The vocabularies for phenotypes should be listed

[chandryou]

The vocabularies for phenotypes should be listed in the wiki

[Alexdavv]

Hi @chandryou! Do you need any help with terminology here?

[cgreich]

Starting with that checklist. We need to create standard conventions for:

• Covid-19 testing
• Intubation
• Mechanical ventilation
• Extracorporeal membrane oxygenation (ECMA)
• Acute respiratory distress syndrome
• Presumptive case (diagnosis), confirmed case (diagnosis)
• Exposure to animal, acute respiratory distress patient, covid-19 patient, hospitalized covid-19 patient
• Travel to Wuhan, Hubei, China

Symptoms:

• Fever >38°C (100.4F)
• Subjective fever (felt feverish)
• Muscle aches (myalgia)
• Runny nose (rhinorrhea)
• Cough (new onset or worsening of chronic cough)
• Shortness of breath (dyspnea)
• Nauseaor vomiting
• Headache
• Abdominal pain
• Diarrhea (≥3 loose/looser than normal stools/24hr period)

Want to give it a shot, @Alexdavv?

[chandryou]

I'll try to reach Korean CDC and request the data of questionnaires from patients with the covid-19. We need convention how to convert these questionnaires into CDM.

[chandryou]

I added the @cgreich 's list to the wiki page

[Alexdavv]

Want to give it a shot, @Alexdavv?

I'd love to.

@chandryou @cgreich, How about adding/elaboration on:

• Other clinical forms (viral pneumonia without ARDS, only upper respiratory symptoms, asymptomatic, encephalitis?).
• COVID coinfections (seasonal influenza, pneumococcal pneumonia or other respiratory pathogens).
• Symptomatic treatment options (non-invasive oxygen support / invasive ventilation, corticosteroids, normal immunoglobulin, mycophenolate mofetil).
• Treatment/prevention of associated infections (influenza vaccination, neuraminidase inhibitors, Cap-dependent endonuclease inhibitors, antibacterial/antifungal therapy).
• Potential COVID specific therapy (interferon alfa/beta, ribavirin, lopinavir/ritonavir, remdesivir, ganciclovir?, stell cells?).
• COVID laboratory confirmation (RNA in respiratory samples / RNAaemia / serology testing when will be available).
• Comorbidities and risk factors (hypertension, chronic obstructive lung disease, smoking).
• Symptoms/criteria/complications (fatigue, throat pain, productive cough, haemoptysis, breath rate > 30/min, hypoxemia, CT/X-ray detected infiltration of lungs, lymphopenia, secondary nosocomial infection, acute cardiac injury).
• Outcome/prognosis (home/healthcare setting isolation, hospitalization, ICU admission, recovery, death).
• Belonging to the risk groups (healthcare workers, border guards, isolation in healthcare settings, etc.) - probably people will not identify themselves being exposed to the ill person due to individual protection measures, but they have a higher risk to be exposed.
• Exposure to seafood.
• Travel history to other regions (Korea, Iran, Italy, Diamond Princess/other cruise ships).

[cgreich]

Sure. Add them to Chan's list. We don't have to invent anything, just check out what we have, make a concept list, and let's make recommendations for de-novo data what concepts to use.

[chandryou]

@Alexdavv I've added you to the collaborator of this github. You can write and edit the wiki now :)

Thank you for your support!

[chandryou]

Should we develop the conventions for WHO's CRF?

[vojtechhuser]

I would like to help but I am not able to edit the wiki. e..g., https://github.com/OHDSI/Covid-19/wiki/Vocabulary-for-phenotypes

Is Mark Suchard the admin of this repo?

[chandryou]

@vojtechhuser I invited you to the collaborator if this github. Thank you for helping this!

[SSMK-wq]

Hi,

Is this open for everyone to participate? Meaning for guys who write SQL, Python as well? May I know what is the intent of this group? Is it to identify the concept ids to be used for each of the conditions listed in github?

[chandryou]

I've uploaded sql queries to identify standard vocabulary for co-morbid diseases based on previous study

[chandryou]

@SSMK-wq Yes, this is open to anyone who can participate :) You call pull request.

[chandryou]

I've updated Korean source code to define intensive cares (oxygen therapy /ICU care/ intubation /ventilator care / ECMO/ hemo) in the wiki

[Alexdavv]

Hi @chandryou and @vojtechhuser,

The vocabulary team has started working on it. At the first step, we are reviewing both the CRFs to identify existing concepts as well as remaining gaps. We will contribute to the existing wiki entry for phenotypes and help completing it. For missing concepts, we are looking into updating of existing vocabularies or providing new extension concepts. We welcome any input on the progress and on priority for extensions for certain phenotypes.

As we can see, EDI is one of the vocabularies that are not currently mapped. So we need to add the mappings for the concepts of interest. What are the other non-mapped vocabularies are expected to represent the COVID-related data?

In the sql queries you've mentioned you are focusing on ICD9CM codes and related Standard equivalents. What we are planning to do is: (a) identify the Standard parent concepts for the concept-sets of required phenotypes; (b) review the mappings between these Standard concepts (including their descendants) and source vocabularies; (c) search among the source vocabularies to confirm that all the related concepts are covered by the list b.

Could you please invite @TinyRickC137 as a collaborator to be able to edit the wiki?

[chandryou]

Thank you @Alexdavv I invited @TinyRickC137 to this repo.

I'll post each of job you mentioned in separate issue. And I'll make a mapping between EDI code and standard concept, today.

[Alexdavv]

@chandryou, We've updated the wiki page.

Please review the format in the first 2 examples, including the following sections:

• phenotype name with a link to code;
• a table with the parent Standard concepts for concept set;
• a collapsible list with mappings of source codes to the parent Standard concepts and their descendants (grouped by source_vocabulary_id). Not all the descendants are specified - just those that have a mapping from the source_codes.

Please let me know if any adjustments are needed.

[Alexdavv]

Hi @chandryou,

On Monday we're planning to start working on COVID-related mapping gaps between Source vocabularies and Standard terms. If something is already done for EDI, can you please share so that we can ingest it and focus on the rest.

Are there coding guidelines in Korea that define the rules for dual coding to reflect the form of the COVID-19? Something like the CDC has issued, e.g.:

For a pneumonia case confirmed as due to the 2019 novel coronavirus (COVID-19), assign codes J12.89, Other viral pneumonia, and B97.29, Other coronavirus as the cause of diseases classified elsewhere.

We're planning to create the pre-coordinated concepts and publish the mapping guidelines for ETLers.

[Alexdavv]

@chandryou Please add @Tsemharb as a collaborator.

[chandryou]

I added @Tsemharb

[shyamvis]

In the Accrual of patients to Clinical Trials (ACT) network, we are starting to collect new and old codes for Covid-19 to build an ontology. See https://github.com/shyamvis/covid-phenotyping and https://github.com/shyamvis/covid-phenotyping/blob/master/codes.md

[Alexdavv]

In the Accrual of patients to Clinical Trials (ACT) network, we are starting to collect new and old codes for Covid-19 to build an ontology. See https://github.com/shyamvis/covid-phenotyping and https://github.com/shyamvis/covid-phenotyping/blob/master/codes.md

@shyamvis Great job! If you’d like to take a look at the work the OHDSI vocab team is doing please ping me by email.

[chandryou]

@Alexdavv Please review my mapping for EDI (https://github.com/OHDSI/Covid-19/blob/master/Vocabulary/covid_kor_source_to_concept_map.csv)