From 637456958a425f70089f1816b22b0fb4b1ba1b2d Mon Sep 17 00:00:00 2001
From: "Benjamin M. Gyori" <ben.gyori@gmail.com>
Date: Sat, 2 Nov 2024 08:55:49 -0400
Subject: [PATCH] Add prefix: gtdb (#1242)

Closes #1239

---------

Co-authored-by: Charles Tapley Hoyt <cthoyt@gmail.com>
Co-authored-by: i alarmed alien <556057+ialarmedalien@users.noreply.github.com>
---
 src/bioregistry/data/bioregistry.json | 54 +++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)

diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json
index 88beb237b..bd20912b7 100644
--- a/src/bioregistry/data/bioregistry.json
+++ b/src/bioregistry/data/bioregistry.json
@@ -48006,6 +48006,60 @@
     "pattern": "^\\d{6}$",
     "uri_format": "http://purl.obolibrary.org/obo/GSSO_$1"
   },
+  "gtdb": {
+    "contact": {
+      "email": "donovan.parks@gmail.com",
+      "github": "donovan-h-parks",
+      "name": "Donovan Parks",
+      "orcid": "0000-0001-6662-9010"
+    },
+    "contributor": {
+      "email": "aireland@lbl.gov",
+      "github": "ialarmedalien",
+      "name": "AJ Ireland",
+      "orcid": "0000-0003-1982-9065"
+    },
+    "description": "The Genome Taxonomy Database (GTDB) is an initiative to establish a standardized microbial taxonomy based on genome phylogeny.",
+    "example": "g__Prochlorococcus_A",
+    "github_request_issue": 1242,
+    "homepage": "https://gtdb.ecogenomic.org",
+    "name": "Genome Taxonomy Database",
+    "pattern": "^[cdfgops]__\\w+\\S+$",
+    "publications": [
+      {
+        "doi": "10.1038/s41564-021-00918-8",
+        "pubmed": "34155373",
+        "title": "A standardized archaeal taxonomy for the Genome Taxonomy Database",
+        "year": 2021
+      },
+      {
+        "doi": "10.1093/nar/gkab776",
+        "pmc": "PMC8728215",
+        "pubmed": "34520557",
+        "title": "GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy",
+        "year": 2021
+      },
+      {
+        "doi": "10.1038/s41587-020-0501-8",
+        "pubmed": "32341564",
+        "title": "A complete domain-to-species taxonomy for Bacteria and Archaea",
+        "year": 2020
+      },
+      {
+        "doi": "10.1038/nbt.4229",
+        "pubmed": "30148503",
+        "title": "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life",
+        "year": 2018
+      }
+    ],
+    "reviewer": {
+      "email": "cthoyt@gmail.com",
+      "github": "cthoyt",
+      "name": "Charles Tapley Hoyt",
+      "orcid": "0000-0003-4423-4370"
+    },
+    "uri_format": "https://gtdb.ecogenomic.org/tree?r=$1"
+  },
   "gtex": {
     "biocontext": {
       "prefix": "GTEX"