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Rephrase and fix spelling
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sandertan committed Nov 24, 2022
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4 changes: 2 additions & 2 deletions README.md
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# Dutch Medical Concepts
This repository contains instructions and code to create concept tables of Dutch medical names, such as primary names, synonyms, abbreviations, and common misspellings. By basing a concept table on UMLS, which includes MeSH, MedDRA, ICD-10 and ICPC, and adding SNOMED CT and our own translations, a comprehensive set of words commonly used in Dutch medical language is generated. Workflows for creating SNOMED and HPO based concept tables are also in this repository.
This repository contains instructions and code to create concept tables of Dutch medical names, such as primary names, synonyms, abbreviations, and common misspellings. By basing a concept table on UMLS, which includes MeSH, MedDRA, ICD-10 and ICPC, and adding SNOMED CT and a few manually added names, a comprehensive set of words commonly used in Dutch medical language is generated. Workflows for creating SNOMED and HPO based concept tables are also in this repository.

The resulting concept tables can be used in named entity recognition and linking methods, such as MedCAT, to identify entities in Dutch medical text.

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## Generate HPO concept table
Method in: [dutch-hpo_to_concept-table.ipynb](dutch-hpo_to_concept-table.ipynb)

Most HPO names were translated to Dutch by Radboudumc's Clinical Genetics team via [CrowdIn](https://crowdin.com/project/hpo-translation/nl). This is the primary source in creating a concept table of Dutch HPO concepts. In an effort to make a more complete set of synonyms, names from UMLS and SNOMED, as well as some of our own translations, are added.
Most HPO names were translated to Dutch by Radboudumc's Clinical Genetics team via [CrowdIn](https://crowdin.com/project/hpo-translation/nl). This is the primary source in creating a concept table of Dutch HPO concepts. In an effort to make a more complete set of synonyms, names from UMLS and SNOMED, and a few manually created names, are added.

## Generate MedCAT models
To generate MedCAT models from the concept table, see the instructions in the [MedCAT](https://github.com/CogStack/MedCAT) repository. For Dutch language, use these parameters in the configuration:
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4 changes: 2 additions & 2 deletions dutch-snomed_to_concept-table.ipynb
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"id": "faa7cba8",
"metadata": {},
"source": [
"To select the types relevant for named entity linking, we assessed the performance of a MedCAT model on a set of example documents using the unfiltered SNOMED terms. We noticed some types are not useful for our general purpose (named entity recognition), and introduce false positives and ambiguity. We exclude the less usefull types from our concept table."
"To select the types relevant for named entity linking, we assessed the performance of a MedCAT model on a set of example documents using the unfiltered SNOMED terms. We noticed some types are not useful for our general purpose (named entity recognition), and introduce false positives and ambiguity. We exclude the less useful types from our concept table."
]
},
{
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"id": "f435a509",
"metadata": {},
"source": [
"| tui | usefullness for NER | useful examples for NER | useless examples for NER |\n",
"| tui | usefulness for NER | useful examples for NER | useless examples for NER |\n",
"| :- | :- | :- | :-|\n",
"|aandoening |good|hypertensie, boezemfibrilleren, av-blok| |\n",
"|monster|good|trombocyten, leukocyten,basofiele granulocyten||\n",
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