search

monarch-initiative / helpdesk

The Monarch Initiative Helpdesk
BSD 3-Clause "New" or "Revised" License
7 stars 0 forks source link

neurodevelopmental disorder MONDO:0700092, gene associations #51

Closed ValWood closed 2 years ago

ValWood commented 2 years ago

If your bug report is about Mondo, please file a ticket here instead: https://github.com/monarch-initiative/mondo/issues

Describe the problem with the Monarch website or APIs

I'm wondering why I see no genes associated with this term in Monarch? neurodevelopmental disorder MONDO:0700092

A clear and concise description of what the issue is.

Expected behavior

A clear and concise description of what you expected to happen.

To reproduce

Please include any information you can about what, where, when, and why this happened. Please include any URLs involved in the issue.

Screenshots

If applicable, add screenshots to help illustrate the problem.

Additional context

Add any other context about the issue that you feel may be important. e.g. browser version, time of day.

kshefchek commented 2 years ago

This is a newly introduced class in Mondo 2021-10-01 and does not have any direct annotations, or any subclasses in which we could infer indirect annotations. It looks like it has been fully incorporated in the 2021-11-01 version so this page should get some indirect annotations in the next data load. Please reopen if this sounds incorrect!

ValWood commented 2 years ago

I don't understand this. We already have it in PomBase with many children? https://www.pombase.org/term/MONDO:0700092 Heve these been removed recently?

kshefchek commented 2 years ago

Which version is PomBase using? I'm looking at the files here https://github.com/monarch-initiative/mondo/releases/tag/v2021-10-01 and it looks like it's a new term without subclasses in this version.

ValWood commented 2 years ago

mondo: releases/2021-11-01/reasoned.owl.owl

ValWood commented 2 years ago

Which version is Monarch using?

kshefchek commented 2 years ago

We're using the October release currently

ValWood commented 2 years ago

Ah OK, maybe the next update will be OK. Do you know when that will be? I am looking for disease gene use cases for a workflow.

kshefchek commented 2 years ago

I don't think we'll get another release out in the near term but defer to @putmantime

in the meantime is there another disease class that could serve as a proxy? perhaps https://monarchinitiative.org/disease/MONDO:0100038 ?

ValWood commented 2 years ago

That term does not work so well it's a smaller gene set for fission yeast orthologs and loses the microtubule-associated subset I am filtering down to. I know the set of genes associated with the term in fission yeast, and I am trying to see how much larger the total human set is. No hurry, this isn't urgent because I can probably check this in other ways by locating the current children in the ontology and summing the associations to get an approximation.

I do have another question though. Is there a way to download the set of causal genes for (associations to) a MONDO disease term from Monarch? I could not see how to do this.