check on unmatched phenotypes.

[harryhoch]

@yuanzhou - please look into the unmatched phenotypes and see if it is working correctly.

[yuanzhou]

@harryhoch I tried to see how the output of unmatched phenotypes look like, but there's nothing showed up after I clicked that checkbox, and the Homo sapiens says there's no Unmatched phenotypes. Do I need to add some random phenotypes in the config to see this?

[harryhoch]

Yes, that’s probably worth a try.

On 27 Jul 2015, at 9:00 AM, yuanzhou notifications@github.com wrote:

@harryhoch I tried to see how the output of unmatched phenotypes look like, but there's nothing showed up after I clicked that checkbox, and the Homo sapiens says there's no Unmatched phenotypes. Do I need to add some random phenotypes in the config to see this?

— Reply to this email directly or view it on GitHub.

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Harry Hochheiser University of Pittsburgh Department of Biomedical Informatics harryh@pitt.edu 412 648 9300

[davism84]

Possible solution for the refactoring unmatched list that Joe and I talked about:

1. include unmatched phenotypes within the full grid listing, but have the font as strike-through or grayed out.
2. include in the control options panel an checkbox option to toggle on/off the unmatched items (could also default them to be turned-off and provide an indicator that notes there are unmatched sources

note: if we add these to grid, they will be sorted by frequency of which the will appear at the bottom of the list

[harryhoch]

how does #2 differ from what we have now?

[davism84]

the toggle is the same, but what we are proposing it to just keep unmatched within the grid verse at the bottom of the screen.

[harryhoch]

at the bottom. They could become cumbersome in the grid

[davism84]

ok, no problem

[yuanzhou]

Unmatched phenotypes is working now.

• refactored the unmatched HTML rendering/jquery toggle (replaced table view with list view), and
• used serverURL instead of the local browser base URL for each link, also
• added ajax to fetch the unmatched phenotype label since it's not presented in the unmatchedPhenotypes array.
• moved the call to _buildUnmatchedPhenotypeDisplay() from _createYLables() into _addPhenogridControls() since it's inside the phenogrid control container

Notes:

• For phenotype page, the id format in URL, e.g., HP_0000746 will be redirected to HP:0000746
• For monarch-app json API, phenotype id format must be HP:0000746, don't use HP_0000746, because http://beta.monarchinitiative.org/phenotype/HP_0000746.json will be redirected to http://beta.monarchinitiative.org/phenotype/HP:0000746 (.json extension will be missing after redirection)

[yuanzhou]

Further debugging with Mike showed us that the phenotype label is not in the unmatchedPhenotypes array. But when embed phenogrid into monarch-app, the disease page returns the phenotype_list based that that disease, and the returned array contains label of each phenotype. That's why it worked with monarch-app, but didn't work as a standalone app.