Summary and Provisional Assertion for GDM

[hitz]

This is a view of the GDM that calculates the current summary and provisional assertions.

Apparently summaries and assertions are PER curator. Summary is autogenerated.

[kgliu0101]

page to create a new provisional.

[kgliu0101]

page to edit existing provisional data. First, have a view of login user's provisional.

then, click button Calculate Again will get new summary below

[selinad]

HI @kgliu0101 Thanks so much for this!

Here are a few comments:

PAGE TO CREATE A NEW PROVISIONAL

• "Calcaleted" should be spelled "Calculated"
• Our bad, but I believe the Scoring Details should go right under the Calculated CVC (Clinical Validity Classification) and then the boxes to change and explain would go below Scoring Details.
• What is the default for change box for Classifciation? I think we should put it as No Selection and make it a required field ...see next few comments
• Change Provisional Clinical Validity Classification" -> Select Provisional Clinical Validity Classification
• Make the above field required
• Add Note above the explain reasons box -> **Note: If your selected Clinical Validity Classification is different from the Calculated value, provide a reason to expain why you changed it."
• The "Back to GDM" button should say "Return to Record Curation" as it does throughout interface. Users will not recognize GDM
• We will need a little more description for Scoring details - see below for example:

Number of years since first clinical publication Score: 2 Year of First Publication: 1994

Number of clinical publications with clincial evidence Score: 2 Number of Publcations: x

Number of probands associated with a pathogenic variant Score: 2 Individual probands not associated with Family: 1 Individual probands associated with Family: 3

Experimental Data Combined Score: 3.5

[indent these]

Expression (0.5 points each) Score: 1.0 Number of pieces of evidence: 2

Protein Interactions (0.5 points each) Score: 0.5 Number of pieces of evidence: 1

Protein Interactions (0.5 points each) Score: 0.5 Number of pieces of evidence: 1

Model Systems (2 points each) Score: 2 Number of pieces of evidence: 1

[end indent]

---

Total Score: 9.5

[selinad]

PAGE TO EDIT PROVISIONAL DATA

• For all titles, the "AND" should be lower case: "Summary and Provisional Classification"
• Kang, could this work more like how @forresttanaka implemented editing a variant assessment? See his newest instance. Do you need this page, or can you just have the next one you show? (Curation - New Calculation)
• Titles should be as @forresttanaka has done throughtout interface for VIew (View: Summary and Provisional Classification or maybe View/Reclassify Summary and Provisional Classification)
• Once you have figured out above, can you please seek advice from @forresttanaka as to blue bars and label names? They should be in sync with his styling.

[selinad]

I think Recalculate (rather than Calculate again) button should be on GDM page - you can't recalculate from the Summary page. The curator could Edit their classification, but that is different from recalculating from the evidence.

[selinad]

@kgliu0101 I'm not sure I understand the red note - it just changes their classification, not any data underneath (also, I don't think @forresttanaka has any red notes - red is reserved for errors).

[kgliu0101]

Add Summary data, link and button in record title panel.

gdm with Summary and Provisional Classification.

gdm with pathogenic data and assessed as Supports, but without Summary.

gdm without assessed pathogenic data.

[kgliu0101]

Display Summary data as one line in record title panel.

[selinad]

Hi @kgliu0101 - looking good - here is my similar version with some changes in wording

[kgliu0101]

matching above?

[selinad]

Thanks @kgliu0101 Looks good!

• Since there is room, I think it could say [Edit Classification] rather than just [Edit]
• Could the button hug the right side a little less? Would like to see more gray around it.
• Also, I realize it should say "Current Summary & Provisional Classification" - if there were no Provisional Classifciation, there could be a "None" or "Not yet provided"

There is one more thing you could try, if you like, since there is more room than I thought.

You could put the following in a 2nd column:

Total Score: 17 (Definitive) Provisional Classification: Strong [Edit Classification]

That way, you would have 3 columns:

1. Current Summary Generated: 2015....

2. Total Score: 17 (Definitive) Provisional Classification: Strong [Edit Classification]

3. [Button]

This might highlight the scoring part.

[kgliu0101]

3 columns, button moves left little, Summary & Provisional Classification, Edit Classification.

[kgliu0101]

Note for new calculation.

[selinad]

Hi @kgliu0101 - thanks so much - it's coming along!

I like the addition of the note since the header still has the Summary/Classification from before the user hit Generate New Summary.

Slight change to wording - @forresttanaka, do we need a blue box for a note here?: The calculated values below are based on the set of curated evidence saved prior to selecting "Generate New Summary." To save these values as the "Current Summary & Provisional Classification" calculated values and make a new Provisional Classification, click the Save button below.

Could you implement the following text changes?

[kgliu0101]

@selinad Have a look

[selinad]

Great! Thanks, @kgliu0101

2 things (both on me):

• Note - change to: The calculated values below are based on the set of saved evidence that exists when the "Generate New Summary" is clicked. To save these values as the "Current Summary & Provisional Classification" calculated values and make any changes to the Provisional Classification, you must click the Save button below.
• Under Proband score, can you make "Proband from Families" and "Proband from Individuals" have Proband in the plural form?

Also, are you requiring a reason if they change the Provisional Score, or did we decide we could not implement that?

Thanks!

[kgliu0101]

changed Note and Proband(s)

[kgliu0101]

change "Proband(s) from Families" to "Number of proband ..."

[selinad]

Thanks @kgliu0101 - let's use the 2nd one.

Change the text under Proband Score to be: Number of probands with variants assessed as "supports" pathogenicity

[kgliu0101]

Changed. But it's pretty long and hard to stay as one line

[selinad]

Great! The "16" is still floating inbetwen - can it be on the same line as "Number of probands....supports"?

Thanks! Selina

[kgliu0101]

"16" at top line

[selinad]

Excellent! Thanks for your hard work on this, @kgliu0101

[selinad]

Thanks @kgliu0101 - I can't see it...?

[kgliu0101]

this one

[kgliu0101]

change to Definitive

[kgliu0101]

should be this one

[selinad]

Thank you @kgliu0101 - that looks perfect!

[selinad]

Hi Kang,

I don't have time for thorough testing by any means - @tsneddon can test more thoroughly on Monday. A couple of quick things:

• Generate Summary page did not appear after 2 families and 1 Individual proband added. When I added Experimental it appeared.
• The first variant I entered (11111) I was never able to assess - it did not save any of the information even after hitting save - no sticky appeared on the button either. This is the one associated with experimental, if that gives a clue.
• I had a proband (not in a a family) with 2 variants (22222 and 33333) and did not get a count for it
• I am not getting a score for an Individual proband with 1 variant with supports as pathogenicity....
• Added experimental to variant 44444 AFTER had already assessed on it for individual and assessment was erased (see second item - seems to be a problem with experimental and assessment, maybe because you aren't counting experimental towards variant count?)
• Double check when header with variants is supposed to show - it did not show on experimental submit page
• Tried to hit Save on a Generate Summary with an experimental count (since probands weren't counting) and I got this error: Cannot read property 'length' of undefined
• Here is the URL for my GDM: https://90-kl-summary-and-provisional-c326264-kangliu.demo.clinicalgenome.org/curation-central/?gdm=25b7c65b-5af3-41a2-a98e-465bd8623e91&pmid=123

Sorry I can't test any more before I go! Thanks for your hard work putting up the instance on a Friday night.

[tsneddon]

Yes, there seems to be issues with generating a summary. One I can add is that I can assess on a variant without selecting any of the drop-downs. However, when I make a summary all the scores are zero. I only get the correct score if I select one of the drop-downs from 'Evaluation of Pathogenicity'. If this is required it should be stated in the Edit Variant Information view and a user should not be able to make an assessment without selecting one of the drop-downs or putting some text in the comments box. This is the GDM in progress: https://90-kl-summary-and-provisional-c326264-kangliu.demo.clinicalgenome.org/curation-central/?gdm=3e144866-16d9-11e5-b451-60f81dc5b05a Let me know when this and Selina's issues are fixed and I will review the new instance.

[kgliu0101]

@tsneddon and @selinad, currently, pathogenicity of one variant in a gdm is shared in all curators. And each curator assesses to the variant pathogenicity. That is different to the mechanism that each curator makes his/her own pathogenicity and assesses to it only (can not assess other's). Please let me know which one you prefer and I will edit relevant code.

[tsneddon]

@kgliu0101 I'm a little confused by your last message. Please clarify what the current situation is and what alternative you are proposing.

[tsneddon]

Another comment: I added Exp 1 to the following instance and saved as 'Supports': https://90-kl-summary-and-provisional-c326264-kangliu.demo.clinicalgenome.org/curation-central/?gdm=3e144866-16d9-11e5-b451-60f81dc5b05a&pmid=2345676 I also added variationID:177872 but I can NOT save any information including an assessment on this variant.

[forresttanaka]

I also added variationID:177872 but I can NOT save any information including an assessment on this variant.

Traced this to an object not being embedded, so there will have to be a change to __init__.py. I’ll work on that first thing this morning in a new branch.

[forresttanaka]

I just noticed the 90_kl_summary_and_provisional branch is 82 commits behind dev. I’ve made embedding changes (including for this exact problem) in recent dev merges, so I think we can assume for now that I fixed this problem already.

[tsneddon]

Thanks @forresttanaka, so I can continue to assess on this instance?: https://90-kl-summary-and-provisional-c326264-kangliu.demo.clinicalgenome.org/

[kilodalton]

@kgliu0101 Your branch should be updated and a new instance brought up.

@tsneddon I would recommend that you not continue to test on this instance until the the code base behind it (on a new instance) is brought up to date.

[forresttanaka]

@tsneddon I can only address assessing variants, and I worked on that towards the end of last week, probably within the 82-commit window. So how much assessing variants proves on this instance, I’m not clear.

[selinad]

Please move these comments if they should be somewhere else (I've lost track from afar):

Here is the GDM URL for the following: https://90-kl-summary-and-provisional-fa45a47-kangliu.demo.clinicalgenome.org/curation-central/?gdm=34adcf73-a559-41d8-985a-b0eb947fc2a3

Here's what I tried in order, generated summary, and it worked!:

• Add proband with variant 11111 from Family from PMID1 - works
• Add proband with variant 11111 from Individual from PMID1 - works
• Add proband with variant 11111 from Individual from PMID2 - works
• Add proband with variant 22222 from Individual from PMID1 - works
• Add Exp B experimental (with variant 22222) - works

What did not work:

• Add Models experimental (with variant 22222) - score not added for Models

Features:

• Could we blank out Generate Summary button on Summary page since it does not work (or make it work even though same page generated)
• We need to return # pieces clinical and experimental contradictory evidence (I think OK for the production version, not necessary for beta @tsneddon ?)

[selinad]

Experimental Count is showing but not Experimental Score

[kgliu0101]

I can see "Final Experimental Score" 3. If you mean no score for each experimental evidence (Expression, Biochemical Function, Model System), that is what we decided last week. Since Final Experimental Score is range-based but not directly equal to sum of each evidence score, we decided not showing them.

[selinad]

Hmm...I vaguely remember this, but not necessarily for experimental. Fine for beta and we can discuss again.

Let me check Models again - I may have been confused, it may be working ok.

[selinad]

@kgliu0101 I have to stop testing now, but I think the scoring is all working well!!!

[tsneddon]

@selinad - I think we are OK not including the # of pieces of contradictory evidence for this initial release but it should be a priority for the next 3-week release. I will start testing now...

[tsneddon]

Initial comments:

1. On Edit Individual Information there is a field "Shared Phenotype(s) (free text):". This should just be "Phenotype(s) (free text):". It is correct on the View Individual page.
2. Not for this release but it would be useful to have a Summary View, especially if it was done by a different curator e.g. this record was created by me. Only Selina has added a PMID. The record evidence is empty in my view but the status is "Summary/Provisional Classifications" - is this a feature or a bug? @selinad have you previously assessed on this record?: https://90-kl-summary-and-provisional-fa45a47-kangliu.demo.clinicalgenome.org/curation-central/?gdm=fae4c241-7417-4a29-9453-f1ecac8c96cc&pmid=21217753
3. I can't save an assessment on this Experimental piece of evidence: https://90-kl-summary-and-provisional-fa45a47-kangliu.demo.clinicalgenome.org/experimental-curation/?editsc&gdm=9ffd7c1e-16d9-11e5-b283-60f81dc5b05a&evidence=bb3432ca-1788-11e5-aefb-60f81dc5b05a&experimental=6be668d4-2a6e-11e5-804a-60f81dc5b05a
4. @selinad - Experimental Rescue count works for me - with and without an associated/assessed variant. However, a previous Experimental piece of Protein Interaction data was previously assessed by me as supports but it is not included in the summary score: https://90-kl-summary-and-provisional-fa45a47-kangliu.demo.clinicalgenome.org/experimental/72341d2e-2a6e-11e5-bdd7-60f81dc5b05a/?gdm=9ffd7c1e-16d9-11e5-b283-60f81dc5b05a
5. I have set this family segregation as Reviewed: https://90-kl-summary-and-provisional-fa45a47-kangliu.demo.clinicalgenome.org/families/e659bd3a-18f8-11e5-9d3a-60f81dc5b05a/?gdm=9ffd7c1e-16d9-11e5-b283-60f81dc5b05a This is the only family associated I have with an assessed variant. However, I am still getting a proband count. Why is this?

...still testing...

[mrmin123]

@tsneddon Regarding item 3... do you get an error message in the console (command+option+i in Chrome) when you try to set an assessment?

[kgliu0101]

@tsneddon Item 1. I changed tile of field "Shared Phenotype(s) (free text):" to "Phenotype(s) (free text):". Item 2. GDM status is currently set as "Summary/Provisional Classifications" if there is a summary generated, no who did it. Is it necessary to set the status per user?

[kgliu0101]

other items are related to test data in gdm 9ffd7c1e-16d9-11e5-b283-60f81dc5b05a. Some of them may missing required item because of schema change. I suggest starting from a new gdm for testing.

[tsneddon]

@mrmin123 - no error, just nothing happens when I click on save.

[tsneddon]

@kgliu0101 - re: #2, I don't see a summary and there is no evidence added so I don't think Selina could have made a summary. Why then is Status: Summary/Provisional Classifications and not Status: In progress?