# MedCAT model for SNOMED-CT

**URL:** <https://discourse.cogstack.org/t/medcat-model-for-snomed-ct/212>\
**Category:** MedCAT\
**Tags:** medical-ontologies\
**Created:** [June 6, 2023, 10:11am UTC](https://discourse.cogstack.org/t/medcat-model-for-snomed-ct/212 "2023-06-06T10:11:25Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![Jaya](https://avatars.discourse-cdn.com/v4/letter/j/22d042/32.png) [@Jaya](https://discourse.cogstack.org/u/Jaya)\
**Post date:** [June 6, 2023, 10:11am UTC](https://discourse.cogstack.org/t/medcat-model-for-snomed-ct/212/1 "2023-06-06T10:11:25Z")

</div>

Hello,

I am facing some issues loading up the SNOMED-CT model for MedCAT. The purpose is to run some text through this model in order to get the values and SCTIDs for some pre-specified pain terms.

Versions  
MedCAT: 1.7.0  
SpaCy: 3.5.3  
Python: 3.10.5

I have downloaded the snomed model from the [https://medcat.rosalind.kcl.ac.uk/](https://medcat.rosalind.kcl.ac.uk/) website, as suggested on the GitHub repo.

When I try to load the model using:

`MODEL_DIR = "./models/"`  
`model_pack_path = MODEL_DIR + "/mc_modelpack_snomed_int_16_mar_2022_25be3857ba34bdd5.zip"`

I get a validation error:

```auto
---------------------------------------------------------------------------
ValidationError Traceback (most recent call last)
Input In [15], in <cell line: 2>()
      1 model_pack_path = MODEL_DIR + "/mc_modelpack_snomed_int_16_mar_2022_25be3857ba34bdd5.zip"
----> 2 cat = CAT.load_model_pack(model_pack_path)

File /opt/conda/lib/python3.10/site-packages/medcat/cat.py:372, in CAT.load_model_pack(cls, zip_path, meta_cat_config_dict, load_meta_models, load_addl_ner)
    368 for meta_path in meta_paths:
    369 meta_cats.append(MetaCAT.load(save_dir_path=meta_path,
    370 config_dict=meta_cat_config_dict))
--> 372 cat = cls(cdb=cdb, config=cdb.config, vocab=vocab, meta_cats=meta_cats, addl_ner=addl_ner)
    373 logger.info(cat.get_model_card()) # Print the model card
    374 return cat

File /opt/conda/lib/python3.10/site-packages/medcat/cat.py:101, in CAT. __init__ (self, cdb, vocab, config, meta_cats, addl_ner)
     99 self._meta_cats = meta_cats
    100 self._addl_ner = addl_ner if isinstance(addl_ner, list) else [addl_ner]
--> 101 self._create_pipeline(self.config)

File /opt/conda/lib/python3.10/site-packages/medcat/cat.py:109, in CAT._create_pipeline(self, config)
    107 # Build the pipeline
    108 self.pipe = Pipe(tokenizer=spacy_split_all, config=config)
--> 109 self.pipe.add_tagger(tagger=tag_skip_and_punct,
    110 name='skip_and_punct',
    111 additional_fields=['is_punct'])
    113 if self.vocab is not None:
    114 spell_checker = BasicSpellChecker(cdb_vocab=self.cdb.vocab, config=config, data_vocab=self.vocab)

File /opt/conda/lib/python3.10/site-packages/medcat/pipe.py:66, in Pipe.add_tagger(self, tagger, name, additional_fields)
     64 name = name if name is not None else component_factory_name
     65 Language.factory(name=component_factory_name, default_config={"config": self.config}, func=tagger)
---> 66 self._nlp.add_pipe(component_factory_name, name=name, first=True)
     68 # Add custom fields needed for this usecase
     69 Token.set_extension('to_skip', default=False, force=True)

File /opt/conda/lib/python3.10/site-packages/spacy/language.py:786, in Language.add_pipe(self, factory_name, name, before, after, first, last, source, config, raw_config, validate)
    782 pipe_component, factory_name = self.create_pipe_from_source(
    783 factory_name, source, name=name
    784 )
    785 else:
--> 786 pipe_component = self.create_pipe(
    787 factory_name,
    788 name=name,
    789 config=config,
    790 raw_config=raw_config,
    791 validate=validate,
    792 )
    793 pipe_index = self._get_pipe_index(before, after, first, last)
    794 self._pipe_meta[name] = self.get_factory_meta(factory_name)

File /opt/conda/lib/python3.10/site-packages/spacy/language.py:679, in Language.create_pipe(self, factory_name, name, config, raw_config, validate)
    676 cfg = {factory_name: config}
    677 # We're calling the internal _fill here to avoid constructing the
    678 # registered functions twice
--> 679 resolved = registry.resolve(cfg, validate=validate)
    680 filled = registry.fill({"cfg": cfg[factory_name]}, validate=validate)["cfg"]
    681 filled = Config(filled)

File /opt/conda/lib/python3.10/site-packages/confection/ __init__.py:728, in registry.resolve(cls, config, schema, overrides, validate)
    719 @classmethod
    720 def resolve(
    721 cls,
   (...)
    726 validate: bool = True,
    727 ) -> Dict[str, Any]:
--> 728 resolved, _ = cls._make(
    729 config, schema=schema, overrides=overrides, validate=validate, resolve=True
    730 )
    731 return resolved

File /opt/conda/lib/python3.10/site-packages/confection/ __init__.py:777, in registry._make(cls, config, schema, overrides, resolve, validate)
    775 if not is_interpolated:
    776 config = Config(orig_config).interpolate()
--> 777 filled, _, resolved = cls._fill(
    778 config, schema, validate=validate, overrides=overrides, resolve=resolve
    779 )
    780 filled = Config(filled, section_order=section_order)
    781 # Check that overrides didn't include invalid properties not in config

File /opt/conda/lib/python3.10/site-packages/confection/ __init__.py:832, in registry._fill(cls, config, schema, validate, resolve, parent, overrides)
    830 schema. __fields__ [key] = copy_model_field(field, Any)
    831 promise_schema = cls.make_promise_schema(value, resolve=resolve)
--> 832 filled[key], validation[v_key], final[key] = cls._fill(
    833 value,
    834 promise_schema,
    835 validate=validate,
    836 resolve=resolve,
    837 parent=key_parent,
    838 overrides=overrides,
    839 )
    840 reg_name, func_name = cls.get_constructor(final[key])
    841 args, kwargs = cls.parse_args(final[key])

File /opt/conda/lib/python3.10/site-packages/confection/ __init__.py:911, in registry._fill(cls, config, schema, validate, resolve, parent, overrides)
    909 exclude_validation = set([ARGS_FIELD_ALIAS, *RESERVED_FIELDS.keys()])
    910 validation.update(result.dict(exclude=exclude_validation))
--> 911 filled, final = cls._update_from_parsed(validation, filled, final)
    912 if exclude:
    913 filled = {k: v for k, v in filled.items() if k not in exclude}

File /opt/conda/lib/python3.10/site-packages/confection/ __init__.py:933, in registry._update_from_parsed(cls, validation, filled, final)
    931 final[key] = value
    932 if isinstance(value, dict):
--> 933 filled[key], final[key] = cls._update_from_parsed(
    934 value, filled[key], final[key]
    935 )
    936 # Update final config with parsed value if they're not equal (in
    937 # value and in type) but not if it's a generator because we had to
    938 # replace that to validate it correctly
    939 elif key == ARGS_FIELD:

File /opt/conda/lib/python3.10/site-packages/confection/ __init__.py:929, in registry._update_from_parsed(cls, validation, filled, final)
    927 continue # skip aliases for reserved fields
    928 if key not in filled:
--> 929 filled[key] = value
    930 if key not in final:
    931 final[key] = value

File /opt/conda/lib/python3.10/site-packages/medcat/config.py:34, in FakeDict. __setitem__ (self, arg, val)
     33 def __setitem__ (self, arg: str, val) -> None:
---> 34 setattr(self, arg, val)

File /opt/conda/lib/python3.10/site-packages/pydantic/main.py:384, in pydantic.main.BaseModel. __setattr__ ()

ValidationError: 1 validation error for Config
linking -> filters -> cuis
  value is not a valid set (type=type_error.set)

```

Has anyone else come across this, or know how to resolve it?

Thanks!

Jaya

---

<div class="post-metadata">

**Author:** ![anthony.shek](https://avatars.discourse-cdn.com/v4/letter/a/b782af/32.png) [@anthony.shek](https://discourse.cogstack.org/u/anthony.shek)\
**Post date:** [June 7, 2023, 1:58pm UTC](https://discourse.cogstack.org/t/medcat-model-for-snomed-ct/212/2 "2023-06-07T13:58:51Z")

</div>

That free demo model is not compatible with the latest MedCAT version.

If you downgrade your version of MedCAT.  
`pip install medcat==1.5 `  
This version will work with the demo.

---

<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:** [June 20, 2023, 6:38am UTC](https://discourse.cogstack.org/t/medcat-model-for-snomed-ct/212/3 "2023-06-20T06:38:18Z")

</div>

For future reference, this also has a fix for newer versions of medxat as described in the following PR:

> <https://github.com/CogStack/MedCAT/pull/313>
>
> When loading 1.2 models with 1.3+, there's an issue due to the validation of dat…a types in 1.3+. A \`{}\` (which is parsed as an empty \_dict\_) is not valid for \`config.linking.filters.cuis\` where a \_set\_ is expected instead.
> 
> This PR adds the possibility of fixing the specific issue (i.e "update").
> 
> This PR add the \`medcat.utils.versioning\` module that helps with this.
> 
> It's a runnable module. One can use the following to fix the config issue:
> \`\`\`
> python -m medcat.utils.versioning fix-config \<model\_pack\_zip\_path\> \<new\_model\_pack\_zip\_path\>
> \`\`\`

Though that’s not yet a part of any release. Hopefully we’ll have the next release up soon.

TLDR:  
If you’ve got the GitHub version of medcat installed (or you’re reading in a future where a version after 1.7.0 has been released), you can run:  
`python -m medcat.utils.versioning fix-config <model_pack_path> <new_model_pack_path>`