One area that's illuminating is the effort to annotate the results of whole-genome sequencing projects. Tagging stretches of the genome which represent coherent units of some sort, and then relating them to some functional capability of the organism, is not at all a solved problem.
Here's an overview from 2011 where they're struggling to even get a good tagging system up for single-celled microorganisms (a much easier problem than multicellar genomes like humans):
> "Highlights include the development of annotation assessment tools, community acceptance of protein naming standards, comparison of annotation resources to provide consistent annotation, and improved tracking of the evidence used to generate a particular annotation. The development of a set of minimal standards, including the requirement for annotated complete prokaryotic genomes to contain a full set of ribosomal RNAs, transfer RNAs, and proteins encoding core conserved functions, is an historic milestone."
Here's an overview from 2011 where they're struggling to even get a good tagging system up for single-celled microorganisms (a much easier problem than multicellar genomes like humans):
https://pubmed.ncbi.nlm.nih.gov/22180819/
> "Highlights include the development of annotation assessment tools, community acceptance of protein naming standards, comparison of annotation resources to provide consistent annotation, and improved tracking of the evidence used to generate a particular annotation. The development of a set of minimal standards, including the requirement for annotated complete prokaryotic genomes to contain a full set of ribosomal RNAs, transfer RNAs, and proteins encoding core conserved functions, is an historic milestone."