From 05fde552c5655455a720780a67729af68308b311 Mon Sep 17 00:00:00 2001 From: Nalika Palayoor Date: Fri, 17 Jan 2025 16:20:20 -0500 Subject: [PATCH] Modified seed prefix to be seed.subsystems --- src/bioregistry/data/bioregistry.json | 146 +++++++++++++------------- 1 file changed, 73 insertions(+), 73 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index f2cd760ed..156459e15 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -104392,79 +104392,6 @@ "uri_format": "https://sed-ml.org/urns.html#language:$1" } }, - "seed": { - "biocontext": { - "prefix": "SEED" - }, - "contributor_extras": [ - { - "email": "aireland@lbl.gov", - "github": "ialarmedalien", - "name": "AJ Ireland", - "orcid": "0000-0003-1982-9065" - }, - { - "email": "seaver@anl.gov", - "github": "samseaver", - "name": "Sam Seaver", - "orcid": "0000-0002-7674-5194" - } - ], - "go": { - "description": "Project to annotate the first 1000 sequenced genomes, develop detailed metabolic reconstructions, and construct the corresponding stoichiometric matrices", - "homepage": "http://www.theseed.org", - "name": "The SEED;", - "prefix": "SEED", - "uri_format": "http://www.theseed.org/linkin.cgi?id=$1" - }, - "mappings": { - "biocontext": "SEED", - "go": "SEED", - "miriam": "seed", - "n2t": "seed", - "ncbi": "SEED" - }, - "miriam": { - "deprecated": true, - "description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.", - "id": "00000552", - "name": "SEED Subsystem", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "seed", - "sampleId": "Biotin_biosynthesis" - }, - "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": "Biotin_biosynthesis", - "homepage": "http://seed-viewer.theseed.org/seedviewer.cgi", - "name": "SEED Subsystem at Argonne National Laboratory", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "seed", - "uri_format": "http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1" - }, - "name": "SEED Subsystem", - "ncbi": { - "example": "fig|83331.1.peg.1", - "homepage": "http://www.theseed.org", - "name": "The SEED Database", - "prefix": "SEED" - }, - "publications": [ - { - "doi": "10.1093/nar/gki866", - "pmc": "PMC1251668", - "pubmed": "16214803", - "title": "The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes", - "year": 2005 - } - ], - "repository": "https://github.com/TheSEED", - "synonyms": [ - "seed.subsystem" - ] - }, "seed.compound": { "biocontext": { "prefix": "SEED.COMPOUND" @@ -104533,6 +104460,79 @@ "uri_format": "http://modelseed.org/biochem/reactions/$1" } }, + "seed.subsystems": { + "biocontext": { + "prefix": "SEED.SUBSYSTEMS" + }, + "contributor_extras": [ + { + "email": "aireland@lbl.gov", + "github": "ialarmedalien", + "name": "AJ Ireland", + "orcid": "0000-0003-1982-9065" + }, + { + "email": "seaver@anl.gov", + "github": "samseaver", + "name": "Sam Seaver", + "orcid": "0000-0002-7674-5194" + } + ], + "go": { + "description": "Project to annotate the first 1000 sequenced genomes, develop detailed metabolic reconstructions, and construct the corresponding stoichiometric matrices", + "homepage": "http://www.theseed.org", + "name": "The SEED;", + "prefix": "SEED.SUBSYSTEMS", + "uri_format": "http://www.theseed.org/linkin.cgi?id=$1" + }, + "mappings": { + "biocontext": "SEED.SUBSYSTEMS", + "go": "SEED.SUBSYSTEMS", + "miriam": "seed.subsystems", + "n2t": "seed.subsystems", + "ncbi": "SEED.SUBSYSTEMS" + }, + "miriam": { + "deprecated": true, + "description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.", + "id": "00000552", + "name": "SEED Subsystem", + "namespaceEmbeddedInLui": false, + "pattern": "^\\w+$", + "prefix": "seed.subsystems", + "sampleId": "Biotin_biosynthesis" + }, + "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": "Biotin_biosynthesis", + "homepage": "http://seed-viewer.theseed.org/seedviewer.cgi", + "name": "SEED Subsystem at Argonne National Laboratory", + "namespaceEmbeddedInLui": false, + "pattern": "^\\w+$", + "prefix": "seed.subsystems", + "uri_format": "http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1" + }, + "name": "SEED Subsystem", + "ncbi": { + "example": "fig|83331.1.peg.1", + "homepage": "http://www.theseed.org", + "name": "The SEED Database", + "prefix": "SEED.SUBSYSTEMS" + }, + "publications": [ + { + "doi": "10.1093/nar/gki866", + "pmc": "PMC1251668", + "pubmed": "16214803", + "title": "The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes", + "year": 2005 + } + ], + "repository": "https://github.com/TheSEED", + "synonyms": [ + "seed" + ] + }, "seinet": { "contributor": { "email": "cthoyt@gmail.com",