In an ordinary undirected graph, each edge $e$ links an unordered pair of vertices $x$ and $y$ (perhaps allowing for the possibility that $x = y$, as in the case of a loop). Hypergraphs generalize this, allowing a “hyperedge” to link any set of “hypervertices”. Abstracting everything away but the incidence relation between hypervertices and hyperedges, a hypergraph can be modelled as an arbitrary heterogenous relation, or more generally as a span.
As with “graph”, the word “hypergraph” does not have an entirely standardized meaning. We take as our starting point (Schmidt & Ströhlein), who define hypergraphs as heterogenous relations (usually presented as boolean-valued matrices) and give an appropriate notion of morphism. We call these “simple” hypergraphs, since they are a special case of a more general definition given below.
The category of simple hypergraphs $SimpHGrph$ has objects consisting of a pair of sets $(V,E)$ equipped with a relation $R \subseteq V \times E$, and morphisms $(R \subseteq V \times E) \to (R' \times V' \times E')$ consisting of pairs of functions $(f : V \to V', g : E \to E')$ which preserve the relation, i.e., such that for all $v\in V, e \in E$, if $(v,e) \in R$ then $(f v,g e) \in R'$.
The category of simple hypergraphs could also be referred to more dryly as “the category of binary relations”, although this has potential for confusion with Rel (whose morphisms are binary relations).
In a simple hypergraph, a hypervertex can be incident to a hyperedge at most once, but in some situations one wants to allow a hypervertex to be incident to a hyperedge multiple times. To define hypergraphs in this more general sense, we keep the intuition of hypergraphs-as-heterogenous-relations, but generalize relations to spans.
The category of hypergraphs $HGrph$ has objects consisting of a pair of sets $(V,E)$ equipped with a span $V \overset{v}\leftarrow R \overset{e}\rightarrow E$, and morphisms $(V \overset{v}\leftarrow R \overset{e}\rightarrow E) \to (V' \overset{v'}\leftarrow R' \overset{e'}\rightarrow E')$ consisting of triples of functions $(f : V \to V', g : E \to E', h:R \to R')$ such that $v'\circ h = f\circ v$ and $e'\circ h = g\circ e$.
Note that $HGrph$ is just the category of presheaves over the “walking cospan” $\bullet \rightarrow * \leftarrow \circ$, and that $SimpHGrph$ is a full subcategory of $HGrph$.
In Lawvere (1986 p.6, 1989 pp.283-4) it is pointed out that $Set^{\bullet\leftarrow\bullet\rightarrow\bullet}$ is a spatial topos since it is equivalent to the topos of sheaves on the space $X=\{a,b,c\}$ with topology $\tau=\{\emptyset,\{a\},\{b\},\{a,b\},\{a,b,c\}\}$ i.e. $X$ has two isolated points $a,b$ and another one $c$ whose only neighborhood is the whole space.
The lattice of subtoposes of $Set^{\bullet\leftarrow\bullet\rightarrow\bullet}$ consists (besides the two obvious subtoposes) of one closed and two open copies of $Set$, two closed copies of the Sierpinski topos complementing the open copies of $Set$ respectively and an open $Set\times Set=Sh(\{a,b\})=Sh_{\neg\neg}(Set^{\bullet\leftarrow\bullet\rightarrow\bullet})$ complementing the closed copy of $Set$. In particular, $Set^{\bullet\leftarrow\bullet\rightarrow\bullet}$ is a scattered topos.
There is a classical equivalence between hypergraphs and 2-colored (hence bipartite) graphs. Given a hypergraph $H$, define a graph $G(H)$ whose vertex set is the disjoint union of the hypervertices and the hyperedges of $H$, and with an edge $x_v \sim x_e$ in $G(H)$ whenever the corresponding pair $(v,e)$ are incident in $H$ (creating multiple edges in the case of multiple incidence). By coloring vertices corresponding to hypervertices in black and vertices corresponding to hyperedges in white, we satisfy the requirement that no pair of vertices sharing an edge have the same color. Conversely, this construction is clearly reversible: any 2-colored graph $G$ determines a hypergraph $H(G)$ by interpreting black vertices as hypervertices and white vertices as hyperedges that connect all of their (black vertex) neighbors.
Giving a vertex coloring of a graph $G$ with $n$ colors is equivalent to building a graph homomorphism $G \to K_n$ into the complete graph on $n$ vertices, and so graphs equipped with a $2$-coloring are naturally organized as a slice category over $K_2$. The classical equivalence between hypergraphs and 2-colored graphs can then be expressed formally as an equivalence of categories
between the category of hypergraphs and the slice over $K_2$ of the category of graphs, where by the latter we mean “pseudographs” in the greatest level of generality, allowing for loops, multiple edges between vertices, and dangling half-edges (as described in this definition). Moreover, this equivalence restricts to an equivalence
where $LoopGraph$ is the category of “loop graphs”, i.e., the full subcategory of $Grph$ whose objects are symmetric relations.
T. R. S. Walsh, Hypermaps Versus Bipartite Maps, Journal of Combinatorial Theory (B) 18, 155-163 (1975).
W. Dörfler and D. A. Waller, A category-theoretical approach to hypergraphs, Archiv der Mathematik, Volume 34, Number 1, (1980) 185-192, DOI: 10.1007/BF01224952
Gunther Schmidt and Thomas Ströhlein (1993), Relations and Graphs: Discrete Mathematics for Computer Scientists, EATCS Monographs on Theoretical Computer Science, Springer.
F. William Lawvere, Categories of Spaces may not be Generalized Spaces as Exemplified by Directed Graphs, Revista Colombiana de Matemáticas XX (1986) pp.179-186. Reprinted with commentary in TAC 9 (2005) pp.1-7. (pdf)
F. William Lawvere, Qualitative Distinctions between some Toposes of Generalized Graphs , Cont. Math. 92 (1989) pp.261-299.