Remove implicit taxonomic scope from votu_class_appr, votu_seq_comp_appr, votu_db

[thomasstjerne]

Current term details
Please supply the current details of the term that you would like to update:

Term name - vOTU database
Term ID - MIXS:0000087
Structured comment name - votu_db
Definition - Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" vOTUs, if any
Expected value - database and version
Value syntax - {database};{version}
Example - NCBI Viral RefSeq;83
Preferred unit - 
Package(s) - 

Suggested update(s)
Please supply the new suggestions for any of the details listed below (only insert text to those details that should be updated):

Term name - OTU database
Term ID - MIXS:0000087
Structured comment name - otu_db
Definition - Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" OTUs, if any
Expected value - database and version
Value syntax - {database};{version}
Example - NCBI Viral RefSeq;83, UNITE;8.3
Preferred unit - 
Package(s) -  

Additional context
We have been working with different communities to draft a guide on how to publish DNA-derived data to ALA, GBIF, OBIS and similar systems. During this work it was pointed out that the terms UViGs and vOTU in field names votu_class_appr, votu_seq_comp_appr, votu_db refer to Uncultivated Virus Genome (MIUViG) and virus Operational Taxonomic Units.

Is there a reason that these terms are taxonomically scoped? If not, we suggest to remove the implicit taxonomic scope and make them relevant for a broader spectrum of DNA derived data (Fungi, Prokaryotes, Animals etc.).
See also gbif/doc-publishing-dna-derived-data#133

[only1chunts]

Thanks for bringing this up, personally I agree with your suggestion. I will add it to the agenda for the next working group call (24th May) for wider discussion. Notes will be added here after the call.

[lschriml]

I think this suggestion is a good idea.
Lynn

[lschriml]

Agreement on this update on the CIG call.
Will update in the spreadsheet.

[thomasstjerne]

Thanks for addressing this so fast!
Will this then apply to MIxS v6 already?
i.e.:

Structured comment name	MIxS ID
otu_class_appr	MIXS:0000085
otu_seq_comp_appr	MIXS:0000086
otu_db	MIXS:0000087

[only1chunts]

Yes all 3 MIXS ID (term names, structured comment names, and definitions) will be updated in the v6 update coming soon. Thanks.

[lschriml]

Yes

…

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On May 25, 2021, at 4:58 AM, Chris Hunter ***@***.***> wrote:  Yes all 3 MIXS ID (term names, structured comment names, and definitions) will be updated in the v6 update coming soon. Thanks. — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or unsubscribe.

[only1chunts]

The following updates have been made in the MIxS6 spreadsheet "MIUVIG_Checklist_v6" tab:
MIXS:0000085

Term name - OTU classification approach
Structured comment name -  otu_class_appr 
Definition - Cutoffs and approach used when clustering “species-level” OTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside OTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis

MIXS:0000086

Term name -  OTU sequence comparison approach
Structured comment name - otu_seq_comp_appr 
Definition - Tool and thresholds used to compare sequences when computing "species-level" OTUs

MIXS:0000087

Term name -  OTU database
Structured comment name - otu_db
Definition - Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" OTUs, if any