CDR Tickets

Issue Number 3069
Summary Glossary Term Concept by Type Report
Created 2010-01-28 12:14:29
Issue Type Improvement
Submitted By Beckwith, Margaret (NIH/NCI) [E]
Assigned To Kline, Bob (NIH/NCI) [C]
Status Closed
Resolved 2010-02-02 16:20:35
Resolution Fixed
Path /home/bkline/backups/jira/ocecdr/issue.107397
Description

BZISSUE::4745
BZDATETIME::2010-01-28 12:14:29
BZCREATOR::Margaret Beckwith
BZASSIGNEE::Bob Kline
BZQACONTACT::William Osei-Poku

There are several issues with the Glossary Term Concept by Type report:
1. If you select HP as the audience, the report is not showing the definitions and should be. If you select Patient as the audience the report works correctly.
2. The report inserts empty parens for terms that don't have pronunciations.

There are also a couple of questions that Robin H had about the display of the HP terms on Cancer.gov. These will probably turn out to be separate issues but I wanted to discuss them before putting in the issues.

1. In the pop-up boxes that a user gets when they click on a glossary term in the HP Genetics summaries, the terms are shown with the pronunciations if they have one. The only reason a few of the terms have a pronunciation is that they also have a patient definition and appear in the Dictionary of Cancer Terms. Would there be any way of suppressing the pronunciations for the HP terms?
2. Similar question about the images. The media link is actually in the patient definition block, but is showing in the HP term pop-up on Cancer.gov. This is fine but Robin was wondering why it was showing up?
3. I know this is a Cancer.gov question, but we were wondering if there was any way to publish the stand-alone Genetics Dictionary from the CDR? Right now it is maintained completely manually.

Comment entered 2010-02-02 09:36:06 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2010-02-02 09:36:06
BZCOMMENTOR::Bob Kline
BZCOMMENT::1

(In reply to comment #0)

> 1. If you select HP as the audience, the report is not showing the
> definitions and should be. If you select Patient as the audience the
> report works correctly.

The software is behaving correctly in both cases. See William's answer to the second question in http://verdi.nci.nih.gov/tracker/show_bug.cgi?id=4486#c4 .

> 2. The report inserts empty parens for terms that don't have pronunciations.

I modified the script to drop the parentheses when the pronunciation is missing.

Comment entered 2010-02-02 09:57:31 by Beckwith, Margaret (NIH/NCI) [E]

BZDATETIME::2010-02-02 09:57:31
BZCOMMENTOR::Margaret Beckwith
BZCOMMENT::2

I am not sure what you mean by the report is working the way it should.

Also, it seems to me that this report would be more useful if you didn't have to specify a term name in order to run it. For example, I would like to see all of the Genetics terms or all of the Levels of Evidence terms, with an audience of HP and I can't do that.

Comment entered 2010-02-02 10:37:49 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2010-02-02 10:37:49
BZCOMMENTOR::Bob Kline
BZCOMMENT::3

(In reply to comment #2)

> I am not sure what you mean by the report is working the way it should.

I meant that we implemented the requirements William gave us. From http://verdi.nci.nih.gov/tracker/show_bug.cgi?id=4486#c4:

> >
> > * Does the radio button selection for audience control which definitions
> > are searched, which definitions are displayed, or both?
>
> Yes. It does control both.

What else could that mean, if not that we were supposed to display definitions only if they matched the audience the user selected?

> Also, it seems to me that this report would be more useful if you didn't have
> to specify a term name in order to run it. For example, I would like to see
> all of the Genetics terms or all of the Levels of Evidence terms, with an
> audience of HP and I can't do that.

The SQL wildcard character (%) works just like it does in the advanced search interface: if you put % in the Term Name field I think you'll get what you're looking for.

Comment entered 2010-02-02 10:40:52 by Beckwith, Margaret (NIH/NCI) [E]

BZDATETIME::2010-02-02 10:40:52
BZCOMMENTOR::Margaret Beckwith
BZCOMMENT::4

I am sorry to be so dense about this.
"What else could that mean, if not that we were supposed to display definitions
only if they matched the audience the user selected?"
Doesn't this mean that if I select HP as the audience I would see the HP definitions?

Comment entered 2010-02-02 10:55:24 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2010-02-02 10:55:24
BZCOMMENTOR::Bob Kline
BZCOMMENT::5

I think I see what's happening. The specs had us looking for "Health Professional" and the data has "Health professional." That didn't make any difference when we were selecting documents using the query-term table, because SQL Server ignores case, but it did make a difference when we are actually looking inside the documents we've selected to decide which parts to display. I have modified the script (on Mahler) to ignore case there as well. Please take a look.

Comment entered 2010-02-02 13:26:22 by Beckwith, Margaret (NIH/NCI) [E]

BZDATETIME::2010-02-02 13:26:22
BZCOMMENTOR::Margaret Beckwith
BZCOMMENT::6

This looks great. Please promote.

Comment entered 2010-02-02 14:39:29 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2010-02-02 14:39:29
BZCOMMENTOR::Bob Kline
BZCOMMENT::7

Promoted to Bach and Franck.

Comment entered 2010-02-02 16:20:35 by Beckwith, Margaret (NIH/NCI) [E]

BZDATETIME::2010-02-02 16:20:35
BZCOMMENTOR::Margaret Beckwith
BZCOMMENT::8

This looks good so I am closing the issue. I also copied the information about cancer.gov enhancements for genetics glossary to the issue which has the collection of cancer.gov issues.

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