Re: Working on CORD-19 semantic annotations?

This is very interesting-i do wish we could have a global standard for exchanging case information; we have been doing so with GA4GH Phenopackets<https://phenopackets-schema.readthedocs.io/en/latest/>, a demonstration is in covidaware.me<https://covidaware.me/>, but Phenopackets does not have all of the related metadata (but might enable more open sharing of a subset of phenotypic information).

In the US there are multiple initiatives to create standardized RedCap CRFs. Here is a nice one from UPenn: https://redcap.med.upenn.edu/surveys/?s=CE83CNHFRT

(Marylyn is copied).

Cheers,
Melissa



On Apr 7, 2020, at 8:36 AM, João Moreira (UTwente) <j.luizrebelomoreira@utwente.nl<mailto:j.luizrebelomoreira@utwente.nl>> wrote:

Hi David,

Here in the University of Twente we're participating in the Virus Outbreak Data Network (VODAN) of GO-FAIR:
https://www.go-fair.org/implementation-networks/overview/vodan/


The first project within this network aims at supporting clinical/screening data collection based on WHO case record form (CRF) for Corona ("rapid" version):
https://www.who.int/docs/default-source/coronaviruse/who-ncov-crf.pdf


A semantic data model representing this CRF was just launched in:
https://github.com/FAIRDataTeam/WHO-COVID-CRF

URI: http://purl.org/vodan/whocovid19crfsemdatamodel


This will be used by Electronic Data Capture (EDC) web-apps, such as Castor, to allow healthcare institutes to register patient data in a standardized way. There are some eCRF initiatives using the WHO CRF willing to annotate their data with this model.

It would be interesting to come with some alignments between FHIR RDF (predicates used in CORD-19-on-FHIR) and this CRF semantic model.

Kind regards,

João Luiz Rebelo Moreira, PhD
Assistant Professor
Services and Cyber-Security (SCS)
Electrical Engineering, Mathematics and Computer Science
University of Twente, PO Box 217
7500AE Enschede, The Netherlands
Office: Zilverling 2009
E: j<mailto:l.o.bonino@utwente.nl>.luizrebelomoreira@utwente.nl<mailto:luizrebelomoreira@utwente.nl>


On Mon, 6 Apr 2020 at 18:48, David Booth <david@dbooth.org<mailto:david@dbooth.org>> wrote:
This call will be tomorrow (Tuesday) 11am Boston time.  If you are doing
semantic annotation of CORD-19 and did not already respond, please so do
now so that I can send you call details.

Thanks,
David Booth

On 4/2/20 10:29 PM, David Booth wrote:
> The CORD-19 dataset is a dataset of 44k journal articles on COVID-19 and
> related topics.  We previously announced our CORD19-on-FHIR release,
> which adds semantic annotations to the CORD-19 dataset, using FHIR RDF:
> https://github.com/fhircat/CORD-19-on-FHIR

>
> Since other efforts using CORD-19 have also started elsewhere, to
> coordinate efforts, we would like to have a web teleconference with
> anyone else who is working on semantic annotation of the CORD-19 dataset.
>
> If you are working on semantic annotation of CORD-19, please: (a) let me
> know; and (b) answer the following doodle poll, for scheduling:
> https://doodle.com/poll/kpfpcix6gvbtkk8y

>
> Thanks,
> David Booth <david@dbooth.org<mailto:david@dbooth.org>>, Yosemite Project
> Harold Solbrig, Johns-Hopkins University
> Guoqian Jiang, Mayo Clinic
>


Melissa Haendel, PhD
Director of Translational Data Science, Oregon State University
Director of the Center for Data to Health, Oregon Health & Science University

melissa@tislab.org<mailto:melissa@tislab.org>
503-407-5970
www.monarchinitiative.org

Appointments:
Brandon White
admin@tislab.org

Received on Tuesday, 7 April 2020 15:50:52 UTC