We study the ideals of the partition, Brauer, and Jones monoid, establishing various combinatorial results on generating sets and idempotent generating sets via an analysis of their Graham–Houghton graphs. We show that each proper ideal of the partition monoid Pn is an idempotent generated semigroup, and obtain a formula for the minimal number of elements (and the minimal number of idempotent elements) needed to generate these semigroups. In particular, we show that these two numbers, which are called the rank and idempotent rank (respectively) of the semigroup, are equal to each other, and we characterize the generating sets of this minimal cardinality. We also characterize and enumerate the minimal idempotent generating sets for the largest proper ideal of Pn, which coincides with the singular part of Pn. Analogous results are proved for the ideals of the Brauer and Jones monoids; in each case, the rank and idempotent rank turn out to be equal, and all the minimal generating sets are described. We also show how the rank and idempotent rank results obtained, when applied to the corresponding twisted semigroup algebras (the partition, Brauer, and Temperley–Lieb algebras), allow one to recover formulae for the dimensions of their cell modules (viewed as cellular algebras) which, in the semisimple case, are formulae for the dimensions of the irreducible representations of the algebras. As well as being of algebraic interest, our results relate to several well-studied topics in graph theory including the problem of counting perfect matchings (which relates to the problem of computing permanents of {0,1}-matrices and the theory of Pfaffian orientations), and the problem of finding factorizations of Johnson graphs. Our results also bring together several well-known number sequences such as Stirling, Bell, Catalan and Fibonacci numbers.