ICO-Clinical Evaluation: Identified gaps and import of non-BFO compliant terms

[lizumberfield]

During evaluation of clinical consent forms and the regulatory literature for reuse of residual clinical biospecimens and health data, the following terms were identified as gaps in coverage within ICO and OBO Foundry ontologies. These terms were taken from NCI Thesaurus (NCIT) and Experimental Condition Ontology (XCO), which do not follow the BFO hierarchy. However, these classes' text definitions and labels are appropriate for our use.

I recommend import of the following terms under new parent hierarchies, following community deliberation on which ontology is the best fit for each term (may be ICO, may be another OBO Foundry Ontology).

Terms

• NCIT:C13235 | Fetus
• NCIT:C16423 | Child
  (consider importing all age group and at-risk population terms)
• NCIT:C15380 | Telemedicine
• NCIT:C142640 | Postmarketing Surveillance
• NCIT:C163409 | Safety Monitoring
• NCIT:C43960 | Health Care Organization
• NCIT:C54131 | Company
• NCIT:C64262 | Biologic Sample Preservation Procedure
• XCO:0000527 | Genetic Manipulation

Elizabeth Umberfield
https://orcid.org/0000-0001-5029-1158

[linikujp]

Thank you Elizabeth! I think most of them will need to be submitted to other ontologies.
At least I know that OBI is discussing the telemedicine term.
I am interested in where the postmarketing surveilance, and safety monitoring will reside. - I know OBI is discussing a term about surveilance. However, the postmarketing surveilance sounds like a regulatory term, or OBI can take it since they took surveilance.
Other things may also can be found in OBI are: Biologic Sample Preservation Procedure, and Health Care Organization (OMSE possible also?) Genetic Manipulation can be possibly found in OBI as well.

Please specify the meaning of "Use"..

Not sure about Fetus and Child. Fetus is exist in FMA, but maybe ask UBERON also?

I suggest to submit all the terms to OBI, and ask what them think. And I will do that for you.

[lizumberfield]

Thanks, Asiyah. I am going to delete "use" from the original post (just realized that Cooper added a 'data use' term for another effort recently, which will meet my need).

Thanks for pushing to OBI. I will also plan to discuss with @cstoeckert and the OBIB community during our next call on 10/15/2020.

[fjmanion]

Liz, I'm glad to see this work being done. We knew there were many terms missing from ICO, and this gap analysis is good to see. My recollection on the fetus/child terms is that we also looked at these during my work on the common rule ontology. We encountered conflicting definitions of them in OMRSE and other OBO aligned ontologies. I personally like the idea of looking to the NCIt for guidance because of (1) the importance and relative size of the cancer community in the clinical trials area, and (2) tremendous broad scale of community engagement across many disciplines that has gone into the construction of the NCIt text definitions. Consequently, I support your recommendation on the process.

…

-- Frank

On 10/2/20 11:14 AM, Asiyah Yu Lin wrote: Thank you Elizabeth! I think most of them will need to be submitted to other ontologies. At least I know that OBI is discussing the telemedicine term. I am interested in where the postmarketing surveilance, and safety monitoring will reside. - I know OBI is discussing a term about surveilance. However, the postmarketing surveilance sounds like a regulatory term, or OBI can take it since they took surveilance. Other things may also can be found in OBI are: Biologic Sample Preservation Procedure, and Health Care Organization (OMSE possible also?) Genetic Manipulation can be possibly found in OBI as well. Please specify the meaning of "Use".. Not sure about Fetus and Child. Fetus is exist in FMA, but maybe ask UBERON also? I suggest to submit all the terms to OBI, and ask what them think. And I will do that for you. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#25 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAI2EGRE5UD3VZP46J3MTVDSIXU4VANCNFSM4SBZHIGA>.

-- Frank J. Manion, Ph.D. Research Investigator University of Michigan School of Nursing Email: [email protected] Ph: (734) 276-0111

[linikujp]

Fantastic! I recently got re-connected with Melanie Courtot from DUO group, and offered to them that I will volunteer as an early developer of ICO. Liz, the child consent related representation was in my mind when I first worked on ICO. Glad that you take it to the next level! I will try to join OBI's call on Monday if there is no conflict. Please update the result from OBI's call here to us. Thanks, Asiyah On Fri, Oct 2, 2020 at 12:03 PM Frank Manion <[email protected]> wrote:

…

Liz, I'm glad to see this work being done. We knew there were many terms missing from ICO, and this gap analysis is good to see. My recollection on the fetus/child terms is that we also looked at these during my work on the common rule ontology. We encountered conflicting definitions of them in OMRSE and other OBO aligned ontologies. I personally like the idea of looking to the NCIt for guidance because of (1) the importance and relative size of the cancer community in the clinical trials area, and (2) tremendous broad scale of community engagement across many disciplines that has gone into the construction of the NCIt text definitions. Consequently, I support your recommendation on the process. -- Frank On 10/2/20 11:14 AM, Asiyah Yu Lin wrote: > > Thank you Elizabeth! I think most of them will need to be submitted to > other ontologies. > At least I know that OBI is discussing the telemedicine term. > I am interested in where the postmarketing surveilance, and safety > monitoring will reside. - I know OBI is discussing a term about > surveilance. However, the postmarketing surveilance sounds like a > regulatory term, or OBI can take it since they took surveilance. > Other things may also can be found in OBI are: Biologic Sample > Preservation Procedure, and Health Care Organization (OMSE possible > also?) Genetic Manipulation can be possibly found in OBI as well. > > Please specify the meaning of "Use".. > > Not sure about Fetus and Child. Fetus is exist in FMA, but maybe ask > UBERON also? > > I suggest to submit all the terms to OBI, and ask what them think. And > I will do that for you. > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#25 (comment)>, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AAI2EGRE5UD3VZP46J3MTVDSIXU4VANCNFSM4SBZHIGA >. > -- Frank J. Manion, Ph.D. Research Investigator University of Michigan School of Nursing Email: ***@***.*** Ph: (734) 276-0111 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#25 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACCPEPO2G3LUXITHFTJPZFDSIX2WNANCNFSM4SBZHIGA> .

[cstoeckert]

Discussed on OBIB call Oct. 29, 2020.
For fetus and child, the need is for consent on behalf of these or data sharing to the fetus or child in the future. Maybe start with consent roles for these.
Telemedicine: would be a type of health care encounter so belongs in OGMS
NCIT:C142640 | Postmarketing Surveillance: consider using OBI's 'surveillance process'
NCIT:C163409 | Safety Monitoring: can also use 'surveillance process' for safety monitoring.
NCIT:C43960 | Health Care Organization: there are different types of health organizations (hospital, home health care, dental health care) but not a general health care. Perhaps try OGMS? OMRSE?
NCIT:C54131 | Company: For-profit organization. Can use OBI's organization as a more general term.
NCIT:C64262 | Biologic Sample Preservation Procedure. Use OMIABIS 'fixation' in OBIB
XCO:0000527 | Genetic Manipulation: look at OBI's induced mutation or genetic transformation