GenomicsStandardsConsortium / mixs

Minimum Information about any (X) Sequence” (MIxS) specification
https://w3id.org/mixs
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rel_to_oxygen "facultative" clarification? #393

Open turbomam opened 2 years ago

turbomam commented 2 years ago

"facultative" is a permissible value for rel_to_oxygen

We assume that means "facultative anaerobe" but does it need to be clarified? There is some precedent for the phrase "facultative aerobe"

Are these two phrases just synonyms?

One motivation for this question is that both "facultative anaerobes" and "facultative anaerobes" can be found in the rel_to_oxygen column in https://ftp.ncbi.nlm.nih.gov/biosample/biosample_set.xml.gz. BBOP/NMDC have a project to repair suspect values like that.

There are other unexpected values for rel_to_oxygen in biosample_set.xml... how interested is this group in going over them?

turbomam commented 2 years ago

Are we talking about environments or organisms here?

See also https://en.wikipedia.org/wiki/Aerobic_organism

The INSDC biosample dataset (biosample_set.xml) has some numeric rel_to_oxygen values... is a mapping possible?