It's great to see the judgment for this case, however, it will not stop virtual patents in the pharma world (or in software either). Patent lawyers know the system very well, and will use what they learned here to make sure that all virtual patents are tied to a mechanical process or an apparatus. In this case, specifically for US Patent 6420139, evaluating the safety of immunization could become using a simple lab on a chip (the apparatus) that will take the samples from all patients and evaluate their effectiveness in correlation with the schedule of treatment*. The lab on a chip will be novel for detection of a certain disease, virus, etc., which will allow this to be patentable for each new immunization/screening that is needed (with minor tweaks of course).
*Note: this has been written about now, therefor prior art now exists. You may not use this to validate this patent, or others.