Skip to content

Commit

Permalink
Update prefix: seed --> seed.subsystem (#1365)
Browse files Browse the repository at this point in the history 
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url, as the old one seems to be outdated.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 <ben.gyori@gmail.com>
  • Loading branch information
@nalikapalayoor @bgyori
nalikapalayoor and bgyori authored Jan 18, 2025
1 parent ffd5863 commit 32b809f
Show file tree
Hide file tree
Showing 2 changed files with 73 additions and 72 deletions.
143 changes: 72 additions & 71 deletions src/bioregistry/data/bioregistry.json
View file
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/$1"
},
"n2t": {
"description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.",
"example": "cpd15380",
"homepage": "http://modelseed.org/",
"name": "SEED Compound at Argonne National Laboratory",
"namespaceEmbeddedInLui": false,
"pattern": "^cpd\\d+$",
"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/$1"
}
},
"seed.subsystem": {
"biocontext": {
"prefix": "SEED"
},
Expand Down Expand Up @@ -104509,76 +104577,9 @@
],
"repository": "https://github.com/TheSEED",
"synonyms": [
"seed.subsystem"
]
},
"seed.compound": {
"biocontext": {
"prefix": "SEED.COMPOUND"
},
"mappings": {
"biocontext": "SEED.COMPOUND",
"miriam": "seed.compound",
"n2t": "seed.compound"
},
"miriam": {
"deprecated": false,
"description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.",
"homepage": "http://modelseed.org/",
"id": "00000553",
"name": "SEED Compound",
"namespaceEmbeddedInLui": false,
"pattern": "^cpd\\d+$",
"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
View file
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

0 comments on commit 32b809f

Please sign in to comment.