Closed wrightmw closed 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!
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:
Once the modal opens, the LHS text in the modal should say something like:
βSelect disease sourceβ
Note: the βiβ in NCIt should be a capital letter in all instances where you display it
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?
@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.
Ok, perfect -- thx @wrightmw !
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
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.
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
@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.
@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...
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...
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) .
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, I can disallow the entry of OMIA IDs in the add disease modal.
@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!):
[x] As we spoke about, a GDM is editable (by creator only) until someone adds a PMID (doesn't matter who) -- if we have time, we will make it so the creator can edit until a 2nd participant has added evidence to the GDM. This means the Disease Edit button will be available next to the Gene:Disease name for the creator until a PMID is added to the record by anyone
[x] For full text -- the curators will need to be able to view the Description (paragraph length) and HPO terms, as well as the term. They should be able to get to this after entering the free text in GDM, next to the disease term int he GDM record's header, and wherever it is displayed in the interface (first 2 most important). A couple of ideas for implementation:
hover over that gives description / HPO terms
display part of text in header under disease with the dotted underline so scroll over shows all of the text (for Description)
View button that pops up non-editable modal (see next task item though)
[x] Editing free text term name: The term name (phrase) is not editable except as is allowed for a MonDO term (i.e. behaves just like an ID). If they want to change it to an ontology term, we will help them with this rather than allowing this to be changed to a term (at least for this version)
[x] For the free text Description, and HPO terms here are a list of options -- you can decide based on implementation time (from least preferred to most preferred)
allow them to be edited in same circumstances as MonDO term and free text term name
allow creator to ADD information at any time (not edit -- that can only happen before PMID added to GDM)
allow any participant to ADD information to it at any time
[x] For diseases within a Group, Family, Individual
can we allow them to copy free text term from GDM to the G, F, or I -- @wrightmw and I think this would help a lot
put edit button by each disease term (MonDO or free text) -- they can only delete a free text term, they could delete or change a MonDO term; we would also need a +Disease button (to add an additional disease)
We think all of the above will work, but happy to walk through it with you! -S
The flow of add/delete diseases within a Group, Family, Individual and Interpretation:
Notes from our discussion today: ( @wrightmw please feel free to make any edits)
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"
@jimmyzhen As we just discussed, Case-Control also has a Disease field (in addition to G, F, I and the Create GDM).
Hi @selinad, @wrightmw,
Below are the UIs I have implemented for Group so far:
Two questions:
Looks great @jimmyzhen !
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."
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.
@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.
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) π
@jimmyzhen you are incredible!
Note: the following work great!
Next times:
Wow! Works really well -- I tried every permutation I could think of wrt to adding / editing disease and everything held. π
Also works great! Can copy disease to individual
Small items:
[x] Could the Group disease that could be copied be returned in bold above the Copy button? For some reason, they it doesn't jump out at user and they are in bold when returned on modal and in header, so user used to it TEXT CHANGE
[x] Individual: The error button when disease is not included appears up by disease rather than by Save button -- can it move down by Save button like other error messages? Right now, there is no feedback by Save button as to why form is not saving, so it seems like it is frozen. Also, the placement of error message is a little funny with the buttons (not a big deal for this release) ![screen shot 2017-05-28 at 12 09 17 pm] BETTER TO HAVE ~1/2 DAY (https://cloud.githubusercontent.com/assets/11320314/26531475/994f8742-439e-11e7-9884-6176b6c05a1c.png)
[x] Related to above issue with disease not being required for proband created with Family. When I tried to save that individual without a disease, got error, as I should. But then when I copied the disease from Family using the button, freezes on Save RELATED TO ABOVE BUG:
[x] @wrightmw do you think we should remove ability to "Copy disease from Gene-Disease Record" for a new individual that is not a proband? RESOLVED -- LEAVE AS IS
I'll keep testing -- there is a lot going on. Absolutely fantastic, hard work, @jimmyzhen -- thank you!
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) π
I've fixed the bug mentioned above and patched the current instance with the fix.
@jimmyzhen -- does this explain the bug or are you saying this is a new issue?
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.
Hi @jimmyzhen Thank you! Nice!
[x] Works great!
[x] The yellow box is directly on top of the check box free text FIXED ON LOCAL
[x] I'm wondering if the Delete button should be red? @wrightmw ? I think it would be similar to other delete buttons in the interface QUICK CHANGE
[x] Links in header for disease work great, and header title looks great!
[x] Change error message to "Either a description or HPO term(s) (e.g. HP:0000001) is required" FIXED
[x] Free text works great! Displays correctly in header and title, is editable
[x] Is there a place we could show Description of disease term when it exists, as in GCI?
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
Note: I tried to repeat this and could not.
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).
@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:
@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....
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
@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.
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?
HI @jimmyzhen -- a couple of small things:
@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
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)
@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:
Is there an easy way for you to find them (I'll keep adding as I see).
In the GDM, once a curator Saves free text, e.g. below: 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: 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.
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...
@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...
p.s. not a big deal for R11 if time consuming MOVE TO R12
@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
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 (ok for next release too)
Thx! - Selina
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
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:
Hi @selinad, @wrightmw,
Here is how the disease and MOI buttons look in VCI:
I like it @jimmyzhen !
I like it also!
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.
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.
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