CDR Tickets

We are still reviewing this for more features elements that we may want changes. In the meantime, here is what Linda has provided:

Glossary Docs:

• GTN 46047, GTC 621832
• GTN 721252, GTC 721250
• GTN 791168, GTC 791167

There are a few cases where gene term name is inside a placeholder in the GTC and would like to be able to display the gene name in italics.

We would also like to be able for words inside EmphasisTags to display in italics.

Media Docs:

• Philadelphia chromosome-Spanish, 558048. Would like to be able to use gene tags for gene names in labels, caption and content description.

Additional information from Amy.

Here are a couple of additional examples of glossary terms where we would use gene tags. Sometimes, we’ll also reference gene names in definitions for drugs or genetic syndromes/conditions:

For media, we don’t use gene names in images very often, other than in the example Linda mentioned above. However, as we’re developing more genetics-related content, we will most likely be using them more so having the option to add the gene tags in the caption, content description, and label name fields in the media doc would be great.

~oseipokuw, it appears you are adding three different items within this one ticket:

1. gene name mark-up within glossary term concept definition ✔

2. gene name mark-up within a placeholder of the glossary term concept definition

3. gene name mark-up within media caption

I've tested the first of these three and have identified that this change would be a WCMS ticket. The mark-up gets created and applied - as you can see by the fact that the QC reports display gene name mark-up in italics - and pushed to Gatekeeper but the Gatekeeper process doesn't preserve/convert the information properly.

For the other two items I would like for you to create a sample on DEV to ensure I'm covering the situations as needed.

For the other two items I would like for you to create a sample on DEV to ensure I'm covering the situations as needed.

From Linda & Amy:

ALK gene (GTN: 721252; GTC: 721250):

I added a GeneName element to the definition text; however, we can’t add an element to placeholders in a definition. We can only use attributes (e.g., TERMNAME or EP1, etc), so I tried a different approach and changed the attribute to EP1 and added EP1 replacement text to the GTN (721252). Here, I typed in the term name (ALK gene) and added a ScientificName element (note: there is not a GeneName element option for replacement text in GTN docs). It looks like the ScientificName element does the same thing as the GeneName element because it put the gene name in italics.

Philadelphia Chromosome (Media doc : 533336)

The media doc only allows me to add a GeneName element to the captions. We’d like to be able to also use this element in the Content Descriptions and in the label names, but currently this element is not an option in these fields.

I marked up the following document on DEV

Gen ROS1 (ROS1 gene)

GTC CDR ID: 779659

I used the GeneName element where the gene name appears in the definition.

gene name mark-up within a placeholder of the glossary term concept definition

Sounds to me there are three issues here:

1. Update Schema to allow GeneName markup within Placeholder elements, like ScientificName

2. Modify filter(s) to display GeneName in italics within QC reports in addition to the blue/yellow background display

3. Modify filter(s) and/or Gatekeeper processing to display GeneName mark-up on Cancer.gov

Does this sound right to you?

The media doc only allows me to add a GeneName element to the captions. We’d like to be able to also use this element in the Content Descriptions

May I ask why we want to add mark-up to the content description? The content description of the Media docs is used to populate the alt tags on Cancer.gov. As far as I know, the alt tag content is used by screen readers to explain the image. Unless this text is also displayed somewhere else, the screen reader will most likely ignore any kind of markup.

I would have the same question regarding the element LabelName. To my knowledge this element is only used in the QC reports.
Is the goal here to add markup text to the QC report although the element is never displayed on Cancer.gov?

Christina also mentioned to me that gene names are not rendered within the drug information summaries. We should discuss whether to make this a separate ticket.

Are the gene names rendered in the QC report?  If that's the case it would again indicate that it's likely Gatekeeper who isn't able to handle the markup.

Would you happen to have a sample of a DIS with gene name?  I'd like to double-check if we're providing the markup.

The Vemurafenib DIS is a good example; it has gene tags around “BRAF.”

CDR ID: 709542

Cancer.gov: https://www.cancer.gov/about-cancer/treatment/drugs/vemurafenib

It appears to be a Gatekeeper issue. I'll file a separate ticket.

I'll let you estimate this one, ~volker, since you been working on it already.

I think this ticket needs a little discussion and we will likely need to split it into multiple tickets.  Plus, I added a few questions we may already have been discussed in our meetings but I don't remember the answer.  I'll try to summarize in this comment the multiple tasks that may need to be addressed

Gene Name/Emphasis within DefinitionText

• PublishPreview Report: Vendor output correct; needs fixing at WCMS end

• Full GTC report: needs to be fixed (2 pt)

• GTC report: OK

• GTN with concept: OK

Gene Name/Emphasis within PlaceHolder Element

• Modify schema to allow GeneName markup within PlaceHolder elements

• PublishPreview Report: Vendor output needs modification (3 pt); also will need fixing at WCMS end

• Full GTC report: needs to be fixed (2 pt)

• GTC report: OK

• GTN with concept: OK

Gene Name/Emphasis within Media Content Description

• I posted the question why we want to markup text that will not get displayed on Cancer.gov?

Gene Name/Emphasis within Media LabelName

• Same as above

Gene Name/Emphasis within Media Caption

•  Media QC report: needs fixing (2 pt)

• PublishPreview Report: needs fixing (2 pt); will likely need fixing at WCMS end

Based on this I'll estimate the ticket with 10 pt assuming the content description and label name requests will not be addressed.

This ticket is in the same boat as OCECDR-4763 (Spanish Genetics Dictionary).  The dictionary API will replace the currently used Gatekeeper processing of glossary and drug terms and any changes to the glossary display we're doing now would be thrown away with the new API.

Therefore, we should do what I had recommended in my last comment and split this task into separate tickets.

• Glossary Term Concept - Full QC Report (GeneName not marked up)

• Drupal API/Elastic Search loader (GeneName not marked up) (i.e. PublishPreview)

• GTC documents - ability to use markup inside PlaceHolder elements

• Media docs - markup inside captions (may require DTD change)

• Media docs - markup inside labels (requires schema change, QC Report only?)

• Media docs - markup inside content description (requires schema change, QC Report only?)

• Media QC Report - (GeneName not marked up inside caption)

• Summaries - Are media captions coming from Summary/Media document marked up?

• GTN - Allow GeneName and Emphasis to be used inside ReplacementText elements, just like ScientificName and ForeignWord. (Schema, DTD change)

Gene Name/Emphasis within Media Content Description

• I posted the question why we want to markup text that will not get displayed on Cancer.gov?

Gene Name/Emphasis within Media LabelName

• Same as above

Please do not implement the above. As you rightly said, they are either for internal use only or meant for screen readers. Thanks!

We had discussed in our last CDR meeting to postpone the changes for the Glossary documents until the Glossary API is published and use this ticket to address the display of the GeneName elements within the media captions.

I prepared a document on DEV (CDR799644) and see that all inline elements (GeneName, Emphasis, Strong, ScientificName) are properly marked up for both, captions coming from the Summary and captions coming from the Media document itself.  This holds true for the QC reports as well as the PP reports.

I'm unsure at this point what it is that needs to be modified.

I think the main issue has to do with displaying the gene names in italics in pub preview and Cancer.gov. So, it is more a WCMS issue than a CDR issue.

Again, I don't see any problems with the display of these elements.  Please see my screenshot from running PP on my test summary on DEV.

What I checked was the display in definition text. At least when I checked last week, gene names were not italicized.

OK, that's part of the changes for GTN/GTC which are currently postponed due to the implementation of the Dictionary API.

In that case, since this ticket in now only addressing the media captions, there are no additional changes needed.  I will go ahead and mark the ticket as fixed and create a replacement for the GTN/GTC work in Maxwell.

It doesn't look like there is anything to test for this issue.

In that case, since this ticket in now only addressing the media captions, there are no additional changes needed.  I will go ahead and mark the ticket as fixed and create a replacement for the GTN/GTC work in Maxwell.

~volker It looks like we missed getting this done in Maxwell. Should I create a new ticket for Newton ?

Yes, please go ahead and create a new ticket for the markup of GeneNames in the glossary definition.