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Update prefix: seed --> seed.subsystem #1365

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merged 7 commits into from
Jan 18, 2025
Merged

Update prefix: seed --> seed.subsystem #1365

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50f6720
Update seed to be seed.subsystems
nalikapalayoor Jan 17, 2025
0535955
Reverted mistaken updates in seed.subsystem prefix
nalikapalayoor Jan 17, 2025
606a989
Merge branch 'main' into update_seed
bgyori Jan 17, 2025
d16eaef
Merge branch 'main' into update_seed
bgyori Jan 18, 2025
fadab01
Update prefix in mismatch.json
bgyori Jan 18, 2025
6a6b885
Override URI format for seed
bgyori Jan 18, 2025
62e6ec2
Revert more changes in mapped content
bgyori Jan 18, 2025
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143 changes: 72 additions & 71 deletions src/bioregistry/data/bioregistry.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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/$1"
},
"n2t": {
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"description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.",
"example": "cpd15380",
"homepage": "http://modelseed.org/",
"name": "SEED Compound at Argonne National Laboratory",
"namespaceEmbeddedInLui": false,
"pattern": "^cpd\\d+$",
"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/$1"
},
"mappings": {
"biolink": "SEED.REACTION",
"miriam": "seed.reaction",
"n2t": "seed.reaction"
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},
"miriam": {
"deprecated": false,
"description": "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions.",
"homepage": "http://modelseed.org/biochem/reactions/",
"id": "00000692",
"name": "SEED Reactions",
"namespaceEmbeddedInLui": false,
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"pattern": "^rxn\\d+$",
"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/$1"
}
},
"seed.subsystem": {
"biocontext": {
"prefix": "SEED"
},
Expand Down Expand Up @@ -104509,76 +104577,9 @@
],
"repository": "https://github.com/TheSEED",
"synonyms": [
"seed.subsystem"
]
},
"seed.compound": {
"biocontext": {
"prefix": "SEED.COMPOUND"
},
"mappings": {
"biocontext": "SEED.COMPOUND",
"miriam": "seed.compound",
"n2t": "seed.compound"
},
"miriam": {
"deprecated": false,
"description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.",
"homepage": "http://modelseed.org/",
"id": "00000553",
"name": "SEED Compound",
"namespaceEmbeddedInLui": false,
"pattern": "^cpd\\d+$",
"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": {
Expand Down
2 changes: 1 addition & 1 deletion src/bioregistry/data/mismatch.json
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Original file line number Diff line number Diff line change
Expand Up @@ -207,7 +207,7 @@
"bartoc": "1756",
"lov": "sao"
},
"seed": {
"seed.subsystem": {
"fairsharing": "FAIRsharing.68b03f"
},
"string": {
Expand Down
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