iv_an_ru (iv_an_ru) wrote,

COVID-19 datasets

Better late than never --- people are preparing datasets about "corona".

Call to Action to the Tech Community on New Machine Readable COVID-19 Dataset
announces "the COVID-19 Open Research Dataset (CORD-19) of scholarly literature about COVID-19, SARS-CoV-2, and the Coronavirus group" at https://pages.semanticscholar.org/coronavirus-research and https://www.kaggle.com/allen-institute-for-ai/CORD-19-research-challenge
There's a derivative, CORD-19-on-FHIR, annouced by Guoqian Jiang (Mayo Clinic), Harold Solbrig (Johns Hopkins University),
and FHIRCat team. The data are represented in FHIR RDF to facilitate semantic linkage with other biomedical datasets.

>- 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

Data Wrangling and Progressive LOD Cloud Knowledge Graph Enhancement
lists some open data publishers related to the genomic epidemiology, testing coverage by country etc., and examples of their use via SPARQL, Google Docs etc.

lod.openlinksw.com/fct and lod.openlinksw.com/sparql , uriburner.com , dbpedia.org/sparql , bio2rdf.org/sparql are all under unusually high load. If something is jammed or in brownout we'll try to recover soon, bu we can't promise 100% uptime. If you need them for works other than healthcare-related and you emit complicated queries or just lot of queries, please consider using your own Virtuoso instance. If you are learning SPARQL, please don't use these services as sandboxes these weeks, Virtuoso Open Source can be installed locally in few minutes and let you use your own data sets in many ways other than just SPARQL.

For complicated debugging cases, I have some spare double- and quad-Xeons, some of them right at home. So if you report your case to tech. support and indicate there that it is about HCLS and ping me directly via skype iv_an_ru I can make a user account for you at my own boxes to debug your case in four hands.

P.S. Despite all "public" activities like LOD and Bio2RDF, OpenLink Software is a business, not a charity. If you want to donate then please donate to the right HCLS people, not to us. If you want to support us, just visit https://www.openlinksw.com/ and buy a good product for a good price.
Tags: rdbms

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