Bird.java

/**
 * Created by vrt on 23/01/2017.
 */
public class Bird {
    private String name;
    private String latinName;
    private int observations;

    public Bird(String name, String latinName) {
        this.name = name;
        this.latinName = latinName;
    }

    public String toString(){

        return String.format("%s (%s): %d observations", name, latinName, observations);
    }

    public String getName() {
        return name;
    }

    public void setName(String name) {
        this.name = name;
    }

    public String getLatinName() {
        return latinName;
    }

    public void setLatinName(String latinName) {
        this.latinName = latinName;
    }

    public int getObservations() {
        return observations;
    }

    public void setObservations() {
        this.observations++;
    }
}

Database.java

import java.util.ArrayList;

/**
 * Created by vrt on 23/01/2017.
 */
public class Database {

    private ArrayList<Bird> lista;

    public Database() {
        lista = new ArrayList<>();
    }

    public void addBird(Bird pajaros) {

        lista.add(pajaros);
    }

    public void observed(String name) {
        if (checkName(name)) {
            for (Bird pajaro : lista) {
                if (pajaro.getName().trim().toLowerCase().contains(name.trim().toLowerCase())) {
                    pajaro.setObservations();
                }
            }

        }else System.out.println("Is not a bird!");
    }

    public boolean checkName(String name) {
        for (Bird pajaro : lista) {
            if (pajaro.getName().trim().toLowerCase().contains(name.trim().toLowerCase())) {
                return true;
            }

        }
        return false;
    }

    public void statistics() {
        for (Bird pajaro : lista) {
            System.out.println(pajaro.toString());
        }
    }

    public void show(String name){
        if(checkName(name)){
        for (Bird pajaro : lista) {
            if (pajaro.getName().trim().toLowerCase().contains(name.trim().toLowerCase())) {
                System.out.println(pajaro.toString());
            }
        }}else {
            System.out.println("Is not a bird!");}
    }

}

Main.java

import java.util.Scanner;

public class Main {

    public static void main(String[] args) {
        String command;

        Scanner scanner = new Scanner(System.in);
        Database db = new Database();
        // implement your program here
        // do not put all to one method/class but rather design a proper structure to your program

        // Your program should use only one Scanner object, i.e., it is allowed to call
        // new Scanner only once. If you need scanner in multiple places, you can pass it as parameter


        do {
            System.out.print("?: ");
            command = scanner.nextLine();
            if (command.trim().toLowerCase().equals("quit")) {
                break;
            }
            switch (command.trim().toLowerCase()) {

                case "add":
                    addBird(scanner,db);
                    break;
                case "observation":
                    observation(scanner, db);
                    break;
                case "statistics":
                    statistics(db);
                    break;
                case "show":
                    show(scanner, db);
                    break;

            }

        } while (true);

    }

    private static void addBird(Scanner scanner, Database db ) {
        String name;
        String latinName;
        System.out.print("Name: ");
        name = scanner.nextLine();
        System.out.print("Latin Name: ");
        latinName = scanner.nextLine();
        if (!name.equals("") && !latinName.equals("")){
            Bird pajaro = new Bird(name, latinName);
            db.addBird(pajaro);
        }

    }

    private static void observation(Scanner scanner, Database db) {

        System.out.println("What was observed:? ");
        db.observed(scanner.nextLine());
    }

    private static void statistics(Database db) {

        db.statistics();
    }

    private static void show(Scanner scanner, Database db) {
        System.out.println("What? ");
        db.show(scanner.nextLine());
    }

}