Hi,
I have a question about how the molecule (CHEBI:25367) and ion (CHEBI:24870) classes work. The definitions say that a molecule is
Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
and an ion is
A molecular entity having a net electric charge.
This implies to me that these classes are disjoint - a molecular entity can be either neutral or charged, but not both. However, this does not reflect the current practice in ChEBI. I found 2,257 classes that subclasses of both ion and molecule. Am I missing something here?
Here are some examples of larger classes in ChEBI that have both superclasses:
| chebi_id |
name |
number of subclasses |
| 64482 |
phosphatidylcholine |
1100 |
| 63048 |
1,3-thiazolium cation |
31 |
| 57875 |
2-acyl-sn-glycero-3-phosphocholine |
35 |
| 57880 |
1-phosphatidyl-1D-myo-inositol(1-) |
75 |
| 47811 |
penamcarboxylate |
33 |
| 64583 |
sphingomyelin |
322 |
| 58168 |
1-O-acyl-sn-glycero-3-phosphocholine |
74 |
| 36702 |
2-acyl-1-alkyl-sn-glycero-3-phosphocholine |
66 |
| 190712 |
epoxy monocarboxylic acid anion |
49 |
@amalik01 I believe we already had an exchange via mail about phosphocholines where you suggesting separating the class into a neutral phosphocholines and a charged phosphocholines(1+). This would probably solve this for the majority of classes. Maybe one can do something similar for the other classes as well?
I have attached a full list of molecule-ion classes in ChEBI (not including classes that have superclasses that also fall into the intersection).
molecule_ion_overlap.csv
Hi,
I have a question about how the
molecule(CHEBI:25367) andion(CHEBI:24870) classes work. The definitions say that a molecule isand an ion is
This implies to me that these classes are disjoint - a molecular entity can be either neutral or charged, but not both. However, this does not reflect the current practice in ChEBI. I found 2,257 classes that subclasses of both ion and molecule. Am I missing something here?
Here are some examples of larger classes in ChEBI that have both superclasses:
@amalik01 I believe we already had an exchange via mail about phosphocholines where you suggesting separating the class into a neutral
phosphocholinesand a chargedphosphocholines(1+). This would probably solve this for the majority of classes. Maybe one can do something similar for the other classes as well?I have attached a full list of molecule-ion classes in ChEBI (not including classes that have superclasses that also fall into the intersection).
molecule_ion_overlap.csv