Accessing Lab data via FHIR – part 4

In this final post for the lab series, we’ll take the terminology resources that we created in the previous post and use them to map codes from the laboratory bespoke coding system to the (mostly) LOINC based NZPOC set.

A quick reminder of what those resources were:

  • A CodeSystem and ValueSet that held the descriptions of the bespoke lab codes
  • A ValueSet for NZPOC, plus the CodeSystem for the non-LOINC codes.
  • A ConceptMap that defined the mappings from lab code to NZPOC (and we’re assuming that all the bespoke codes could be mapped – in practice you’d need a strategy for codes that couldn’t be mapped.)

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Accessing lab data via FHIR – part 1

This will be the first post in a short series that considers a very useful interaction – accessing Laboratory data such as blood tests from a repository of data via (of course) a FHIR API. The actual repository we use doesn’t really matter – it could be a part of an EHR, or an interface that the lab exposes or it could be a standalone data repository such as a regional or National store – it’s the API that counts.

There are a number of different perspectives that we can take, of which two are:

  • Accessing data about a particular person – whether by the person themselves or an authorized clinician.
  • Accessing data from the perspective of the ordering clinician – e.g. all the tests they have ordered, but not yet reviewed. This would return the results belonging to multiple people.

In this post we’ll take a look at the first perspective – accessing a single person’s data. We’ll consider the clinicians perspective in a subsequent post.

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clinFHIR stock take

I’ve been asked to give a short talk about clinFHIR to a course at Johns Hopkins this month – what it is and what you’d use it for, so to organize my thoughts I decided to write a ‘stock take’ of clinFHIR modules. This is actually part of a project I’ve been working on for a little while – learning FHIR with clinFHIR – so it’s a perfect time to be doing it.

The idea for clinFHIR started shortly after FHIR started to gain prominence within HL7 – coming up to 10 years ago now. The technical folk understood what the developers were trying to do – utilize internet standards to share healthcare data – but it was harder for the clinical folk to gain that understanding and appreciate the significance.

clinFHIR (Clinical FHIR) was envisaged as a way to visualize FHIR – particularly resources and the references between them – so that the committees within HL7 responsible for authoring resources could advance their development. We worked closely with the members of the ‘Patient Care’ committee in particular – they had sessions at most Working Group Meetings called ‘Clinicians on FHIR’, and we developed clinFHIR as one of the main tools for them.

(And I’d like to recognize all the work they put into this – it was an on-going balance between evolving the application to meet identified needs, and dealing with the bugs that a rapid development cycle brings!)

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FHIR enabling an Immunization registry – part 4

So we’ve talked about how to represent an immunization program both in the abstract (the overall definition of a national plan) and the specific (the plan applied to an individual). In addition, we discussed how to submit the actual administrations to the registry.

What we haven’t really talked about is how to measure the performance of an individual against the plan.

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FHIR enabling an Immunization registry – part 3

So we’ve made a few proposals in the last couple of posts:

The next thing to think about is how to generate the ImmunizationRecommendation (IR) from the PlanDefinition.

This could be really complicated, depending on the circumstances around the generation. For example, if we just wanted the recommendation for a new born then it’s quite easy. If we wanted more ‘smarts’ – e.g. the recommendation for someone of a given age considering their immunization and clinical history, then it becomes rather more complicated. In this post we’ll keep it simple and not look at the patient’s history, focusing on the ‘mechanics’ of the generation.

As a background to the discussion, let’s think about how a client might use the registry API.

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FHIR enabling an immunization registry – part 2

In the previous post we discussed how an immunization registry might receive Immunization resources documenting the administration of vaccines to an individual (complicated), and how to expose those resources to a client (easy).

But vaccine administrations don’t exist in a vacuum – they’re generally related to some particular plan consisting of multiple administrations of different vaccines over a period of time with the intent of providing the recipient with protection against specific diseases. (And, as COVID has emphasized, protection of the planetary population as a whole).

So we need a way to represent that general plan, customize it for an individual – and then a way to link individual vaccine administrations back to that plan so we can be sure that an individual is receiving the vaccinations they should be. And we want to be able to report on this administration at a population level as well as the individual.

That’s a bit more complicated than it might appear.

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Extending a required binding on ContactPoint

So we’ve got an interesting issue in New Zealand (from a FHIR perspective of course). We’re in the process of creating extensions to be used nationally, and one of the requirements we have is to be able to store the HealthLink EDI number – an ‘address’ used to send information electronically between healthcare providers.

Some background: in New Zealand we have a messaging service that is operated by a private company (HealthLink) which has national coverage that connects Primary care with Hospitals, Laboratories and other services such as eReferrals. It’s actually been running for a number of decades and has certainly helped with electronic sharing of information. The company provides vendors with client-side applications they they use to interact with the service.

Users of the service are assigned a unique code (the EDI number) that acts as a delivery address for the user (which can be an individual or an organization). For example, when a hospital wishes to send a Discharge Summary to the patient’s General Practitioner (their Primary / Ambulatory care provider) then they will send the summary to the service, asking for it to be delivered to that EDI account.

As we move into FHIR, the question is how do we represent that number? For the purposes of this discussion, we’ll assume that we wish to attach it to a Practitioner resource, though it will also need to be applied to others such as Organization or PractitionerRole.

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Slicing with Sushi

As readers will know, I’m a big fan of FHIR Shorthand as a way of making it much easier to create Implementation Guides and examples in conjunction with the IG publisher. In fact, I’m coming to the conclusion that all systems that expose FHIR API’s should have an IG that describes it (along with the CapabilityStatement resource of course) – and unless you have experience with creating StructureDefinitions directly, then FSH – and SUSHI – is the way to go.

Of course, creating IG’s is still not easy (it’s just easier) so I thought it would be a good idea to write about common patterns that you might want to express – and serve as a reminder for me when I forget! Read more of this post

Custom Implementation Guide templates

As you’ll likely be aware, FHIR uses Implementation Guides (IG) to describe how to use FHIR for specific scenarios or use cases. In the past it has been technically challenging to create these guides, but this is changing – in large part due to new tooling/approaches like shorthand and sushi, but also because the FHIR community (and especially Lloyd) have been working on a template based publisher.

The idea behind the template based publisher is that there are a number of standard templates for specific purposes such as an ‘official’ HL7 FHIR IG or a plain template, and these can then be adapted for specific purposes – such as a National IG or a vendor specific one describing a FHIR based implementation. The project is still relatively new, but becoming stable enough that people are able to use it. However, the newness means that the documentation is still catching up, so when my colleague Jose Costa Teixeira offered to write a ‘beginners guide to creating your very own template’ I said great!

He’s published it on his blog, but kindly allowed me to reproduce it here.

Without further ado, take it away Jose… Read more of this post

Creating examples

Examples are probably one of the more useful things to an implementer – yet likely the least exciting part of building an Implementation Guide (IG) to the designer. And not only are they useful to the implementer, they are a good way to double check the actual IG – it’s surprising how often having to create an example finds issues with the artifacts within an IG.

But the tooling to create examples is not that great. Generally you’re using a generic JSON or XML tool which offers no editing support to ensure that the example is valid (you can use the $validate operation that I’ve discussed before, but the workflow is tedious). I’ve tried to use clinFHIR for that – and it does work, though chokes some of the more complex profiles, and is still quite slow to create the resource instance.

There is an alternative that I’m currently using that seems to resolve these issues – the shorthand spec (with associated sushi reference implementation) that I blogged about last week. As well as producing profiles, it can also create resource instances using the same syntax as for profiles, and even better – when you run sushi to generate the resources, it will pick up the more egregious errors.

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