The commuting graph of a finite non-commutative semigroup $S$, denoted $\cg(S)$, is a simple graph whose vertices are the non-central elements of $S$ and two distinct vertices $x,y$ are adjacent if $xy=yx$. Let $\mi(X)$ be the symmetric inverse semigroup of partial injective transformations on a finite set $X$. The semigroup $\mi(X)$ has the symmetric group $\sym(X)$ of permutations on $X$ as its group of units. In 1989, Burns and Goldsmith determined the clique number of the commuting graph of $\sym(X)$. In 2008, Iranmanesh and Jafarzadeh found an upper bound of the diameter of $\cg(\sym(X))$, and in 2011, Dol\u{z}an and Oblak claimed (but their proof has a GAP) that this upper bound is in fact the exact value.
The goal of this paper is to begin the study of the commuting graph of the symmetric inverse semigroup $\mi(X)$. We calculate the clique number of $\cg(\mi(X))$, the diameters of the commuting graphs of the proper ideals of $\mi(X)$, and the diameter of $\cg(\mi(X))$ when $|X|$ is even or a power of an odd prime. We show that when $|X|$ is odd and divisible by at least two primes, then the diameter of $\cg(\mi(X))$ is either 4 or 5. In the process, we obtain several results about semigroups, such as a description of all commutative subsemigroups of $\mi(X)$ of maximum order, and analogous results for commutative inverse and commutative nilpotent subsemigroups of $\mi(X)$. The paper closes with a number of problems for experts in combinatorics and in group or semigroup theory.