# Trouble creating ICD10 codes mappings for NER

**URL:** <https://discourse.cogstack.org/t/trouble-creating-icd10-codes-mappings-for-ner/290>\
**Category:** MedCAT\
**Created:** [March 25, 2024, 9:29pm UTC](https://discourse.cogstack.org/t/trouble-creating-icd10-codes-mappings-for-ner/290 "2024-03-25T21:29:23Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![acortis](https://dub1.discourse-cdn.com/flex017/user_avatar/discourse.cogstack.org/acortis/32/59_2.png) [@acortis](https://discourse.cogstack.org/u/acortis)\
**Post date:** [March 25, 2024, 9:29pm UTC](https://discourse.cogstack.org/t/trouble-creating-icd10-codes-mappings-for-ner/290/1 "2024-03-25T21:29:23Z")

</div>

Hi noob here 😉

I am trying to do some entity recognition, but I am confused as how to actually report them in the results.  
For instance:

```auto
In [1]: from medcat.cat import CAT
In [2]: cat = CAT.load_model_pack('./medmen_wstatus_2021_oct.zip')
In [3]: cat.get_entities("epilepsy", only_cui=False)
Out[3]: 
{'entities': {0: {'pretty_name': 'Epilepsy',
   'cui': 'C0014544',
   'type_ids': ['T047'],
   'types': ['Disease or Syndrome'],
   'source_value': 'epilepsy',
   'detected_name': 'epilepsy',
   'acc': 0.6693785786848553,
   'context_similarity': 0.6693785786848553,
   'start': 0,
   'end': 8,
   'icd10': [],
   'ontologies': [],
   'snomed': [],
   'id': 0,
   'meta_anns': {'Status': {'value': 'Affirmed',
     'confidence': 0.7051243185997009,
     'name': 'Status'}}}},
 'tokens': []}

```

and the `icd10` field is empty.  
Then I followed the [https://htmlpreview.github.io/?https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/specialised/Preprocessing\_SNOMED\_CT.html](https://tutorial) and  
I am able to get to the point where we **doc**

```auto
In [91] cdb.addl_info['cui2icd10'] = sctid2icd10
In [92] cdb.save("SNOMED_cdb.dat")

```

But I am not able to create a `model_pack` from this `cdb`.

Could you please help me out?

Thanks

Andrea

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<div class="post-metadata">

**Author:** ![mart.ratas](https://avatars.discourse-cdn.com/v4/letter/m/e79b87/32.png) [@mart.ratas](https://discourse.cogstack.org/u/mart.ratas)\
**Post date:** [March 26, 2024, 10:02am UTC](https://discourse.cogstack.org/t/trouble-creating-icd10-codes-mappings-for-ner/290/2 "2024-03-26T10:02:30Z")

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I am not quire sure what’s stopping you from creating a model pack.

But for reference, you create a model pack using the `CAT` instance, not the `CDB` instance. The model pack includes the CDB and the Vocab. When saved on disk, it’ll also save the `spacy` model used along with the additional NER models or MetaCAT models if applicable.

Here’s how you do it, in a nutshell:

```auto
# relevant imports
cat = CAT.load_model_pack('./medmen_wstatus_2021_oct.zip')
cdb = cat.cdb # reference to the CDB involved in the model pack
# relevant changes to the CDB - in your case, adding the cui2icd10 mappings
save_folder = '' # path to where you want to save the new model pack
cat.create_model_pack(save_folder)

```

Note that the `CAT` instance keeps track of the `CDB` instance so changes you’ve made to the CDB will be saved on disk as part of the model pack.

---

<div class="post-metadata">

**Author:** ![acortis](https://dub1.discourse-cdn.com/flex017/user_avatar/discourse.cogstack.org/acortis/32/59_2.png) [@acortis](https://discourse.cogstack.org/u/acortis)\
**Post date:** [March 26, 2024, 2:05pm UTC](https://discourse.cogstack.org/t/trouble-creating-icd10-codes-mappings-for-ner/290/3 "2024-03-26T14:05:05Z")

</div>

> [@mart.ratas](#):
>
> `relevant changes to the CDB - in your case, adding the cui2icd10 mappings`

mhmm … I guess this is the part where I am confused for `medmen` and `snomed`.

Could you please help me out filling in the `???` in the codes below ? Thanks!

```auto
# --- code 1
from medcat.cat import CAT
cat = CAT.load_model_pack('./medmen_wstatus_2021_oct.zip')
# cat.cdb.addl_info['cui2icd10'] = ???
cat.get_entities("epilepsy", only_cui=False)
ents = cat.get_entities("epilepsy", only_cui=False)
assert ents['entities'][0]['icd10'] == ['G40.909']
cat.create_model_pack('medmen_with_icd10')

```

```auto
# --- code 2
from medcat.cdb import CDB
from medcat.cat import CAT
cdb = CDB.load('SNOMED_cdb.dat')
def get_direct_refset_mapping(in_dict: dict) -> dict:
    ret_dict = dict()
    for k, vals in in_dict.items():
        ret_dict[k] = [v['code'] for v in svals]
    return ret_dict
from medcat.utils.preprocess_snomed import Snomed
snomed = Snomed('SnomedCT_InternationalRF2_PRODUCTION_20240301T120000Z')
icd_dict = snomed.map_snomed2icd10()
sctid2icd10 = get_direct_refset_mapping(icd_dict)
cdb.addl_info['cui2icd10'] = get_direct_refset_mapping(sctid2icd10)

# cat = CAT(cdb=cdb, config=cdb.config, vocab=???)

```

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<div class="post-metadata">

**Author:** ![mart.ratas](https://avatars.discourse-cdn.com/v4/letter/m/e79b87/32.png) [@mart.ratas](https://discourse.cogstack.org/u/mart.ratas)\
**Post date:** [April 2, 2024, 8:59am UTC](https://discourse.cogstack.org/t/trouble-creating-icd10-codes-mappings-for-ner/290/4 "2024-04-02T08:59:35Z")

</div>

I see you’re first (in `code 1`) loading the MedMentions model. That’s a UMLS based model.

You’re then (in `code 2`) seemingly loading a SNOMED based CDB. And then using our preprocessing tools to get and add the SNOMED to ICD10 mappings from the 2024 SNOMED International release.  
As far as I know, this should work just fine.

Now, if you want to relate the UMLS terms in the MedMentions model to ICD10 you would need to use the UMLS version that this model was created with (different versions you may have unforeseen conflicts) and look for the corresponding ICD10 terms for each of the concepts where possible. Though this may not always be straight forward since there can be one-to-many or many-to-one mappings.  
Off the top of my head, I think this will involve looking into MRCONSO.RRF (but potentially some others as well) and looking at lines where the source is ICD10. In that case the source ID should be the ICD10 ID and should allow you to link it to the UMLS concept.