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monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Temporal ordering of phenotypes in both the curated data and algorithms #454

Open jmcmurry opened 7 years ago

jmcmurry commented 7 years ago

Include temporal ordering of phenotypes in both the curated data and algorithms, allowing search for models that recapitulate patterns of phenotype progression

As per R24 here

cc: @pnrobinson

pnrobinson commented 7 years ago

@jmcmurry @mellybelly @cjm This aim doesnt seem to be a Dipper item, at least not in first instance? But it would be good to review all of the aims and make sure were are on track.

jmcmurry commented 7 years ago

I kinda agree, Peter but I looked in HPO repo and there was nothing explicitly mentioned yet. I think we need a general monarch-wide approach to patterns of temporal progression that transcends any one specific species.

jmcmurry commented 6 years ago

@cmungall, @pnrobinson can we revisit in light of recent harmonization efforts?

pnrobinson commented 6 years ago

Let's discuss this this week! I have a few ideas, but not sure how to put this into dipper.

pnrobinson commented 6 years ago

@jmcmurry These are the things that we have on the ground now

  1. A refactoring of the annotation file format together with a refactoring of the Java code we are using to work with the annotations. This will allow us to exploit onset data better for rare disease
  2. We now have a concrete plan for the data model for common disease that will allow us to start curating and developinig algorithms to exploit temporal data. I would say this is a focus for the second half of the R24.
jmcmurry commented 6 years ago

OK great; where is this plan documented?

pnrobinson commented 6 years ago

see email

jmcmurry commented 6 years ago

Spans datamodel for curation, devising the algorithms, etc. Needs leadership to break down into component tickets. @cmungall @mellybelly @julesjacobsen @pnrobinson Please help. cc: @nlharris

nlharris commented 6 years ago

Reassigned to algorithms cat-herder (Kent) as suggested by Chris.

nlharris commented 2 years ago

Close as not planned?

jmcmurry commented 2 years ago

For humans this might now covered by Poet? @pnrobinson ? If so, it isn't species agnostic. Curious to know @cmungall thoughts on that.

pnrobinson commented 2 years ago

We delayed working on this in order to finish the Phenopacket Schema, one of whose use cases is to support temporal modeling. We are now working on a first analysis with chronic kidney disease. Stay tuned! POET is for MAxO annotations (and after more testing for HPO annotations). We are also close to finishing a REST API and Web app for making phenopackets. Phenopackets are human centric.

jmcmurry commented 2 years ago

What's the update as to when is Poet going to be released?

pnrobinson commented 2 years ago

Here you go: https://poet.jax.org/ We have started to use this and are testing intensively