I agree. Integration is exceedingly complex. Data is stored and interpreted differently in every system, even if they share the same EMR, due to configuration differences in workflow, data setup, software versions, etc.
You can't exchange data without thoroughly understanding the clinic workflows that generated it or will be using it. It's all time-consuming and hard.
I work on a patient portal consuming data from the EMR, and even that is tremendously complicated to present medical data safely and correctly to a person.
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Sibling comment mentioned wanting to work in Health IT. The big market problem in healthcare is small companies doing good innovation (usable patient-side workflows, modern clinical tools, shiny things) running into the consolidated, massive EMR systems. The first question when they approach a healthcare system will be "Are you integrated with Epic/Cerner/whatever?" and if not, they will be sent away. Or be ready to embark on a very long, slow process and integrate deeply into workflows, data APIs, etc.
When a system consolidates their EMR (driven by real needs but also Meaningful Use incentives), it forces standardization and special one-offs become much harder. Getting a doctor interested in using a new device or software means working within the whole EMR - the staff doesn't have the time or leeway to go use tools that don't integrate, just because a doctor really wants it. That doctor needs to align large groups, get agreement, and it's going to take a lot of time and money.
It all comes down to interoperability/integration. Building cool stuff in healthcare is really easy since most of the tech in use is outdated and slow moving. But interoperability - required to sell into healthcare systems - is really, really tough.