snomed refset processing update #294
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baixiac
reviewed
Jan 18, 2023
medcat/utils/preprocess_snomed.py
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| while len(stack) != 0: | ||
| # remove the last element from the stack | ||
| current_snomed = stack.pop() | ||
| current_snomed_parent = pt2ch.get(current_snomed, []) |
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Should the LHS be named as *_children rather than *_parent?
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Thanks will change.
medcat/utils/preprocess_snomed.py
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| Retrieves all the children of a given SNOMED CT ID (SCTID) from a given parent-to-child mapping (pt2ch) via the "IS A" relationship. | ||
| pt2ch can be found in a MedCAT model in the additional info via the call: cat.cdb.addl_info['pt2ch'] | ||
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| Parameters: |
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This is different from Google-style docstrings used at other places so pls check if the existing doc-gen will honour this.
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| def map_snomed2opcs4(self) -> pd.DataFrame: | ||
| """Map SNOMED to OPSC4. | ||
| def map_snomed2opcs4(self): |
| snomed2opcs4df = self._map_snomed2refset()[1] | ||
| return self._refset_df2dict(snomed2opcs4df) | ||
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| def _check_path_and_release(self): |
medcat/utils/preprocess_snomed.py
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| This function takes a SNOMED refset DataFrame as an input and converts it into a dictionary. | ||
| The DataFrame should contain the columns 'referencedComponentId','mapTarget','mapGroup','mapPriority','mapRule','mapAdvice'. | ||
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| Parameters: |
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Again, pls check if the existing doc-gen will honour this.
| 'mapAdvice': row['mapAdvice']} for _, row in group.iterrows()]).to_dict() | ||
| return refset_dict | ||
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| def _map_snomed2refset(self): |
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Ready for merge if everyone is okay with it |
mart-r
pushed a commit
to mart-r/MedCAT
that referenced
this pull request
Jun 14, 2023
snomed refset processing update
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Main change has been to the processing of snomed refsets to the required medcat models formats.