NTR: phosphatidylinositol 4-phosphate biosynthetic process

[ValWood]

Please provide as much information as you can:

• Suggested term label:

• phosphatidylinositol 4-phosphate biosynthetic process

(see below)

• Definition (free text)

• standard def

• Reference, in format PMID:#######

• PMID:39239853
  Title | Fission yeast Duc1 links to ER-PM contact sites and influences PM lipid composition and cytokinetic ring anchoring.
  -> PMID: 28784611

• Gene product name and ID to be annotated to this term

f.y stt4 at first

• Parent term(s)

phosphatidylinositol phosphate biosynthetic

• Synonyms (please specify, EXACT, BROAD, NARROW or RELATED)

• PI4P biosynthesis
• 1-phosphatidyl-1D-myo-inositol biosynthetic process
• phosphatidylinositol (PI)-4- phosphate biosynthetic process
• phosphatidylinositol-4-phosphate synthesis
• 1-phosphatidyl-1D-myo-inositol 4-phosphate biosynthesis

• Any other information

seven PIP species found in eukaryotic cells, PM phosphatidylinositol (PI)-4- phosphate (PI4P) and the most abundant PM PIP species, PI-4,5-bisphosphate [PI(4,5)P2], are important for the fidelity of cell division in diverse organisms (Eggert et al., 2004; Emoto et al., 2005; Field et al., 2005; Janetopoulos et al., 2005; Snider et al., 2017b, 2018b; Wong et al., 2005).

we have

GO:1903102 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate biosynthetic process is_a
GO:1902635 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process is_a
GO:0036092 phosphatidylinositol-3-phosphate biosynthetic process is_a
GO:1904563 phosphatidylinositol 5-phosphate biosynthetic process

This request adds one more, so we are still missing 2
We also need to standardise and use either 1-phosphatidyl-1D-myo-inositol or phosphatidylinositol in these labels.
I think Rhea uses 1-phosphatidyl-1D-myo-inositol but in practice everyone uses "phosphatidylinositol"
all need synonyms and common names adding

(not to self stt4)

[ValWood]

also note for some of these the common names are in comments
these aren't searchable:

[ValWood]

@pgaudet @sjm41
what should the standardization be with hyphens here?

phosphatidylinositol 4-phosphate synthesis
or
phosphatidylinositol-4-phosphate synthesis

We have both
phosphatidylinositol-3-phosphate synthesis
phosphatidylinositol 5-phosphate synthesis

[sjm41]

Funny you mention this - @rozaru and I were talking about exactly this issue (in another context) earlier this week.
We couldn't work out if there is a 'correct' standardisation, or what this should be, right Rossana? (though we didn't look too hard).
For the terms we were looking at, I think we looked at the relevant enzyme entries in EC and used their hyphenation.
In this case, I guess the authority would be ChEBI - that is, we use whatever hyphenation they use?

[ValWood]

Also some labels use
1-phosphatidyl-1D-myo-inositol
and some use
phosphatidylinositol

Rhea uses 1-phosphatidyl-1D-myo-inositol but in practice everyone uses "phosphatidylinositol"
Does GO need to follow Rhea for process the same way we do for enzymes?

[ValWood]

GO:1902635 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process

• Comments
  Phosphatidylinositol-4,5-bisphosphate, PtdIns(4,5)P(2) common name.
  migrated to synonyms

[ValWood]

Have used phosphatidylinositol 4-phosphate biosynthetic process here,
will open a new ticket to resolve the inconsistencies

logical def uses
1-phosphatidyl-1D-myo-inositol 4-phosphate ChEBI ID | CHEBI:17526
but CHEBI mustn't be consistent because

'biosynthetic process'
and ('has primary output' some 'phosphatidylinositol 3-phosphate')

[ValWood]

I used
1-phosphatidyl-1D-myo-inositol 4-phosphate ChEBI ID | CHEBI:17526
but that gives

if [ -s 'tmp_referenced_chebi_nums_not_7_3.txt' ]; then echo "ERROR: CHEBI IDs should be mapped to pH 7.3:" && cat tmp_referenced_chebi_nums_not_7_3.txt && exit 1; else exit 0; fi
ERROR: CHEBI IDs should be mapped to pH 7.3:
17526

I don't know how to fix that so for now I will remove the logical def.
@pgaudet

[ValWood]

1-phosphatidyl-1D-myo-inositol 4-phosphate(3−)