CDR Tickets

As a first step to look into Robin's question of genetics board sub-groups I said I would summarize how the information if currently prepared:

The SummaryMetaData block in the summaries contains an element "PDQBoard" for the "PDQ Cancer Genetics Board".

This PDQBoard is parent element to the child elements "BoardMember", which link to the member's Person document.

In filter CDR335242 (Denormalization Filter: Summary), we use a SQL query to select the BoardMember's name and affiliation from the BoardMember document based on the PersonID of the BoardMember link.  We create a new element "LeadReviewer" as part of the SummaryMetaData and include the board information in it's required format, i.e. "Suzanne C. O'Neill, PhD (Georgetown University)"

In the final filter CDR157 (Vendor Filter: Summary) the "LeadReviewer" elements are extracted from the SummaryMetaData and inserted into the misc. document’s Placeholder element that has the attribute "LeadReviewers". The Misc document is CDR684055 (About this PDQ Summary)

As discussed in a previous meeting, we've made some decisions (in consultation with the Genetics Board) about how we'd like this information to be displayed on Cancer.gov in the About This PDQ Summary Section. I've attached a mock-up of what we'd like to have displayed in this section. This will likely require some schema changes to capture "lead" and "contributing" working groups for the genetics summaries and filter changes to adjust what is displayed for the genetics board to be these working groups as opposed to individual Board members. Additionally, I expect we'll need to create one or two more miscellaneous documents to be added into the About This PDQ Summary section to include a new statement about working groups and a new acknowledgment statement. We can discuss this more in an upcoming meeting._Acknowledging contributors and reviewers for PDQ Genetics Summaries for 4_26_24.docx

Is this change limited to a single board or will we apply this change to all boards?

Originally, I was under the impression we wanted to list the working groups along with the members of each working group.  Looking at the sample provided, it appears that we only display the working group names.  If this is correct, I would think we're adding new elements to the Summary schema, likely as child elements to the "PDQBoard" element with a name like "WorkingGroups" and then list the working groups as children (WorkingGroupName).  The WorkingGroupName element will have an attribute "Lead=Yes".

<SummaryMetaData>
...<PDQBoard>

...
<BoardMember cdr:ref="CDR0000791232">Lee, Valerie</BoardMember>
<LeadReviewer lname="Lee">Valerie Lee, MD (Johns Hopkins University)</LeadReviewer>
<BoardMember cdr:ref="CDR0000812405">Pappas, Leon</BoardMember>
<LeadReviewer lname="Pappas">Leon Pappas, MD, PhD (Dana-Farber Cancer Institute)</LeadReviewer>
</PDQBoard>
<WorkingGroups>
{{   <WorkingGroupName Lead="yes">Prostate Cancer working group</WorkingGroupName>}}
{{   <WorkingGroupName>Skin Cancer working group</WorkingGroupName>}}
{{   <WorkingGroupName>Pancreatic Cancer working group</WorkingGroupName>}}
</WorkingGroups>{{}}
<MainTopics>
<Term cdr:ref="CDR0000038736">small intestine cancer</Term>
</MainTopics>{{}}{}...{}{}</SummaryMetaData>{}{{  }}

I still will need to inspect the filters in more detail but with a structure like this it should be fairly straight forward to make those proposed changes.

In the misc. document we're using a placeholder called [LeadReviewer] to prepare the list of reviewers in the section.  This is done using a specific filter template.  For our new approach we want to create a new placeholder element called WorkingGroups (or similar) to trigger the modified template to insert our list of working groups.

For my information: The misc document is CDR684055 (About this PDQ Summary).

Here are some proposed summary schema changes (~volker , please let me know if you have other ideas):

Please add "WorkingGroups" as a child element to "PDQBoard"

Please add "WorkingGroupName" as a child element to "WorkingGroups"

Please add an attribute to "WorkingGroupName" – the attribute name is "Lead" with a possible value of "Yes"

We will want a set of defined values for the WorkingGroupName. Let me check with Kavitha on those and provide them in a subsequent comment.

(Working groups that don't have the "Lead" attribute would effectively be "contributing" working groups)

I assume (from the name of the wrapper) that the WorkingGroupName children should allow multiple occurrences. I'll hold off until Volker and Kavitha have had a chance to weigh in on the requirements.

Yes, that's correct. It should allow multiple occurrences. Thank you!

Here are the working group name values we'd like to use to populate the WorkingGroupName element.

• Genetics of Breast and Gynecologic Cancers

• Genetics of Gastrointestinal Cancers

• Genetics of Hematologic Malignancies

• Genetics of Endocrine Neoplasias

• Genetics of Kidney Cancer

• Genetics of Pediatric Cancers

• Genetics of Prostate Cancer

• Genetics of Skin Cancer

• Genetic Counseling and Psychosocial Aspects of Hereditary Cancer

Schema enhancements installed on CDR DEV.

https://github.com/NCIOCPL/cdr-server/commit/7c90237

Is it possible to have more than one "Lead" working group for a summary?

I've made some changes to the filters and to the misc. document so that we have something to talk about.  At the moment I'm displaying both, the individual members and the working groups.  We need to talk about which summaries would receive one or the other and how to organize the misc. document based on this decision.

My understanding is that only the genetics summaries will include the working groups but we want to keep the current display for all other summaries.  This would require a separate misc document which replaces the placeholder [LeadReviewers] with the placeholder [WorkingGroups].

I met with Kavitha and Jessica this week to go over the process of updating summaries with the new element and maintaining the text of the Misc. Doc. Kavitha also spent time testing and reviewing the process on her own.  The new features worked well and we were able to confirm the changes. The only question Kavitha had is quoted below:

• "Will we need a separate miscellaneous document for Genetics summaries or is there another way to have different wording and working groups be listed instead of lead reviewers? "

From the status meeting: It would be helpful to have a few examples of exactly what we'd like to appear in the About section (including text about working groups, lead/contributing WGs, link to roster, and acknowledgment text). We should include at least one page that's unaffected by the changes (maybe a Peds summary without acknowledgment text), a couple of genetics examples (some with lead/contributing WGs and at least one with acknowledgment text) and a Peds example with acknowledgment text.

I met with Kavitha, Crystal and Jess yesterday to get clarification on the requirements for the ticket. I have attached the Word document Kavitha provided that outlines the use cases and exception for this change. We also talked about the placement of the proposed acknowledgment text and the preference was for the text to go in the About This PDQ Summary section, and under the Reviewers and Updates subsection, specifically before the last paragraph in the section of the Reviewers and Updates subsection.  CDR Genetics Summaries Scenarios for About This Summary 11_13_24.docx

The Word document includes some requirements that should best be captured in a comment for the ticket.  I'm pasting those here:

Lead working group added in CDR (almost all Genetics summaries, see exceptions below):

• In the “Reviewers and Updates” section, replace sentence “Changes to the summaries are made through a consensus process in which Board members evaluate the strength of the evidence in the published articles and determine how the article should be included in the summary.” with “The PDQ Cancer Genetics Editorial Board is organized into subgroups called working groups. Each working group covers a specific topic. A working group evaluates the strength of the evidence in the published articles and determines how the articles should be included in the summary. Based on these articles, the working group drafts changes to the summary. The Board then reviews and modifies or approves the text through a consensus process.”

• Then list lead working group under “The lead working group for the [summary title] summary is:”

• If other working groups are added in the CDR, list under the lead working group with “The following working groups contribute to the [summary title] summary:”

• After listing the working group(s), add sentence “For more information about the Board members in these working groups, see [link to Cancer.gov roster].”

... and also:

Summaries that are collaborations between Genetics and Pediatric Boards:

• Both Boards will be listed in the CDR. In the first sentence in “Reviewers and Updates” section, will continue to list both Boards (This summary is reviewed regularly and updated as necessary by the PDQ Cancer Genetics Editorial Board and the PDQ Pediatric Treatment Editorial Board, which are editorially independent of the National Cancer Institute (NCI).).

• Above changes apply. Will list “Genetics of Pediatric Cancers” as the lead working group.

If a lead working group is not listed in the CDR (likely only the Cancer Genetics Overview summary):

• Keep text in “Reviewers and Updates” the same as other HP summaries.

• List any Board members linked to the summary as lead reviewers.

The first bullet point requests to have text sections replaced.  We don't want to do this within the filters.  Instead, we should create a new misc. document to be used for (almost all) Genetics summaries containing the required text - and Placeholders.

The third bullet point indicates we may have one or more working groups.  Is it possible to have none?
I will need to think about how to handle situations with 2 or more working groups.  We may need to add the text described in bullet 3 and 4 in a secondary misc. document.

If I remember correctly, Robin mentioned another section that may be included for "special individuals" to be named.  I would like to see a sample that shows how such a section would be displayed and if that special section would be part of the CDR content or added by filters.

The second part of this comment indicates that the Genetics Overview summary should be handled like any non-genetics summary.  Is that correct?

We are planning to add a new misc. document to be added to all (almost all) genetics summaries.  We will need an indicator that allows the filters to identify which of the summaries would be handled differently despite the fact that they are genetics summaries.

Yes, I believe you're referring to the "Acknowledgment text" for which I have the following comment below.

We also talked about the placement of the proposed acknowledgment text and the preference was for the text to go in the About This PDQ Summary section, and under the Reviewers and Updates subsection, specifically before the last paragraph in the section of the Reviewers and Updates subsection. 

PS:

I have scheduled a meeting with Kavitha for Tuesday next week to discuss your questions.

 The second part of this comment indicates that the Genetics Overview summary should be handled like any non-genetics summary.  Is that correct?

Unlike other non-genetics summaries, the Genetics Overview summary does not list any reviewers so it should be handled differently from other non-genetics summaries. note: The screening and prevention summaries also do not list reviewer names so that would be more like the Overview summaries.

The first bullet point requests to have text sections replaced.  We don't want to do this within the filters.  Instead, we should create a new misc. document to be used for (almost all) Genetics summaries containing the required text - and Placeholders.

The new misc. doc on DEV is CDR0000817118. Kavitha has finished updating it. Should it get a new Type? We used the For more information - Health professional summary type for now. 

The third bullet point indicates we may have one or more working groups.  Is it possible to have none?

Every genetics summary with the exception of the Genetics Overview summary will have a working group.

The third bullet point indicates we may have one or more working groups. Is it possible to have none?
I will need to think about how to handle situations with 2 or more working groups. We may need to add the text described in bullet 3 and 4 in a secondary misc. document.

Are you proposing something different from the way you currently handing lead/contributing working groups?

~oseipokuw , I forgot which genetics summaries have been prepared on DEV to run our tests and I can't find the CDR-IDs listed in this ticket.  

Do you have that information?