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This week we released two new vocabularies to Athena:
CIM10 - The French version of the ICD10 classification, at this point created from the 2020 version and presumably lacking some historic, now deprecated, entries.
Release Notes
NCCD - The Normalized Chinese Clinical Drug knowledge base
Release Notes
This week we released a couple new vocabularies to Athena:
ICD10GM - The German version of the ICD10 classification. It has been created using stacked versions of the ICD10 catalogs provided by Dresden University. Codes that were not present in the ICD10 International version have been auto-translated and uphill mapping applied to less specific parent codes. This delta list of codes is preserved for a later follow up to apply more specific mappings.
Release Notes
A first version of a set of Cancer and Gene variant vocabularies that at this point are focused to support cancer classification use cases and are not entirely complete. These vocabularies will receive ongoing updates over the course of the following months.
| Name | Description |
|---|---|
| CIViC | Clinical Interpretation of Variants in Cancer (civicdb.org) |
| CGI | Cancer Genome Interpreter (Pompeu Fabra University) |
| ClinVar | ClinVar (NCBI) |
| JAX | The Clinical Knowledgebase (The Jackson Laboratory) |
| NCIt | NCI Thesaurus (National Cancer Institute) |
| HGNC | Human Gene Nomenclature (European Bioinformatics Institute) |
Release Notes #1
Release Notes #2
@Christian_Reich will be able to provide more background soon.
This week, we released two new vocabularies to Athena:
OPS - The German procedure coding catalog
OPS is provided by the DIMDI institute and the source material was provided under these licensing conditions.
This initial release of the OPS vocabulary does not feature a comprehensive mapping but contains around 9000 mappings to standard concepts, with a substantial part of these mappings provided by Averbis and TriNetX. Not mapped concepts remain as non standard for now, with the intention to continue mapping based on community feedback and collaboration.
CCAM - The French procedure and measures coding catalog
The “Classification Commune des Actes Médicaux” is issued by the French Health Insurance (Assurance Maladie).
This initial release of CCAM does not contain any mappings to standard concepts. A collaborative approach is required by French OHDSI members to enrich the vocabulary with mappings and provide them back to OHDSI for distribution through Athena.
Last week, we released one new vocabulary to Athena:
Oncotree is provided by the Memorial Sloan Kettering Cancer Center and is in use by the GENIE project.
Its concepts are mostly mapped to ICD-O.
While it is not exactly a new vocabulary, it might be worth mentioning that in the latest vocabulary release we have updated (v 9.2) the PHDSC vocabulary (Payer Typology) and at the same time replaced it with its proper name SOPT. In the unlikely case that you have explicitly referenced to the vocabulary ID “PHDSC” in your coding, please replace this reference with “SOPT”.
We have done it again… in the latest vocabulary release we have fixed previous misconceptions about the VA Product vocabulary and updated it to the latest version. In this process we have also renamed VA Products to its proper name VANDF. So, again, if in your coding “VA Products” has been referenced as a vocabulary id, please replace it with “VANDF”.
We have released a new vocabulary again: The OMOP Investigational Drugs, a compilation of non-standard drug entries mapped into standard concepts with essentially two features: