Redo: [EXTERNAL] Re: Announcing CORD-19-on-FHIR: A FHIR RDF dataset for COVID-19 research

On 3/30/20 12:03 PM, Kingsley Idehen wrote:
> On 3/29/20 5:36 PM, Jiang, Guoqian, M.D., Ph.D. wrote:
>> 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
>
>
> Hi Guoqian,
>
> We've loaded the COVID-19 research dataset into our LOD Cloud cache.
>
> Here are some query examples, based on tweaks of your sample queries [1]:
>
> [1]Diseases and MESH Cross References
> <http://lod.openlinksw.com/sparql?default-graph-uri=&query=PREFIX+rdf%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%0D%0APREFIX+fhir%3A+%3Chttp%3A%2F%2Fhl7.org%2Ffhir%2F%3E%0D%0APREFIX+pmc%3A+%3Chttps%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%23%3E%0D%0A%0D%0Aselect+distinct+iri%28concat%28%27https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fmesh%2F%27%2Creplace%28%3Fpmc_identifier%2C%27MESH%3A%27%2C%27%27%29%2C%27%23%27%29%29+as+%3Fmesh_id+%0D%0A++++++++++++++++%3Fpmc_type+%3Fpmc_identifier+%3Ftext+%28count%28%3Ftext%29+as+%3Fcount%29+%3Fg%0D%0Awhere+%7B+%0D%0A++++graph+%3Fg+%7B%3Fpmc+pmc%3Aannotations+%3Fannotations+.%0D%0A++++%3Fannotations+pmc%3Ainfons+%3Fpmc_infons+.%0D%0A++++%3Fpmc_infons+pmc%3Aidentifier+%3Fpmc_identifier+.%0D%0A++++%3Fpmc_infons+pmc%3Atype+%3Fpmc_type+.%0D%0A++++%3Fannotations+pmc%3Atext+%3Ftext+.%0D%0A++++FILTER+%28%3Fpmc_type%3D%27Disease%27%29.+%7D%0D%0A++++%0D%0A++++%0D%0A%7D+%0D%0Agroup+by+%3Fg+%3Fpmc_type+%3Fpmc_identifier+%3Ftext+%0D%0Aorder+by+DESC%28%3Fcount%29%0D%0Alimit+100&format=text%2Fhtml&timeout=30000&debug=on&run=+Run+Query+>
> -- note that I had to mint a Linked Data URI for live MESH cross
> references
>
> [2] Source Query Text for the above
> <http://lod.openlinksw.com/sparql?default-graph-uri=&qtxt=PREFIX+rdf%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%0D%0APREFIX+fhir%3A+%3Chttp%3A%2F%2Fhl7.org%2Ffhir%2F%3E%0D%0APREFIX+pmc%3A+%3Chttps%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%23%3E%0D%0A%0D%0Aselect+distinct+iri%28concat%28%27https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fmesh%2F%27%2Creplace%28%3Fpmc_identifier%2C%27MESH%3A%27%2C%27%27%29%2C%27%23%27%29%29+as+%3Fmesh_id+%0D%0A++++++++++++++++%3Fpmc_type+%3Fpmc_identifier+%3Ftext+%28count%28%3Ftext%29+as+%3Fcount%29+%3Fg%0D%0Awhere+%7B+%0D%0A++++graph+%3Fg+%7B%3Fpmc+pmc%3Aannotations+%3Fannotations+.%0D%0A++++%3Fannotations+pmc%3Ainfons+%3Fpmc_infons+.%0D%0A++++%3Fpmc_infons+pmc%3Aidentifier+%3Fpmc_identifier+.%0D%0A++++%3Fpmc_infons+pmc%3Atype+%3Fpmc_type+.%0D%0A++++%3Fannotations+pmc%3Atext+%3Ftext+.%0D%0A++++FILTER+%28%3Fpmc_type%3D%27Disease%27%29.+%7D%0D%0A++++%0D%0A++++%0D%0A%7D+%0D%0Agroup+by+%3Fg+%3Fpmc_type+%3Fpmc_identifier+%3Ftext+%0D%0Aorder+by+DESC%28%3Fcount%29%0D%0Alimit+100&format=text%2Fhtml&timeout=30000&debug=on&run=+Run+Query+>
>
>
> [3] Top Gene Instances and NCBI Cross References
> <http://lod.openlinksw.com/sparql?default-graph-uri=&query=%0D%0A%0D%0APREFIX+rdf%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%0D%0APREFIX+fhir%3A+%3Chttp%3A%2F%2Fhl7.org%2Ffhir%2F%3E%0D%0APREFIX+pmc%3A+%3Chttps%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%23%3E%0D%0Aselect+distinct+iri%28concat%28%27https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fgene%2F%27%2Creplace%28%3Fpmc_identifier%2C%27MESH%3A%27%2C%27%27%29%2C%27%23%27%29%29+as+%3Fncbi_id%0D%0A++++++++++++++++%3Fpmc_type+%3Fpmc_identifier+%3Ftext+%28count%28%3Ftext%29+as+%3Fcount%29+%0D%0Awhere+%7B+%0D%0A++++%3Fpmc+pmc%3Aannotations+%3Fannotations+.%0D%0A++++%3Fannotations+pmc%3Ainfons+%3Fpmc_infons+.%0D%0A++++%3Fpmc_infons+pmc%3Aidentifier+%3Fpmc_identifier+.%0D%0A++++%3Fpmc_infons+pmc%3Atype+%3Fpmc_type+.%0D%0A++++%3Fannotations+pmc%3Atext+%3Ftext+.%0D%0A++++FILTER+%28%3Fpmc_type%3D%27Gene%27%29.%0D%0A++++%0D%0A++++%0D%0A%7D+%0D%0Agroup+by+%3Fpmc_type+%3Fpmc_identifier+%3Ftext+%0D%0Aorder+by+DESC%28%3Fcount%29%0D%0Alimit+100&format=text%2Fhtml&timeout=30000&debug=on&run=+Run+Query+>
> -- I had to mint a Linked Data URI for live NCBI cross references
>
> [4] Source Query Text for the above
> <http://lod.openlinksw.com/sparql?default-graph-uri=&qtxt=%0D%0A%0D%0APREFIX+rdf%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%0D%0APREFIX+fhir%3A+%3Chttp%3A%2F%2Fhl7.org%2Ffhir%2F%3E%0D%0APREFIX+pmc%3A+%3Chttps%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%23%3E%0D%0Aselect+distinct+iri%28concat%28%27https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fgene%2F%27%2Creplace%28%3Fpmc_identifier%2C%27MESH%3A%27%2C%27%27%29%2C%27%23%27%29%29+as+%3Fncbi_id%0D%0A++++++++++++++++%3Fpmc_type+%3Fpmc_identifier+%3Ftext+%28count%28%3Ftext%29+as+%3Fcount%29+%0D%0Awhere+%7B+%0D%0A++++%3Fpmc+pmc%3Aannotations+%3Fannotations+.%0D%0A++++%3Fannotations+pmc%3Ainfons+%3Fpmc_infons+.%0D%0A++++%3Fpmc_infons+pmc%3Aidentifier+%3Fpmc_identifier+.%0D%0A++++%3Fpmc_infons+pmc%3Atype+%3Fpmc_type+.%0D%0A++++%3Fannotations+pmc%3Atext+%3Ftext+.%0D%0A++++FILTER+%28%3Fpmc_type%3D%27Gene%27%29.%0D%0A++++%0D%0A++++%0D%0A%7D+%0D%0Agroup+by+%3Fpmc_type+%3Fpmc_identifier+%3Ftext+%0D%0Aorder+by+DESC%28%3Fcount%29%0D%0Alimit+100&format=text%2Fhtml&timeout=30000&debug=on&run=+Run+Query+>
>
> [5] Top Mutation Instances and Gene Card References
> <http://lod.openlinksw.com/sparql?default-graph-uri=&query=%0D%0A%0D%0APREFIX+rdf%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%0D%0APREFIX+fhir%3A+%3Chttp%3A%2F%2Fhl7.org%2Ffhir%2F%3E%0D%0APREFIX+pmc%3A+%3Chttps%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%23%3E%0D%0Aselect+distinct+iri%28concat%28%27https%3A%2F%2Fwww.genecards.org%2FSearch%2FKeyword%3FqueryString%3D%27%2Creplace%28%3Fpmc_identifier%2C%27MESH%3A%27%2C%27%27%29%2C%27%23%27%29%29+as+%3Fgene_card_id+%3Fpmc_type+%3Fpmc_identifier+%3Ftext+%28count%28%3Ftext%29+as+%3Fcount%29+where+%7B+%0D%0A++++%3Fpmc+pmc%3Aannotations+%3Fannotations+.%0D%0A++++%3Fannotations+pmc%3Ainfons+%3Fpmc_infons+.%0D%0A++++%3Fpmc_infons+pmc%3Aidentifier+%3Fpmc_identifier+.%0D%0A++++%3Fpmc_infons+pmc%3Atype+%3Fpmc_type+.%0D%0A++++%3Fannotations+pmc%3Atext+%3Ftext+.%0D%0A++++FILTER+%28%3Fpmc_type%3D%27Mutation%27%29.%0D%0A++++%0D%0A++++%0D%0A%7D+%0D%0Agroup+by+%3Fpmc_type+%3Fpmc_identifier+%3Ftext+%0D%0Aorder+by+DESC%28%3Fcount%29%0D%0Alimit+100&format=text%2Fhtml&timeout=30000&debug=on&run=+Run+Query+>
> -- I had to mint a Linked Data URI for live Gene Card cross references
>
> [6] Source Query Text for the above
> <http://lod.openlinksw.com/sparql?default-graph-uri=&qtxt=%0D%0A%0D%0APREFIX+rdf%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%0D%0APREFIX+fhir%3A+%3Chttp%3A%2F%2Fhl7.org%2Ffhir%2F%3E%0D%0APREFIX+pmc%3A+%3Chttps%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%23%3E%0D%0Aselect+distinct+iri%28concat%28%27https%3A%2F%2Fwww.genecards.org%2FSearch%2FKeyword%3FqueryString%3D%27%2Creplace%28%3Fpmc_identifier%2C%27MESH%3A%27%2C%27%27%29%2C%27%23%27%29%29+as+%3Fgene_card_id+%3Fpmc_type+%3Fpmc_identifier+%3Ftext+%28count%28%3Ftext%29+as+%3Fcount%29+where+%7B+%0D%0A++++%3Fpmc+pmc%3Aannotations+%3Fannotations+.%0D%0A++++%3Fannotations+pmc%3Ainfons+%3Fpmc_infons+.%0D%0A++++%3Fpmc_infons+pmc%3Aidentifier+%3Fpmc_identifier+.%0D%0A++++%3Fpmc_infons+pmc%3Atype+%3Fpmc_type+.%0D%0A++++%3Fannotations+pmc%3Atext+%3Ftext+.%0D%0A++++FILTER+%28%3Fpmc_type%3D%27Mutation%27%29.%0D%0A++++%0D%0A++++%0D%0A%7D+%0D%0Agroup+by+%3Fpmc_type+%3Fpmc_identifier+%3Ftext+%0D%0Aorder+by+DESC%28%3Fcount%29%0D%0Alimit+100&format=text%2Fhtml&timeout=30000&debug=on&run=+Run+Query+>
>
>
> Links:
>
> [1] https://github.com/fhircat/CORD-19-on-FHIR/wiki/PubTator-Dataset
> -- Your Query Examples Page.
>
>
> Kingsley
>

All,

I am re-sharing the links above, as they haven't actually come through
in generally usable form when viewed online (for instance).

[1] https://tinyurl.com/sdcl3e3 --  Diseases and MESH Cross References

[2] https://tinyurl.com/udnghrx -- Source Query Text for the above

[3] https://tinyurl.com/s95wjs5 -- Top Gene Instances and NCBI Cross
References

[4] https://tinyurl.com/wychdsn -- Source Query Text for the above

[5] https://tinyurl.com/truzv9e --  Top Mutation Instances and Gene Card
References

[6] https://tinyurl.com/vdregdc -- Source Query Text for the above

-- 
Regards,

Kingsley Idehen       
Founder & CEO 
OpenLink Software   
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