A Resource reference binding could not be found for the jdbc/mydb resource CWNEN0044E

You need to add the binding in ibm-web-bnd.xml:

<resource-ref name="jdbc/mydb" binding-name="jdbc/jndi" />

jdbc/jndi: You will configure jndi in websphere admin console,
Reference name: resource-ref name should match with res-ref-name

<resource-ref>
    <res-ref-name>jdbc/mydb</res-ref-name>
    <res-type>javax.sql.DataSource</res-type>
    <res-auth>Container</res-auth>
    <res-sharing-scope>Shareable</res-sharing-scope>
 </resource-ref>

You should also make sure that <web-app version of web.xml file should be 2.5 or up and use schema not dtd. If you use older version of J2EE you have to use ibm-web-bnd.xmi file instead of xml.