A pharmaceutical company has a lot at risk since pretty much all its intellectual property is in the form of electronically...
stored compounds and trial data, which is very valuable. For instance, consider a blockbuster drug that has the potential to be a multi-billion-dollar business. Clearly the focus of the assessment should be on protecting those kinds of assets.
Once polices are to make sure they adequately set the stage to protect critical assets, it's time to see whether the rubber meets the road by conducting some vulnerability testing. I'm a fan of both electronic testing, as well as human testing. So perform automated scans (to find obvious stuff) and use penetration testing tools (for both networks/systems and applications) to view your environment as a hacker sees it.
Periodically an organization should administer a manual pen test, where a skilled attacker uses social engineering techniques and looks for logic flaws in an environment. Most regulations require a formal "assessment" at least once per year -- so these are probably already happening.
Relative to ISO 17799 and its successor, ISO 27001, those are relatively comprehensive frameworks laying out all of the things (policies and procedures) that can be protected, as opposed to all of the assets that should be protected.
If you need a list of things to "assess," one of the ISO frameworks can be used as a starting point. But I would consider it a default if it's already understood what's protected and how the attackers can get the data.
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