ROBOT report - need to check that we have no clashes with HPO

nicolevasilevsky commented 4 years ago

Per our Mondo call on 05/08, could we get a check in the ROBOT report to check that Mondo terms do not have any clashes with HPO terms.

For example: MONDO_0001627 'dementia (disease)' MONDO_0002280 'anemia (disease)'

joeflack4 commented 3 years ago

I've moved the main discussion for this issue here: https://github.com/INCATools/ontology-development-kit/issues/482

Put label 'needs clarification' on this for now until some questions in that issue addressed.

matentzn commented 3 years ago

This problem actually needs to be solved here in the Mondo repo, as this is very specific to Mondo, and ROBOT/ODK extensions apply to all ontologies! You are thinking in the right direction though.

What needs to happen here is: 1) Inputs: tmp/mondo-labels.tsv, tmp/hpo-labels.tsv (using ROBOT query, and a sparql query that obtains a list of IDs with their labels (that query already exists in the repo). These to make goals do not exist yet and need to be created in mondo.Makefile 2) a python script that reads the two tables, does some preprocessing on the labels and then spits put an error if two labels clash.

A more amazing, alternative solution (which I dont know if and how it would work, but could be a challenge) 1) you merge mondo.owl and hp.owl 2) write a single SPARQL query that checks for duplicate labels.. after preprocessing (this requires some pretty advanced SPARQL skills a hand-width beyond my own though)

joeflack4 commented 3 years ago

Just copying over my questions from here. I refined my questions based on Nico's last comment. Maybe another one to add to the qc-call.

@matentzn

[x] 1. Is this the correct repo for this issue? The original issue is under Mondo: ROBOT report - need to check that we have no clashes with HPO monarch-initiative/mondo#1499
[x] 2. Can you point me towards best directory/file(s) in repo where I should be working? Edit: It looks like the src/ontology/tmp/ directory, but those files are .gitignoreed. I might be misunderstanding, but it sounds like you are saying that I need to create some make targets in order to create these files first and then use them as inputs? And I think the python scripts should go in src/scripts.
[x] 3. Anything else I should know ahead of time before I start working on ROBOT stuff? Edit: Looks like this doesn't need to be in the ROBOT repo, but I'm not too familiar with ROBOT yet; not sure where it comes in here. @nicolevasilevsky
[x] 4. can you expand more on "HPO terms"? Where is a list of such terms?
[x] 5. What is an example of a "clash"? I know I'm missing the context of this earlier meeting w/ Dazhi, but in your example, they look like perfectly good terms to me.

nicolevasilevsky commented 3 years ago

The issue here is that we have terms in Mondo that are diseases and sometimes there are terms in Human Phenotype Ontology (HPO) that have the same label. Examples: MONDO_0001627 dementia and HP:0000726 Dementia MONDO_0002280 anemia and HP:0001903 Anemia

You can view the entire HPO here: https://hpo.jax.org/app/ (or download the owl file here

I can't remember what our ultimate goal is though - do we not want to have overlapping terms in Mondo and HPO?

I'll add this to the QC call agenda.

matentzn commented 3 years ago

For now, the action item should be:

[ ] create an SSSOM file with "exact matches" between HPO and and Mondo
[ ] bring table to curation call and discuss strategy with Chris.

As I describe in my last comment above, you can generate the tables using ROBOT report - @sabrinatoro is also now expert and can help you do it :D

nicolevasilevsky commented 3 years ago

2) best directory - should go to into mondo.make file temp files should go to into tmp directory src/scripts

3) ROBOT report is a function inside of ROBOT tool to generate a standardized QC that is the same across all OBO ontologies

The point of this ticket is some diseases match phenotypes - we need an exact match table. Then we'll discuss what to do with these on the Mondo call.

5) where the label (after stemming, lowercasing, removing abnormal) matches. Could start by looking at exact matches. stemming is a preprocessing step (can google what this means). May not be necessary.

start with case insensitive matches

psiotwo commented 2 years ago

Not sure whether it is related to this issue, but e.g. the following MONDO concepts share a definition with HPO concepts: MONDO:0005260, MONDO:0001014.

matentzn commented 2 years ago

It fits in here! But its a slightly adjacent issue. Thank your for reporting!

monarch-initiative / mondo

ROBOT report - need to check that we have no clashes with HPO #1499