Open MelaniePhilofsky opened 1 year ago
In you are in the N3C Enclave you can reference O2 device concept set.
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?
@stephanieshong I only see SNOMED codes, not OHDSI concept_ids.
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 |
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?
@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.
@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.
@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.
@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.
@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
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?