We prove that the annihilating-ideal graph of a commutative semigroup with unity is, in general, not weakly perfect. This settles the conjecture of DeMeyer and Schneider [‘The annihilating-ideal graph of commutative semigroups’, J. Algebra469 (2017), 402–420]. Further, we prove that the zero-divisor graphs of semigroups with respect to semiprime ideals are weakly perfect. This enables us to produce a large class of examples of weakly perfect zero-divisor graphs from a fixed semigroup by choosing different semiprime ideals.

In this paper, it is proved that the complement of the zero-divisor graph of a partially ordered set is weakly perfect if it has finite clique number, completely answering the question raised by Joshi and Khiste [‘Complement of the zero divisor graph of a lattice’, Bull. Aust. Math. Soc. 89 (2014), 177–190]. As a consequence, the intersection graph of an intersection-closed family of nonempty subsets of a set is weakly perfect if it has finite clique number. These results are applied to annihilating-ideal graphs and intersection graphs of submodules.