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SILVA #1306

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jplfaria opened this issue Dec 12, 2024 · 6 comments · May be fixed by #1307
Open

SILVA #1306

jplfaria opened this issue Dec 12, 2024 · 6 comments · May be fixed by #1307
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New Used in combination with prefix, metaprefix, or collection for new entries Prefix

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@jplfaria
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jplfaria commented Dec 12, 2024

Prefix

silva

Name

SILVA rRNA database project

Homepage

https://www.arb-silva.de/

Source Code Repository

No response

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.

License

CC-BY-SA-4.0

Publications

doi:10.1093/nar/gks1219 | doi:10.1093/nar/gkt1209

Example Local Unique Identifier

11084

Regular Expression Pattern for Local Unique Identifier

^\d+$

URI Format String

https://www.arb-silva.de/search?q=$1

Wikidata Property

No response

Contributor Name

Jose P. Faria

Contributor GitHub

jplfaria

Contributor ORCiD

0000-0001-9302-7250

Contributor Email

[email protected]

Contact Name

Frank Oliver Glöckner

Contact ORCiD

0000-0001-8528-9023

Contact GitHub

frankolivergloeckner

Contact Email

[email protected]

Additional Comments

No response

@jplfaria jplfaria added New Used in combination with prefix, metaprefix, or collection for new entries Prefix labels Dec 12, 2024
@github-actions github-actions bot linked a pull request Dec 12, 2024 that will close this issue
@cthoyt
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cthoyt commented Dec 12, 2024

Thanks @jplfaria. I made a few updates, including putting @frankolivergloeckner as the contact person - it's Bioregistry policy to have a single point of contact and not a group email.

@cthoyt
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cthoyt commented Dec 12, 2024

@jplfaria however, it's not clear what's the actual semantic space here. The URI format doesn't seem to work when using your example. Can you link me to a page that shows something for the example acccession number 11084?

@cthoyt
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cthoyt commented Dec 12, 2024

Is it possible that https://www.arb-silva.de/browser/ssu-138.2/AJ001010 is actually the accession numbers that SILVA creates, and 11084 was an NCBI Taxonomy id?

@jplfaria
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jplfaria commented Dec 12, 2024

I was going off the folder I believe it has taxonomy data:
https://www.arb-silva.de/no_cache/download/archive/current/Exports/taxonomy/
In that folder in specific my plan was to work ith the file https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/tax_slv_ssu_138.2.txt.gz take a look at the contents there and let me know if that makes any sense. There are additional files with mappings, etc, but I was going to start just with that. Also, I decided only to make this ontology file for the SSU data since that is the most commonly used. We could, in theory, have a separate ontology file for the LSU data or merge both, which I am not sure is a good idea.

@cthoyt
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cthoyt commented Dec 12, 2024

Archaea;Crenarchaeota;Nitrososphaeria;Nitrosotaleales;	42950	order		138
Archaea;Crenarchaeota;Nitrososphaeria;Nitrosotaleales;Nitrosotaleaceae;	42951	family		138
Archaea;Crenarchaeota;Nitrososphaeria;Nitrosotaleales;Nitrosotaleaceae;Candidatus Nitrosotalea;	42952	genus		138

here are a few lines in that file, I think it corresponds to https://www.arb-silva.de/browser/ssu-121/AB050229/ but I can't figure out where any of the numbers (42950, 42951, 42952) are on the web page. Or, what does AB050229 mean?

@jplfaria
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jplfaria commented Dec 12, 2024

We are bpth having issues understanding what is going on here. Maybe starting this entry could have been more timely. I will spend more time trying to understand the resource to be able to properly represent this entry.

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