From a550c06962297b7b69e9219c12604aa157fe9439 Mon Sep 17 00:00:00 2001 From: jplfaria Date: Thu, 12 Dec 2024 06:16:26 +0000 Subject: [PATCH 1/4] [create-pull-request] automated change --- src/bioregistry/data/bioregistry.json | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index acec93843..d582f62a2 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -105164,6 +105164,31 @@ "orcid": "0000-0003-4423-4370" } }, + "silva": { + "contributor": { + "email": "jplfaria@anl.gov", + "github": "jplfaria", + "name": "Jose P. Faria", + "orcid": "0000-0001-9302-7250" + }, + "description": "SILVA is a comprehensive, quality-checked, and regularly updated resource of aligned ribosomal RNA (rRNA) gene sequences for Bacteria, Archaea, and Eukaryotes. It provides a consistent taxonomic framework, commonly used in microbial ecology and diversity studies.", + "example": "11084", + "github_request_issue": 1306, + "homepage": "https://www.arb-silva.de/", + "license": "CC-BY-SA-4.0", + "name": "SILVA rRNA database project", + "pattern": "^\\d+$", + "publications": [ + { + "doi": "10.1093/nar/gks1219" + }, + { + "doi": "10.1093/nar/gkt1209" + } + ], + "repository": "bioregistry", + "uri_format": "https://www.arb-silva.de/search?q=$1" + }, "sio": { "aberowl": { "description": "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. It provides vocabulary for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.", From 7de7e09e267ca17a86d281bb37dc8ab6ddb2b3d9 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Thu, 12 Dec 2024 10:40:56 +0100 Subject: [PATCH 2/4] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 25 +++++++++++++++++++++++-- 1 file changed, 23 insertions(+), 2 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index d582f62a2..05452ba02 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -105165,6 +105165,12 @@ } }, "silva": { + "contact": { + "email": "fog@mpi-bremen.de", + "github": "frankolivergloeckner", + "name": "Frank Oliver Glöckner", + "orcid": "0000-0001-8528-9023" + }, "contributor": { "email": "jplfaria@anl.gov", "github": "jplfaria", @@ -105176,17 +105182,32 @@ "github_request_issue": 1306, "homepage": "https://www.arb-silva.de/", "license": "CC-BY-SA-4.0", + "logo": "https://www.arb-silva.de/fileadmin/graphics_general/main/dissemination/silva-sticker-1_2_ext_33.png", "name": "SILVA rRNA database project", "pattern": "^\\d+$", "publications": [ { - "doi": "10.1093/nar/gks1219" + "doi": "10.1093/nar/gkt1209", + "pmc": "PMC3965112", + "pubmed": "24293649", + "title": "The SILVA and \"All-species Living Tree Project (LTP)\" taxonomic frameworks", + "year": 2014 }, { - "doi": "10.1093/nar/gkt1209" + "doi": "10.1093/nar/gks1219", + "pmc": "PMC3531112", + "pubmed": "23193283", + "title": "The SILVA ribosomal RNA gene database project: improved data processing and web-based tools", + "year": 2012 } ], "repository": "bioregistry", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, "uri_format": "https://www.arb-silva.de/search?q=$1" }, "sio": { From f1bd8e5d174ed1e16535b2860c2926057bdc66bb Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Mon, 27 Jan 2025 18:35:29 +0100 Subject: [PATCH 3/4] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 4ee191119..3db9c755e 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -106696,20 +106696,14 @@ "orcid": "0000-0003-4423-4370" } }, - "silva": { - "contact": { - "email": "fog@mpi-bremen.de", - "github": "frankolivergloeckner", - "name": "Frank Oliver Glöckner", - "orcid": "0000-0001-8528-9023" - }, + "silva.taxon": { "contributor": { "email": "jplfaria@anl.gov", "github": "jplfaria", "name": "Jose P. Faria", "orcid": "0000-0001-9302-7250" }, - "description": "SILVA is a comprehensive, quality-checked, and regularly updated resource of aligned ribosomal RNA (rRNA) gene sequences for Bacteria, Archaea, and Eukaryotes. It provides a consistent taxonomic framework, commonly used in microbial ecology and diversity studies.", + "description": "SILVA is a resource of aligned ribosomal RNA (rRNA) gene sequences for Bacteria, Archaea, and Eukaryotes.\n\nIt assigns internal, auto-incremented integer identifiers to taxa. However, these identifiers are not persistent nor unique - if the label for a taxon is changed, it assigned a new identifier and the old identifier is removed.", "example": "11084", "github_request_issue": 1306, "homepage": "https://www.arb-silva.de/", @@ -106733,14 +106727,12 @@ "year": 2012 } ], - "repository": "bioregistry", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" - }, - "uri_format": "https://www.arb-silva.de/search?q=$1" + } }, "sio": { "aberowl": { From 37f420d47a234fce94a6ae6c0c20f57158850756 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Tue, 28 Jan 2025 10:20:42 +0100 Subject: [PATCH 4/4] Update bioregistry.json --- src/bioregistry/data/bioregistry.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 3db9c755e..509b88050 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -106706,10 +106706,10 @@ "description": "SILVA is a resource of aligned ribosomal RNA (rRNA) gene sequences for Bacteria, Archaea, and Eukaryotes.\n\nIt assigns internal, auto-incremented integer identifiers to taxa. However, these identifiers are not persistent nor unique - if the label for a taxon is changed, it assigned a new identifier and the old identifier is removed.", "example": "11084", "github_request_issue": 1306, - "homepage": "https://www.arb-silva.de/", + "homepage": "https://www.arb-silva.de", "license": "CC-BY-SA-4.0", "logo": "https://www.arb-silva.de/fileadmin/graphics_general/main/dissemination/silva-sticker-1_2_ext_33.png", - "name": "SILVA rRNA database project", + "name": "SILVA Taxon", "pattern": "^\\d+$", "publications": [ {