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IHCC-cohorts / GECKO

Genomics Cohorts Knowledge Ontology
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Add CSV export for IHCC view #24

Closed beckyjackson closed 3 years ago

beckyjackson commented 3 years ago

Resolves #23

Currently ordered by ID, but please let me know if you'd like it to be ordered a different way (e.g., label or parent).

Lines 115-120 are a bit weird because the PDRO definition for that term contains line breaks... not sure if we want to do something about this. It displays OK in Excel.

jamesaoverton commented 3 years ago

@mcourtot You can preview the table here: https://github.com/IHCC-cohorts/GECKO/blob/2d13448f5c5e72854d978f4dd0bc0696654d0a27/views/ihcc-gecko.csv

jamesaoverton commented 3 years ago

@mcourtot Does this table look good to you? https://github.com/IHCC-cohorts/GECKO/blob/2d13448f5c5e72854d978f4dd0bc0696654d0a27/views/ihcc-gecko.csv

mcourtot commented 3 years ago

I'm going to ask for my ideal outcome in case it's easy to tweak, if it is too much work the table above is ok

  1. Can we have the columns order be, from the left: Category (ie subclass of), ID, label, definition (suspect trivial)
  2. Can we have the categories in order/depth. For example consider the hierarchy physio measurement > anthropometry > height Can we have left most column be physio measurement, then next one be anthropometry then next be all subclasses height etc? To emulate the structure of https://docs.google.com/spreadsheets/d/1ZXqTMIhFtGOaodw7Fns5YghvY_pWos-RuSa2BFnO5l4/edit#gid=0 with broad category, sub-category etc (suspect hard, but maybe having all the IHCC facets be broad category could be a good intermediate solution (ie we would have 'physio measurement' as broad category, then anthropometry and height in same column)
beckyjackson commented 3 years ago

I just pushed some changes. @mcourtot could you please check out this table and let me know if this is what you're thinking? https://github.com/IHCC-cohorts/GECKO/blob/8b2e43bd6e9f90e5f30ba9098c2f232c4f17a59d/views/ihcc-gecko.csv

Also, I can always remove the "definition" column if you think it doesn't really help.

jamesaoverton commented 3 years ago

@mcourtot We're just waiting for your feedback on this PR.