@Entity
@Table(name = "base_object")
public class BaseObject implements Serializable {
    @Id
    @Column(name = "id")
    @GeneratedValue(strategy = GenerationType.AUTO)
    private Integer id;
    @Column(name = "name", nullable = false, unique = true)
    private String name;
    @ManyToMany
    @JoinTable(
            name = "related_objects",
            joinColumns = @JoinColumn(name = "base_name", referencedColumnName = "name"),
            inverseJoinColumns = @JoinColumn(name = "related_name", referencedColumnName = "name")
    )
    private Set<RelatedObject> related = new HashSet<>();
}

@Entity
@Table(name = "related_object")
public class RelatedObject {
    @Id
    @Column(name = "id")
    @GeneratedValue(strategy = GenerationType.AUTO)
    private Integer id;
    @Column(name = "name", nullable = false, unique = true)
    private String name;
}

        BaseObject b = entityManager.find(BaseObject.class, bId);
        RelatedObject r = entityManager.getReference(RelatedObject.class, rId);
        b.getRelated().add(r);
        entityManager.flush();