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Add provider for metacyc prefix and consider new prefix for unique IDs #1294

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Add provider for metacyc prefix and consider new prefix for unique IDs #1294

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31d938e
Add provider for metacyc
nagutm Dec 6, 2024
9f24be8
lint
nagutm Dec 7, 2024
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53 changes: 52 additions & 1 deletion src/bioregistry/data/bioregistry.json
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Original file line number Diff line number Diff line change
Expand Up @@ -66749,6 +66749,23 @@
"name": "Metabolic Pathway Database",
"prefix": "10"
},
"providers": [
{
"code": "plantcyc.compound",
"description": "A resource for compounds associated with plant metabolism",
"homepage": "https://pmn.plantcyc.org",
"name": "PlantCyc Compound",
"publications": [
{
"doi": "10.1093/nar/gkae991",
"pubmed": "39558185",
"title": "Plant Metabolic Network 16: expansion of underrepresented plant groups and experimentally supported enzyme data",
"year": 2024
}
],
"uri_format": "https://pmn.plantcyc.org/compound?orgid=PLANT&id=$1"
}
],
"publications": [
{
"doi": "10.1093/nar/gkv1164",
Expand Down Expand Up @@ -66809,6 +66826,23 @@
"github_request_issue": 1012,
"homepage": "https://metacyc.org",
"name": "Metabolic Encyclopedia for Pathway/Genome Databases",
"providers": [
{
"code": "plantcyc.pathway",
"description": "A resource for pathways associated with plant metabolism",
"homepage": "https://pmn.plantcyc.org",
"name": "PlantCyc Pathway",
"publications": [
{
"doi": "10.1093/nar/gkae991",
"pubmed": "39558185",
"title": "Plant Metabolic Network 16: expansion of underrepresented plant groups and experimentally supported enzyme data",
"year": 2024
}
],
"uri_format": "https://pmn.plantcyc.org/pathway?orgid=PLANT&id=$1"
}
],
"publications": [
{
"pubmed": "31586394",
Expand Down Expand Up @@ -66877,7 +66911,24 @@
"pattern": "^RXN-\\d{5}$",
"prefix": "metacyc.reaction",
"uri_format": "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1"
}
},
"providers": [
{
"code": "plantcyc.reaction",
"description": "A resource for reactions associated with plant metabolism",
"homepage": "https://pmn.plantcyc.org",
"name": "PlantCyc Reaction",
"publications": [
{
"doi": "10.1093/nar/gkae991",
"pubmed": "39558185",
"title": "Plant Metabolic Network 16: expansion of underrepresented plant groups and experimentally supported enzyme data",
"year": 2024
}
],
"uri_format": "https://pmn.plantcyc.org/reaction?orgid=PLANT&id=$1"
}
]
},
"metanetx.chemical": {
"biocontext": {
Expand Down
1 change: 1 addition & 0 deletions src/bioregistry/data/curated_papers.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -71,3 +71,4 @@ pubmed relevant orcid date_curated relevancy_type pr_added notes
39498478 1 0009-0009-5240-7463 2024-11-25 new_publication 1283 Publication for gold
39498484 1 0009-0009-5240-7463 2024-11-27 unclear 1288 Provider for ensembl IDs, issue with curation due to multiple URI formats. Similar case: (PMID: 39104285)
39526381 1 0009-0009-5240-7463 2024-12-01 new_publication 1290 Publication for refseq
39558185 1 0009-0009-5240-7463 2024-12-03 new_provider 1294 Provider for metacyc
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