From 32b809f5fc5d9d50fa9585b6e20e20c23d116690 Mon Sep 17 00:00:00 2001 From: Nalika Palayoor Date: Sat, 18 Jan 2025 11:47:53 -0500 Subject: [PATCH] Update prefix: seed --> seed.subsystem (#1365) After reviewing the current prefixes associated with The Seed, we decided to update the name of the 'seed' prefix to be 'seed.subsystems', and have 'seed' be a synonym for it instead. This PR makes this update, and also updates the 'uri_format' for 'seed.subsystems' to be a working url, as the old one seems to be outdated. Fixes #1339 --------- Co-authored-by: Benjamin M. Gyori --- src/bioregistry/data/bioregistry.json | 143 +++++++++++++------------- src/bioregistry/data/mismatch.json | 2 +- 2 files changed, 73 insertions(+), 72 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 31c129fae..8ee82a33f 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -104439,7 +104439,75 @@ "uri_format": "https://sed-ml.org/urns.html#language:$1" } }, - "seed": { + "seed.compound": { + "biocontext": { + "prefix": "SEED.COMPOUND" + }, + "mappings": { + "biocontext": "SEED.COMPOUND", + "miriam": "seed.compound", + "n2t": "seed.compound" + }, + "miriam": { + "deprecated": false, + "description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.", + "homepage": "http://modelseed.org/", + "id": "00000553", + "name": "SEED Compound", + "namespaceEmbeddedInLui": false, + "pattern": "^cpd\\d+$", + "prefix": "seed.compound", + "sampleId": "cpd15380", + "uri_format": "http://modelseed.org/biochem/compounds/$1" + }, + "n2t": { + "description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.", + "example": "cpd15380", + "homepage": "http://modelseed.org/", + "name": "SEED Compound at Argonne National Laboratory", + "namespaceEmbeddedInLui": false, + "pattern": "^cpd\\d+$", + "prefix": "seed.compound", + "uri_format": "http://modelseed.org/biochem/compounds/$1" + }, + "repository": "https://github.com/TheSEED" + }, + "seed.reaction": { + "biolink": { + "is_identifiers": false, + "is_obo": false, + "prefix": "SEED.REACTION", + "uri_format": "https://modelseed.org/biochem/reactions/$1" + }, + "mappings": { + "biolink": "SEED.REACTION", + "miriam": "seed.reaction", + "n2t": "seed.reaction" + }, + "miriam": { + "deprecated": false, + "description": "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions.", + "homepage": "http://modelseed.org/biochem/reactions/", + "id": "00000692", + "name": "SEED Reactions", + "namespaceEmbeddedInLui": false, + "pattern": "^rxn\\d+$", + "prefix": "seed.reaction", + "sampleId": "rxn00001", + "uri_format": "http://modelseed.org/biochem/reactions/$1" + }, + "n2t": { + "description": "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions.", + "example": "rxn00001", + "homepage": "http://modelseed.org/biochem/reactions/", + "name": "SEED Reactions", + "namespaceEmbeddedInLui": false, + "pattern": "^rxn\\d+$", + "prefix": "seed.reaction", + "uri_format": "http://modelseed.org/biochem/reactions/$1" + } + }, + "seed.subsystem": { "biocontext": { "prefix": "SEED" }, @@ -104509,76 +104577,9 @@ ], "repository": "https://github.com/TheSEED", "synonyms": [ - "seed.subsystem" - ] - }, - "seed.compound": { - "biocontext": { - "prefix": "SEED.COMPOUND" - }, - "mappings": { - "biocontext": "SEED.COMPOUND", - "miriam": "seed.compound", - "n2t": "seed.compound" - }, - "miriam": { - "deprecated": false, - "description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.", - "homepage": "http://modelseed.org/", - "id": "00000553", - "name": "SEED Compound", - "namespaceEmbeddedInLui": false, - "pattern": "^cpd\\d+$", - "prefix": "seed.compound", - "sampleId": "cpd15380", - "uri_format": "http://modelseed.org/biochem/compounds/$1" - }, - "n2t": { - "description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.", - "example": "cpd15380", - "homepage": "http://modelseed.org/", - "name": "SEED Compound at Argonne National Laboratory", - "namespaceEmbeddedInLui": false, - "pattern": "^cpd\\d+$", - "prefix": "seed.compound", - "uri_format": "http://modelseed.org/biochem/compounds/$1" - }, - "repository": "https://github.com/TheSEED" - }, - "seed.reaction": { - "biolink": { - "is_identifiers": false, - "is_obo": false, - "prefix": "SEED.REACTION", - "uri_format": "https://modelseed.org/biochem/reactions/$1" - }, - "mappings": { - "biolink": "SEED.REACTION", - "miriam": "seed.reaction", - "n2t": "seed.reaction" - }, - "miriam": { - "deprecated": false, - "description": "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions.", - "homepage": "http://modelseed.org/biochem/reactions/", - "id": "00000692", - "name": "SEED Reactions", - "namespaceEmbeddedInLui": false, - "pattern": "^rxn\\d+$", - "prefix": "seed.reaction", - "sampleId": "rxn00001", - "uri_format": "http://modelseed.org/biochem/reactions/$1" - }, - "n2t": { - "description": "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions.", - "example": "rxn00001", - "homepage": "http://modelseed.org/biochem/reactions/", - "name": "SEED Reactions", - "namespaceEmbeddedInLui": false, - "pattern": "^rxn\\d+$", - "prefix": "seed.reaction", - "uri_format": "http://modelseed.org/biochem/reactions/$1" - } + "seed" + ], + "uri_format": "https://pubseed.theseed.org/SubsysEditor.cgi?page=ShowSubsystem&subsystem=$1" }, "seinet": { "contributor": { diff --git a/src/bioregistry/data/mismatch.json b/src/bioregistry/data/mismatch.json index 65da6b416..b87cd0016 100644 --- a/src/bioregistry/data/mismatch.json +++ b/src/bioregistry/data/mismatch.json @@ -207,7 +207,7 @@ "bartoc": "1756", "lov": "sao" }, - "seed": { + "seed.subsystem": { "fairsharing": "FAIRsharing.68b03f" }, "string": {