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[bioontology-support] [BioPortal] Feedback from Michele LeNoue-Newton

Michael Dorf mdorf at stanford.edu
Fri Feb 28 15:05:59 PST 2020


Hi Michele,

The reprocessing of NCIT has been completed. Looks like the search is now working properly. Let me know if any of the terms you are expecting to find are still missing.

Thank you,

Michael



On Feb 28, 2020, at 2:31 PM, Lenoue-newton, Michele Laura <michele.l.lenoue-newton at vumc.org<mailto:michele.l.lenoue-newton at vumc.org>> wrote:

Hi Michael,

Thanks for the update!

-Michele

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, February 28, 2020 4:29 PM
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: Lenoue-newton, Michele Laura <michele.l.lenoue-newton at vumc.org>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Michele LeNoue-Newton

Hi Michele,

Upon further inspection, it looks like the latest version did process correctly, but the part that generates the index for searches had not fully completed. I’ll try to re-indexing it on my and and see if that addresses your issue. I’ll keep you posted.

Thanks!

Michael


On Feb 28, 2020, at 2:09 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

Hi Michele,

Thank you for your email. The version of NCIT we host in BioPortal is provided to us directly by the NIH/NCI staff. I’ve CCd Gilberto Fragoso from NIH/NCI, who has been in charge of maintaining the BioPortal version of NCI Thesaurus. It looks like a new version (20.02d) of the ontology was uploaded to us recently (2/24/20). I hope Gilberto can offer some light on what changes have been introduced since the previous version (20.01d).

Sorry, I couldn’t be more helpful, but Gilberto should be able to offer some assistance with your concerns.

Thanks!

Michael


----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
mdorf at stanford.edu<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------


On Feb 28, 2020, at 8:03 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Michele LeNoue-Newton
Email: michele.l.lenoue-newton at vumc.org<mailto:michele.l.lenoue-newton at vumc.org>
Location: https%3A%2F%2Fbioportal.bioontology.org<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2F2fbioportal.bioontology.org%2F&data=02%7C01%7Cmichele.l.lenoue-newton%40vumc.org%7C926ba63db983428b4bab08d7bc9da39e%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637185257549416662&sdata=DT9yxtP9ADb0bgzr8mahw7qdHgpqPS0uB5C3lm9%2BiOY%3D&reserved=0>%2Fontologies%2FNCIT

Feedback:
The latest version of the NCIT released in the BioPortal and used in applications like REDCap appears to be incomplete. It no longer contains many critical terms, including major disease classifications (Melanoma, Lung Adenocarcinoma) or single drug entities (carboplatin, cisplatin).

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