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monarch-initiative / monarch-app

Monarch Initiative website and API
https://monarchinitiative.org/
BSD 3-Clause "New" or "Revised" License
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Create a Multiterm Composed Phenotype Ingest #711

Open putmantime opened 2 years ago

putmantime commented 2 years ago

FLybase and SGD have more complex multi-term phenotypes that require special consideration in the modeling.

We need to plan and implement ingests for these.

putmantime commented 1 year ago

This is still unresolved, we are only getting single term association from Flybase and SGD currently.

putmantime commented 1 year ago

This could be modeled with qualifiers. This should be a topic at a Data meeting soon. @sagehrke @monicacecilia @matentzn

matentzn commented 1 year ago

I would like to be involved in this issue, and I think it should be discussed at the next call!

sagehrke commented 1 year ago

This is on the agenda for the second half (30 minutes) of the Data call on February 16th, 2023.

matentzn commented 9 months ago

We need to upgrade the importance of this issue, as we are loosing a lot of phenotype relations without a solution in place. Can we resurface this at the next data call?

sagehrke commented 9 months ago

I have added this to the second half of the data call agenda for 2023-Jan-04 FYI: @kevinschaper

matentzn commented 9 months ago
  1. @sierra-moxon will check if we need to do anything for GO annotations (gene to process ---> gene to "abnormal process")
  2. @kevinschaper and @matentzn meet to decide where best to fit the generation of the "abnormal phenotype" module in a way that circularity is avoided
  3. Once we have a plan, we will find someone to execute it, potentially @souzadevinicius under supervision of @caufieldjh and me.
monicacecilia commented 6 months ago

Dear @matentzn, @sierra-moxon, @kevinschaper, @souzadevinicius, @caufieldjh - I would like to kindly ask for a status update for the tasks described in Nico's last comment on this ticket. Please let us know about progress and whether there are PRs to review. Thanks!

  1. @sierra-moxon will check if we need to do anything for GO annotations (gene to process ---> gene to "abnormal process")
  2. @kevinschaper and @matentzn meet to decide where best to fit the generation of the "abnormal phenotype" module in a way that circularity is avoided
  3. Once we have a plan, we will find someone to execute it, potentially @souzadevinicius under supervision of @caufieldjh and me.
kevinschaper commented 6 months ago

For 2, we're avoiding circularity by having an upstream process to produce the anatomy to upheno mappings and provide them to both annotation ingests and upheno

For 3, progress is happening in the uphenotizer (sorry, the name is my fault) repo at the the steady rate of about an hour a week

matentzn commented 6 months ago

Slowly but firmly edging towards a solution. ETA for full circle delivery is end of April, but pipeline could be done 9th April.

sierra-moxon commented 6 months ago

No GO updates needed here.

ChristopherMancuso commented 5 months ago

We use the tsv files found at https://data.monarchinitiative.org/monarch-kg/latest/tsv/gene_associations/index.html in a gene set enrichment like method and would love to have one for fly. I was wondering when this issue is cleared up, will the data bucket I linked to automatically be updated to include a fly tsv, or should I start an GitHub issue to request that? Thanks!

monicacecilia commented 4 months ago

Slowly but firmly edging towards a solution. ETA for full circle delivery is end of April, but pipeline could be done 9th April.

Hi @matentzn, checking in with ourselves for full circle status update. Is this ready?

matentzn commented 4 months ago

@kevinschaper just because this is so urgent, can you perhaps just commit the basic SGD ingest up so I can take over and finalise the patternisation stuff?