Feedback form - Sierra Moxon - Thank you for the lovely new interface! I was searching a...

[monarch-issues-tracker[bot]]

Name Sierra Moxon

Email smoxon@lbl.gov

GitHub Username @sierra-moxon

Details Page: /feedback Browser: Chrome 120.0.0.0 Device: Apple Macintosh OS: Mac OS 10.15.7 Engine: Blink 120.0.0.0

Thank you for the lovely new interface!

I was searching around for the equivalent of this: https://previous.monarchinitiative.org/analyze/phenotypes in the new UI and couldn't find it. Maybe this is just a me-problem w/re to "Tools" vs. "Explore" :)

Kevin pointed me to this: http://monarchinitiative.org/explore#phenotype-explorer. I didn't figure out that I could enter a disease in the second box, nor that I could request to find diseases because the pulldowns both start with "phenotype" and I couldn't figure out how to ask it to "just show me diseases that have matching phenotypic profiles". The old UI had a really good user walk-through. It gave me help up front if I needed it, clearly asked me to define whether I wanted all diseases or one particular disease back, and had some intermittent feedback about the terms I put in matching the terms it had.

I guess the third issue (and most important, UI aside), is that I don't get diseases back (using the old UI) when the disease is a "grouping term" for other diseases. E.g. if I search for all the phenotypes of the two sub-types of Cerebral Palsy, I would expect to get Cerebral Palsy back in the results of diseases that match my phenotypic profile. Instead I only get some sub types of the disease. Same for Marfan Syndrome and Ehlers-Danlos.

[sagehrke]

Thank you for submitting this feedback @sierra-moxon! The technical team will take a look and identify where we may be able to assist. 🙂

[amc-corey-cox]

I just want to capture this all here in case the March 20 shutdown takes this offline (it likely will).

Phenotype Profile Search This Phenotype Profile Search enables you to find phenotypically similar diseases or genes in a variety of organisms, then visualize their overlap. Begin by constructing a "profile" (a collection of phenotypes) then create a comparison profile.

1. Create a Profile of Phenotypes Do you have a phenotype list you would like to paste? Yes | No, I'll need some help

   Yes: Gives box for comma-separated values of phenotypes.

No, I'll need some help:

Generate List from Gene | Generate list from phenotype Either section gives box for search for ... with correct item selected.

Help Section: Creating Starting Profile To begin, you can create a profile by pasting a list of phenotypes (Human Phenotype Ontology) and confirming your profile. As an alternative you can build a profile of phenotypes by choosing a gene or disease. The associated phenotypes to those entities will be populated for you.

2. What do you want to compare against? Show me everything | I know what I want to compare Show me everything: All matching genes | All matching diseases

   All matching genes - gives single select for which taxon Both - gives button for Run similarity analysis (after selection)

I know what I want to compare: A specific gene | A specific disease | I will paste a comparison list of phenotypes

A specific gene - gives search box for gene A specific disease - gives search box for disease I will paste a comparison list of phenotypes - gives box to paste phenotype list.

Help Section Creating Comparison Profile The next step is to choose what to compare your profile to. You may choose to conduct a blanket search by selecting either all genes from a single species or all human diseases. Once you make a selection, you may run the analysis. For a more fine grained search, you can again build a profile by selecting a specific disease or gene, as well as pasting another list of phenotypes. Finally, you can run the analysis.

[amc-corey-cox]

Sierra, I'm working now on incorporating this sort of help/how-to section into a larger how-to section for the new monarch site. I'm having a little trouble capturing the same sort flow as this widget gives due to the new more unified interphase for phenotype profiling. I'd love to have your insight when I've made some progress. Would you be willing to take a look at it when I have a demo available?

[sierra-moxon]

absolutely - let me know how I can help :) - and thank you in advance for taking the time to consider this!