I am trying to map an existing domain into HL7 FHIR.
So far it was pretty easy to find FHIR resources that more or less represent the same data and can be used for that purpose. But now I am running into a problem of which I am not sure how to solve it.
The existing domain allows that data can be anonymized depending on the users access level. e.g. a patient's name or address might be removed and marked as anonymized. Other data will be pseudonymised, for example a the birthdate in 1980 will be replaced with 01.01.1980. An Age of 37 will be replaced with a category of 30-40.
So I am unsure how to integrate that into the FHIR domain. I was thinking I could create an extension holding a boolean, indicating if a value was anonymized or not and always replace or remove the original value. This might work, but I will run into big problems when the anonymized value is of a different type than the original value (e.g. Age is replaced by a range of values)
Is that even a valid approach? I thought this might be common problem, but I could not find any examples where people described methods of how to mark data as altered. Unfortunately the documentation at http://build.fhir.org/extensibility-registry.html does not contain anything that would help my case.
You can use security labels for this purpose (Resource.meta.security). Take a look at REDACTED and SUBSETTED in the security label value set: https://www.hl7.org/fhir/valueset-security-labels.html
If you need to convey a data type other than the one allowed by the resource (e.g. wanting to convey a range rather than a birthdate), you'd need to use an extension. (Note that dates are valid even if you only include the year.)
Related
In the docs for FieldMask the paths use the field names (e.g., foo.bar.buzz), which means renaming the message field names can result in a breaking change.
Why doesn't FieldMask use the field numbers to define the path?
Something like 1.3.1?
You may want to consider filing an issue on the GitHub protocolbuffers repo for a definitive answer from the code's authors.
Your proposal seems logical. Using names may be a historical artifact. There's a possibly relevant comment on an issue thread in that repo:
https://github.com/protocolbuffers/protobuf/issues/3793#issuecomment-339734117
"You are right that if you use FieldMasks then you can't safely rename fields. But for that matter, if you use the JSON format or text format then you have the same issue that field names are significant and can't be changed easily. Changing field names really only works if you use the binary format only and avoid FieldMasks."
The answer for your question lies in the fact FieldMasks are a convention/utility developed on top of the proto3 schema definition language, and not a feature of it (and that utility is not present in all of the language bindings)
While you’re right in your observation that it can break easily (as schemas tend evolve and change), you need to consider this design choice from a user friendliness POV:
If you’re building an API and want to allow the user to select the field set present inside the response payload (the common use case for field masks), it’ll be much more convenient for you to allow that using field paths, rather then binary fields indices, as the latter would force the user of the gRPC/protocol generated code to be “aware” of the schema. That’s not always the desired case when providing API as a code software packages.
While implementing this as a proto schema feature can allow the user to have the best of both worlds (specify field paths, have them encoded as binary indices) for binary encoding, it would also:
Complicate code generation requirements
Still be an issue for plain text encoding.
So, you can understand why it was left as an “external utility”.
I'm trying to port our Anesthesia record software to using FHIR. But I'm struggling to find any sort of "official" way to structure the record.
The final product should contain everything you'd see on a typical sedation record (which are relatively standardized.
For a sample, see this: https://az184419.vo.msecnd.net/rcdso/pdf/RCDSO_4522_PC%20Sedation%20Sample%20Record_V8_Fillable_RD.pdf
I'm trying to avoid just making up my own way to do this within FHIR if there are already established patterns for it.
Currently my plan is to use a document, by creating a FHIR Composition and using the "section" field each with corresponding "entry" fields containing referenced resources like the vital signs Observations, etc.
But currently, I'm just making up "section" titles, etc.
My question is: Is there already a formalized structure for anesthesia records or even a standard set of section titles a sedation record should include? I would love to see some sort of "official" sample of what one might look like.
I am writing an app that has a sign-up form. This article made me doubt everything I knew about human names. My question is: does a person's name necessarily have positive length? Or can I validate names in this way and be confident that I have not denied anyone their identity?
P.S.: one might ask why am I validating at all. The answer is that this is for a school project and proper validation is a part of the mark. The article above proves that person's name can be pretty much any string of positive length but I don't know if zero length is OK.
With all types of programming, you have to draw a distinction between what is meaningful in the real world, and what is meaningful for your software solution.
How the data is to be used will validate what type of validation is required.
For instance, if your software interfaces with a government API, and the government API requires a first name and surname, you should do the same.
If you're interacting with bank accounts, you may have a single string which represents that account name, which many or may not be a human name or not, but may have other constraints around length.
If the name is only to be used for display purposes, maybe there is no point to capture the name at all, and instead you should capture a preferred display name (which doesn't needlessly assume a certain number of name components).
When writing software, you should target to make as few assumptions as possible, unless those assumptions will cause an increase in complexity of your software solution. If the software requires people to have non-empty names, then you should validate at the border that this is true.
In addition, if you were my student, you would have already lost marks for conflating null, and an empty string. In this instance, null would represent you lack data about the name, and an empty string would indicate that user has specified that their name is empty.
Also, if you decide not to validate something, you should at least leave a comment to indicate that you thought of it. If you do something unusual, it's possible a future developer may come along and fix the "bug". In addition, this helps you avoid losing marks.
I need my chatbot to query the user for an address and therefore I need the rasa NLU to return the address components (e.g. zip code, house number, street name, etc.) contained in the messages as entities.
Of course, one obvious way to do it would be to create a training file containing appropriate training data. But since this surely is a common problem, I hoped there might be another solution. Besides, it is not obvious to me where one might get loads of labeled addresses in various formats.
In this blog post some evaluations were done which show that the entity extractor ner_crf performs quite well for addresses if you add enough training data. In the blog post addresses were annotated as follows:
Take me to [123 Washington Street](address) please
You could support the recognition by supplying some regular expressions
Depending whether you have a list of possible street names you could also use lookup tables
Can anyone provide some insight on the required syntax to use to search LOINC using FHIR for a specific string in the labs descriptive text portion of an Observation resource?
Is this even possible?
The documentation is all over the place and I can't find an example for this generic kind of search.
I found similar examples here: https://www.hl7.org/fhir/2015Sep/valueset-operations.html
Such as: GET "[base]/ValueSet/23/$validate-code?system=http://loinc.org&code=1963-8&display=test"
But none of them are providing a general enough case to do a global search of the LOINC system for a specific string in an Observation resource.
None of my attempts to use the FHIR UI here, http://polaris.i3l.gatech.edu:8080/gt-fhir-webapp/search?serverId=gatechreadonly&resource=Observation , have been successful. I keep getting a 500 Internal Server Error because I don't know the correct syntax to use for the value part of the search, and I can't find any documentation out of all the copious documents online that explains this very simple concept.
Can anyone provide some insight?
Totally frustrated at this point.
Observation?code=12345-6
or
Observation?code=http://loinc.org|12345-6
where 12345-6 is whatever LOINC code you want to look for (e.g. 39802-4)
The second ensures you'll only match on LOINC codes as opposed to codes from other systems, though given the relatively unique format of LOINC codes, you're mostly safe without including that.
If you want to search for a set of codes, then you can separate the codes or the tuples with commas: E.g.
Observation?code=12345-6,12345-7
or
Observation?code=http://loinc.org|12345-6,http://loinc.org|123456
If you expect to search by a really long list of codes frequently, you can define a value set that includes all the desired codes and then filter by value set:
Observation?code:in=http://somwhere.org/whatever/ValueSet/123
Note: for readability, I haven't escaped the URL contents, but you'll need to escape the URL values appropriately.