"HES Specialty" vocabulary - Two codes are merged (& and Null) #1007
Comments
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Not sure I understand what you are trying to do. So, there is a funny code "&" which apparently stands for "other maternity event", which really is not a specialty and is not listed in the official NHS website. Why should this be split? What are the two codes? What are the two concept_names? |
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@cgreich: "Null = Other Maternity Event" as reported in the NHS lookups provided by NHS digital, which I shared above: HES APC TOS tab, MAINSPEF in row 166 ("The specialty under which the consultant is contracted.") and TRETSPEF in row 299 ("The specialty in which the consultant was working during the period of care.") fields, column H, look at the bottom. Unfortunately, there are discrepancy in the NHS documentations, but these values are present in the data and the spreadsheet is kept updated. If you look at the screenshot I shared is looks that "&" means "Null = Other maternity event" which is wrong and makes no sense ("&" means "Not Known" and "Null" means "Other maternity event") All the codes in the "HES Specialty" vocabulary should have "Class" = "Physicial Specialty" and "Domain" = "Provider" (not "Observation") because they are used as attributes for the consultants who provided the service associated to an event: the consultant is already an attribute of the event. I agree that the wording chosen by NHS sometimes is confusing, but this is how these "HES Specialty" vocabulary codes are used in the HES APC data. |
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I am trying, @adelmestri. The website you linked to does not contain the word "specialty" anywhere. The only thing is a download of a spreadsheet HES+TOS+V2.01.xlsx, which also does not contain any specialty information. Where is this lookup? I only found the lookup I linked. It's fine to split up that code. But we need to map them accordingly. Two questions:
Happy to create a non-standard concept 44777731 | & | Not known |Physician Specialty| null | Valid | Provider | HES Specialty with no "Maps to" relationship, as flavors of Null have to be represented by the concept_id=0. In fact, all we have to do is to remove the "Other Maternity Event" from the name and fix the Concept Class. |
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@cgreich:
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@cgreich: there are other concepts in "HES Specialty" vocabulary which are not in the correct Class/Domain: would you be OK if I send you a list of those? |
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Ok. Looks like this is a bigger construction site. First, there are missing codes. I assume you want to add them? 108 | Spinal Surgery Second, you want to review the domains. Right now, we have the following non-specialty domain records: 190 | Not a treatment function | Observation You are saying they in fact are all specialty of a provider, rather than a visit/observation? |
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Exactly @cgreich: I did not want to overload you with requests, but you are spot on. Thanks! |
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And what exactly is: 324 | Anticoagulant These are specialties? Or conditions of the patients? |
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And what exactly is: 324 | Anticoagulant These are specialties? Or conditions of the patients? |
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@cgreich: they are all Specialties of the doctors who treated the patients: In "TRETSPEF" (The specialty in which the consultant was working during the period of care.) your list is reported as: 324 = Anticoagulant Service (From 1 April 2004) meaning that the consultant has the specialty provided by the service |
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I see. We would have to link them up to the hierarchy, so they become part of more general specialties, since in the rest of the world there is no such thing as "anticoagulant service". I guess that would be under Internal Medicine. But again, there are more missing from the two tables combined. And you are saying that these things are specialties. Need to sort that out. |
You are too kind. :-) But seriously. These visits and observations are not visits and observations, but actually badly described specialties of providers? So, "Postnatal clinic" is not a visit to a postnatal clinic, but a provider who cares for newborn babies? |
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@cgreich: exactly! These fields are attribute of episodes, for which lots of other information are provided, including a id for a consultant. These lookups describe the consultants specialties. I guess it is because visit costs are based on the consultant specialty, and these are administrative data. |
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Great conversation going on here :) Let's summarise what needs to be done
Did I miss something? @adelmestri would you mind helping us by submitting community contributions with these changes? |
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Thanks @TinyRickC137. |
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Like this:
? |
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@cgreich : Not sure if your comment was for me or for @TinyRickC137 |
@adelmestri, if you would like to contribute, there is a formal process that you can follow. Here is the link to the guidelines: https://github.com/OHDSI/Vocabulary-v5.0/wiki/Community-contribution:-non%E2%80%90drug-vocabularies-p.I. In general, issues placed in the backlog and prioritized against other maintenance needs. HES Specialty vocabulary is not on the roadmap and we do not have an estimate on when this request will be fulfilled. Submitting a formal contribution would enable faster incorporation of the proposed changes. |
Describe the problem in content or desired feature
In the "HES Specialty" vocabulary the following row should be split into 2, "Class" should be "Physicial Specialty" and "Domain" should be "Provider" (not "Observation"):
44777731 | & | null = Other maternity event | Observation | Non-standard | Valid | Observation | HES Specialty
As the link below shows:
https://digital.nhs.uk/data-and-information/data-tools-and-services/data-services/hospital-episode-statistics/hospital-episode-statistics-data-dictionary
in the "HES Specialty" lookup used for Hospital Episode Statistics specialties, the following codes/descriptions are reported, which have been merged together in the Athena vocabulary:
"Null = Other Maternity Event"
"& = Not Known"
Moreover, from the link above, these codes represent
"The specialty in which the consultant was working during the period of care. It can be compared with MAINSPEF, the specialty under which the consultant is contracted. Prior to 1 April 1996, this data item contained the code for the sub-specialty. From April 2004 a new list of treatment specialities was introduced, which describes the specialised service within which the patient was treated."
This means that they are attributes of the providers associated to an observation (not the observation itself) and define their specialty, so the domain should be "Provider" and the class "Physician Specialty" for both
How to find it
In Athena, select the "HES Specialty" vocabulary, click on "Code": the first row is the one that needs to be split into 2 and corrected
Expected adjustments
The 1 row/concept reported above should be split into two as follows
44777731 | & | Not known |Physician Specialty| <Standard?> | Valid | Provider | HES Specialty
| null | Other maternity event | Physician Specialty| <Standard?> | Valid | Provider | HES Specialty
Screenshots
Additional context
Add any other context about the problem here.
44777731 & null = Other maternity event Observation Non-standard Valid Observation HES Specialty
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