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Re: Working on CORD-19 semantic annotations?

From: UTwente <j.luizrebelomoreira@utwente.nl>
Date: Tue, 14 Apr 2020 14:54:24 +0200
Message-ID: <CAMmh81D2ufxw9ayMNy6=nrx3MpK+M00dNcaZ6d+Zq7mBMUXVwA@mail.gmail.com>
To: Melissa Haendel <haendel@ohsu.edu>
Cc: David Booth <david@dbooth.org>, w3c semweb HCLS <public-semweb-lifesci@w3.org>, "Ritchie, Marylyn" <marylyn@pennmedicine.upenn.edu>, "Xirasagar, Sandhya (NIH/NIAID) [E]" <xirasasa@mail.nih.gov>, Christopher Chute <chute@jhu.edu>, Tudor Groza <tudor.groza@pryzm.health>, "craig.mcnamara@pryzm.health" <craig.mcnamara@pryzm.health>, Kenneth Gersing <Kenneth.gersing@nih.gov>, monarch-leadership <monarch-leadership@googlegroups.com>
Hi all,

Please consider participating on this tomorrow:

*Enabling the Collection and Exploration of COVID-19 Data via FAIR
Principles *- 2-part session scheduled *April 15th, 2020 from 9:00 - 10:00
AM (PDT). *Register here <https://tinyurl.com/sqsa7l6> to join this webinar

   1. *VODAN: FAIR Data Work in Action *presented by *Albert Mons (Phortos
   Consultants) and Luiz Bonino (GO FAIR)*
      - One of the projects under the VODAN Implementation Network is
      developing a FAIR Data Point (FDP) with semantics based upon the World
      Health Organization eCRF forms
      Up to six countries will deploy a Proof of Concept securing and keeping
      sensitive data at the data source yet remaining available for distributed
      learning. Learn about the semantic model, the ontologies used and the
      deployment of an FDP for COVID-19 data and how this may be relevant for
      your organization.
   2. *The SARS-Cov-2-SPOKE Molecular Explorer: A Public Knowledge Graph
   Visualization Tool *presented by *Sergio Baranzini and Sharat Israni
   (University of California, San Francisco)*
   - SPOKE is a knowledge graph containing more than 25 widely used
      databases in the biomedical domain. In this webinar, we will present the
      basic features of the neighborhood explorer with a particular emphasis on
      COVID-19 molecular pathways and potential drugs that could
target the virus


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 <l.o.bonino@utwente.nl>.luizrebelomoreira@utwente.nl

On Tue, 7 Apr 2020 at 17:50, Melissa Haendel <haendel@ohsu.edu> wrote:

> 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, 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> 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 <l.o.bonino@utwente.nl>.luizrebelomoreira@utwente.nl
> On Mon, 6 Apr 2020 at 18:48, David Booth <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>, 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
> 503-407-5970
> www.monarchinitiative.org
> Appointments:
> Brandon White
> admin@tislab.org
Received on Tuesday, 14 April 2020 12:54:34 UTC

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