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

Excellent! This looks really useful, and it looks really straightforward to
upload annotations, hopefully we will see lots soon!

On Fri, Mar 20, 2020 at 10:21 AM Hunter, Larry <LARRY.HUNTER@cuanschutz.edu>
wrote:

> Yes, Jin-Dong Kim is organizing just this with PubAnnotation, see
> http://pubannotation.org/collections/LitCovid  There’s also a planned
> hackathon in early April
> https://github.com/virtual-biohackathons/covid-19-bh20/wiki
>
> Larry
>
> On Mar 20, 2020, at 11:17 AM, Chris Mungall <cjmungall@lbl.gov> wrote:
>
> More generally: I'm becoming aware of other efforts to annotate relevant
> texts, either the CORD-19 corpus, or supersets (e.g general coronavirus
> literature). Is anyone aware of any attempts to loosely coordinate these
> efforts? It would be great to have a resource for people to download all
> text annotations in a single format combining annotations from groups
> specializing in NER vs relation extraction, clinical markup vs omics
> markup, ...
>
> On Fri, Mar 20, 2020 at 10:11 AM Chris Mungall <cjmungall@lbl.gov> wrote:
>
>> This looks great!
>>
>> Is there a dummies guide on how to use this?
>>
>> It looks like there is a FHIR datamodel for modeling textual spans and
>> you are using this to represent the results of NER. What NER tool was used?
>>
>> It looks like snomed was the main vocabulary used - this makes sense for
>> marking up conditions, medications, and procedures. But what about genes
>> (human and viral), mechanisms (e.g. viral gene function) - do you plan to
>> run this with any OBO ontologies?
>>
>> On Thu, Mar 19, 2020 at 8:44 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
>>>
>>>
>>>
>