai.sri.com", + "github": "pkarp111", + "name": "Peter Karp", + "orcid": "0000-0002-5876-6418" + }, "fairsharing": { "abbreviation": null, "description": "MetaCyc is the largest curated collection of metabolic pathways currently available. It provides a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways, and are curated from the primary scientific literature. Most reactions in MetaCyc pathways are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. As of 2022 MetaCyc describes 3,000 pathways and 17,000 reactions curated from 71,000 publications.\n", @@ -57901,6 +57907,12 @@ ] }, "metacyc.pathway": { + "contact": { + "email": "pkarp@ai.sri.com", + "github": "pkarp111", + "name": "Peter Karp", + "orcid": "0000-0002-5876-6418" + }, "contributor": { "github": "hrshdhgd", "name": "Harshad Hegde", @@ -57940,6 +57952,12 @@ "prefix": "metacyc.reaction", "uri_format": "http://identifiers.org/metacyc.reaction:$1" }, + "contact": { + "email": "pkarp@ai.sri.com", + "github": "pkarp111", + "name": "Peter Karp", + "orcid": "0000-0002-5876-6418" + }, "mappings": { "biocontext": "METACYC.REACTION", "biolink": "metacyc.reaction", From 0307b5ecc093e8be29fe6a4caee1a6ca2ae130bc Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Thu, 7 Dec 2023 18:40:42 +0100 Subject: [PATCH 4/4] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index fd9299d9d..68a4b5777 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -57925,13 +57925,19 @@ "name": "Metabolic Encyclopedia for Pathway/Genome Databases", "publications": [ { - "pubmed": "31586394" + "pubmed": "31586394", + "title": "The MetaCyc database of metabolic pathways and enzymes - a 2019 update", + "year": 2019 }, { - "pubmed": "23746312" + "pubmed": "23746312", + "title": "The challenge of constructing, classifying, and representing metabolic pathways", + "year": 2013 }, { - "pubmed": "21523460" + "pubmed": "21523460", + "title": "A survey of metabolic databases emphasizing the MetaCyc family", + "year": 2011 } ], "reviewer": {