Is there a mapping of FHIR systems to OMOP vocabularies?
The FHIR messages I’m working with are using things like this:
SNOMED http://snomed.info/sct
RxNorm http://www.nlm.nih.gov/research/umls/rxnorm
…and OMOP uses things like this:
So, I need something that will tell me when I see “http://snomed.info/sct” in my FHIR message I should be looking for the OMOP vocabulary with the vocabulary_id of “SNOMED”
There's a set of candidate mappings here: https://docs.google.com/spreadsheets/d/1ykzbW-RMRJV4doIpZANibu45WveLFoFA/edit?usp=sharing&ouid=111904620053364392286&rtpof=true&sd=true
Note that these are just candidates that I made up. They're not approved by either the FHIR or OMOP communities. There's a joint working party between HL7 and OHDSI working through those proposed mappings checking them and filling in the blanks.
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I am developing chatbot using Rasa for a Contract Manager Organisation. I am facing few issues and after reading a lot on the forums and Rasa blog, I am unable to conclude to a solution for this. I have several similar intents with similar examples like -
“inform_supplier_start_date” and “inform_contract_start_date”.
“inform_supplier_email” and “inform_customer_email” and “inform_reviewer_email”
Now the issue is, for both the categories of intents the example sentence in nlu.md is same. What I exactly mean is-
##intent:inform_suppler_start_date
-what is the supplier [Microsoft] (supplier_name) start date
-[EON Digital] (supplier_name) start date
##intent:inform_contract_start
1) start-date of [O2 Mobile phones] (contract_name)
2) [O2 Mobile phones] (contract_name) start date
The model isnt able to differentiate and identify the correct intent. It is getting confused and identifying the wrong intent, since the words in these intents are similar.
I need correct intents to be recognised ,so that accordingly, In custom action i can query the Database and get the corresponding result for supplier and contract.
I have many fields like this for which the example data and user queries will be same. For Example-
customer_email & supplier_email & reviewer_email
total_spend_contract & total_spend_supplier & total_spend_customer
contract_number_for_supplier & contract_number_of_contract & contract_number_organisation
What exactly I should be doing to get correct classification. One solution i am thinking of is merging the intents like “supplier_start_date” and "contract_start_date" as one “start_date” and check for the extracted entity inside custom actions in both supplier and contract database. But I dont think that would be proper usage of Natural Language.
Please Suggest, I shall be highly greatful for the same. Regards.
As the examples for your intents are very similar, the model will not be able to differentiate between them. Also the intent is actual the same, inform_suppler_start_date and inform_contract_start inform the bot about a start date. What kind of start date it is should be figured out via the entity recognition. So I would propose to merge the similar intents and check what the entity recognition detected as entities. Depending on whether a supplier or a contract was found, you can execute query A or B.
I find that the nickname and reference_id fields work differently across platforms and I'd like to get clarification on how they should be used.
With the API, I can retrieve and set both these fields.
In the web-based dashboard, both fields are displayed and can be edited if present, but there's no way to enter a nickname when creating a new customer.
In the Register iOS app, none of these fields are shown or editable. They're also absent when creating a new customer.
What I want to do is map Square Customers to our existing members, but we're facing three problems:
reference_id seems to map perfectly with our existing member numbers but, as mentioned, it's nowhere to be seen in the Register app.
Searching customers in the Register app only searches in names and emails. It would really help us if it searched in reference_id as well.
CustomerGroupInfo is read-only via the API (and not even an endpoint). We would map these to our membership levels.
As of now, I'm looking at ugly workarounds, but I wanted to know if something in the roadmap could help us out. Thanks in advance to the people at Square!
Trying to understand the concept of the code datatype in hl7-fhir. Looking at the appointment (https://www.hl7.org/fhir/appointment.html) resource as an example it has a status parameter with suggested values of "proposed | pending | booked" etc.
Given an existing database with it's own custom status' (Attended, Confirmed, Attended but late) what is the correct way to handle a hl7-fhir response to a consumer?
If the "code" data type is used, then the FHIR binding strength is always "required" - which means you are required to use the FHIR-defined list of codes and no others.
It appears that two of your statuses - "Attended" and "Attended but late" aren't actually statuses of the appointment - the booking, but are instead commentary about the resulting encounter. So I would capture those as extensions. "confirmed" sounds similar to "booked", though I'd need to know the definition to know for sure. Do you have any appointment statuses for appointments that are not yet confirmed (let alone attended)?
To extend on Lloyds notes, you will want to put the extension under the status property, and map your existing values to the provided FHIR values, and put your local actual value in the extension underneath.
This way when other systems read the resource and don't know about your extension status values, they will still be able to act sensibly based on the core values.
<status value="fulfilled">
<extension url="http://yourorg.com/fhir/.../ExtendedAppointmentStatuses">
<valueCoding>
<code value="abl" />
<display value="Attended but late" />
</valueCoding>
</extension>
</status>
Reading the API Blueprint specification, it seems set up to allow one to specify 'Data Structures' like:
Address
street: 100 Main Str. (string) - street address
zip: 77777-7777 (string) - zip / postal code
...
Customer:
handle: mrchirpy (string)
address: (address)
And then in the model, make a reference to the data structure:
Model
[Customer][]
It seems all set up that by referencing the data structure it should generate documentation and examples in-line with the end points.
However, I can't seem to get it to work, nor can I find examples using "fully normalized data abstraction". I want to define my data structures once, and then reference everywhere. It seems like it might be a problem with the tooling, specifically I'm using aglio as the rendering agent.
It seems like all this would be top of the fold type stuff so I'm confused and wondering if I'm missing something or making the wrong assumptions about what's possible here.
#zanerock, I'm the author of Aglio. The data structure support that you mention is a part of MSON, which was recently added as a feature to API Blueprint to describe data structures / schemas. Aglio has not yet been updated to support this, but I do plan on adding the feature.
I am looking for a good example to lock a document in elastic search. The below link explain how to do this in elasticsearch.
http://www.elasticsearch.org/guide/en/elasticsearch/guide/current/concurrency-solutions.html
How can i achieve this using NEST. can someone suggest an approach to start with.
To start with, read the NEST Quick Start article. In particular, note the following:
NEST is a high level elasticsearch client that still maps very closely to the original elasticsearch API. Requests and Responses have been mapped to CLR objects and NEST also comes with a powerful strongly typed query dsl.
Consider also, that you may not require the added level of abstraction that NEST provides, and may prefer to directly utilise Elasticsearch.NET. Read also, it's own Quick Start article.
With that in mind, implementing the steps in the Solving concurrency issues article using NEST / Elasticsearch.NET is simply a matter of identifying the .NET methods that correspond to the necessary Elasticsearch API methods. The first one for example:
PUT /fs/lock/global/_create
{}
In NEST would look something like:
var createGlobalLockResponse = esClient.Index<object>(new object(), f => f
.Index("fs")
.Type("lock")
.Id("global")
.OpType(global::Elasticsearch.Net.OpType.Create));
Regarding the check of whether "this create request fails with a conflict exception", check the properties on the createGlobalLockResponse object. In particular, Created and if you're intending to get a bit more specific in the handling, ServerError.