Many thanks, @dodobot, for this post- it’s good to see the topic explored. I’d like quickly to add two comments.
First, if a Material Sample does indeed relate to organisms cultured in a dish (or similar), these may be just as robustly identified as any observable specimen. A subset of data in our global network has always come from living culture collections, where live strains of microorganisms and maintained for long-term reference and use. In such cases, even if BasisOfRecord is MaterialSample, we’d be better off treating it the same as a specimen.
Secondly, you are quite correct to give guidance on recognising and filtering records that derive purely from DNA/RNA but it would be sad if readers simply assume that such data are always worse than data from othe sources. (You don’t say this!) In particular, all methods vary in their ability to derect all species in a sample or community, so that is not a unique weakness of metagenomics, and all methods lead to some proportion of misidentifications.As we proceed, it will be good to make the basis of evidence clear rather than just the basis of record and for us to develop models of uncertainty and repeatability around different methods/protocols (including selection of different sequencing platforms, primers, etc.).