The Wikidata:WikiProject Chemistry is the primary source describing the data models used for chemistry in Wikidata. It is also the place where discussions are held about these topics. Over time, the model has evolved. We do not intend to repeat all the content, but we will highlight some aspects reflecting how Wikidata thinks about chemistry and the quality of the chemistry data in Wikidata.
Most of the modelling of chemical entries in Wikidata is described in the aforementioned WikiProject_Chemistry. The project provides many guidelines of the structure of methods.
An overview of guidelines is given in https://www.wikidata.org/wiki/Wikidata:WikiProject_Chemistry/Guidelines
A principle guideline is that any chemical is modelled instance of (P31) type of chemical entity (Q113145171) for specific chemical, but as one of the many available metaclasses.
This page describes the main classes of chemical entities, such as structural class of chemical entities (Q47154513), group of stereoisomers (Q59199015), and class of chemical entities with similar applications or functions (Q56256173). A full overview is found at https://www.wikidata.org/wiki/Wikidata:WikiProject_Chemistry/Guidelines/Basic_metaclasses_and_relations
Specific guidelines exist, such as for undefined isomeric or isotopic features: https://www.wikidata.org/wiki/Wikidata:WikiProject_Chemistry/Guidelines/Entities_with_undefined_isomeric_or_isotopic_features
https://www.wikidata.org/wiki/Wikidata:WikiProject_Chemistry/Guidelines/Naming_conventions
https://www.wikidata.org/wiki/Wikidata:WikiProject_Chemistry/Guidelines/Illustrations
Part of these models can be expressed as shape expressions. For this, Wikidata uses ShEx (see shex.io). These shape expressions formalize a data model and allow a computer to report inconsistency complementary and extending the propery constraints. The use of of shape expressions has previously been used for viruses, proteins, and genes [1].
Some of them are linked to their corresponding item, some are not, see: https://w.wiki/FqRc
The following entity schema describe the basic models of: