Automate deepening of BPs using RHEA; example from lactate biosynthetic process

[cmungall]

"lactate biosynthesis" is a broad term that IMO should be do-not-annotate. In general both the form (L/D) and the mechanism are well known.

Here is the current distribution of annotations

• [] GO:0009058 ! biosynthetic process
  • [i] GO:1901617 ! organic hydroxy compound biosynthetic process
    • [i] GO:0019249 ! lactate biosynthetic process (34)
      • [i] GO:0036530 ! protein deglycation, methylglyoxal removal (2)
      • [i] GO:0019248 ! D-lactate biosynthetic process from methylglyoxal via (R)-lactaldehyde
      • [i] GO:0019244 ! lactate biosynthetic process from pyruvate (15)
        • [i] GO:0019246 ! L(+)-lactate biosynthetic process from pyruvate
        • [i] GO:0019245 ! D(-)-lactate biosynthetic process from pyruvate

Aside: we should consider fermentation synonyms to be consistent with MetaCyc, unipathways, and a lot of the literature.

LDHA
https://www.uniprot.org/uniprotkb/P00338/entry
Process: "lactate metabolism" (should be do-not-annotate)
Reaction: (S)-lactate + NAD+ = pyruvate + NADH + H+
Unipathways: Fermentation; pyruvate fermentation to lactate; (S)-lactate from pyruvate: step 1/1

LDHC
https://www.uniprot.org/uniprotkb/P07864/entry
Process:
"lactate metabolism" (IBA - why not deeper for IBA?)
lactate biosynthetic process from pyruvate (still not deep enough)
Unipathways:Fermentation; pyruvate fermentation to lactate; (S)-lactate from pyruvate: step 1/1.

• LDHD
  https://www.uniprot.org/uniprotkb/Q86WU2/entry
  Involved in D-lactate, but not L-lactate catabolic process.
  Process: lactate catabolic process
  Reaction: D-lactate dehydrogenase

In all these cases we could be using the reactions to make the process annotations at the correct level. The metabolism here is well understood, it's not clear how we ended up with such high level annotations in the first place.

Aside: for mouse, this publication
https://amigo.geneontology.org/amigo/reference/PMID:20935145

yields an annotation of mouse tp53 to glucose catabolic process to lactate via pyruvate but it's clearly acting as a regulator