strain-code 0.3.2 → 0.3.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/data/catalogues.yaml +200 -73
- data/lib/strain-code/version.rb +1 -1
- metadata +1 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 6159bc3ec462d7488fec929a9ae5f2436f9141a9505e1152c2d454cdd07c80b4
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4
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data.tar.gz: 371fa4ba53eb5a6fb33b193081c60edadcc25c1643d01a4fed8556f88cc17b3d
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 94107d5d9dbabfa236ad24778bf16442208f267691f8592e2ea6dff03a011c54310eec60aaa77b407e894b958a347233a32bdef86860f0a9fb7c37f16ec2cf09
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7
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data.tar.gz: 5d99e6cfd28d4b2749d7fc66486884557a088875560ce7c8b57b6c3a422507bc6a3a5406bd7584e65396e88bc3c095dcb48ee0147ae0f343bde482f35297ebaa
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data/data/catalogues.yaml
CHANGED
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@@ -11,15 +11,16 @@
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# - url: URL of the catalogue's main website
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# - url_pattern: URL pattern indicating how to form links to catalogue entries,
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# with "%s" indicating the non-code part of the culture number
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#
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#
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# Additionally, fields starting with `_` are ignored in the basecode, and
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# notably include `_examples` (an array of strain numbers) and `_tested`
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# (the date in which the website was last tested)
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# (the date in which the website was last tested), as well as `_notes`
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#
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# See also:
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# - https://ftp.ncbi.nih.gov/pub/taxonomy/Ccode_dump.txt
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# - https://jcm.brc.riken.jp/en/abbr_e
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catalogues:
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#--- A
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- codes: [ ABB ]
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country_code: KR
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name: Asian Bacterial Bank
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@@ -41,7 +42,7 @@ catalogues:
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name: Anaerobe Reference Laboratory, Helsinki Collection
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- codes: [ AHU ]
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country_code: JP
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name:
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name: >-
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Laboratory of Culture Collection of Microorganisms,
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Faculty of Agriculture, Hokkaido University
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organization: Hokkaido University
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@@ -63,66 +64,23 @@ catalogues:
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name: American Type Culture Collection
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url: 'https://www.atcc.org'
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url_pattern: 'https://www.atcc.org/products/%s'
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-
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name: Colección Española de Cultivos Tipo
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name_en: Spanish Collection of Type Cultures
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organization: University of Valencia
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url:
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'https://www.uv.es/uvweb/coleccion-espanola-cultivos-tipo/es/coleccion-espanola-cultivos-tipo-1285872233521.html'
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url_pattern: 'https://www.cect.org/vstrn2.php?cect=%s'
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- codes: [ DSM ]
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country_code: DE
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name: Deutsche Sammlung von Mikroorganismen und Zellkulturen
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name_en: German Collection of Microorganisms and Cell Cultures
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organization: |
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Leibniz Institute DSMZ - German Collection of Microorganisms and
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Cell Cultures GmbH
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url: 'https://www.dsmz.de/collection/catalogue'
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url_pattern:
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'https://www.dsmz.de/collection/catalogue/details/culture/DSM-%s'
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- codes: [ IFO, NBRC ]
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country_code: JP
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name: 'NITE Biological Resource Center'
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organization: 'NITE: National Institute of Technology and Evaluation'
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url: 'https://www.nite.go.jp/nbrc/catalogue/'
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url_pattern:
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'https://www.nite.go.jp/nbrc/catalogue/NBRCCatalogueDetailServlet?ID=IFO&CAT=%s'
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- codes: [ JCM ]
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country_code: JP
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name: 'Japan Collection of Microorganisms'
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organization: RIKEN
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url: 'https://jcm.brc.riken.jp/en/'
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url_pattern: 'https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=%s'
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- codes: [ KCTC ]
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country_code: KR
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name: Korean Collection for Type Cultures
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organization:
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'KRIBB: Korea Research Institute of Bioscience and Biotechnology'
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url: 'https://kctc.kribb.re.kr/en/collection/'
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url_pattern: 'https://kctc.kribb.re.kr/collection/view?sn=%s'
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_examples: [ KCTC 92132 ]
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_tested: 2025-03-18
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- codes: [ NCTC ]
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country_code: UK
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name: National Collection of Type Cultures
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organization: Health Security Agency
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url: 'https://www.culturecollections.org.uk/products/bacteria-and-mycoplasmas/'
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url_pattern:
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'https://www.culturecollections.org.uk/products/bacteria/detail.jsp?collection=nctc&refId=NCTC+%s'
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#--- B
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- codes: [ BCRC ]
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country_code: TW
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name: Bioresource Collection and Research Center
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organization: Food Industry Research and Development Insitute
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url: 'https://catalog.bcrc.firdi.org.tw/'
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url_pattern: 'https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=%s'
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#--- C
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- codes: [ CAIM ]
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country_code: MX
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name: Collection of Aquatic Important Microorganisms
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organization: 'CIAD: Centro de Investigación en Alimentación y Desarrollo'
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url:
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url: "https://www.ciad.mx/caim"
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url_pattern:
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"https://www.ciad.mx/caim/busqueda.php?searchtype=caim&criterio=%s"
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- codes: [ CCALA ]
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name: Culture Collection of Autotrophic Organisms
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organization: Czech Academy of Sciences
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@@ -133,27 +91,40 @@ catalogues:
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organization: Masaryk University
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country_code: CZ
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url_pattern: 'https://www.sci.muni.cz/ccm/bakterie/camb/%s'
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- codes: [ CGMCC, AS ]
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name: China General Microbiological Culture Collection Center
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organization: National Science and Technology Infrastructure
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country_code: CN
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url_pattern: 'https://cgmcc.net/english/search?stn=%s'
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# From NCBI Taxonomy (not working):
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# 'http://www.cgmcc.net/english/cata.php?stn=CGMCC%%20%s'
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_examples: [ CGMCC 1.19149 ]
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_tested: 2025-03-18
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- codes: [ CCMP ]
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name:
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name: >-
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NCMA: National Center for Marine Algae and Microbiota,
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formerly Culture Collection for Marine Phytoplankton
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organization: Bigelow Laboratory for Ocean Sciences
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country_code: US
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url_pattern: 'https://ncma.bigelow.org/CCMP%s'
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- codes: [ CCTCC ]
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country_code: CN
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name: China Center for Type Culture Collection
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organization: Wuhan University
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- codes: [ CCUG ]
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name: Culture Collection University of Gothenburg
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organization: University of Gothenburg
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country_code: SE
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url_pattern: 'https://www.ccug.se/strain?id=%s'
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- codes: [ CECT ]
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country_code: ES
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name: Colección Española de Cultivos Tipo
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name_en: Spanish Collection of Type Cultures
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organization: University of Valencia
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url:
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"https://www.uv.es/uvweb/coleccion-espanola-cultivos-tipo/es/\
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coleccion-espanola-cultivos-tipo-1285872233521.html"
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url_pattern: 'https://www.cect.org/vstrn2.php?cect=%s'
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- codes: [ CGMCC, AS ]
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name: China General Microbiological Culture Collection Center
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organization: National Science and Technology Infrastructure
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country_code: CN
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url_pattern: 'https://cgmcc.net/english/search?stn=%s'
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# From NCBI Taxonomy (not working):
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# 'http://www.cgmcc.net/english/cata.php?stn=CGMCC%%20%s'
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_examples: [ CGMCC 1.19149 ]
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_tested: 2025-03-18
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- codes: [ CICC ]
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name: China Center of Industrial Culture Collection
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organization:
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@@ -167,46 +138,165 @@ catalogues:
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country_code: FR
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url_pattern:
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'https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%%20%s'
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#--- D
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- codes: [ DSM ]
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country_code: DE
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name: Deutsche Sammlung von Mikroorganismen und Zellkulturen
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name_en: German Collection of Microorganisms and Cell Cultures
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organization: >-
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Leibniz Institute DSMZ - German Collection of Microorganisms and
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Cell Cultures GmbH
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url: 'https://www.dsmz.de/collection/catalogue'
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url_pattern:
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'https://www.dsmz.de/collection/catalogue/details/culture/DSM-%s'
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#--- E
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#--- F
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- codes: [ FRR ]
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country_code: AU
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name: Division of Food Research, Food Research Laboratory
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organization: >-
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CSIRO: The Commonwealth Scientific and Industrial Research Organisation
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#--- G
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- codes: [ GDMCC ]
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country_code: CN
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name: Guangdong Microbial Culture Collection Center
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organization: Guangdong Academy of Sciences
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url:
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'http://english.gdim.cn/research/researchdivisions/guangdongmicrobialculturecollectioncentergdmcc/'
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- codes: [ GIFU, GTC ]
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country_code: JP
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name: Gifu Type Culture Collection
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organization: Gifu University School of Medicine
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#--- H
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- codes: [ HAMBI ]
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country_code: FI
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name: >-
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Culture Collection of the Department of Microbiology,
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Faculty of Agriculture and Forestry, University of Helsinki
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organization: University of Helsinki
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url: "https://www.helsinki.fi/en/infrastructures/biodiversity-collections/\
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infrastructures/microbial-domain-biological-resource-centre-hambi"
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url_pattern: 'https://kotka.luomus.fi/culture/bac?q="HAMBI%20%s"'
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_example: [ HAMBI 1518 ]
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_tested: 2025-03-20
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_notes: url_pattern points to a search result form
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#--- I
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- codes: [ IAM ]
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country_code: JP
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name: >-
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IAM Culture Collection, Center for Cellular and Molecular Research,
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Institute of Molecular and Cellular Biosciences
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organization: The University of Tokyo
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_notes: Transferred to JCM
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- codes: [ ICMP, PDDCC ]
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country_code: NZ
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name: >-
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International Collection of Microorganisms from Plants,
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Plant Diseases Division
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organization: "DSIR: Department of Scientific and Industrial Research"
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url: "https://www.landcareresearch.co.nz/tools-and-resources/collections/\
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icmp-culture-collection/"
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url_pattern: "https://scd.landcareresearch.co.nz/Specimen/ICMP_%s"
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_examples: [ ICMP 123 ]
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_tested: 2025-03-20
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- codes: [ IFO, NBRC ]
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country_code: JP
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name: 'NITE Biological Resource Center'
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organization: 'NITE: National Institute of Technology and Evaluation'
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url: 'https://www.nite.go.jp/nbrc/catalogue/'
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url_pattern:
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'https://www.nite.go.jp/nbrc/catalogue/NBRCCatalogueDetailServlet?ID=IFO&CAT=%s'
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- codes: [ ITM ]
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-
name:
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name: >-
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Belgian Coordinated Collections of Microorganisms (BCCM),
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Institute of Tropical Medicine Antwerp Mycobacteria Collection
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organization: 'BELSPO: Belgian Science Policy'
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country_code: BE
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url_pattern:
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'https://bccm.belspo.be/catalogues/bm-details?accession_number=ITM%%20%s'
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#--- J
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- codes: [ JCM ]
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country_code: JP
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name: Japan Collection of Microorganisms
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organization: RIKEN
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url: 'https://jcm.brc.riken.jp/en/'
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url_pattern: 'https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=%s'
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- codes: [ JMRC ]
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name: Jena Microbial Resource Collection
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organization: Friedrich Schiller University Jena
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country_name: DE
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url_pattern: 'http://www.jmrc.uni-jena.de/data.php?fsu=%s'
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+
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#--- K
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- codes: [ KACC ]
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name: Korean Agricultural Culture Collection
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organization: National Academy of Agricultural Science
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country_code: KR
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url_pattern:
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url_pattern:
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'https://genebank.rda.go.kr/eng/mic/cat/MicrobeSearch.do?sSearchWith=no&sTxt1=%s'
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- codes: [ KCTC ]
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country_code: KR
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name: Korean Collection for Type Cultures
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organization:
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'KRIBB: Korea Research Institute of Bioscience and Biotechnology'
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url: 'https://kctc.kribb.re.kr/en/collection/'
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url_pattern: 'https://kctc.kribb.re.kr/collection/view?sn=%s'
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_examples: [ KCTC 92132 ]
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_tested: 2025-03-18
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#--- L
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195
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- codes: [ LMG ]
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196
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name:
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256
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name: >-
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197
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Belgian Coordinated Collections of Microorganisms (BCCM),
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198
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Bacteria Collection Laboratorium voor Microbiologie Universiteit Gent
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name_en:
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name_en: >-
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200
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Belgian Coordinated Collections of Microorganisms (BCCM),
|
|
201
261
|
Bacteria Collection Laboratory of Microbiology, University of Ghent
|
|
202
|
-
organization:
|
|
262
|
+
organization: "BELSPO: Belgian Science Policy"
|
|
203
263
|
country_code: BE
|
|
204
|
-
|
|
264
|
+
url: "https://bccm.belspo.be/catalogues"
|
|
265
|
+
url_pattern: "https://bccm.belspo.be/catalogues/lmg-strain-details?NUM=%s"
|
|
266
|
+
|
|
267
|
+
#--- M
|
|
268
|
+
- codes: [ MAFF ]
|
|
269
|
+
country_code: JP
|
|
270
|
+
name: Ministry of Agriculture, Forestry and Fisheries Genebank
|
|
271
|
+
organization: Ministry of Agriculture Forestry and Fisheries
|
|
272
|
+
url: "https://www.gene.affrc.go.jp/index_en.php"
|
|
273
|
+
url_pattern: "https://www.gene.affrc.go.jp/\
|
|
274
|
+
databases-micro_search_detail_en.php?maff=%s"
|
|
275
|
+
_examples: [ MAFF 210265 ]
|
|
276
|
+
_tested: 2020-03-20
|
|
205
277
|
- codes: [ MCCC ]
|
|
206
278
|
name: Marine Culture Collection of China
|
|
207
279
|
organization: Third Institute of Oceanography
|
|
208
280
|
country_code: CN
|
|
209
|
-
url_pattern:
|
|
281
|
+
url_pattern: "https://mccc.org.cn/detailRecord3.asp?bcbh=%s"
|
|
282
|
+
|
|
283
|
+
#--- N
|
|
284
|
+
- codes: [ NCTC ]
|
|
285
|
+
country_code: UK
|
|
286
|
+
name: National Collection of Type Cultures
|
|
287
|
+
organization: Health Security Agency
|
|
288
|
+
url: 'https://www.culturecollections.org.uk/products/bacteria-and-mycoplasmas/'
|
|
289
|
+
url_pattern:
|
|
290
|
+
'https://www.culturecollections.org.uk/products/bacteria/detail.jsp?collection=nctc&refId=NCTC+%s'
|
|
291
|
+
- codes: [ NCIB ]
|
|
292
|
+
country_code: UK
|
|
293
|
+
name: National Collection of Industrial Bacteria
|
|
294
|
+
organization: Torry Research Station, Aberdeen, Scotland
|
|
295
|
+
_notes: Incorporated with NCIMB
|
|
296
|
+
- codes: [ NCIMB ]
|
|
297
|
+
country_code: UK
|
|
298
|
+
name: National Collection of Industrial, Food and Marine Bacteria
|
|
299
|
+
organization: NCIMB Ltd., Aberdeen, Scotland
|
|
210
300
|
- codes: [ NEPCC ]
|
|
211
301
|
name: North East Pacific Culture Collection
|
|
212
302
|
organization: The University of British Columbia
|
|
@@ -222,19 +312,33 @@ catalogues:
|
|
|
222
312
|
name: Division of Biological Sciences, National Research Council of Canada
|
|
223
313
|
organization: National Research Council
|
|
224
314
|
- codes: [ NRRL ]
|
|
225
|
-
|
|
315
|
+
country_code: US
|
|
316
|
+
name: >-
|
|
226
317
|
Agricultural Research Service Culture Collection,
|
|
227
318
|
formerly Northern Regional Research Laboratory
|
|
228
319
|
organization: National Center for Agricultural Utilization Research
|
|
229
|
-
country_code: US
|
|
230
320
|
url_pattern:
|
|
231
321
|
'https://nrrl.ncaur.usda.gov/cgi-bin/usda/prokaryote/report.html?nrrlcodes=%s'
|
|
322
|
+
|
|
323
|
+
#--- O
|
|
324
|
+
- codes: [ OCM ]
|
|
325
|
+
country_code: US
|
|
326
|
+
name: Oregon Collection of Methanogens
|
|
327
|
+
organization: Portland State University
|
|
328
|
+
|
|
329
|
+
#--- P
|
|
232
330
|
- codes: [ PCC ]
|
|
233
331
|
name: Pasteur Cultures of Cyanobacteria
|
|
234
332
|
organization: Institut Pasteur
|
|
235
333
|
country_code: FR
|
|
236
334
|
url_pattern:
|
|
237
335
|
'https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=PCC%%20%s'
|
|
336
|
+
|
|
337
|
+
#--- Q
|
|
338
|
+
|
|
339
|
+
#--- R
|
|
340
|
+
|
|
341
|
+
#--- S
|
|
238
342
|
- codes: [ SAG ]
|
|
239
343
|
name: Sammlung von Algenkulturen
|
|
240
344
|
name_en: Culture Collection of Algae
|
|
@@ -242,26 +346,49 @@ catalogues:
|
|
|
242
346
|
country_code: DE
|
|
243
347
|
url_pattern:
|
|
244
348
|
'https://sagdb.uni-goettingen.de/detailedList.php?str_number=%s'
|
|
349
|
+
|
|
350
|
+
#--- T
|
|
245
351
|
- codes: [ TBRC ]
|
|
246
352
|
name: Thailand Bioresource Research Center
|
|
247
353
|
organization: Thailand Bioresource Research Center
|
|
248
354
|
country_code: TH
|
|
249
355
|
url_pattern: 'https://tbrcnetwork.org/microb_detail.php?code=TBRC_%s'
|
|
356
|
+
|
|
357
|
+
#--- U
|
|
358
|
+
- codes: [ UAMH ]
|
|
359
|
+
country_code: CA
|
|
360
|
+
name: University of Alberta Mold Herbarium and Culture Collection
|
|
361
|
+
organization: University of Alberta
|
|
362
|
+
url: 'https://www.uamh.ca/index.html'
|
|
363
|
+
url_pattern: 'https://www.uamh.ca/details.php?id=%s'
|
|
364
|
+
_examples: [ UAMH 2956 ]
|
|
365
|
+
_tested: 2025-03-20
|
|
250
366
|
- codes: [ ULC ]
|
|
251
|
-
name:
|
|
367
|
+
name: >-
|
|
252
368
|
Belgian Coordinated Collections of Microorganisms (BCCM),
|
|
253
369
|
University of Liège Cyanobacteria Collection
|
|
254
370
|
organization: 'BELSPO: Belgian Science Policy'
|
|
255
371
|
country_code: BE
|
|
256
372
|
url_pattern:
|
|
257
373
|
'https://bccm.belspo.be/catalogues/bm-details?accession_number=ULC%%20%s'
|
|
374
|
+
|
|
375
|
+
#--- V
|
|
258
376
|
- codes: [ VKM ]
|
|
259
377
|
name: ВСЕРОССИЙСКАЯ КОЛЛЕКЦИЯ МИКРООРГАНИЗМОВ
|
|
260
378
|
name_en: All-Russian Collection of Microorganisms
|
|
261
|
-
organization:
|
|
379
|
+
organization: >-
|
|
262
380
|
Pushchino Scientific Center for Biological Research of the
|
|
263
381
|
Russian Academy of Sciences
|
|
264
382
|
country_code: RU
|
|
265
383
|
url_pattern: 'http://www.vkm.ru/strains.php?vkm=%s'
|
|
384
|
+
|
|
385
|
+
#--- W
|
|
386
|
+
|
|
387
|
+
#--- X
|
|
388
|
+
|
|
389
|
+
#--- Y
|
|
390
|
+
|
|
391
|
+
#--- Z
|
|
392
|
+
|
|
266
393
|
manifest:
|
|
267
394
|
update: 2025-03-18
|
data/lib/strain-code/version.rb
CHANGED