Suggested "do not annotate" terms

[ValWood]

See https://github.com/geneontology/go-annotation/issues/4115 Also GOC presentation. This is a selection of high-level terms used in annotation.

• [x] GO:0034641 cellular nitrogen compound metabolic process [56 direct annotation, 56 ARBA IEA, 0 EXP]
• [x] GO:0006807 nitrogen compound metabolic process [597 direct annotation, IEAs from InterPro, CGD, 97 PAINT IBA, 53 EXP]
• [x] GO:1901564 organonitrogen compound metabolic process [81 direct annotation, All ARBA IEA]
• [x] GO:0044238 primary metabolic process [241 direct annotation, 239 ARBA IEA, 2 EXP]
• [x] GO:0071704 organic substance metabolic process [231 direct annotation, 229 ARBA IEA, 2 EXP]
• [x] GO:0043170 macromolecule metabolic process [383 direct annotation, 377 IEA, 122 ARBA IEA, 3 EXP]
• [x] GO:0110165 cellular anatomical entity [1507 direct annotation, 1505 ARBA IEA, EXP 2]
• [x] GO:0048588 developmental cell growth [70 direct annotation, 52 TAIR IEA, 7 EXP]
• [x] GO:0048856 anatomical structure development [2425 direct annotation, 719 ARBA IEA, 1673 PAINT IBA, 33 EXP]
• [ ] GO:0098771 inorganic ion homeostasis [87 direct annotation, IEA TAIR 78, 1 EXP] TAIR from https://amigo.geneontology.org/amigo/reference/PMID:34562334 (these are predictions)
• [ ] GO:0060560 developmental growth involved in morphogenesis [74 direct annotation, 54 TAIR IEA, 8 EXP] TAIR from https://amigo.geneontology.org/amigo/reference/PMID:34562334 (these are predictions)

[XXX direct annotation, ARBA IEA, EXP]

GO:0043231 intracellular membrane-bounded organelle HOLDING OFF ON THIS ONE HAS 14198 annotations 879 EXP, I wonder why??? 724 are HPA, are these useful? what does it mean? 10,794 are IBA?

• [x] GO:0043414 macromolecule methylation (2 direct) (already present)

• [x] changed "metabolic process" from "do not manually annotate" to "do not annotate"

• [x] GO:1901564 organonitrogen compound metabolic process [101, ARBA IEA]

• [x] organonitrogen compound catabolic process [2 EXP]

• [x] organonitrogen compound biosynthetic process [ 46 ALl IEA]

• [x] GO:0032879 regulation of localization [19 direct annotation, 4 EXP]

• [x] GO:0016310 phosphorylation AND ALL CHILDREN? (for now I did only the term)

• [x] GO:0016311 dephosphorylation AND ALL CHILDREN? (for now I did only the term)

• [x] GO:0046483 heterocycle metabolic process [48 direct annotation, 7 EXP]

[ValWood]

@pgaudet do you agree with these? I can check the direct annotation numbers before proceeding and flag the ones with not so many annotations (usually they only have a small number)

[ValWood]

also

• [x] lip2 | GO:1901576 | organic substance biosynthetic process | IEA with ARBA00026382 |   | GO_REF:0000117 |

[48 direct annotation, mainly ARBA IEA, 0 EXP]

• [x] (also did organic substance catabolic process)

[ValWood]

@pgaudet can I add these? I think most have no annotations but it will prevent future function predictions (at least we can explain /filter them). I think most of these came from function prediction evaluation.

[pgaudet]

Yes yes

[ValWood]

• [-] Response to organic substance (leaving for now, has quite a lot of direct annotation)
• [x] macromolecule modification

[ValWood]

• [x] ion binding
• | − | (46) | DisProt
• | − | (4) | RGD

[gthayman]

4 RGD annotations moved.

[ValWood]

Thanks @gthayman

Closing this one, MODs can fix from the logs.

@pgaudet is this currently a soft check or a hard check?

[pgaudet]

soft check

[ValWood]

Could it be made a hard check for IEA maybe?