Brook Santangelo issues

Results 7 issues of


                                            Brook Santangelo

rename transform input and output folders

merge and competency questions queries

DuckDB code for merging KG

NCBITaxon file ncbitaxon_removed_subset.json is not downloaded before Uniprot api is queried

Need to update download_utils to ensure ncbitaxon_removed_subset.json is present in data/raw before download_from_api is called

Oaklib annotate function does not return all substring containing values as expected

Example: "runoak -i sqlite:obo:chebi annotate “butyrate”" should have returned all strings that contain butyrate, but, butyr, etc but only returns "butyrate" and "b" containing results. result: predicate_id: rdfs:label object_id: CHEBI:17968...

Get only assembled proteomes if available, remove redundant proteomes

Update README.md

fixes to ingest all HGNC genes for uniprot mappings

- HGNC gene IDs were only being mapped for those that exist in the MONDO ontology - Now ingest the HGNC OWL file, and map all human Uniprot IDs to...