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Add semsim-comparison percentage-diff metadata columns #190

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souzadevinicius opened this issue Aug 16, 2023 · 2 comments
Closed

Add semsim-comparison percentage-diff metadata columns #190

souzadevinicius opened this issue Aug 16, 2023 · 2 comments
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@souzadevinicius
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The current semsim-comparison percentage-diff file encodes metadata file as column name like this:

subject_id object_id phenio-hp-hp.semsimian.0.7_jaccard_similarity upheno1-hp-hp.semsimian.0.7_jaccard_similarity diff
HP:0010136 HP:0010147 0.8021978021978022 0.8823529411764706 9.99%
HP:0010147 HP:0010136 0.8021978021978022 0.8823529411764706 9.99%
HP:0008060 HP:0007750 0.8524590163934426 0.9375 9.98%
HP:0007750 HP:0008060 0.8524590163934426 0.9375 9.98%

It needs to be replaced to this:

subject_id object_id jaccard_similarity_left jaccard_similarity_right diff left_file right_file
HP:0010136 HP:0010147 0.8021978021978022 0.8823529411764706 9.99% phenio-hp-hp.semsimian.0.7 upheno1-hp-hp.semsimian.0.7
HP:0010147 HP:0010136 0.8021978021978022 0.8823529411764706 9.99% phenio-hp-hp.semsimian.0.7 upheno1-hp-hp.semsimian.0.7
HP:0008060 HP:0007750 0.8524590163934426 0.9375 9.98% phenio-hp-hp.semsimian.0.7 upheno1-hp-hp.semsimian.0.7
HP:0007750 HP:0008060 0.8524590163934426 0.9375 9.98% phenio-hp-hp.semsimian.0.7 upheno1-hp-hp.semsimian.0.7

PS: Some stats

A file with 265829 lines had its size increased from 16MB using the first template to 30MB compared to the second one.

@matentzn
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Thank you @souzadevinicius I am not sure what is the right answer. I reached out for other opinions. Maybe your original solution (solution 1) is actually preferable after all if the file size increase is so enormous. On the other hand, maybe adding a column compresses well? These 16MB and 30MB files, if you gzip them, what is their difference?

@souzadevinicius souzadevinicius self-assigned this Aug 21, 2023
@souzadevinicius
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Replaced by this approach
monarch-initiative/monarch-semantic-similarity-profiles#9

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