CORD-19-on-FHIR is a Linked Data version of the COVID-19 Open Research Dataset (CORD-19) data, provided by the Allen Institute to support research on COVID-19 / SARS-CoV-2 / Novel Coronavirus. It is represented in FHIR RDF and was produced by data mining the CORD-19 dataset and adding semantic annotations. The purpose is to facilitate linkage with other biomedical datasets and enable answering research questions.

See also: list of other CORD-19 semantic annotation projects

https://github.com/fhircat/CORD-19-on-FHIR/wiki

So far, CORD-19-on-FHIR adds the following semantic annotations to the CORD-19 dataset, based only on parsing the titles and abstracts.See an RDF turtle example here. A number of sparql queries to identify the instances of different data types are aviable at here.

• Condition: 182,231 instances
• Medication: 32,069 instances
• Procedure: 100,260 instances

We plan to parse the full text articles soon, for those that we can access.

If you can generate other semantic linkages, please let us know. Collaboration is invited. Please issue a pull request or contact Guoqian Jiang jiang.guoqian@mayo.edu and Harold Solbrig solbrig@jhu.edu.

We have also added another set of annotations from Pubtator. These are pulled from the Pubtator API via pmcid (PubMed Central id) from metadata file (see below). Not all PMC ids yielded annotations. These annotations have been converted from the source JSON into RDF Turtle format.

We have produced a linked version of the dataset. See an RDF turtle example here. A number of sparql queries to identify the instances of different data types are aviable at here.

• Species: 2,030,458 instances
• Gene: 1,235,829 instances
• Disease: 1,036,954 instances
• Chemical: 778,872 instances
• CellLine: 76,816 instances
• Mutation: 33,413 instances
• Strain: 26,573 instances

LitCovid is a curated literature hub for tracking up-to-date scientific information about the 2019 novel Coronavirus. It is the most comprehensive resource on the subject, providing a central access to 3207 (and growing) relevant articles in PubMed. We have produced a linked version of the dataset. A number of sparql queries to identify the instances of different data types are aviable at here.

• Species 34,945
• Disease 29,106
• Chemical 4,718
• Gene 43,82
• CellLine 460
• Mutation 117

We are developing the COVID-19 PICO Ontology (CPICO) that is an extension of Cochrane PICO Ontology for supporting COVID-19 evidence extraction and formulating COVID-19 research questions. The CPICO Ontology defines specific subtypes for the PICO classes of Population, Intervention, and Outcome. See details here.

• COVID-19 Open Research Dataset (CORD-19)
• COVID-19 Knowledge Accelerator
• EBMonFHIR
• NCBI Pubtator
• LitCovid
• Coronavirus Infectious Disease Ontology
• NCATS CTSA Program National Center for Data to Health (CD2H)
• NCATS Biomedical Data Translator
• OntoText and GraphDB

This dataset was derived from the CORD-19 dataset, and therefore consists of two subsets, having different licenses, that are intermingled in the CORD-19-on-FHIR dataset:

• the CORD-19 dataset, subject to the CORD-19 license; and

• semantic annotations that were added by CORD-19-on-FHIR data mining, subject to a CC0 license.

See LICENSE. By downloading this dataset you are agreeing to the dataset licenses.

Specific licensing information for individual articles in the dataset is available in the metadata file. See also the readme for the metadata file.

• semantic annotations that were added by Pubtator from public domain, using the following public domain notice

# ===========================================================================
#
#                            PUBLIC DOMAIN NOTICE
#               National Center for Biotechnology Information
#
#  This software/database is a "United States Government Work" under the
#  terms of the United States Copyright Act.  It was written as part of
#  the author's official duties as a United States Government employee and
#  thus cannot be copyrighted.  This software/database is freely available
#  to the public for use. The National Library of Medicine and the U.S.
#  Government have not placed any restriction on its use or reproduction.
#
#  Although all reasonable efforts have been taken to ensure the accuracy
#  and reliability of the software and data, the NLM and the U.S.
#  Government do not and cannot warrant the performance or results that
#  may be obtained by using this software or data. The NLM and the U.S.
#  Government disclaim all warranties, express or implied, including
#  warranties of performance, merchantability or fitness for any particular
#  purpose.
===============================================================================
 
 

-Pipfile, Pipfile.lock -- Use by pip python installer

• contexts -- JSON-LD 1.1 @context files used in converting JSON data files into RDF Turtle
• source -- Source data from CORD-19 release, EXCEPT for the commercial subset, which was too big to put on github. It is available here: https://ai2-semanticscholar-cord-19.s3-us-west-2.amazonaws.com/2020-03-13/comm_use_subset.tar.gz
• datasets -- CORD-19-on-FHIR releases. There is one zip for corresponding to each of the CORD-19 source subsets. And there are zip files that, taken together, correspond to the CORD-19 metadata file. Pubtator annotatio release is under the folder Pubtator_RDF.
• examples -- A few sample files, illustrating the content of the datasets directory.