Warning: The CDB was exported by an unknown version of MedCAT.

[plandes]

I'm getting a warning using the latest 3.0 release, which is:

The CDB was exported by an unknown version of MedCAT.

Will you please provide the most recent set of URLs to the CDB, vocabulary and MC status?

Thank you very much for writing this great software.

[plandes]

I managed to solve this. For the sake of others with this issue:

You must use the Available Models (requires UMLS license) link. There appears to be no model that is available to download (without creating an NIH UMLS login).

[plandes]

Looks like I spoke too soon. Now I'm getting this:

You have MedCAT version '1.3.0' installed while the CDB was exported by MedCAT version '1.2.dev361', which may or may not work. If you experience any compatibility issues, please reinstall MedCAT or download the compatible model

Also, this model seems to SNOWMED CUIs. Is there something that converts that to a UMLS CUI, such as 64033007 -> C0022646?

[antsh3k]

MedCAT demo models Thanks for raising this issue. I'll look into updating the demo models to a stable medcat version.

What you are receiving is a warning to say that the model has been built with a different version of the software. In your case you have installed medcat==1.3.0 whilst the model was created with medcat==1.2.dev361. Although this is not an error, one should be careful when using a model created with a different version of medcat. I don't believe that there are any major changes between these versions, so you should be good to go for demo purposes.

Standardised Terminologies As for the terminologies. UMLS nor SNOMED require a respective license to be used. Hence you must obtain a licence from them before we can freely distribute a model.

UMLS contains a mapping of between UMLS-->SNOMED CT

[plandes]

@antsh3k Thanks for the reply.

First regarding the other thread, sounds good--I will use the discussion board next time (thank you for clarifying).

Regarding the version, does it make sense to revert to 1.2.8? Is there a model for 1.3?

Regarding UMLS: yes I understand I need a license (and have one). I also understand the mapping. However, the cui_ field added seems to provide SNOWMED and I'd rather stick to UMLS CUIs (those identifiers that start with C).

[antsh3k]

Use v1.3 and treat medcat==1.2.dev361 as equivalent for the time being. We'll announce in the discourse and news once a new set of demo models have been released.

Which cui_ field are you referring to? What does the concept dictionary: cat.cdb.cui2preferred_name show?

[plandes]

kidney failure gives the following across the two tokens:

• cui_: 64033007, 76797004
• preferred name: Kidney structure, Failure

Note that the previous version would identify kidney failure as one entity for the sentence John was diagnosed with kidney failure.

[antsh3k]

So I am not sure which model you are referring to? There is only one UMLS model I am aware of: umls_sm_wstatus_2021_oct . The concepts that you are mentioned above are SNOMED CT codes (cui_: 64033007, 76797004). It seems to me that you are using a SNOMED model. If it from https://medcat.rosalind.kcl.ac.uk/ then it is a minimally trained snomed model which is for demo purposes only.

[plandes]

I see, so this is a different model, specifically one trained on Snowmed. I thought this might be the case, but then I second guessed it when I could not find a 1.2 or 1.3 version model. Is there no model yet trained using UMLS (as opposed to SNOWMED CT) IDs?

[antsh3k]

Recently our main focus has been on SNOMED CT rather than UMLS. We have an old umls model umls_sm_wstatus_2021_oct just drop us a line at [email protected] and we can send it across.