More comments on FHIR documents

January 14, 2014 1 Comment

With the emphasis on Documents in the coming connectathon, there have been a few questions on the skype chat about that. I suspect that most people who plan to attend connectathon will be monitoring that conversation (if not then you really should!) but just thought I’d post some of them here in case they got missed.

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Server processing of FHIR documents: Connectathon

December 16, 2013 1 Comment

In this post we’re going to think a bit about how the server might process a document that it receives. This is a massive topic, and certainly not one that can be covered in a single post – or by any one individual! Apart from anything else, there are lots of different possibilities – all legitimate in specific circumstances.

This is an important concept for FHIR – it doesn’t seek to drive any particular design or architecture – rather it attempts to support how data is moved around now, and how it may be done the future. It’s up to individual implementations to decide the details, but using common ‘building blocks’.

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FHIR and the Ambulance: Notification of XDS documents

December 6, 2013 4 Comments

We had an interesting discussion today about how to ‘notify’ clinicians that there is a document in a repository for a patient that they are looking after.

The documents in question will be clinical summaries of ambulance visits, and will be held in a highly available repository hosted by the ambulance service, from which authorized users (including the patient) may view them. This repository will be part of an XDS style implementation, so the repository will create a metadata resource (DocumentReference) and send that to the Registry (which we’re terming a ‘Record Locator’ service).

Once there, clinicians and patients will be able to locate and view the documents in the ways that we’ve already discussed.

In addition to storing the document, we also want to be able to create a notification to the patients usual General Practitioner (Primary Care Provider to you US folk) so that they know that an ambulance visit has occurred and there is a new Transfer of Care document for them to review.

The reason for this is that it is very useful for the GP to know that their patient has been seen by the ambulance service, in case follow up is required. In many cases – particularly when the ambulance call does not involve a hospital visit – and hence there is no hospital discharge summary to the GP – they have no way of knowing that the visit occurred. An example of this is where the patient has an asthmatic attack and is nebulized successfully at home.

So the workflow will go something like this:

  1. The Ambulance system creates the document (likely a CDA) and saves it directly in its repository – along with all the other required metadata. (This is the integrated document source/repository actor in XDS).
  2. The Repository will generate a DocumentReference resource, and send that to the Registry.
  3. The Registry will save the DocumentReference resource, and also generate a new resource – the Notification resource – that is directed to the patients usual GP (which will be in the Patient.careProvider property). There’s nothing to stop it creating multiple notifications – eg to a patients care team – if there are business reasons for doing so.

Once this is done, GP’s will be able to receive the notification by means of an RSS feed querying the Notification resource like this:

GET [host]/Other?code='notification'&target=<GP>&_since=<lastQueryTime>

which will return a bundle (Atom feed) of Notification resources for that GP. They can then use the Notification (specifically the DocumentReference property) to retrieve the actual document for viewing.

So what is this Notification Resource? Well, it doesn’t actually exist yet. To implement notifications we need to use the Other resource, which has been specifically designed for situations like this: we need a resource that is not yet defined (or maybe won’t be). It has a simple structure:

  • Code – the type of resource. This will indicate that it is a notification resource.
  • Subject – the patient
  • Author – in this case the ambulance system
  • Created – the date of creation

And then you add as many other properties (as extensions) that you want. We’ll probably need:

  • Type – the type of Notification – eg that there is a new document for them. We could get fancier if we want to…
  • About – the DocumentReference reference
  • Target – a Provider resource reference to the GP

Why have we specified a separate resource for the notification, rather than just storing the GP as an extension to the DocumentReference resource and querying on that? Well:

  • A tight coupling in this way would mean that the ‘notification’ is for DocumentReference resources only, and we may want to support other Use Cases – such as a notification that a patient has been admitted into hospital.
  • More complex workflow – like the ability to record that the notification has been viewed and accepted (or declined) would be tricky. (Actually this is more Task type behaviour – but then, a Notification could be thought of as a type of task)
  • It feels like we’re binding together behaviour that doesn’t belong together.

Some other notes:

  • We’ll probably get the registry to provide a special service for this ‘save metadata and create notification’ functionality – eg POST /service/DocumentReference/saveAndNotify that takes the DocumentReference resource and does the rest. (I’ve grown rather fond of these services since Keith suggested them!)
  • Because the  notification query is based on an extension, the server needs to map the ‘target‘ query parameter to the target extension. We really want to be able to search on the identifier property of the Practitioner resource that is the target property of the Notification, so we’ll need to set up the profile accordingly.

And finally, in our particular situation there are a couple of wrinkles:

  • The delivery timeframe of the project is before the Record Locator service is likely to be in place
  • This design requires that the vendors of Practice Management Systems that the GP’s use need to implement the RSS/Atom query mechanism

For the first wrinkle, the RSS/Atom lookup will initially be provided directly by the Ambulance Repository application. Then, when the remainder of the infrastructure is in place the consumers will simply need to change URL’s to switch to the Record Locator/Registry and the system will otherwise work unchanged.

In the second case, there are a number of portal applications in use in New Zealand – we’ll add the display of notifications to those portals so that when GP’s and patients log into the Portals they will receive the notifications in the same way as they would from within their GP PMS. Hopefully, this will allow the PMS vendors to see the value of this approach, and implement the functionality directly (it’s not that hard for a consumer after all!)

Since writing this post, I’ve written another one, further extending the concept of Notifications, thinking about how to manage workflow.

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FHIR XDS – updating a document

November 20, 2013 Leave a comment

It’s not uncommon for a document to need to be updated after it has been posted to a repository and registry. Sometimes new information has come to hand that affects the document, or there may be normal workflow where a ‘draft’ document is saved, and is subsequently updated or finalized, or maybe the original was just plain wrong and needs to be retracted.

None of these are unique to a document of course, but there are some ‘quirks’ – for want of a better word – to the DocumentReference resource for a couple of reasons:

  • It is a resource whose main role is to refer to another entitity – so there are 2 lifecycles to consider.
  • Documents are often summaries of clinical care (e.g. Discharge Summaries, Progress notes, Clinic notes) and it’s very common for clinical decisions to be made on the contents. Keeping an easily accessible (to the end user) ‘audit trail’ of changes is very important for medico-legal reasons.

When thinking about changes to a document, there are 2 ‘types’ of change to consider:

  • Changes to the metadata (e.g. the document type was incorrect)
  • Changes to the content of the document itself.

We’ll consider these separately.

Changes to the metadata

If the change is only to the metadata – the contents of the DocumentReference resource itself, then it can be updated it in the usual way – i.e. retrieve the existing version, make the changes, and PUT the document back. The standard FHIR versioning process will manage the update of the resource. (Resource versioning is not required by FHIR – but highly recommended). There are some caveats to this approach, as mentioned in a minute…

Changes to the document.

This is more tricky. What we need to do is:

  • Update the document in it’s location (e.g. as a binary resource on a FHIR /Binary endpoint)
  • Update the existing DocumentReference resource that points to it, setting the status property to ‘superseded’
  • Create a new DocumentReference resource that references the updated document (and if it’s a FHIR server that we may want to make this a version specific reference), setting the relatesTo.code to ‘supercedes’, and the relatesTo.target as a reference to the original DocumentReference resource
  • We might also want to create a provenance resource to indicate who has made the change.

Because this needs to be managed as a transaction, we’ll use a FHIR bundle and we’ll use the same pattern as when we submitted the document in the first place – i.e. have the repository server manage the updating process. (Other patterns are possible of course).

So our bundle will contain:

  • The updated document as a base-64 encoded binary resource. It will have a real ID so the server knows to update it
  • The original DocumentReference resource, with updated status. It will also have a real ID so the server knows to update it
  • The new DocumentReference resource – largely a copy of the original with the relatesTo property set. It will have a ‘cid:’ ID so the server knows to add it as new.
  • Optionally a provenance resource with the details of who made the change – and when. The provenance resource refers to the resource being changed (not the other way around) so it will have 2 targets – the 2 DocumentReference resources that are effected in this transaction. It also has a cid: ID.

The repository server will process the bundle as described above.

Although this second approach is more complex, it does make it quite obvious that a significant change has occurred. For this reason, some metadata changes – such as a change of subject or author – might be better managed this way rather than a simple update to the DocumentReference resource. It’s up to you…

All of this does raise an interesting point that we didn’t think about when considering how to query the registry for documents (i.e. a query against /DocumentReference) – the response will include DocumentReference resources that have been superseded as well as current ones.

If we don’t add the status parameter in the query, then we will get back all DocumentReference resource’s – so we will need to check this value when assembling the list of documents for the consumer (Of course, we may want to do this anyway so that we can place some visual indication in the display that changes have occurred – it’s up to the implementer, as it should be…)

Otherwise we can be explicit that we only want current documents, so the examples we gave in the previous post becomes:

GET  http://registryserver/DocumentReference?subject= 100&status=current&period > 2013-01-01

and

GET  http://registryserver/DocumentReference?subject= 100&status=current&type= http://loinc.org|34108-1

And as a last word, and following on from the post that Keith Boone made about task orientated services, we may choose to define specific service end points for this functionality (and even for the ‘add document’ scenario), perhaps:

  • /service/document/new
  • /service/document/update

both of which receive the bundles we’re described.

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Getting documents from a FHIR XDS infrastructure

November 19, 2013 5 Comments

So far in our little mini series on FHIR and XDS we’ve had an overview of how FHIR resources support a document sharing infrastructure, looked at how a document creator can create and submit documents to a repository and/or registry, and spent a bit of time talking about the DocumentReference resource.  Time to think about the consumer of these services.

There are 2 main scenarios that we want to support:

  • Getting a list of documents for a patient (with various search parameters – e.g. a date range, type of document etc.) and displaying the metadata in a list to the consumer
  • Retrieving a particular document to view

Getting the list of documents

Let’s think about the first scenario, and to keep it simple we’ll aim to retrieve all the documents for a patient. Given that the metadata about the document is represented by a DocumentReference resource hosted by the registry server we are using, then this is obviously going to be a query against the DocumentReference endpoint. There are a couple of ways we could to this, and the way we choose depends on whether the have the patients ID or their identity (in fact, it’s exactly the same issue as the document creator had – so refer to that post for more discussion on this).

If we know the patient ID (let’s say it’s 100), then our query will be something like:

GET  http://registryserver/DocumentReference?subject= 100

(assuming that the patient identity is also on the registry server – if not then the patient ID would need to be the absolute reference to the patient resource).

If we don’t have the patient ID, but we do have an identifier (e.g. PRP1660) then we have a couple of options (as always!):

  • Look up the patient ID by a query against the Patient endpoint first
  • Query the DocumentReference with the patient identifier using a chained query, like so:

GET http://registryserver/DocumentReference?subject.identifier= PRP1660

Note that the server is not obliged to support chained queries – check their conformance resource to see if they do. Also, I didn’t include the identifier system in the query – depending on the implementation I may need to do so. Chained queries make a clients life easier (but a servers life harder) – but as the FHIR philosophy is to make it as easy for clients as possible, it’s to be hoped that servers do support that capability.

In either case, the result will be a bundle of DocumentReference resources – the difference between the two being that if we specified the patient ID, then we know that all the DocumentReference resources are for the right person. If we used the identifier, then we are trusting that the identifier is unique (which means that we should probably not be lazy and include the system in the query).

But what if we want a more targeted search? Perhaps we’re only interested in documents created in the past year, or only outpatient summaries?

Well, checking the defined search parameters for DocumentReference we see a period parameter (date of the service) and a type parameter (document type) which would seem to suit our purpose, so (assuming we have the Patient ID):

GET  http://registryserver/DocumentReference?subject= 100&period= >= 2013-01-01

and

GET  http://registryserver/DocumentReference?subject= 100&type= http://loinc.org|34108-1

And of course we can mix and match parameters as we need to (provided the server supports them as documented in their conformance resource)

Retrieve a particular document.

So now we have a list of documents which we can display to our user, how do we retrieve a particular document for them? Well, hopefully the DocumentReference resource that describes the document we want has the location property. Then it’s just an HTTP call away. If the repository where the document is stored doesn’t support a direct GET, then you’ll need to drop back to the XDS ‘Retrieve Document’ profile, the access details for which should be on the DocumentReference.service property.

Assuming you can make a GET call, the repository should include the HTTP standard headers in the response like content-type (which is also recorded in the DocumentReference.mimeType property of course), so rendering by the viewer should be straightforward. Of course, it can get a lot more complex than that – especially in the case of a structured document like a CDA or FHIR-document, when specialized client-side renderers (like XSLT stylesheets) will be required. The metadata in the DocumentReference resource (and possibly HTTP headers)  should indicate what renderer is going to be needed, so all should be well.

Note that the GET call will return the document directly, whatever it is – eg a PDF or CDA document – not a FHIR resource of any sort.

A short (and grossly incomplete) comment on FHIR security.

FHIR itself doesn’t define security protocols – rather it provides the ‘hooks’ that a security framework can use when deciding whether to deliver up a particular document – or even whether to include the document metadata in the original list of documents.

There is an assumption that anyone accessing any of these services is authenticated (identified) and oAuth is the recommended (though not mandated) way to do this.

FHIR supports the concepts of tags – that can be applied to any resource, and allow a privacy policy framework to apply rules when determining whether to deliver up information p and those rules can become arbitrarily complex.  In addition, the DocumentReference resource has the specific confidentiality property that can also be used.

There is also the SecurityEvent resource (analogous to the IHE ATNA profile) that can be used to record significant events such as the release of a document to a viewer. This resource can then be used as the basis of functionality such as “Who has viewed my data?”, and can be created at any time that is appropriate in the overall workflow. The provenance resource indicates the context in which a resource was obtained – e.g. the person who created it.

So, it is the responsibility of the governing body for the document sharing infrastructure to make these policy decisions – and to enforce them! And the IHE ‘Affinity Domain’ concept is a good source of information.

Incidentally, for health security issues in general, check out John Moehrkes blog as a good source of inspiration!

We’re getting towards the end of our little mini series – one of the longer ones so far! We’ll wrap up the loose ends in the final post – in particular we need to think about the best approach when a document source needs to update a document it has already sent to a repository.

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The FHIR DocumentReference resource

November 12, 2013 13 Comments

In the previous FHIR-XDS post we discussed how a document source actor (ie a system that creates a document) could create a document and DocumentReference resource and send them to the Repository server. (Actually, we described a couple of ways that this could be done – and there are a few subtleties yet to discuss about server behaviour – but we’ll hold that for later).

However, we didn’t have a lot of time to talk about the DocumentReference resource itself. This resource represents the metadata about the document and allows a consumer to search the registry (or any server hosting these resources) to retrieve matching documents. From these results, a consumer can then generate a list of documents so that a consumer can select one to view.

The documents themselves can be of any allowed type (CDA, PDF, FHIR document, text etc) and can be stored on any server accessible via HTTP – and they do not need to be FHIR servers. It is quite legitimate for a DocumentReference resource to refer to a static document on any server (or, for that matter, a URL that generates a document ‘on the fly’, though you’d want some way to persist the generated document for medico-legal reasons as described in the ‘IHE on-demand document‘ profile). And, if one is being particularly pedantic, then even HTTP is not really required – you could use FTP or any other supported protocol.

It is important to note that although the DocumentReference resource was developed to support some of the requirements of an XDS infrastructure, it is not restricted to that purpose and can be used in any situation where the business requirement is to create a ‘list of available documents’, from which one or more can be chosen for viewing.

In fact, the FHIR specification defines a specific XDS profile that describes how the DocumentReference resource is to be used in the context of an XDS installation – for example some fields that are optional in the resource, are required when acting as a proxy to XDS. The link also gives guidance for mapping between XDS and FHIR elements, including fields required for XDS that are not in the DocumentReference and so represented by extensions.

The following description refers to the generic DocumentReference resource. Note that there are a number of properties whose value should come from a ValueSet defined by the governance body that oversees the overall installation (an Affinity Domain in XDS-speak – though the affinity domain covers much more than just code sets). We will talk a bit more about ValueSet’s after this list.

  • The masterIdentifier is the identifier of the document as created by the source. It is version specific – i.e. a new one is required if the document is updated (We’ll talk about updating documents in a separate post).
  • There can be any number of other document identifiers that make sense. For example, there might be a version independent identifier here.
  • The subject is who the document is about. Generally this is a patient, but the specification also supports a Practitioner, a Group or a Device.
  • The type and class indicate what kind of document this is- (eg a discharge summary). A ValueSet should be defined for each. (Note that ‘class’ has been called ‘sub-type’ in some versions of this resource)
  • There is at least one author, which is a Practitioner.
  • There can be an Organization which is the custodian of the document – responsible for maintaining the document
  • There’s a policyManager link to a URL that describes the access policies to the document.
  • The authenticator of the document can be an Organization or a Practitioner.
  • The created date is when the document was created (not necessarily related to the period of the service that the document may describe – this is in the context.period element).
  • The indexed date which is when the DocumentReference resource was created.
  • The status allows minimal workflow of this DocumentReference resource (NOT the underlying document). Options are current, superseded or error. We’ll talk more about this status when we talk about updating a document in a later post.
  • The docStatus and supercedes allow a document to be updated (superseded) or otherwise have it’s status changed. This is a CodeableConcept, and so can accommodate a specific workflow defined by the affinity domain such as preliminary, final, amended or whatever, as documented in the ValueSet.
  • The description is the title of the document. If you’re displaying list of documents then this would be a good property to use.
  • The Confidentiality property allows a privacy policy to control the access to a document. The policy can also use the generic tags functionality in FHIR.
  • The PrimaryLanguage element indicates exactly that – no surprises here. It is a code, and is bound to the IETF Language tag.
  • mimeType and format indicate how the document is represented – eg xml, pdf, msword etc.
  • Size allows a client to estimate download time of the document, and the hash can ensure integrity.
  • The Location is a URI that indicates from where the document can be downloaded. This does not need to be a FHIR server. The client will (generally) not know what this is when creating the resource as it will be related to the ID that the server assigns. However, either it or the service property is required, so it may be necessary to create a ‘dummy’ resource using the cid: prefix so the server knows it is not real – or define a service. You would define a local policy to describe this, which could be identified in the policyManager link above.
  • The service is used if the location is not known. You would use this if you weren’t using simple FHIR REST, so for the moment we’ll ignore it.
  • The context allows you to specify the clinical context of the document – at least the context that is useful in searching or displaying the document list. The period that the document refers to and the facility type are present, but you can add codes that make sense here as well.

For reference, the following fields need to have their options defined by the governing body using a ValueSet. These can either be defined directly in the ValueSet or be a sub-set of an external Terminology like LOINC or SNOMED.

  • type
  • subtype
  • docStatus
  • confidentiality
  • mimeType
  • format
  • context.code
  • context.facilityType

The recommended way to document this is to create a Profile resource that describes the implementation, and refers to the appropriate ValueSets – with the whole lot being saved in FHIR server/s so that they can be easily located. The option below shows a minimal profile that sets the ValueSet for the confidentiality property.

&lt;Profile xmlns=&quot;http://hl7.org/fhir&quot;&gt;
     &lt;text&gt;
         &lt;status value=&quot;additional&quot;/&gt;
         &lt;div xmlns=&quot;http://www.w3.org/1999/xhtml&quot;&gt;Minimal profile for confidentiality codes in DocumentReference&lt;/div&gt;
     &lt;/text&gt;
     &lt;name value=&quot;Elbonian XDS Profile&quot;/&gt;
     &lt;status value=&quot;draft&quot;/&gt;
     &lt;structure&gt;
         &lt;type value=&quot;DocumentReference&quot;/&gt;
         &lt;name value=&quot;XDSDocumentReference&quot;/&gt;
         &lt;element&gt;
             &lt;path value=&quot;DocumentReference.confidentiality&quot;/&gt;
             &lt;name value=&quot;ConfidentialityOptions&quot;/&gt;

             &lt;definition&gt;
                 &lt;short value=&quot;Confidentiality Code options&quot;/&gt;
                 &lt;formal value=&quot;Confidentiality Code options&quot;/&gt;
                 &lt;min value=&quot;1&quot;/&gt;
                 &lt;max value=&quot;1&quot;/&gt;
                 &lt;isModifier value=&quot;false&quot;/&gt;
                 &lt;binding&gt;
                     &lt;name value=&quot;List of confidentiality options&quot;/&gt;
                     &lt;isExtensible value=&quot;false&quot;/&gt;
                     &lt;referenceResource value=&quot;/ValueSet/ConfidentialityOptions&quot;/&gt;
                 &lt;/binding&gt;
             &lt;/definition&gt;
         &lt;/element&gt;
     &lt;/structure&gt;
 &lt;/Profile&gt;

and the ValueSet that it references could look like:

&lt;ValueSet xmlns=&quot;http://hl7.org/fhir&quot;&gt;
     &lt;text&gt;
         &lt;status value=&quot;additional&quot;/&gt;
         &lt;div xmlns=&quot;http://www.w3.org/1999/xhtml&quot;&gt;The value set for confidentiality codes in the elbonian document sharing
         project. The codes are defined directly by the valueset, rather than references to an external terminology&lt;/div&gt;
     &lt;/text&gt;
     &lt;name value=&quot;ConfidentialityOptions&quot;/&gt;
     &lt;description value=&quot;ConfidentialityOptions&quot;/&gt;
     &lt;status value=&quot;draft&quot;/&gt;
     &lt;!-- Define the  options in the resource rather than an external terminology--&gt;
     &lt;define&gt;
         &lt;system value=&quot;http://fhir.moh.elbonia.com/confidentiality&quot;/&gt;
         &lt;concept&gt;
             &lt;code value='N'/&gt;
             &lt;display value=&quot;Normal&quot;/&gt;
             &lt;definition value=&quot;That the document is of normal confidentiality - is able to be viewed for any authenticated user&quot;/&gt;
         &lt;/concept&gt;
         &lt;concept&gt;
             &lt;code value='H'/&gt;
             &lt;display value=&quot;High&quot;/&gt;
             &lt;definition value=&quot;Then the document is Highly confidential - eg Mental health - and can only be viewed by people authorized to access documents at that level&quot;/&gt;
         &lt;/concept&gt;
     &lt;/define&gt;
 &lt;/ValueSet&gt;

Finishing up…

In the previous post I promised that I would talk about the DocumentManifest resource. This is a new addition to the FHIR family, and has been introduced to support the ability for a document source to submit a collection of documents in a single batch as XDS does.

In truth, I’m not entirely clear how this resource should be used. It does have the recipient element, which provides the basis for a notification system, but beyond that the main value would seem to be that there can be more than a single document in a batch submission to the Repository server. I’ll update the post when I learn more.

So, we have saved a document in the repository and updated the registry. In the next post, we’ll switch our attention to the Document Consumer and discuss how to query the registry for documents, and to get the actual document itself.

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