CDR Tickets

Names for the ad-hoc queries:

• Drug Terms - published to Drug Dictionary

• Drug Terms  - NOT published

The following path has to be added to the list of query terms.  All term documents will need to be re-indexed on all tiers:

/Term/Definition/DefinitionText 

Hi Volker,

Would you be able to modify the query to include Other Names in a column separated by semi colons?

Thanks,

William

The queries have been created on all tiers.  The drug terms have been reindexed.

Please check out the 2 new queries.

Thanks ~volker. When I run the first query Drug terms on published to Cancer.gov,  it retrieves 7261 however, on Cancer.gov the total number appears to be 7845. I am not sure where the discrepancy is coming from but it appears to be significant.

I see that Cancer.gov lists brand names as a separate entry, therefore inflating the numbers we list since it would count a drug multiple times, once for the preferred name and once for the brand name.

I'm still looking at the possibility that some terms aren't listing the C-code properly in the field for the NCIThesaurusConcept.  A term without this element would be dropped on the list.

I looked through the output for one letter (Z) to compare and find any differences between the Cancer.gov list and the ad-hoc query output:

• The total number of drugs listed on Cancer.gov is 113

• 55 of those are brand names and need to be excluded: Total on Cancer.gov - 58

• 2 terms are missing on Cancer.gov because of an incorrect SemanticType (this is a bug in our export software)
  Total on Cancer.gov: 60

•  

• Ad-hoc query lists 59

• 1 term is excluded from Cancer.gov because of a missing definition (missing ReviewStatus)
  Total ad-hoc: 58

• 2 terms are excluded from ad-hoc query because of missing C-code
  Total ad-hoc: 60

It appears the numbers are matching between both lists when the missing data elements are considered.

These are the terms with issues:

• 803278 - zelenoleucel: SemanticType

• 803287 - zirconium Zr 89-DFO-fianlimab: SemanticType

• 764414 - zirconium Zr 89-girentuximab: missing ReviewStatus

• zirconium Zr 89-desferrioxamine B monoclonal antibody huJ591: missing C-code

• zirconium Zr 89-labeled anti-PIGF monoclonal antibody RO5323441: missing C-code

• zirconium Zr 89˗DFO˗REGN3504
  For this term the dash ('-') character is not a dash and is displayed as question mark in the ad-hoc query.

Could you please include only terms with a Drug/Agent semantic type. Currently the spreadsheet include terms that are not drug terms. Like:

 **

The query has been updated on PROD.

The errors have been fixed. Thank  you!

Looks good on PROD. Thank you!

Adding offline conversation with about this ticket. 

From: Englisch, Volker (NIH/NCI) [C] <volker@mail.nih.gov>
Sent: Thursday, November 19, 2020 5:14 PM
To: Osei-Poku, William <William.Osei-Poku@icf.com>
Subject: Re: CDR oddity this week

In that case, why don’t we remove the definition from the query but keep the query with a comment and delete the query term?

Deleting the query_term will prevent the warning message to pop up with every save and the comment should remind us what to do the next time we need to run this query again if the definition needs to be included.

Plus, we should add a comment to the ticket.

Thanks,

        Volker

Volker Englisch
NCI OCPL – Office of Communications & Public Liaison

Contractor: publicis sapient
NCI: 240-276-6583

From: "Osei-Poku, William" <William.Osei-Poku@icf.com>
Date: Thursday, November 19, 2020 at 3:48 PM
To: Volker Englisch <volker@mail.nih.gov>
Subject: RE: CDR oddity this week

1. We can remove it from the query terms and the report for now as we’ve already generated a spreadsheet to send to EVS. However, I am sure at some point, they will ask for another one so we may have to repeat this whole thing again.

Thanks,

William

From: Englisch, Volker (NIH/NCI) [C] <volker@mail.nih.gov>
Sent: Thursday, November 19, 2020 3:46 PM
To: Osei-Poku, William <William.Osei-Poku@icf.com>
Subject: Re: CDR oddity this week

I think the only way to avoid this would be to remove the DrugDefinitionText  from the query terms and remove it from the new ad-hoc report or create the report via a Python script.

It’s just a notification and therefore not really something to be concerned about but I can see how  it might get annoying.  

Thanks,

        Volker

Volker Englisch
NCI OCPL – Office of Communications & Public Liaison

Contractor: publicis sapient
NCI: 240-276-6583

From: "Osei-Poku, William" <William.Osei-Poku@icf.com>
Date: Thursday, November 19, 2020 at 3:22 PM
To: Volker Englisch <volker@mail.nih.gov>
Subject: RE: CDR oddity this week

Should we just ignore it ?

Thanks,

William

From: Englisch, Volker (NIH/NCI) [C] <volker@mail.nih.gov>
Sent: Thursday, November 19, 2020 2:57 PM
To: Osei-Poku, William <William.Osei-Poku@icf.com>
Subject: Re: CDR oddity this week

I don’t think it’s a limit on drug definitions but on indexed terms.  I had to add the drug definitions to the query_term index table for your ad-hoc report.  That’s likely why you’re now seeing this because the query_term table gets updated with every save.

Thanks,

        Volker

Volker Englisch
NCI OCPL – Office of Communications & Public Liaison

Contractor: publicis sapient
NCI: 240-276-6583

From: "Osei-Poku, William" <William.Osei-Poku@icf.com>
Date: Thursday, November 19, 2020 at 2:46 PM
To: Volker Englisch <volker@mail.nih.gov>
Subject: FW: CDR oddity this week

Hi Volker,

Are you aware that there is an 800 character limit on Drug definitions ?

Thanks,

William

From: Barnstead, Mary (NIH/NCI) [C] <mary.barnstead@nih.gov>
Sent: Thursday, November 19, 2020 2:44 PM
To: Osei-Poku, William <William.Osei-Poku@icf.com>
Subject: RE: CDR oddity this week

Hi William,

I first started seeing it yesterday.

Thanks

Mary

From: Osei-Poku, William <William.Osei-Poku@icf.com>
Sent: Thursday, November 19, 2020 2:27 PM
To: Barnstead, Mary (NIH/NCI) [C] <mary.barnstead@nih.gov>
Subject: RE: CDR oddity this week

Hi Mary,

Is this the first time you’re seeing this or you’ve seen it before.

Thanks,

William

From: Barnstead, Mary (NIH/NCI) [C] <mary.barnstead@nih.gov>
Sent: Thursday, November 19, 2020 8:53 AM
To: Osei-Poku, William <William.Osei-Poku@icf.com>
Subject: CDR oddity this week

Hi William,

In term records, I’ve started getting this message when there is a long definition:

Is this anything to worry about?

Thanks!

Mary

______________________________________________________________________________________

Mary Barnstead, MS PMP

CIAT Terminology and Drug Information Manager – NCI/ICF

(301) 407-6640 (office) (240) 449-9762 (cell)