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Add custom upheno lexical pipeline to phenio-utils #53

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matentzn opened this issue Jun 28, 2023 · 0 comments
Open

Add custom upheno lexical pipeline to phenio-utils #53

matentzn opened this issue Jun 28, 2023 · 0 comments
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@matentzn
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Addition to #51

Add https://github.com/obophenotype/upheno-dev/blob/master/src/scripts/lexical_mapping.py

to the phenio toolkit, as

phenio-utils upheno-lex -i ....

And change the output to be a valid SSSOM file.

Try it! Here is a simple example to start: https://github.com/mapping-commons/sssom/blob/master/examples/external/example1.sssom.tsv

You don't need all columns, for now, just add the ones that are already there!

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