Problems with ICDO ontology on ontobee

[cmungall]

http://www.ontobee.org/ontology/ICDO

The name of this is confusing - ICDO is already taken as a name for "The International Classification of Diseases for Oncology"

The ontobee ICDO is an ontological representation of ICD9/10/11 which is completely different

There are other issues with the ontology

• the URIs don't resolve
• it mints new numbers that could be confused with actual IDs (whether ICDO or 9 or 10 or 11...)
• the URIs look like OBO purls, but they include a .owl in them, and this is not registered with. obo

[yongqunh]

Good comments. I will forward the comments to Dr. Eric Wan who is the primary developer of ICDO.

Tentative replies:
"The International Classification of Diseases for Oncology" appears to be always abbreviated as ICD-O, with a "-" in between ICD and O.

The new numbers were generated to show that they are ICD version neutral. ICDO also includes mapping to the actual IDs in ICD 9 or 10 or 11. Ideally, ICDO IDs represents the IDs of the terms at the sense of ontology realism using the BFO realism meaning, and they map to the concept IDs in different ICD systems like -9, -10, or -11. See more detail in the ICDO paper which was also presented in the InCOB-2020 conference:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8522253/
The ICDO work was first presented by Eric in the ICBO-2019 conference:
http://ceur-ws.org/Vol-2931/ICBO_2019_paper_30.pdf

It is true that the ICDO URIs don't resolve, which is because ICDO was not included yet in OBO ontology library. ICDO was develoed by following the OBO ontology development principles. I will suggest to Eric and ask him to apply for the OBO library inclusion.

[cmungall]

I would urge changing the name of the ontology. A dash is not a good disambiguator.

[mbaudis]

+1 @cmungall

[cmungall]

Any progress on this? I strongly recommend ontobee chooses a different prefix for the ontologization of ICD, otherwise this will always cause confusion.

[matentzn]

+1 @cmungall

[yongqunh]

Thanks, Chris, for checking. Thanks, Nico, for discussion. I have recently discussed with Eric, the primary developer of the ontology. Although we have not made our final decision, we are open for discussion.

What about "OICD"? It stands for "Ontology of ICD".

I checked in Google, and did not find any relevant confusion with the "OICD".

[yongqunh]

Also, we expect some major updates on the ontology by this summer. An undergraduate student who previously worked on this project has expressed her interest in continuing this work. We will likely hire some more student(s) in the summer. Eric has also found another student who is intereted in this project.
We also welcome comments, suggestions, and collaborations. Probably we can schedule some meeting together this month or next month to discuss this project in more details.
Thanks!

[cmungall]

I think that is much better!

…

On Wed, Mar 2, 2022 at 8:17 AM Yongqun Oliver He ***@***.***> wrote: Thanks, Chris, for checking. Thanks, Nico, for discussion. I have recently discussed with Eric, the primary developer of the ontology. Although we have not made our final decision, we are open for discussion. What about "OICD"? It stands for "Ontology of ICD". I checked in Google, and did not find any relevant confusion with the "OICD". — Reply to this email directly, view it on GitHub <#163 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMON4O2LQZQZWKIKOYA3U56H73ANCNFSM5IUMNXAA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[matentzn]

OICD sounds good to me as well!

[mbaudis]

+1 Still a good claim of the space ¯\_(ツ)_/¯