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monarch-initiative / monarch-ingest

Data ingest application for Monarch Initiative knowledge graph using Koza
https://monarchinitiative.org
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Consider adding Dictybase gene to phenotype associations #134

Closed kevinschaper closed 1 year ago

kevinschaper commented 2 years ago

http://dictybase.org/Downloads/

This one doesn't look entirely straightforward, but in the all-mutants-ddb_g.txt file I see

Systematic_Name Strain_Descriptor   Associated gene(s)  DDB_G_ID    Phenotypes
DBS0350195   [act15]:acbA(Y72A) acbA    DDB_G0270658    decreased binding
DBS0350059   mcln-  mcln    DDB_G0291275    aberrant post-lysosome organization and biogenesis | increased growth rate
DBS0235412  1C7 gp130   DDB_G0279921    decreased cell-substrate adhesion | delayed development | increased growth rate
DBS0235414  2F5 gp130   DDB_G0279921    decreased cell-substrate adhesion | delayed development | increased growth rate
DBS0238601  5NT-    5NT DDB_G0287199    multiple tips in culminant | delayed tip formation | multiple tips in mound

This file could be filtered for rows with single associated genes, and the text phenotype names can be matched against a lookup of DDPHENO terms.

matentzn commented 2 years ago

@pfey03 may be able to help with answering anything dictybase related.

pfey03 commented 2 years ago

HI Kevin,

I know this table from our outgoing database is not perfect as it has no phenotype Ids. Also, since I edited the phenotype ontology a lot I need to check if this list still updates as it says. End of November there should be another update if the mechanism still works. I will check it end of this month and update the list status here.

Our old database is in some places broken but many things remarkably still work, all needs checking.

In our upcoming new database, eventually we will have better data to download but we are a very small team and other things are more pressing currently.

kevinschaper commented 1 year ago

I'm going to close this issue, as this ingest is implemented. It seems to have a bug (issue monarch-initiative/monarch-app#551), but none-the-less, it's there.