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[bioontology-support] [BioPortal] Feedback from David Rogers

Rogers, David W drogers at fredhutch.org
Thu May 10 17:58:11 PDT 2018


Interesting. So the custom ontology would appear in the list when I used my apikey?





Sent from my Verizon, Samsung Galaxy smartphone


-------- Original message --------
From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Date: 5/10/18 5:18 PM (GMT-08:00)
To: "Rogers, David W" <drogers at fredhutch.org>
Cc: support at bioontology.org
Subject: Re: [bioontology-support] [BioPortal] Feedback from David Rogers

Hi David,


On May 10, 2018, at 3:40 PM, Rogers, David W <drogers at fredhutch.org<mailto:drogers at fredhutch.org>> wrote:

We have numerous projects which use REDCap to select CTCAE ontologies provided through BioPortal. Much like ICD codes, one doesn’t normally switch to a different version (e.g., ICD9 –> ICD10) in the middle of a research study. My request is for you guys to do the same thing with CTCAE as you have done with ICD codes – provide multiple versions – at least the most recent prior version as well as the current version in the api.


I wanted to offer some clarification with regard to ICD. Roughly 5 years ago, we started doing twice annual imports of the ontologies that are part of the National Library of Medicine’s UMLS [1]. The UMLS includes copies of both ICD9 and ICD10, which is why you see both in BioPortal. In other words, there was no internal decision to offer multiple versions of ICD. This is simply a product of what’s available to import from the UMLS.

Generally speaking, we provide the software infrastructure for publishing biomedical ontologies into our repository. In most cases, we aren’t the authors, and/or maintainers of these ontologies and don’t put restrictions on when ontology authors are allowed to publish new versions. The contact information for CTCAE in BioPortal indicates that it’s maintained by NCI.


So I would see CTCAE and CTCAE4 in the list of available ontologies.


If you’re doing a research study that requires access to a particular version of an ontology, you’re welcome to create a new entry in BioPortal. As the owner/administrator of that entry, you’d be able to ensure that no modifications are made for the duration of your study. To add an entry for an older version of CTCAE in BioPortal, you would need to create an account [2], then navigate to the Tools -> Ontology Browser page, and click the Submit New Ontology button.

Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nlm.nih.gov_research_umls_knowledge-5Fsources_metathesaurus_&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=WgUuXEZxxnXFMyW7y9PgsrcZI3Wdrk7U4ztbdTbhVmo&m=v16cO8iN5aJref9Dc01IEJl0-eByniIewnSjRiScoAs&s=beksTC-3a8JKw6nqdF6PiKhzmVTJBuAZiCUB37EzusI&e=>
[2] https://bioportal.bioontology.org/accounts/new<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_accounts_new&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=WgUuXEZxxnXFMyW7y9PgsrcZI3Wdrk7U4ztbdTbhVmo&m=v16cO8iN5aJref9Dc01IEJl0-eByniIewnSjRiScoAs&s=3_WScNMyFPlU9OLK1t07w3cC7XwOwEWn_KCQu7amTLc&e=>

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