PHR and EMR are two inter-related concepts. First of all, the use cases are different. EMR is the electronic medical record primarily used at the hospital. Typically, it is the healthcare providers such as nurses or physicians use the EMR intensively. PHR is different, it centers around the patient experience. In some healthcare organisations, it is also an important patient/physician communication tool. EMR systems are typically deployed at the hospital, sometime one hospital system has a single EMR system. PHR systems presumably can be deployed independent from the healthcare organisations, in practice, many PHR systems are deployed for each healthcare organisation. The data stored in PHR and EMR are also different, EMR contains medical records including. PHR stores not necessarily medical records only, it can also be used to store other personal health records such as fitness data, insurance explanation of benefits, health device data which typically are out of the reach of the traditional EMR system. Other than HealthVault, other PHR system typically do not store medical imaging, neither does EMR systems. In healthcare organisations, medical imaging typically are stored in PACS system after acquisition, moved to archive when immediate usage does not appear to be in the horizon.
The biggest problem of these record system is the fragmentation. Quite a few of these systems were designed prior to the dot com boom, thus the interoperability of the EMR systems are terrible if not horrible. If you switch from one hospital to the other, you are likely to lose most of your record if you do not explicitly request a transfer. HealthVault is presumably in the position to defrag the EMR systems, however, the progress has been lackluster since its inception. The reason is in order to integrate with HealthVault, EMR providers have to take the action to perform the integration, however, the customers of the EMR systems typically do not have a financial incentive of sharing the healthcare data.