Another option would be annotations that generate code on compile like Project Lombok does [13].
31 An alternative mechanism for readers to communicate discrepancies to other readers would be an annotation system such as PubMed Commons or Pubpeer.
One of the potential applications of a comprehensive resource like tbvar would be for annotation of variants derived from re-sequencing of isolates, especially in clinical settings.
One possible explanation for the difference in the relative proportion of essential genes in these three organisms would be an incomplete/incorrect annotation of the genome of Synechocystis sp. PCC6803.
It would be great if annotations could be implemented in future releases of JSAV.
One promising extension to our approach would be to include 'latent' annotation terms in the CRF structure, to account for additional rare annotation terms for which we would not attempt to obtain a prediction.
Realistically, completely removing the manual stage of annotation would be imprudent, however, improving current automated pipelines may greatly reduce the time spent manually checking the annotation.
An example of this would be a literature-based annotation for a gene to 'protein serine/threonine kinase activity' (GO 0004674) paired with a computationally predicted annotation to 'kinase activity' (GO 0016301).
For example, a literature-based annotation that exactly matched one of the computational predictions and was a parent of another computational annotation would be classified only as 'shallow' and not as both 'exact match' and 'shallow'shallow
Such annotation tier initializations of linguistically interesting phenomena would be useful for annotators.
