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Update seed to be seed.subsystems
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@nalikapalayoor
nalikapalayoor committed Jan 17, 2025
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Showing 1 changed file with 131 additions and 73 deletions.
204 changes: 131 additions & 73 deletions src/bioregistry/data/bioregistry.json
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Original file line number Diff line number Diff line change
Expand Up @@ -661,6 +661,41 @@
"database": "Q111134507"
}
},
"absd": {
"contact": {
"email": "[email protected]",
"name": "Nicolas Maillet",
"orcid": "0000-0003-1611-5243"
},
"contributor": {
"email": "[email protected]",
"github": "nalikapalayoor",
"name": "Nalika Palayoor",
"orcid": "0009-0008-8406-631X"
},
"description": "The AntiBody Sequence Database is a public dataset for antibody sequence data. It provides unique identifiers for antibody sequences, including both immunoglobulin and single-chain variable fragment sequences. These are are critical for immunological studies, and allows users to search and retrieve antibody sequences based on sequence similarity and specificity, and other biological properties.",
"example": "81d0ea69a9ab134f6ba68314e982171a367d3ab739c85c5ba49701dd02170ed3",
"github_request_issue": 1362,
"homepage": "https://absd.pasteur.cloud",
"name": "AntiBody Sequence Database",
"pattern": "^[a-f0-9]{64}$",
"publications": [
{
"doi": "10.1093/nargab/lqae171",
"pmc": "PMC11655285",
"pubmed": "39703430",
"title": "AntiBody Sequence Database",
"year": 2024
}
],
"reviewer": {
"email": "[email protected]",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"uri_format": "https://absd.pasteur.cloud/antibody/$1"
},
"ac": {
"contributor": {
"email": "[email protected]",
Expand Down Expand Up @@ -37448,6 +37483,29 @@
"https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r229"
]
},
"evr": {
"contact": {
"email": "[email protected]",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor": {
"email": "[email protected]",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An open, community-driven registry of conference and event venues.\n\nEVR assigns persistent identifiers (PIDs) to make referencing venues FAIR. This is similar to how ORCID assigns PIDs to researchers and ROR assigns PIDs to research organizations.\n\nThis benefits researchers assembling information about in-person conferences and events by enabling them to refer in an unambiguous way to the venue where it takes place.\n\nThis repository follows the [Open Data, Open Code, Open Infrastructure (O3) principles](https://www.nature.com/articles/s41597-024-03406-w), meaning that the data and code are all in one repository that anyone can contribute to.",
"example": "0000001",
"github_request_issue": 1363,
"homepage": "https://cthoyt.com/evr",
"license": "CC0-1.0",
"name": "Event Venue Registry",
"pattern": "^\\d{7}$",
"repository": "https://github.com/cthoyt/evr",
"uri_format": "https://cthoyt.com/evr/$1"
},
"exac.gene": {
"biocontext": {
"prefix": "EXAC.GENE"
Expand Down Expand Up @@ -104334,79 +104392,6 @@
"uri_format": "https://sed-ml.org/urns.html#language:$1"
}
},
"seed": {
"biocontext": {
"prefix": "SEED"
},
"contributor_extras": [
{
"email": "[email protected]",
"github": "ialarmedalien",
"name": "AJ Ireland",
"orcid": "0000-0003-1982-9065"
},
{
"email": "[email protected]",
"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"
Expand Down Expand Up @@ -104475,6 +104460,79 @@
"uri_format": "http://modelseed.org/biochem/reactions/$1"
}
},
"seed.subsystems": {
"biocontext": {
"prefix": "SEED.SUBSYSTEMS"
},
"contributor_extras": [
{
"email": "[email protected]",
"github": "ialarmedalien",
"name": "AJ Ireland",
"orcid": "0000-0003-1982-9065"
},
{
"email": "[email protected]",
"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": "https://modelseed.org/",
"name": "SEED Subsystem at Argonne National Laboratory",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "seed.subsystems",
"uri_format": "https://pubseed.theseed.org/SubsysEditor.cgi?page=ShowSubsystem&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": "[email protected]",
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