'Secondary GO ID' errors in some sessions

[jseager7]

(References https://github.com/pombase/canto/issues/2255)

The PHI-Canto GAF export has errors related to usage of a 'Secondary GO ID' in two curation sessions:

• 'innate immune response-activating signal transduction' (GO:0009870) in PMID:20601497, and
• 'hyphal growth' (GO:0075061) in PMID:29567712.

According to the OLS, both the above terms are obsolete, and replaced by the following:

• GO:0009870 replaced by GO:0002758 'innate immune response-activating signal transduction';
• GO:0075061 replaced by GO:0030448 'hyphal growth'.

@ValWood @CuzickA I haven't assigned this issue to anyone, because I'm not sure who wants to fix it.

---

On a related note, I think this error provides evidence that GO don't want annotations made to alternative GO IDs, since GO:0075061 is an alternative ID for its successor, GO:0030448.

[kimrutherford]

On a related note, I think this error provides evidence that GO don't want annotations made to alternative GO IDs, since GO:0075061 is an alternative ID for its successor, GO:0030448.

Sounds like if we fix https://github.com/pombase/canto/issues/2362 then these GAF errors will go away.

[jseager7]

I've checked the sessions again: for the primary terms, PMID:20601497 now has GO:0002758 'innate immune response-activating signal transduction', and PMID:29567712 now has GO:0030448 'hyphal growth'.

However, there is a part_of annotation extension in PMID:20601497 that still has the (merged) GO:0009870 term ID, presumably because Canto doesn't check annotation extension terms in the same way.

@CuzickA could you fix this one remaining extension by deleting and re-adding it with the same term, or by amending the term ID to GO:0002758 using edit as text? I can try doing it if you're happy for the change to be made.

[CuzickA]

I've made the change. Closing ticket.