unclear on difference between `host_taxid` & `specific_host`

[mslarae13]

host_taxid https://genomicsstandardsconsortium.github.io/mixs/0000250/ Description: NCBI taxon id of the host, e.g. 9606 Name Description Checklist/Extension PlantAssociated A collection of terms appropriate when collecting samples and sequencing samp... Extension HostAssociated A collection of terms appropriate when collecting samples and sequencing samp... Extension SymbiontAssociated A collection of terms appropriate when collecting samples and sequencing samp... Extension FoodFarmEnvironment A collection of terms appropriate when collecting samples and performing sequ... Extension Agriculture A collection of terms appropriate when sequencing samples obtained in an agri... Extension

specific_host https://genomicsstandardsconsortium.github.io/mixs/0000029/ Description: Report the host's taxonomic name and/or NCBI taxonomy ID Name Description Checklist/Extension MigsVi Minimal Information about a Genome Sequence: virus Checklist Miuvig Minimum Information About an Uncultivated Virus Genome Checklist MigsPl Minimal Information about a Genome Sequence: plasmid Checklist MigsEu Minimal Information about a Genome Sequence: eukaryote Checklist MigsBa Minimal Information about a Genome Sequence: cultured bacteria/archaea Checklist Agriculture A collection of terms appropriate when sequencing samples obtained in an agri... Extension

These seem to be the same descriptions. I think this should be in extensions, not checklists.

Are these terms different? Should they be consolidated?

[mslarae13]

linked to https://github.com/GenomicsStandardsConsortium/mixs/issues/128

[lschriml]

host_taxid is intended to capture the NCBI taxonomy ID

specific_host is used when there is no defined NCBI taxonomy ID or the taxonomy ID is from a source other than NCBI.

Keep both terms.

[mslarae13]

@lschriml could we re-open this and add clarity? You said "specific_host is used when there is no defined NCBI taxonomy ID or the taxonomy ID is from a source other than NCBI."

But the description of specific host says "Report the host's taxonomic name and/or NCBI taxonomy ID" ... so we should change the description to "Report the host's taxonomic name when an NCBI taxonomy ID is unavailable or the taxonomu ID is from a source other than NCBI"

yes?

[lschriml]

Hello Montana, Good point, I'll re-open the ticket and get more input/decision from CIG.

Cheers, Lynn