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Not really a task yet but following discussion was had with Harry Nov 2015:
Jules is going to start looking into the REST stuff as his next big task which should make things easier. We did do that work for AMIA to export Exomiser results in a suitable format for PhenoGrid so sure some of that could be reused.
One thing I would like to see is if I can reuse PhenoGrid for is to show phenotype match results for just a single disease/patient vs a single gene in the IMPC portal and possibly Exomiser individual results. So for IMPC instead of different genes from different species on the horizontal axis I would have different models from mouse for the same gene. For Exomiser, upon clicking on something to dynamically load for each gene result, we would show a PhenoGrid with human, mouse and fish results on the horizontal axis. I am figuring that current PhenoGrid should be capable of taking a bunch of any objects associated with phenotype terms for the horizontal axis and it should not matter if they are genes from diff species, diff models for the same gene etc?
I do get the political aspect of combining our tools though so we can try and do the simpler experiment of course of just showing PhenoGrid for the top 50 Exomiser ranked candidates. I was also wondering if we should try and do all this integration in the context of Tudor's Patient Archive. Are we planning to have a PA installation on the Monarch site eventually anyway. Tudor has already done a nice job of pulling in Exomiser so wondering if we should not kill 2 birds with one stone and see if we can plug PhenoGrid in there?
The text was updated successfully, but these errors were encountered:
Now that Phenogrid has been heavily refactored for more generic usage this is doable.
Re-write PhenoGridAdaptor to write out the new phenogrid input format - see IMPC implementation for details.
Remove phenogrid specific code from Organism
Remove phenogrid specific Json annotations from PhenotypeTerm and PhenotypeMatch
Look into refactoring PhenotypeTerm to follow same model as PFX OntologyClass.of(id, label) pattern, moving the IC into the PhenotypeMatch. This isn't strictly the correct place for it (it's a function of the LCS), but makes for cleaner coding. Given these are constants the builder should probably be backed by a cache to prevent multiple instances of the same thing.
Not really a task yet but following discussion was had with Harry Nov 2015:
Jules is going to start looking into the REST stuff as his next big task which should make things easier. We did do that work for AMIA to export Exomiser results in a suitable format for PhenoGrid so sure some of that could be reused.
One thing I would like to see is if I can reuse PhenoGrid for is to show phenotype match results for just a single disease/patient vs a single gene in the IMPC portal and possibly Exomiser individual results. So for IMPC instead of different genes from different species on the horizontal axis I would have different models from mouse for the same gene. For Exomiser, upon clicking on something to dynamically load for each gene result, we would show a PhenoGrid with human, mouse and fish results on the horizontal axis. I am figuring that current PhenoGrid should be capable of taking a bunch of any objects associated with phenotype terms for the horizontal axis and it should not matter if they are genes from diff species, diff models for the same gene etc?
I do get the political aspect of combining our tools though so we can try and do the simpler experiment of course of just showing PhenoGrid for the top 50 Exomiser ranked candidates. I was also wondering if we should try and do all this integration in the context of Tudor's Patient Archive. Are we planning to have a PA installation on the Monarch site eventually anyway. Tudor has already done a nice job of pulling in Exomiser so wondering if we should not kill 2 birds with one stone and see if we can plug PhenoGrid in there?
The text was updated successfully, but these errors were encountered: