ClinGen / clincoded

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Allowing multiple ID types and free text to represent the disease in the GDM #1328

Closed wrightmw closed 7 years ago

wrightmw commented 7 years ago

Currently when creating a GDM, a disease can only be identified by an Orphanet ID. This needs to be opened up to include DO, NCIT and OMIM IDs, and when none of these IDs are available then the curator should be able to add free text instead.

  1. In the GDM allow any of the following ID types: Orphanet DO OMIM NCIt
screen shot 2017-04-11 at 3 31 38 pm
  1. We currently populate the disease name automatically based on the Orphanet ID entered, this functionality will need to be expanded to include pulling in the disease names based on OMIM, DO and NCIt disease names.

  2. If none of the above disease IDs are available then the curator should have the option of clicking a button to add free text. However they must: i)first enter some sort of confirmation that they have checked all of the ontologies ii)have option of including phenotypes, so another curator can match to it

screen shot 2017-04-11 at 3 47 15 pm
  1. The curator must have a means of changing the disease once they've entered it
screen shot 2017-04-11 at 3 59 55 pm
jimmyzhen commented 7 years ago

Hi @selinad, @wrightmw,

Here is the instance for you to review the prototype of the modal for users to enter disease information: https://1328-jz-disease-id-types-043b3aa-jzhen.demo.clinicalgenome.org

There are still quite a few details to be worked out (e.g. free text entry confirmation, HPO id validation).

Most importantly, the disease information CAN NOT be saved into the GDM object at the moment. I will need to discuss with Karen on how the GDM schema shall be changed to deal with the disease property that no longer links to the Orphanet object (with implications on existing GDM data in production).

I look forward to all your feedback on this prototype. Thanks!

wrightmw commented 7 years ago

Hi @jimmyzhen Wow, you've come so far on this already! Great work!

I'm going to have a play with it. However, two quick things:

Currently I don't feel it's that obvious to the user that the magnifying glass is how they look-up/add disease gene names...it looks like they can just type IDs into the box, but I think we want people to only use the modal to add disease names? How about greying out the box and having a button on the RHS of the greyed-out box...e.g. re-using the buttons from the VCI: screen shot 2017-05-02 at 5 09 40 pm screen shot 2017-05-02 at 5 26 04 pm

Once the modal opens, the LHS text in the modal should say something like:

β€œSelect disease source”

Note: the β€˜i’ in NCIt should be a capital letter in all instances where you display it

selinad commented 7 years ago

Hi @jimmyzhen -- I tested a bit yesterday, and will do more thorough testing this afternoon. The API is great and I agree with @wrightmw that you implemented this very quickly and it's a fantastic improvement. Every disease I checked worked perfectly and I love having the descriptions come back.

One quick comment -- it would be great to have the UI for this mimic (as much as possible) the UI for the ClinVar modal, etc. I think @wrightmw is on the right track with respect to it looking like adding a disease in the VCI, but need to think through a bit more. I'll add some more ideas when visiting it again.

I'm a bit worried about the edit button -- are we going to allow people to edit a disease once evidence has been added to the GDM?

wrightmw commented 7 years ago

@selinad The edit disease button is vital on the GDM selection page so that curators can go in and edit when they have entered the wrong disease. Once they click through to curation central it's a different story, they would only have the edit disease button when free text has been entered so that they can change it to one of the disease IDs, when available.

selinad commented 7 years ago

Ok, perfect -- thx @wrightmw !

selinad commented 7 years ago

Hi @jimmyzhen -- here is what we discussed (I know you already have some under development)

Create GDM page:

On modal window:

After term returned (back on Create GDM page)

Free text choice:

@wrightmw let me know if I've forgotten anything

jimmyzhen commented 7 years ago

Hi @selinad, @wrightmw,

I've spun up a new instance of the add-disease modal for you to review: https://1328-jz-disease-id-types-7b8fb1d-jzhen.demo.clinicalgenome.org

The changes are so far only implemented for the GDM, and you can now save the GDM.

selinad commented 7 years ago

First -- wow! Lots of progress and many things working great! Here are maybe more comments than you need for this instance (meaning I know you have been working on data model changes and you may not have had a chance to get there yet) and a few bugs.

Super work, @jimmyzhen ! thank you.

Comments:

Bug

selinad commented 7 years ago

@jimmyzhen -- it may be that you have it that another curator can't edit the disease if the first has entered evidence -- I'm finding that! Apologies, that might not be a bug. Testing a bit more to check behavior.

selinad commented 7 years ago

@jimmyzhen -- great! A second curator cannot edit the disease. However, it does seem the first curator who created the disease term name with free text can edit it AFTER a second curator has added a piece of evidence -- it may be in your plans already, but want to disallow this ( @wrightmw do you agree?)

p.s. this instance does not remove the logic, so 2 curators can't curate from same paper -- not certain whether this will change anything...

selinad commented 7 years ago
selinad commented 7 years ago

Hopefully, no one would enter this, but if we can block it, it's always better -- let me know; I can make a ticket for July.

@wrightmw we are going to need to create help documentation for using MonDO...

wrightmw commented 7 years ago

I think the FreeText ID should be internal... we shouldn't display it. @selinad The current help docs need to be updated based on the changes to the interfaces, and it would be desirable to add some MonDO help documentation at the same time but I think this is desirable rather than essential (i.e. if we have not had time to add this MonDO help doc then I don't think our release should be delayed to wait for this) .

selinad commented 7 years ago

thx @wrightmw I agree re the FREETEXT ID

It's rare, but I disagree re help -- we need to explain they can only pick terms with MONDO in blue box on the OLS (they will want to know why they can't use ORPHA15, for example), etc. I don't think it has to be complicated, but they will need some guidance. I believe JG mentioned this on a call already, too. They are likely to have had little/no exposure to MonDO.

selinad commented 7 years ago
jimmyzhen commented 7 years ago

@selinad, I can disallow the entry of OMIA IDs in the add disease modal.

selinad commented 7 years ago

@jimmyzhen thx re OMIA -- let me know if that is time intensive and we can evaluate against other features.

Here is what @wrightmw and I drew up for editing diseases ( @jimmyzhen I'm trying out the task list, although it may not be appropriate for this list!):

We think all of the above will work, but happy to walk through it with you! -S

jimmyzhen commented 7 years ago

The flow of add/delete diseases within a Group, Family, Individual and Interpretation:

img_5611

selinad commented 7 years ago

Notes from our discussion today: ( @wrightmw please feel free to make any edits)

Create GDM page

Modal before save

Modal after save

Free text

Resulting Create GDM (following save)

Group/Family/Individual pages

VCI

selinad commented 7 years ago

One more potential change, @jimmyzhen as I see you may already have a check next to the item -- seeking @wrightmw 's opinion first:

For the checkbox -- how about: "Check this box to indicate you were unable to find a suitable ontology term and need to create a free text term"

selinad commented 7 years ago

@jimmyzhen As we just discussed, Case-Control also has a Disease field (in addition to G, F, I and the Create GDM).

jimmyzhen commented 7 years ago

Hi @selinad, @wrightmw,

Below are the UIs I have implemented for Group so far: image image

Two questions:

  1. Shall we modify the text messages in the yellow warning box?
  2. How would you want the button arrangement to look like for Family and Individual if we also need to include ability to copy disease from the group (e.g. "Copy Orphanet IDs from Associated Group")?
selinad commented 7 years ago

Looks great @jimmyzhen !

  1. Yes, we should definitely alter the yellow box. How about "Please enter a disease term and/or phenotype(s); phenotypes may be entered using HPO ID(s) (preferred) or free text when there is no appropriate HPO ID."

  2. Did we talk about having 2 buttons for F and I? e.g. Copy disease from Gene-Disease Record" and "Copy disease from Group"? We were thinking we didn't need to add logic now if the GDM disease = Group disease.

selinad commented 7 years ago

@jimmyzhen per our pow-wow with @wrightmw too, let's revise answer to number 2 above so that we don't have Copy disease from Gene-Disease record on F and I pages. Instead, just on the G page and then the F and I pages have "Copy disease from Group" (or whatever current language is), "Copy disease from Family."

One item: For Case-Control, could we have "Copy disease from Gene-Disease record" there? Not urgent if it doesn't work this release, but maybe it's easier as it will be consistent with Group.

jimmyzhen commented 7 years ago

Hi @selinad, @wrightmw,

I have a new instance spun for what I have so far: https://1328-jz-disease-id-types-fbd3dba-jzhen.demo.clinicalgenome.org

The add-disease modal has been implemented throughout the GCI, but not yet in VCI.

A known issue - if the entered disease is not already in the test database, it is not somehow captured in the curation objects (e.g. group, family, individual) 😭

selinad commented 7 years ago

@jimmyzhen you are incredible!

Create GDM page

Note: the following work great!

Next times:

Modal

Group

Wow! Works really well -- I tried every permutation I could think of wrt to adding / editing disease and everything held. πŸ‘

Family

Also works great! Can copy disease to individual

Small items:

Individual

I'll keep testing -- there is a lot going on. Absolutely fantastic, hard work, @jimmyzhen -- thank you!

jimmyzhen commented 7 years ago

A known issue - if the entered disease is not already in the test database, it is not somehow captured in the curation objects (e.g. group, family, individual) 😭

I've fixed the bug mentioned above and patched the current instance with the fix.

selinad commented 7 years ago

@jimmyzhen -- does this explain the bug or are you saying this is a new issue?

jimmyzhen commented 7 years ago

Hi @selinad, @wrightmw,

I've spun up a new instance for you to review: https://1328-jz-disease-id-types-e668045-jzhen.demo.clinicalgenome.org

This instance includes the new add-disease modal for interpretation in VCI, along those in the GCI. Let me know if you have any questions.

selinad commented 7 years ago

Hi @jimmyzhen Thank you! Nice!

Comments on VCI:

selinad commented 7 years ago

Hi @jimmyzhen -- I tried entering a free text again and found this (free text was the first thing I entered this time). What's strange is no disease term is showing even though the Delete button is active

screen shot 2017-05-30 at 9 47 10 pm

Note: I tried to repeat this and could not.

jimmyzhen commented 7 years ago

Hi @selinad,

The strange behavior (e.g. "The yellow box is directly on top of the check box free text") and console error you were seeing might have something to do with a bug in the "Delete disease" button in the VCI. I've addressed the bug and patched the instance. Please try again after refreshing the browser page.

Also, I've added a "View description" link in the VCI header if a disease term has description.

Lastly, I tried the red delete disease button in the VCI. It seemed a bit too much visually, and so I am using the same blue color for the button (as we do for the mode of inheritance association button).

selinad commented 7 years ago

@jimmyzhen a little confused as I still see the yellow box sitting on top of the text box, but the disease seems to be functioning correctly:

screen shot 2017-05-31 at 10 42 23 am
selinad commented 7 years ago

@jimmyzhen -- the View Description is great, and the link to the OLS for the VCI. The Description box pops up quite a bit below the link, but I think it's great for now -- thanks!

Re Disease button -- I like the icon, but I'm worried about the blue -- would it be easy to see the red? (do you have a screen capture). Also, it would be more consistent with the rest of the UI to use red, I think....

selinad commented 7 years ago

One thought for the MOI button -- could it be the same blue as the update button for evaluations? Delete and Edit are different and we use the lighter blue for "Update" (= Edit) QUICK

wrightmw commented 7 years ago

@jimmyzhen @selinad I like the dustbin on the Delete button but I think it should be red to make it more obvious to a curator that they are about to delete the disease.

selinad commented 7 years ago

Hi @jimmyzhen

Not a big deal -- it would be great if this either worked like the "View Definition" link you have elsewhere or if easier, was an external link rather than something they'd have to copy/paste. MOVE TO R12

Do you mean to send them to OMIM for the Definition?

screen shot 2017-05-31 at 10 51 15 am
selinad commented 7 years ago

screen shot 2017-05-31 at 12 54 26 pm

HI @jimmyzhen -- a couple of small things:

selinad commented 7 years ago

@jimmyzhen is there a way to make the Description text a little wider on return at very minimal time cost -- this is an extreme example. Not worth any amount of time if not. Another possibility would be the "View Description" link that you use elsewhere (if possible from the modal)

The 100 characters works great! MOVE TO R12

screen shot 2017-05-31 at 1 34 54 pm

Also, would it be quick to insert a space between HPO terms on the following display? QUICK ![screen shot 2017-05-31 at 1 37 17 pm] (https://cloud.githubusercontent.com/assets/11320314/26652948/747edeb2-4606-11e7-9822-befc39240262.png)

selinad commented 7 years ago

@jimmyzhen There are other places where OLS is a link (sorry!). Here's an example that will occur on G, F, I and I assume Case-Control: screen shot 2017-05-31 at 1 49 08 pm

Is there an easy way for you to find them (I'll keep adding as I see).

wrightmw commented 7 years ago

In the GDM, once a curator Saves free text, e.g. below: screen shot 2017-05-31 at 2 23 24 pm Then they do not have an option to change the free text to an ID, they are stuck on free text...e.g. see below: screen shot 2017-05-31 at 2 23 32 pm Curators can delete the free text if they refresh the page, but there is no information to tell them this. This is different from the functionality for IDs, which can be changed within the GDM. Which is confusing. @selinad

Also, when curators add the disease in Groups, Individual, etc.. they do get the option to "Delete Disease" and so they can start over, even if they've added free text. It's only in the GDM that we have this restriction.

selinad commented 7 years ago

HI @wrightmw - yes, @jimmyzhen and I talked about this and felt we should hold given all the other things that needed to happen at the time, with the plan to revisit closer to the release when everything else had been implemented. I agree it's potentially confusing -- it's a bigger problem once the record is created and before a PMID added.....but we have provided a lot more functionality that previously existed...

selinad commented 7 years ago

@jimmyzhen I don't think the URL was here before? It's good as it goes to OMIM. Is it coming directly from the API? Could it be the hyperlink to text like "View term at source's site"? (I'm sure there's something better, but I'm thinking it will be hard to pick out OMIM or Disease Ontology, etc...

screen shot 2017-05-31 at 4 24 04 pm

p.s. not a big deal for R11 if time consuming MOVE TO R12

selinad commented 7 years ago

@jimmyzhen -- for the View page when a free text term, Definition and HPO terms added (copied from GDM), it only shows the free text term. It's a bit confusing as there are fields for HPO for phenotype. Could you show the Definition and disease associated HPO terms on the View, maybe below the term name but indented? the fields would be empty if none entered. MOVE TO R12

e.g. (minus line space and the actual bullets)

Short term

screen shot 2017-05-31 at 4 38 15 pm

selinad commented 7 years ago

Hi @jimmyzhen Would it be a quick request to have it so that every time there is a description, use the "View Description" link that you have implemented in header -- I think it could get really long displaying on G, F, I pages like here (even tho this one short) REVISIT IN R12 screen shot 2017-05-31 at 4 48 25 pm (ok for next release too)

selinad commented 7 years ago

Thx! - Selina

wrightmw commented 7 years ago

This is a slightly odd minor bug. I filled out the GDM but the gene symbol was incorrect... I corrected the gene symbol but it would then not let me save the GDM, even though it now had the correct approved symbol: BUG screen shot 2017-05-31 at 5 50 57 pm

I filled out the GDM but the gene symbol was incorrect... I corrected the gene symbol but it would then not let me save the GDM, even though it now had the correct approved symbol.

JZHEN: I was not able to reproduce the bug :man_shrugging:

jimmyzhen commented 7 years ago

Hi @selinad, @wrightmw,

Here is how the disease and MOI buttons look in VCI: image

selinad commented 7 years ago

I like it @jimmyzhen !

wrightmw commented 7 years ago

I like it also!