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Allow passing in of ontology terms on command line when using enrichment in ontology-only mode #770

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cmungall opened this issue May 30, 2024 · 0 comments

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@cmungall
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Currently enrichment allows you to pass in:

  • entity set (typically genes) via -U
  • term set (optional - uses whole ontology to enrich against) - these are the candidates

The command can also be run in ontology-only mode, where instead of genes we just summarize commonalities among terms

It would be handy to pass in the terms as sample set on the command line. Many commands accept @ as a break, so we could allow for:

ontie --stacktrace enrichment --ontology-only -p i i^ONTIE: @ [ .all .not i^ONTIE: ]

This enriches IDs in the ONTIE space against those in the non-ONTIE space in the ONTIE ontology

cmungall added a commit that referenced this issue May 30, 2024
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