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Re: Announcing CORD-19-on-FHIR: A FHIR RDF dataset for COVID-19 research

From: Jiang, Guoqian, M.D., Ph.D. <Jiang.Guoqian@mayo.edu>
Date: Thu, 26 Mar 2020 22:40:57 +0000
Message-Id: <28fddd$dgld4g@ironport10.mayo.edu>
To: W3c Semweb HCLS <public-semweb-lifesci@w3.org>
Cc: Harold Solbrig <solbrig@jhu.edu>, David Booth <david@dbooth.org>, Eric Prud'hommeaux <eric@w3.org>, "Stone, Daniel J." <Stone.Daniel@mayo.edu>

We have updated the release of CORD-19-on-FHIR in accordance with the
latest CORD-19 dataset, and we have expanded the set of semantic
annotations.

The latest CORD-19 dataset contains metadata on 44,000
coronavirus-related research articles through 2020-03-20.  Of these,
29,000 are full text.  The latest CORD-19-on-FHIR release now has
semantic annotations for:

- Condition: 182231 instances
- Medication: 32069 instances
- Procedure: 100260 instances

This release also adds semantic annotations produced by Pubtator:

- Species       2030458 instances
- Gene          1235829 instances
- Disease       1036954 instances
- Chemical      778872 instances
- CellLine      76816 instances
- Mutation      33413 instances
- Strain        26573 instances

More details and download URL are in the original announcement below.

Sincerely,

Guoqian Jiang (Mayo Clinic), Harold Solbrig (Johns Hopkins University),
and FHIRCat team


On 3/19/20, 10:42 PM, "Jiang, Guoqian, M.D., Ph.D."
<Jiang.Guoqian@mayo.edu> wrote:

>
>  We are pleased to announce an initial version of the CORD-19-on-FHIR
>>dataset for COVID-19 research, a dataset of 13202 journal articles
>>relevant to novel coronavirus research.  This dataset extends the
>>CORD-19 dataset (on which it is based) by adding several semantic
>>annotations.  It is represented in FHIR RDF to facilitate semantic
>>linkage with other biomedical datasets.
>>
>>CORD-19-on-FHIR dataset currently adds the following semantic
>>annotations:
>>
>>- Conditions: 103,968 instances
>>- Medications: 16,406 instances
>>- Procedures:  54,720 instances
>>
>>CORD-19-on-FHIR is available on github, and collaboration is invited:
>>https://github.com/fhircat/CORD-19-on-FHIR
>>
>>It is licensed to encourage open COVID-19 research.  See specific terms:
>>https://github.com/fhircat/CORD-19-on-FHIR/blob/master/LICENSE
>>
>>CORD-19-on-FHIR was funded by the FHIRCat research grant, which seeks to
>>enable the semantics of FHIR and terminologies for clinical and
>>translational research:
>>https://github.com/fhircat/FHIRCat
>>
>>Sincerely,
>
>>Guoqian Jiang (Mayo Clinic), Harold Solbrig (Johns Hopkins University),
>>and FHIRCat team
>
Received on Thursday, 26 March 2020 22:41:14 UTC

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