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@rsgoncalves rsgoncalves released this 19 Sep 19:03
· 66 commits to master since this release
v3.6.0
5ec60af

Change Log

User-facing changes:

  • Update the variable codebooks table nhanes_variables_codebooks.tsv with additional codebooks that were previously unattainable using nhanesA, and which we can now get with nhanesA_0.8.0.
  • Add disease locations associated with NCIT and FOODON terms.
    • Also includes locations expressed in universal restrictions (i.e., 'pancreas disease' disease_has_location only 'pancreas').
  • Update ontology set to use EFO v3.57.0, which results in updated ontology mappings (or just updated scores).
  • Include DIsease Ontology (DOID) terms as potential mapping targets.
  • Modify prototype search module nhanes_metadata_search.py to allow queries with multiple search terms.

Internal changes:

  • Use optimized nhanesA v0.8.0 for faster codebook retrieval.
  • Add dedicated module to build a sqlite DB of the metadata, which outputs a (xz compressed) sqlite database file containing all the generated tables.
    • This facilitates browsing and testing the generated tables.
    • The resulting database is used with nhanes_metadata_search.py.
  • Use SemSQL gzip database distributions, which provide more up to date ontology versions.
  • Add argument to include (or not) disease locations associated with ontology terms.
  • Update conditions used to flag if variables are mapped, since we include now in the output table all variables even if they have not been mapped (these get a mapping score of 0).
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