JPA create, edit and delete entities from database

How should I manage the create, edit and delete operations with entites as simple as possible?

For example:

User:

public class User {

    @Id
    @GeneratedValue(strategy = GenerationType.AUTO)
    private Integer id;

    private String name;

    ...

    // Item can't exist without user
    @OneToMany(cascade=CascadeType.ALL,mappedBy = "user",orphanRemoval=true)
    private Set<Item> items = new HashSet<Item>();

    public Set<Item> getItems() { return items; }

    public void addItem(Item item) {
        items.add(item);
    }

    public void removeItem(Item item) {
        if(!items.contains(item)) return;
        items.remove(item);
    }

    // Group can exist without a user
    @ManyToMany(cascade = {CascadeType.MERGE, CascadeType.PERSIST, CascadeType.REFRESH},mappedBy="users")
    private Set<Group> groups = new HashSet<Group>();

    public Set<Group> getGroups() { return groups; }

    public void setGroups(Set<Group> groups) { this.groups = groups; }

    public void addGroup(Group group) {
        groups.add(group);
    }

    publi void removeGroup(Group group) {
        if(!groups.contains(group)) return;
        groups.remove(group);
    }

    ...
}

Group:

@Entity
public class Group {

    @Id
    @GeneratedValue(strategy = GenerationType.AUTO)
    private Integer id;

    private String name;

    ...

    @ManyToMany(cascade = {CascadeType.MERGE, CascadeType.PERSIST, CascadeType.REFRESH})
    @JoinTable(name = "GroupToUser", joinColumns =
    @JoinColumn(name = "GroupId", referencedColumnName="Id"), inverseJoinColumns =
    @JoinColumn(name = "UserId", referencedColumnName="Id"))
    private Set<User> users = new HashSet<User>();

    public Set<User> getUsers() { return users; }

    public void setUsers(Set<User> users) { this.users = users; }

    public void addUser(User user) {
        user.addGroup(this);
    }

    publi void removeUser(User user) {
        if(!users.contains(user)) return;
        users.remove(user);
    }

    ...
}

Item:

@Entity
public class Item {

    @Id
    @GeneratedValue(strategy = GenerationType.AUTO)
    private Integer id;

    private String name;

    ...

    @ManyToOne(cascade = {CascadeType.MERGE, CascadeType.PERSIST, CascadeType.REFRESH})
    @JoinColumn(name="UserId")
    private User user;

    public Set<User> getUser() { return user; }

    public void setUser(User user) {
        this.user = user;
    }

    publi void removeUser() {
        this.user = null;
    }

    ...
}

Am I using the jpa annotations right?

What should I write here?

EntityManager em = getEntityManager();
em.getTransaction().begin();
???
em.getTransaction().commit();

Do I have to just call the em.remove/persist/merge methods for delete/create/edit operations?

And when should I use the javax.persistence.EntityManager.getReference method in these operations?