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monarch-initiative / mondo

Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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[Obsolete] look for terms that are tagged ‘obsoletion candidate’ #1405

Closed nicolevasilevsky closed 3 years ago

nicolevasilevsky commented 4 years ago

Fixing these will help address #834

Adding Shahim, as I am not sure if I know how to filter all the terms that are tagged 'obsoletion candidate'

nicolevasilevsky commented 4 years ago

@matentzn said he would help generate this list (thank you!) Once we have the list, I'll post it here for folks to review.

matentzn commented 4 years ago

@nicolevasilevsky I think @cmungall pretty extensive reports already cover this:

https://github.com/monarch-initiative/mondo/blob/master/reports/obsoletion-candidates.tsv

Isnt this what you are looking for?

nicolevasilevsky commented 4 years ago

this is great, thank you @matentzn!

nicolevasilevsky commented 4 years ago

I sorted this list by label: https://github.com/monarch-initiative/mondo/blob/master/reports/obsoletion-candidates-sorted.tsv

nicolevasilevsky commented 3 years ago

Google spreadsheet here

nicolevasilevsky commented 3 years ago

@matentzn could you please regenerate this list? Looks like many terms have already been obsoleted. Thank you!

matentzn commented 3 years ago

This is how to do this:

sh run.sh make report-query-obsoletion-candidates

Can you add a section to the editors doc how to generate reports?

How to generate reports

Reports are generally created like this:

sh run.sh make report-query-%

For example, the following command...

sh run.sh make report-query-obsoletion-candidates

will run this:

robot --catalog catalog-v001.xml query --use-graphs true -i mondo-edit.obo -f tsv --query ../sparql/reports/obsoletion-candidates.sparql reports/report-obsoletion-candidates.tsv

Which will generate a TSV report here: reports/report-obsoletion-candidates.tsv.

The only requirement for a report is, that a suitable SPARQL query can be found in ../sparql/reports/, for example, ../sparql/reports/obsoletion-candidates.sparql.

If you want to create your very own report, you can

  1. tweak an existing command, for example using Ubergraph (https://api.triplydb.com/s/YfJCi9mrR)
  2. Save the query as a .sparql query in ../sparql/reports/, for example, ../sparql/reports/my-query.sparql.
  3. Run sh run.sh make report-query-my-query to generate the report as above.

Note that the above does not cover automated upload to Google docs (if you want to learn that, put it on a QC meeting agenda).

nicolevasilevsky commented 3 years ago

thank you, will do!

nicolevasilevsky commented 3 years ago

Updated spreadsheet is here

nicolevasilevsky commented 3 years ago

reviewed the list and created separate tickets for this