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When opening an evidence item, the variant_hgvs field should be displayed as 'coordinate:'

Clicking or mousing over should inform a user that they need to log in.

When I select a particular variant (e.g. BRAF V600E) I find myself looking at the table of evidence statements and wondering what their evidence types are (i.e. predictive, prognostic, or diagnostic) and what the evidence directions (i.e. supports vs does not support) of these are.

Actually showing these values would take up way too much space. But they are simple categorical values just like the 'level' (A, B, C, D). I'm wondering if we could include them in a compact way (perhaps as colored icons/symbols. For example,

Evidence type:
T = therapeutic/predictive
D = diagnostic
P = prognostic

Evidence direction
'+' = Support
'-' = Does not support

Clinical significance
green = drug sensitivity (predictive) or good outcome (prognostic) or positive (diagnostic)
red = drug resistance (predictive) or poor outcome (prognostic) or negative (diagnostic)

Clinical significance is harder because it is not so much of a simple categorical variable. In that case maybe you need the full description... Or we need to come up with more tightly defined categories here. Or we rely on synthesizing this in the clinical summary.

This issue seems to be related to #36 (Adding more information to the drug column)

I replaced the contact page with the FAQ page.

Variant Group view should show a data grid for the evidence items in that variant group.

Requiring that each field is filled is a major burden for a curator. Many of these can be back-filled by us post-curation. Required fields should be: Gene Name (Not Entrez ID), Variant Name, Disease (Not DOID), Source (PMID is greatly appreciated but not required), Evidence Summary, Evidence Type, Evidence Level, Clinical Significance, Evidence Direction, Evidence Rating, Comments.

We also need to discuss these... Keeping the barrier to entry as low as possible is my personal priority #-1, but maybe @obigriffith @malachig may feel differently.

When clicking on an evidence item, the clinical significance field is blank.

The Add Evidence Statement form doesn't have a very logical flow at the moment from the standpoint of a curator (in my opinion).

I think a better flow would go as follows:
-Entrez Gene ID (Gene-based data)
-Variant Name (Variant-based data)
-Variant Origin
-Disease Ontology ID (Disease)
-Evidence Summary (Evidence info)
-PubMed ID
-Evidence Level (Evidence Descriptors)
-Evidence Type
-Evidence Direction
-Clinical Significance
-Evidence Rating

Currently, we only accept the original curator's trust rating.

It would be great if this could happen without having to click on "edit evidence statement" but still be tracked in the activity of an evidence statement. Otherwise you have to submit a comment about your evidence statement change which may deter users that just want to vote.

I've been thinking more about this. I already suggested some reorders that took effect and were an improvement. But, I am wondering if the following would be even better.
Left column: Evidence Level, Evidence Direction, Evidence Type, Clinical Significance.
Then, as you read down the items you sort of get a sentence/story. Like: "Clinical" evidence "Supports" a "Predictive" association with "Sensitivity".

The downside is that Drug and Clinical Significance wouldn't appear together. That has a certain logic to it as well. We could at least line them up left to right.

So, for the right column we could have: Citation, Rating, Disease, Drug.

That has the advantage of putting Citation at the top to bring attention to the source more, followed by rating which is really a rating of that publication. Drug is also commonly N/A for non-predictive evidence so I like having it at the bottom.

Thoughts?

I believe this information is being slurped into the back-end. But it is not yet being displayed next to the gene summary.

You must click on an evidence item to see the add evidence tab. Maybe pre-loading each page with the 1st evidence item in the table would work.

To illustrate this, go to the browse page, sort by number of statements, and select one with lost of evidence (e.g. BRAF V600E). Scrolling through the evidence statements is very fast, making it difficult to land in the middle of the table.

Requiring the gene before the variant in quick event search is a bit frustrating, and may lead people to believe a variant is missing. Typing 'V600E' should bring up BRAF V600E. And G12D should drop down all the RAS's with G12 entries.

Use pagination instead on datagrids.

If you click the edit button and change your mind, there currently isn't an obvious "cancel" button/way out.

When I merged in the coordinate information, I made a mistake and we lost the leading zeros on a handful of DOIDs again. This resulted in evidence items without an associated disease (18 to be exact).

Not sure if this is expected behavior, but no matter where you are in the site, if you click on the 'Sign In/Sign Up' button and then the 'Cancel' button, you are returned to home page.

Collapsing the variants on the browse page to allow for a unique list of genes may be nice for people searching for a specific gene but not variant.

I've been stabbing around in the dark for a while and can't figure how to make a new tab/page on the home page. The FAQ file is here: /civic-client/src/app/pages/faq.tpl.html

It would save quite a bit of effort to pre-populate the add evidence form with information from the previous page. This could be Gene, Entrez ID, and Variant

We should still start sorted by Gene, but Variant should be the first column.

Can we get a placeholder page for API documentation and link to it from top or bottom bar?

Type - Direction - Signficance flows better.

When you edit an evidence item and submit it to the queue the admin has the option to commit the change. When the commit button is pressed the change gets updated in the back end but the view does not get updated on the front end

32 characters seems like a lot to explain your change. Ron Bose typed "I added drug info", and ran into character requirement.

It is not obvious how these are sorted now. For example, if we select BRAF V600E, there are currently 31 evidence statements. Not sure what order these are in now. But it would be awesome if they were ordered by 'Level' (A, B, C, D) and then within statements of the same level by 'Rating' (highest rating first). Thoughts?

These should be produced and incorporated into the views

For genes with multiple variant groups. Under the "variant group talk" tab, the ID of the variant group is being displayed prior to the heading. So it says "2 Description" instead of just "Description".

This may be the most desirable initial sorting. Another alternative is level, but I think trust is more useful right now.

In order to display type, direction and significance in the evidence table, it may work to color-code the drug column.

Sensitvity could cause the drug text to be green, resistance red.

Statements without drugs can print evidence type, with Diagnostic in Blue and Prognostic in Purple.

Then the Supports/Refutes could be represented as an arrow?? I don't know if I like this.

We need to add links and explanations of the CC license we've selected on the downloads page and in the page footer.

For example: NCT02279654

Will require different information than Pubmed ID (author, date, journal) to be displayed for evidence item entries. I'm not sure what data at this moment or what the options would be from their API.

It would be nice to have buttons for adding genes/variants. This could land you at the add evidence page, maybe with a prompt that reads "Adding a gene or variant requires at least one evidence statement: Add it here!"

When adding or editing evidence statements we want to enforce a relationship between each 'Evidence Type' and certain 'Clinical Significance' values

A greyed out "Summary" tab is displaying at the top of the page when I click on some Variant Group summaries such as these.
http://0.0.0.0:3001/#/events/genes/25/summary/variant-groups/1/summary (See screenshot below)
http://0.0.0.0:3001/#/events/genes/238/summary/variant-groups/3/summary

But not others:
http://0.0.0.0:3001/#/events/genes/238/summary/variant-groups/2/summary

I've created a new API documentation page, the URL is:

http://localhost:3001/#/api-documentation

The page template is at:

/src/app/pages/apiDocumentation.tpl.html

Currently it just contains lorem-ipsum filler text.

Once imported from the spreadsheets we need to display somatic/germline status in the evidence statement summary.

In all the talk pages under comments it says "Login to post comments." It would be great if the Login was actually a link to the login screen.

It may improve clarity to add a heading above the Variant summaries like the Gene Summary and Clinical summary.

By default the browser sends you to the top of the page when clicking on a link, but for most buttons in the UI we want the interface to stay scrolled to the same position.