Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Relationship between viral lineages #620

Huffmaar opened this issue Jul 26, 2022 · 1 comment

Relationship between viral lineages #620

Huffmaar opened this issue Jul 26, 2022 · 1 comment


Copy link

For CIDO, we represent the different sub-variants of SARS-CoV-2 that emerge, including the PANGO lineage identification (BA.1, BA.2, etc.). However, PANGO lineage identification gives a set of common amino acids that are used to identify if a specific SARS-CoV-2 sequence belongs to a lineage. However, a SARS-CoV-2 virus can be identified as a member of a lineage if it contains a majority of these specific amino acid mutations or it it contains a majority of a set of amino acids from a derived lineage. More relevantly, it is possible for more derived viral lineages to contain a different set of mutations. As CIDO is interested in representing these amino acid mutations, it would not be appropriate to link these lineages by an 'is_a' relationship.
We initially planned and implemented to use 'derives from' (RO:1000100) and 'derives into' (RO:1000101) relationships to link these derived from lineages. However, the definition of these terms are such that it asserts that if X 'derives to' Y, then X ceases to exist in its entirety. This is not necessarily the case for these viral lineages.
As such, we would request RO to add 'evolves from' and 'evolves into' as new relationships. We propose a definition for X 'evolves into' Y as the following: "X 'evolves to' Y such that X is subjected to some evolutionary process such that Y is produced from some an ancestral X". The primary difference is that it is possible for X and Y to coexist. I also did not specify if X or Y as material entities as it is possible to apply evolutionary pressure to symbols and other information content entities. If a more specific relation is desired to limit the range and domain of X and Y, that is fine.

Copy link

addiehl commented Dec 13, 2022

See RO:0002156 'derived by descent from'. Does this satisfy your needs? If so please close this issue. Thanks.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
None yet

No branches or pull requests

3 participants