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Add Biomappings support for the DKG #95

Merged
merged 7 commits into from
Jul 5, 2023
Merged

Add Biomappings support for the DKG #95

merged 7 commits into from
Jul 5, 2023

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cthoyt
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@cthoyt cthoyt commented Dec 2, 2022

Closes #69. This PR does the following:

  1. Adds relevant biomappings into the DKG
  2. Adds a script for constructing a local Gilda cache based on the DKG
  3. Adds a script for adding predicted lexical mappings to Biomappings from a subset of namespaces in the DKG (ones related to epi)
  4. Improves RDF construction (remaps the new synonym predicates and the unqualified biomappings predicates to DeBiO terms)

This also updates code relevant for updates to the PyOBO and bioontologies

@cthoyt cthoyt force-pushed the lexical-merge branch 4 times, most recently from d23a0ae to a5492cb Compare December 8, 2022 13:00
@cthoyt cthoyt force-pushed the lexical-merge branch 2 times, most recently from 8791e9c to 58b67dc Compare June 12, 2023 13:48
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codecov-commenter commented Jun 12, 2023

Codecov Report

Merging #95 (8fe2d81) into main (7f849c7) will not change coverage.
The diff coverage is n/a.

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@@           Coverage Diff           @@
##             main      #95   +/-   ##
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  Coverage   76.45%   76.45%           
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  Files          65       65           
  Lines        4977     4977           
=======================================
  Hits         3805     3805           
  Misses       1172     1172           

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@cthoyt cthoyt requested a review from bgyori June 14, 2023 12:49
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cthoyt commented Jun 14, 2023

@bgyori tested and ready!

@cthoyt cthoyt merged commit 65407db into main Jul 5, 2023
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@cthoyt cthoyt deleted the lexical-merge branch July 5, 2023 11:08
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cthoyt commented Jul 5, 2023

We had several chats about this being ready, I just added a few minor updates for pyobo + bioontologies before merging

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