O2 codes vs concept_ids

[MelaniePhilofsky]

The 'Suggested O2 SNOMED Mappings for N3C' table contains the suggested SNOMED codes we should/could use while mapping our oxygen data. Do you also have a spreadsheet with the concept_ids for these? Or do I need to look them up?

[stephanieshong]

O2 Device data element reference you can use:

[stephanieshong]

In you are in the N3C Enclave you can reference O2 device concept set.

[UzmaHasan]

Hi Stephanie.

Is there any data related to ventilator settings (such as SPO2, PaCO2, PaO2, FiO2, air pressure, etc.) in the O2 device concept set?

[MelaniePhilofsky]

@stephanieshong I only see SNOMED codes, not OHDSI concept_ids.

[stephanieshong]

OHDSI concept_ids are in the O2 device concept set in the Enclave. Hope this helps.

Concept Name	Concept Code	Concept Id	Domain Id	Vocabulary Id
Partial rebreather oxygen mask	425926003	4138748	Device	SNOMED
Oxygen mustache cannula	720744009	36715214	Device	SNOMED
Ambu bag	371785003	4160626	Device	SNOMED
Transtracheal oxygen catheter	426129001	4144319	Device	SNOMED
Blow by oxygen mask	425478008	4137849	Device	SNOMED
Oxyhood	427594004	4145529	Device	SNOMED
Oxygen mask	336602003	4222966	Device	SNOMED
Partial-rebreathing oxygen face mask	464233000	45759146	Device	SNOMED
N3C:Room air	ROOM_AIR	2004208005	Device	N3C
Tracheostomy mask, aerosol	465256000	45759811	Device	SNOMED
T piece without bag	415700003	4188570	Device	SNOMED
Continuous positive airway pressure/Bilevel positive airway pressure mask	706226000	45768222	Device	SNOMED
Aerosol tent, adult	468450007	45762031	Device	SNOMED
Continuing positive airway pressure unit	37874008	4243754	Device	SNOMED
Oxygen reservoir cannula	720742008	36715212	Device	SNOMED
Venturi oxygen face mask	465433006	45759930	Device	SNOMED
Tracheostomy mask, oxygen	465839001	45760219	Device	SNOMED
Oxygen ventilator	426160001	4138916	Device	SNOMED
Aerosol oxygen mask	426851007	4145694	Device	SNOMED
CPAP nasal oxygen cannula	467645007	45761494	Device	SNOMED
Nonrebreather oxygen mask	427591007	4145528	Device	SNOMED
Venturi mask	428285009	4322904	Device	SNOMED
Oxygen pendant cannula	720743003	36715213	Device	SNOMED
BiPAP oxygen nasal cannula	425826004	4138614	Device	SNOMED
High flow oxygen nasal cannula	426854004	4139525	Device	SNOMED
T piece with bag	415698007	4188569	Device	SNOMED
Face tent oxygen delivery device	426294006	4138487	Device	SNOMED
Basic nasal oxygen cannula	466713001	45760842	Device	SNOMED
Aerosol tent, pediatric	701256005	45764548	Device	SNOMED
Non-rebreathing oxygen face mask	463225005	45771595	Device	SNOMED
Ventilator	706172005	45768197	Device	SNOMED
N3C:Other oxygen device	OT_O2_DEVICE	2004208004	Device	N3C
Oxygen administration face tent	464578003	45759373	Device	SNOMED

[mgkahn]

Is there any compelling reason why the OMOP concept_ids are kept only in the Enclave and not included as one additional column in the much more assessable spreadsheet linked in the wiki?

[stephanieshong]

@mgkahn - With your request, we can certainly publish concept set of your interest. We just have not gone around to publishing all of the N3C recommended concept sets from the Enclave to the gitHub. It is my understanding that all of the N3C published papers also publish the concept sets used in the paper.

[stephanieshong]

@UzmaHasan - You may want to reference following concept set defined in the Enclave. [ICU/MODS]IMV, [ICU/MODS]fio2, [ICU/MODS]pao, ICU, Kostka-ECMO, and [DATOS] Vasopressors (v1). in order to find the ICU cohort. You can use these concept set to look for the concept id in the respective domain to find the cohort. You can also create your own concept set that is a super set of all of these concept set mentioned above.

[mgkahn]

@stephanieshong Thank you. I did not know if there were specific policy reasons for keeping the codes in the Enclave rather than on GitHub. There is a higher barrier to accessing the Enclave compared to making the codes available via a link here. I was wondering if N3C had the need for some additional controls, such as logging downloads or tracking provenance, that REQUIRED management within the Enclave. If there is not (as seems to be the case), I would like to propose all codes be moved out of the Enclave and made more accessible here for folks who have not done Enclave training/access. I know that would make life easier for my folks.

[stephanieshong]

@mgkahn - I am informed that currently, concept sets used in N3C publications are being published here: https://zenodo.org/communities/cd2h-covid/?page=1&size=20

In N3C, we have added extra metadata to go with every concept set we define. (i.e. version number, provenance, limitations and any update information that goes with the concept set versions. ) Currently we do not have a way to download /extract those metadata from the Enclave. I will bring up this issue to the N3C issues meeting.

[stephanieshong]

@mgkahn - N3C recommended concept sets are listed here:
https://github.com/National-COVID-Cohort-Collaborative/Data-Ingestion-and-Harmonization/tree/master/concept_sets/n3c-recommended-csets-json