calcium ion

[muthuvenkat]

chebi has:

CHEBI:29108 calcium(2+) [SYNONYM: "CALCIUM ION" (related)] [SYNONYM: "calcium(2+)" (exact)] [SYNONYM: "calcium(II) cation" (related)] [SYNONYM: "Ca2+" (related)] [SYNONYM: "Ca(2+)" (related)] [SYNONYM: "calcium(2+) ion" (exact)] [SYNONYM: "calcium(II) cation" (exact)] [SYNONYM: "Ca" (related)] [SYNONYM: "[Ca++]" (related)] [SYNONYM: "InChI=1/Ca/q+2" (related)]

GO frequently uses the term "calcium ion" embedded in other terms. Sometimes this is qualified specifically as Ca2+ in the definition:

calcium ion binding [DEF: "Interacting selectively with calcium ions (Ca2+)."]

but often it is not.

What is the best practice for talk of calcium ions here? In chebi, this is related to a related synonym rather than exact synonym (why ALL IN CAPS by the way? Can we have these lowercased?)

Is GO being imprecise when it uses the term?

If not, perhaps "calcium ion" can be raised to exact synonym?

Reported by: cmungall

[muthuvenkat]

Logged In: YES user_id=1473024 Originator: NO

Here's the distinction between "of biological interest" and "in biological conditions".

It's EXACT if you're dealing with a biological system, but a spectroscopist, particle physicist or an astronomer might be describing a calcium ion with up to 20 electrons missing.

So for text mining I'd rather not have it as EXACT, but for biomedical ontology alignment it definitely ought to be.

Original comment by: batchelorc

[muthuvenkat]

Logged In: YES user_id=254723 Originator: YES

It is actually possible to have contextual synonyms in obof1.2; you could have a type of synonym just for biologists and another for spectroscopists, and qualify the scope (exact/related/...) with the type.

I would be happy if chebi's structure reflected chemical entities as they exist in reality here; eg

calcium ion %calcium cation %%calcium(2+) %%... %calcium anion %%... %%...

consistency has a lot of benefits in ontology construction; and for end users too

biological ontologies would be free to either reference calcium ion or the more specific Ca2+.

Original comment by: cmungall

[muthuvenkat]

Logged In: YES user_id=802919 Originator: NO

> What is the best practice for talk of calcium ions here? In chebi, this is > related to a related synonym rather than exact synonym (why ALL IN CAPS by > the way? Can we have these lowercased?)

The answer to the last question is NO. The "CALCIUM ION" term is coming from chemPDB (now MSDchem); almost all their names are in uppercase which is clearly the PDB legacy but we are not changing it. (In the same fashion, names from KEGG have the first letter capitalised.)

Just to illustrate the point that not every calcium ion is calcium(2+), I've entered calcium(1+) (CHEBI:39099) which exists in reality but is not common in biological systems.

Original comment by: kiri11

[muthuvenkat]

Logged In: YES user_id=254723 Originator: YES

Ah I see, synonyms in ChEBI a retrospective mappings of how a term is used in another database, similar to xrefs. In other obo ontologies they are added prospectively by the curators to aid human search, text mining etc.

I accept that not evey calcium ion is a Ca(2+) ion but my point is should calcium ion should be a term in its own right, the superclass of Ca(2+) and Ca(1+)?

Original comment by: cmungall

[muthuvenkat]

Logged In: YES user_id=802919 Originator: NO

I just did calcium and other alkaline earth metal cations and ions. Should appear in the next ChEBI release.

Original comment by: kiri11

[muthuvenkat]

• status: open --> closed

Original comment by: kiri11