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[OHDSI Covid19] Literature review on phenotype definitions and evaluations

(Patrick Ryan) #1

I’m opening up this thread to be a place for the ‘lit review on phenotype definition’ sub-team, led by @mattspotnitz, @rchen and @Gowtham_Rao, can have team discussions and share progress. Thanks for all your efforts!

[OHDSI COVID-19 response] Community Update 20 March 2020
[OHDSI COVID-19 response] Community Update 20 March 2020
(Matt Spotnitz) #2

Hi Everyone,

Thank you all for volunteering to help with the research effort about phenotyping conditions, symptoms, lab tests, and procedures that are relevant to the management of COVID-19. It is a privilege to help lead this group with expertise in data science, public health, and clinical medicine. The purpose of this forum is to exchange ideas across the group. Also, please feel free to contact myself, Ray (@rchen), or Gowtham (@Gowtham_Rao) anytime.

We have received a list of phenotypes that are of interest to the community, a data abstraction sheet, and a recommended MESH search algorithm, which I will distribute via e-mail.

We are open to suggestions about how to coordinate the phenotyping review. Here is what has been proposed:

The group of volunteers that has been assigned to a particular phenotype will do a MESH search, perhaps supplemented by an intuitive PubMed search. One of the co-leaders will triage the results. The group will then fill out the data abstraction sheet for that topic and send it to the co-leaders, who will also be available to help as needed.

Please let us know if you would like to have meeting to discuss the start of this research effort. I look forward to working with all of you. I am optimistic that we can make meaningful contributions to COVID-19 research in a short period of time!


(David Vizcaya) #3

Hi @mattspotnitz! thanks for the coordination efforts to you and the other co-leads @rchen and @Gowtham_Rao!
I would appreciate a TC to get guidance on specific tasks around this big topic.

(Ray Chen) #4

Thanks @david_vizcaya! I went ahead and created a when2meet to try to figure out the best time for the call: https://www.when2meet.com/?8901728-HZbIE
I’m not sure where everyone is based around the world, but please be sure to specify the correct time zone on the top left of your screen when filling this out. I also included the weekend in case we really want to move quickly

(David Dorr) #5

I’d like to participate as well - please include me in the emails.

(Matt Spotnitz) #6

That sounds great, @David_Dorr! Welcome!

(Matt Spotnitz) #7

Welcome to the team @david_vizcaya!

(Julianna Kohler) #8

I’m not sure where this goes, so I’m going to post it in a couple of different fora:

From the Global Digital Health Forum (this wasn’t written by me):
I was on the AeHIN COIL webinar today and the presenter mentioned that OpenEHR has a COVID-19 project that has archetypes and templates for COVID19 data in clinical settings. Here is the link: https://www.openehr.org/ckm/projects/1013.30.81

(David Vizcaya) #9

Thanks @rchen Great! If no consensus I can adapt to have a call during weekend

(Miguel A. Mayer) #10

Hi everyone,
Thank you very much for this initiative and efforts. I am interested in participating in this lit thread. Please include me in the emails as well.

(Matt Spotnitz) #11

Welcome Miguel!

(Matt Spotnitz) #12

Are there any members of this group with a particular interest in phenotyping gastrointestinal symptoms?


Thanks @rchen, I’ve filled in my availability

(Asieh Golozar) #14

Hi Matt,

I would like to participate in this as well. Can you please add me to the email list?

(Matt Spotnitz) #15

Absolutely @agolozar! Please send me a message with your e-mail and we will discuss how to get you involved.

(Selva) #16

Hi @mattspotnitz,

I am interested to participate as well. But I am not from clinical background. However I do data analysis using SQL, Python etc. Of course, I can help with Lit review by reading and summarizing the article. Will my participation be of any use to the team?

Please add me to the mailing list as well

(Ray Chen) #17

Hi @SELVA_MUTHU_KUMARAN, all are welcome! The more the merrier, and the better we can dive through literature.

Also, @all, based on the when2meet, seems like the most number of people can meet in 11hours. At 1PM Eastern Time (5PM GMT). Please stay tuned for the virtual meeting link. Look forward to chatting with you all soon!

(Ray Chen) #18

Here is the link for our Zoom meeting at 1PM Eastern Time (5PM GMT)! https://zoom.us/j/542131812

(Matt Spotnitz) #19

This reference has a very thorough list of ICD-09 and ICD-10 codes for conditions associated with hospitalization for influenza. The list is in the supplementary information.

(Matt Spotnitz) #20

I’d like to congratulate the group on finishing the literature review of phenotypes. The data abstraction sheets have been submitted to the OHDSI leadership. With the help of this extraordinary group, we have made a significant contribution to COVID response research in a short period of time. It was an honor and privilege to co-lead this team with @Gowtham_Rao and @rchen!