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Re: [EXTERNAL] 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: Sun, 29 Mar 2020 21:36:20 +0000
Message-Id: <28fddd$dh0fng@ironport10.mayo.edu>
To: Kingsley Idehen <kidehen@openlinksw.com>, "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>, "public-lod@w3.org" <public-lod@w3.org>
Cc: "Stone, Daniel J." <Stone.Daniel@mayo.edu>, Harold Solbrig <solbrig@jhu.edu>, David Booth <david@dbooth.org>, Eric Prud'hommeaux <eric@w3.org>
Hi, Kingsley,

Thanks much for your notes.

We have updated the README.md file, adding links to the turtle file
examples and SPARQL query examples. Hope this would be helpful for
identifying URLs for the datasets. Feel free to let us know if you need
any specific information about the datasets.

Thanks,

-Guoqian






On 3/28/20, 5:40 PM, "Kingsley Idehen" <kidehen@openlinksw.com> wrote:

>On 3/26/20 6:40 PM, Jiang, Guoqian, M.D., Ph.D. wrote:
>> 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
>
>
>Hi Guoqian,
>
>This is a great contribution!
>
>BTW -- would you be able to add a little clarity to the URLs that
>identify RDF documents so that we can quickly load into various LOD
>Cloud instances? 
>
>For example identify the RDF docs (or their zip archive) URLs associated
>with:
>
>- Species       2030458 instances
>- Gene          1235829 instances
>- Disease       1036954 instances
>- Chemical      778872 instances
>- CellLine      76816 instances
>- Mutation      33413 instances
>- Strain        26573 instances
>
>
>Kingsley
>
>
>>
>>
>> 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
>>
>
>-- 
>Regards,
>
>Kingsley Idehen	  
>Founder & CEO 
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Received on Sunday, 29 March 2020 21:38:21 UTC

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