CDR Tickets

BZDATETIME::2010-10-28 15:40:30
BZCOMMENTOR::Robin Juthe
BZCOMMENT::1

Attachment Bevacizumab DIS Mock-up per group agreement.doc has been added with description: Bevacizumab Cancer.gov Mock-Up

BZDATETIME::2010-10-29 14:19:28
BZCOMMENTOR::Volker Englisch
BZCOMMENT::2

I have made changes to the filters and moved around the sections according to the sample document. I realized, however, that there are a few things which we forgot to discuss at our meeting. These do require additional changes.

We will need to make changes to the distribution partner's DTD in order to include the information for the FDA link and the pronunciation to the GateKeeper output.
I suggest to add these elements to the DrugInfoMetaData section.
The TermPronunciation element already exists and can be added as an element but the ExternalRef only exists as an inline element and we'll have to either use the RelatedExternalRef element or create a new element like FdaExternalRef to include the link information.

The relevant part of the DTD currently looks like this:

<!ELEMENT DrugInformationSummary
( DrugInfoMetaData,
DrugInfoTitle,
Section+,
DrugInfoDisclaimer,
DateFirstPublished,
DateLastModified?)>
<!ATTLIST DrugInformationSummary id CDATA #REQUIRED>

<!– Note: The CDR Vendor Filter will ensure that the Section elements
used within a DrugInformationSummary will not contain these
elements: AltTitle, KeyPoints, nested Section elements -->

<!ELEMENT DrugInfoMetaData
( DrugInfoType,
DrugInfoAudience,
DrugInfoDescription,
DrugInfoURL,
Manufacturers?,
FDAApproved?,
TerminologyLink,
GlossaryLink,
USBrandNames?,
Synonyms?,
TermPronunciation?, <<<<< New optional element
FDAExternalRef )> <<<<< New mandatory element

Please feel free to look at the changes that have been done so far on MAHLER.

BZDATETIME::2010-11-04 17:16:36
BZCOMMENTOR::Volker Englisch
BZCOMMENT::3

I have now changed the filters to use the new "section" attribute.

I will be able to finalize the filter changes once we decided how to modify the DTD which in turn will require changes to the GateKeeper code.

This is ready for review on MAHLER.

BZDATETIME::2010-11-08 14:57:23
BZCOMMENTOR::Margaret Beckwith
BZCOMMENT::4

I just want to add a note that after going through all of the changes to the DIS with Deb and Diana, it seems like we should go ahead and have the text for the Clinical Trials search string section come from a Misc. Doc. as we do for all of the summary CT SS sections.

BZDATETIME::2010-11-08 15:25:56
BZCOMMENTOR::Volker Englisch
BZCOMMENT::5

Were you thinking about using the PlaceHolder functionality as we do for the summaries or just create the link for the trials and concatenate the text from a misc. document?

BZDATETIME::2010-11-08 15:28:11
BZCOMMENTOR::Margaret Beckwith
BZCOMMENT::6

I was thinking that you would create the link and place the section in the document but that the explanatory text would come from a Misc. doc. So I guess that is the second option?

BZDATETIME::2010-11-08 15:32:19
BZCOMMENTOR::Volker Englisch
BZCOMMENT::7

Yes, it's the second option (and also the simpler one).

I wasn't sure if the link would still be displayed at the beginning of the text because if it needs to be embedded in the text we would have to use PlaceHolders.

BZDATETIME::2010-11-08 15:33:25
BZCOMMENTOR::Margaret Beckwith
BZCOMMENT::8

No, it would look exactly as it looks now, with the link at the beginning.

BZDATETIME::2010-11-19 09:18:49
BZCOMMENTOR::Robin Juthe
BZCOMMENT::9

I reviewed PubPreview of our favorite DIS, bevacizumab (CDR487564), on Mahler and noticed a couple of things.

1. The FDA approval link is showing up below the "FDA Approved: Yes" line. Could it be placed next to the word "Yes" with a dash ("-") between the word Yes and the link, as in the mockup provided?

2. In the "About this drug" section, I believe one of the new requirements was for the MedlinePlus information to display first in this section, and be followed by the drug dictionary definition. Although the sequence of links in this section is largely due to the sequence of DrugReference blocks in the document, the drug dictionary definition appears to be at the top of the list no matter what (it doesn't have a DrugReference block of its own). How is this link added? Would it be possible to place it after the MedlinePlus information?

Thanks!

BZDATETIME::2010-11-19 12:25:34
BZCOMMENTOR::Volker Englisch
BZCOMMENT::10

(In reply to comment #9)
> 1. The FDA approval link is showing up below the "FDA Approved: Yes" line.
> Could it be placed next to the word "Yes" with a dash ("-") between the word
> Yes and the link, as in the mockup provided?

Yes. This will be fixed once the modified DTD has been updated.

Question: Can we make that new FDAExternalRef element a mandatory field?
Will it always exist or should we add it as an optional element?

BZDATETIME::2010-11-19 16:07:05
BZCOMMENTOR::Volker Englisch
BZCOMMENT::11

I made changes to the DTD and forwarded it to Lee and Blair to replace the current DTD on the GatekeeperGK test server. Until the DTD has been replaced the PublishPreview report will not work anymore.

I modified the order of the sections to display the dictionary definition as the very first paragraph if no MedlinePlus section exists or otherwise it will be displayed right after the MedlinePlus section.
Also, for the time being I am displaying the FDA link and pronunciation in a paragraph before the Used in Cancer Treatment section since this is the only way to display these elements at all in PP.

BZDATETIME::2010-12-06 13:27:36
BZCOMMENTOR::Volker Englisch
BZCOMMENT::12

The DTD has been updated on the GatekeeperGK environment which means that PublishPreview is working again on MAHLER.

BZDATETIME::2010-12-08 15:10:27
BZCOMMENTOR::Volker Englisch
BZCOMMENT::13

I ran a publishing job on MAHLER and pushed data to GatekeeperGK to confirm that the DTD change didn't affect publishing of the old format.

I also made the filter changes publishable and published a reformatted Drug Summary to confirm that the new, optional elements are now accepted by Gatekeeper and the documents are properly processed.

In addition, I ran a publishing job of the DIS documents with the new DTD and the new filters.

Everything appears to be working as expected.

BZDATETIME::2010-12-09 12:08:14
BZCOMMENTOR::Margaret Beckwith
BZCOMMENT::14

I looked at bevacizumab on Mahler using Publish Preview and it looks pretty good. Everything appears to be sorting into the right categories. Is the placement of the FDA Approval info and the pronunciation not correct because it requires changes to the Cancer.gov dtd? When we go live with this we would want to suppress the pronunciation unless it can appear right under the title (drug name). Maybe this is obvious, but I thought I would state it anyway!

BZDATETIME::2010-12-09 12:31:11
BZCOMMENTOR::Volker Englisch
BZCOMMENT::15

(In reply to comment #14)
> Is the placement of the FDA Approval info and the pronunciation not
> correct because it requires changes to the Cancer.gov dtd?

Yes. I added those two elements into a separate paragraph to identify that this content actually does exist in the document. This is only intended for our test phase. when we'll display the reformatted DIS this display will be suppressed.

BZDATETIME::2010-12-14 14:56:54
BZCOMMENTOR::Volker Englisch
BZCOMMENT::16

This should probably be added under its own issue but I thought I'll add it here as some sort of FYI since it relates to this issue.
Ravee talked to me regarding any kind of changes that this or any other request for Cancer.gov might require (i.e. the Genetics Dictionary). He says that there should not be any change from this point forward until the WCM rolled out. He will set up a meeting to discuss the process (and personnel?) of future enhancements to the Gatekeeper.

BZDATETIME::2010-12-15 16:31:55
BZCOMMENTOR::Volker Englisch
BZCOMMENT::17

I've modified the filter
CDR505580 - Module: Vendor Filter: DrugInfoSummary

to remove the two paragraphs displaying the pronunciation and FDA link.
I did need to add an empty paragraph due to spacing issues between the Meta data block and the following section header.

The result is at
http://wwwgk.cancer.gov/cancertopics/druginfo/bevacizumab

BZDATETIME::2010-12-21 15:01:57
BZCOMMENTOR::Robin Juthe
BZCOMMENT::18

Just thought I would add a comment here to say that Margaret and I talked about this issue yesterday and, if we publish these pages in two stages as discussed (1st stage with the sections, 2nd stage with the pronunciations & FDA approval link), then we will need to come up with an interim plan for displaying the FDA approval link in stage 1 before the Cancer.gov changes involved in stage 2 are implemented. Maybe this can be accomplished the way it had been done as a separate paragraph previously? (see comment 15) Another possibility would be to have it in the About-Drug section for the time being.

BZDATETIME::2011-01-04 09:47:11
BZCOMMENTOR::Robin Juthe
BZCOMMENT::19

I had asked Deb if she had a rough idea of when she thought the section attributes would be added to all of the DIS. Here's her comment (today):

"I plan on concentrating on completing the section attribute assignment for all the DIS this week. Diana and I will be “meeting and greeting” Erin soon (later this week or early next week) and will ask her to QC my work on the section attributes as her first DIS/DCS project – hopefully she can get that completed by the time we convene our first DIS/DCS quarterly meeting January 20."

Me again: I believe the vendor filter changes are done, but we should talk about how to address the issue in comment 18 about the FDA approval link in our next meeting since it does look like we will be publishing the changes in 2 stages.

BZDATETIME::2011-01-07 15:09:33
BZCOMMENTOR::Volker Englisch
BZCOMMENT::20

As discussed at our status meeting yesterday, I've added the FDA approval link back into the filter output allowing us to go ahead with Phase I of the conversion once the data is ready.

BZDATETIME::2011-01-21 12:40:51
BZCOMMENTOR::Volker Englisch
BZCOMMENT::21

I've updated the filter and DTD on FRANCK and ran a publishing job. You can view the result on GatekeeperGK here:
http://wwwgk.cancer.gov/cancertopics/druginfo/alphalist

It appears that we didn't check closely enough how the change would affect the Drug Combinations since we're having some problems there.

Also, I will need to make some minor changes because for DIS without an FDA section there needs to be some additional space between the meta data section and the first section heading (see Methotrexate)

BZDATETIME::2011-01-21 13:54:19
BZCOMMENTOR::Volker Englisch
BZCOMMENT::22

I'd like the discussion about the DrugCombinations to continue in Bugzilla.

Email from Deb:
-----------------------------------------------------------------------

From: Price, Deborah (NIH/NCI) [E]
Sent: Friday, January 21, 2011 1:22 PM
To: Englisch, Volker (NIH/NCI) [C]
Cc: Blais, Diana (NIH/NCI) [E]; Beckwith, Margaret (NIH/NCI) [E]; Harrison, Robin (NIH/NCI) [E]
Subject: RE: Drug Combinations

Hi Volker,

Here is the sample reformatted drug combination summary for ADE that displays the changes in format. We decided we wanted to keep the list of drugs included in the combination prominently displayed, followed by the "Use in Cancer," and finish with "About DCS" which pulls in the Drug Dictionary definition.

Unlike the drug information summaries for single drugs, I think most of the DCS reformatting will be a manual task for Erin, Diana, and me.
I hope this helps!

Many thanks,
Deb
---Original Message---
From: Englisch, Volker (NIH/NCI) [C]
Sent: Friday, January 21, 2011 12:58 PM
To: Blais, Diana (NIH/NCI) [E]; Price, Deborah (NIH/NCI) [E]
Cc: Beckwith, Margaret (NIH/NCI) [E]; Harrison, Robin (NIH/NCI) [E]
Subject: Drug Combinations

Hi there,

I ran a publishing job on FRANCK (using the CDR data from 3 days ago) to test the display changes to the DISs.
What I noticed was that I hadn't paid too much attention to the Drug Combinations as you can see here
http://wwwgk.cancer.gov/cancertopics/druginfo/ABVD

I'm not sure, however, what we had decided on how to handle these documents.
Could you give me a little refresher?

BZDATETIME::2011-01-21 13:55:52
BZCOMMENTOR::Volker Englisch
BZCOMMENT::23

This is the sample provided by Deb showing the display of the Drug Combination Summaries.

Attachment ADE mock up showing group agreement.doc has been added with description: Drug Combination Mock-Up

BZDATETIME::2011-01-21 14:05:26
BZCOMMENTOR::Volker Englisch
BZCOMMENT::24

Deb, your explanation helps but I still have questions.

If I understand you correctly you will create the 'Use in Cancer' section manually after the drugs table. This means I will need to suppress printing the automatically generated 'Uses in Cancer Treatment' heading for the DCSs.

I'm assuming there will not be a 'Research Results' section and therefore I will need to suppress this heading from printing for the DCSs as well.

Will you also create the 'About ADE' section manually? If you do I will need to suppress printing this title as well, otherwise the sections will need to be created before we do the switch.

BZDATETIME::2011-01-21 14:37:46
BZCOMMENTOR::Deb Price
BZCOMMENT::25

(In reply to comment #24)
> Deb, your explanation helps but I still have questions.
> If I understand you correctly you will create the 'Use in Cancer' section
> manually after the drugs table. This means I will need to suppress printing
> the automatically generated 'Uses in Cancer Treatment' heading for the DCSs.
> I'm assuming there will not be a 'Research Results' section and therefore I
> will need to suppress this heading from printing for the DCSs as well.
> Will you also create the 'About ADE' section manually? If you do I will need
> to suppress printing this title as well, otherwise the sections will need to be
> created before we do the switch.

Yes Volker, it looks like you will need to suppress the "Use in Cancer" heading and the Research Results heading in the DCS. We will manually create the Use in Cancer" section after the drugs table. The DCS do not have a "Research Results section so that heading is not needed. Also, our group decided to revise the heading in the DIS to "Use in Cancer" instead of "Use in Cancer Treatment.
We can also manually add the "About DCS" heading, too s you can suppres that heading, too. I tried my hand at refomatting our CVP DCS in BACH and think it turned out pretty well.

BZDATETIME::2011-01-21 15:23:07
BZCOMMENTOR::Volker Englisch
BZCOMMENT::26

(In reply to comment #25)
> We can also manually add the "About DCS" heading, too

I've removed the 'Uses in Cancer...' and 'Research Results' sections from the DrugCombinations.
Please let me know if you want me to keep the 'About DCS' or take it out.

Back to the DIS:
The filter is printing the dictionary definition as part of the 'About Drug' section. This requires this section to exist. I came across a DIS without the 'About Drug' section. Do we still want to display the dictionary definition or will the definition be dropped if the section 'About Drug' does not exist?

Again, the latest changes are available for review at
http://wwwGK.cancer.gov/cancertopics/druginfo/alphalist

BZDATETIME::2011-01-21 16:02:59
BZCOMMENTOR::Margaret Beckwith
BZCOMMENT::27

Which is the drug without the link to the Drug Dictionary definition? All of these should have one.

BZDATETIME::2011-01-21 16:06:03
BZCOMMENTOR::Volker Englisch
BZCOMMENT::28

It's Paclitaxel Albumin-stabilized Nanoparticle Formulation because this one is missing an 'About Drug' section.

BZDATETIME::2011-01-21 16:23:26
BZCOMMENTOR::Margaret Beckwith
BZCOMMENT::29

I see. It looks like there are quite a few drugs that don't have an About This Drug section. My vote is to go ahead and add the section and just put the link to the Drug Dictionary in it. Every drug is in the Drug Dictionary, and at least the definition is providing a little bit of additional information about the drug.

BZDATETIME::2011-01-21 17:17:32
BZCOMMENTOR::Volker Englisch
BZCOMMENT::30

I have updated the filter to display the 'About ...' section in all cases to include the drug dictionary link, regardless if a 'About Drug' reference section exists or not.

The documents have been updated on WWWGK.cancer.gov.

BZDATETIME::2011-01-26 12:53:45
BZCOMMENTOR::Volker Englisch
BZCOMMENT::31

Per Deb's request I have changed the title 'Uses in Cancer Treatment' to 'Use in Cancer'.
We have also discussed the differences between the DrugInformation and the DrugCombination summaries and I believe that I have made all of the changes to the filter and the sections are now being displayed properly for both DIS types.

The documents have been updated on
http://wwwgk.cancer.gov/cancertopics/druginfo/alphalist
for your review.

BZDATETIME::2011-02-03 11:07:48
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::32

(In reply to comment #31)
> The documents have been updated on
> http://wwwgk.cancer.gov/cancertopics/druginfo/alphalist
> for your review.

I reviewed a few of the documents and they appear to follow the requirements correctly. The Clinical Trials Accepting Patients section appears to indicate that only Active clinical trials would be retrieved but I found a few Approved-not yet Active trials in some of the search results. I don't know if this is important or not but considering the text: "Check for trials from NCI's list of cancer clinical trials now accepting patients." it seems to me that the results should not include non Active trials.

I will continue to review some more documents...

BZDATETIME::2011-02-11 14:43:56
BZCOMMENTOR::Volker Englisch
BZCOMMENT::33

I've talked to Deb about this issue and she said that from her point-of-view we could put the new filters in production whenever we're ready.
Since we're ready this means Now.

I will schedule to have the DTD copied to Gatekeeper early next week and then we can run a special production job to update all of the DrugInfoSummaries and Combos.

BZDATETIME::2011-02-15 19:52:31
BZCOMMENTOR::Volker Englisch
BZCOMMENT::34

The DTD has been copied to production. We can now go ahead and copy the filters, which I will do tomorrow.

BZDATETIME::2011-02-16 14:18:04
BZCOMMENTOR::Volker Englisch
BZCOMMENT::35

I copied the following filter to FRANCK and BACH:
CDR505580 - Module: Vendor Filter: DrugInfoSummary - R10007

The DrugInfo summaries can now be viewed using publish preview on BACH.

Do we want to run a special publishing job to update these documents or should we wait until Friday's publishing job to have these updated on Cancer.gov.
I prefer to run a separate publishing. In case something goes wrong we would not interrupt the much larger job on Friday.

I could possibly run a publishing job tonight after the nightly job finished.

BZDATETIME::2011-03-10 14:02:23
BZCOMMENTOR::Volker Englisch
BZCOMMENT::36

Per discussion at our status meeting this issue can be closed since it's in production for several weeks now.