The description of each article from the CORD-19 corpus comes in three parts: (1) metadata such as title and authors, (2) annotations about named entities, and (3) argumentative components and PICO elements. Below we exemplify and described these parts.
Below we use the following namespaces:
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.
@prefix owl: <http://www.w3.org/2002/07/owl#>.
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix bibo: <http://purl.org/ontology/bibo/> .
@prefix dce: <http://purl.org/dc/elements/1.1/>.
@prefix dct: <http://purl.org/dc/terms/>.
@prefix fabio: <http://purl.org/spar/fabio/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/>.
@prefix frbr: <http://purl.org/vocab/frbr/core#>.
@prefix oa: <http://www.w3.org/ns/oa#>.
@prefix prov: <http://www.w3.org/ns/prov#>.
@prefix schema: <http://schema.org/>.
@prefix aif: <http://www.arg.dundee.ac.uk/aif#>. # Argument Interchange Format
@prefix amo: <http://purl.org/spar/amo/>. # Argument Model Ontology (Toulmin)
@prefix sioca: <http://rdfs.org/sioc/argument#>. # SIOC Argumentation Module
@prefix umls: <http://bioportal.bioontology.org/ontologies/umls/>.
@prefix covid: <http://ns.inria.fr/covid19/>.
@prefix covidpr:<http://ns.inria.fr/covid19/property/>.Article URIs are formatted as http://ns.inria.fr/covid19/paper_id where paper_id may be either the article SHA hash or its PCM identifier.
Article metadata includes the following items:
- title (
dct:title) - authors (
dce:creator) - publication date (
dct:issued) - journal (
schema:publication) - license (
dct:license) - identifiers
- DOI (
bibo:doi) - Pubmed identifer (
bibo:pmidandfabio:hasPubMedId) - PMC identifer (
fabio:hasPubMedCentralId)
- DOI (
- source of the metadata information (
dct:source) - DOI-based URL (
schema:url) - SHA hash (
foaf:sha1)
Furthermore, each article is linked to its parts (title, abstract, body) as follows:
covidpr:hasTitle <http://ns.inria.fr/covid19/paper_id#title>dct:abstract <http://ns.inria.fr/covid19/paper_id#abstract>covidpr:hasBody <http://ns.inria.fr/covid19/paper_id#body_text>.
Here is an example of article metadata:
<http://ns.inria.fr/covid19/f74923b3ce82c984a7ae3e0c2754c9e33c60554f>
a fabio:ResearchPaper, bibo:AcademicArticle, schema:ScholarlyArticle;
rdfs:isDefinedBy <http://ns.inria.fr/covid19/dataset-1-1>;
dct:title "A real-time PCR for SARS-coronavirus incorporating target gene pre-amplification";
schema:publication "Biochemical and Biophysical Research Communications";
dce:creator "Wong, Freda Pui-Fan", "Tam, Siu-Lun", "Fung, Yin-Wan", "Li, Hui", "Cheung, Albert", "Chan, Paul", "Lin, Sau-Wah", "Collins, Richard", "Dillon, Natalie";
dct:source "Elsevier";
dct:license "els-covid";
dct:issued "2003-12-26"^^xsd:date;
bibo:doi "10.1016/j.bbrc.2003.11.064";
bibo:pmid "14652014";
fabio:hasPubMedId "14652014";
foaf:sha1 "f74923b3ce82c984a7ae3e0c2754c9e33c60554f";
schema:url <https://doi.org/10.1016/j.bbrc.2003.11.064>;
dct:abstract <http://ns.inria.fr/covid19/f74923b3ce82c984a7ae3e0c2754c9e33c60554f#abstract>;
covidpr:hasTitle <http://ns.inria.fr/covid19/f74923b3ce82c984a7ae3e0c2754c9e33c60554f#title>;
covidpr:hasBody <http://ns.inria.fr/covid19/f74923b3ce82c984a7ae3e0c2754c9e33c60554f#body_text>.The named entities identified in an article are described as annotations using the Web Annotations Vocabulary. Each annotation consists of the following information:
- the article it is about (
schema:about) - the annotation target (
oa:hasTarget) describes the piece of text identified as a named entity as follows:- the source (
oa:hasSource) is the part of the article where the named entity was detected - the selecor (
oa:hasSelector) gives the named entity raw text (oa:exact) and its location whithin the source (oa:startandoa:end)
- the source (
- the annotation body (
oa:hasBody) gives the URI of the resource identified as representing the named entity (e.g. a Wikidata URI) - domains related to the named entity (
dct:subject)
Example:
_:b40150806
a oa:Annotation, prov:Entity;
schema:about <http://ns.inria.fr/covid19/f74923b3ce82c984a7ae3e0c2754c9e33c60554f>;
dct:subject "Engineering", "Biology";
covidpr:confidence "1"^^xsd:decimal;
oa:hasBody <http://wikidata.org/entity/Q176996>;
oa:hasTarget [
oa:hasSource <http://ns.inria.fr/covid19/f74923b3ce82c984a7ae3e0c2754c9e33c60554f#abstract>;
oa:hasSelector [
a oa:TextPositionSelector, oa:TextQuoteSelector;
oa:exact "PCR";
oa:start "235";
oa:end "238"
]
];The arguments extracted from an article are described using the Argument Model Ontology, SIOC Argumentation Module and Argument Interchange Format.
In the example below, an argument is defined that consits of 3 components: 2 evidences and a claim, with support/attack relations between the components:
<http://ns.inria.fr/covid19/arg/4f8d24c531d2c334969e09e4b5aed66dcc925c4b>
a amo:Argument;
schema:about covid:f74923b3ce82c984a7ae3e0c2754c9e33c60554f;
dct:creator <https://team.inria.fr/wimmics/>;
prov:wasGeneratedBy covid:ProvenanceActa.
# Argumentative components
amo:hasEvidence <http://ns.inria.fr/covid19/arg/4f8d24c531d2c334969e09e4b5aed66dcc925c4b/0>;
amo:hasEvidence <http://ns.inria.fr/covid19/arg/4f8d24c531d2c334969e09e4b5aed66dcc925c4b/123>;
amo:hasClaim <http://ns.inria.fr/covid19/arg/4f8d24c531d2c334969e09e4b5aed66dcc925c4b/6>;
.
<http://ns.inria.fr/covid19/arg/4f8d24c531d2c334969e09e4b5aed66dcc925c4b/0>
a amo:Evidence, sioca:Justification, aif:I-node;
prov:wasQuotedFrom covid:4f8d24c531d2c334969e09e4b5aed66dcc925c4b;
aif:formDescription "17 patients discharged in recovered condition and 10 patients died in hospital."^^xsd:string;
# evidence 0 supports claim 6
sioca:supports <http://ns.inria.fr/covid19/arg/4f8d24c531d2c334969e09e4b5aed66dcc925c4b/6>;
amo:proves <http://ns.inria.fr/covid19/arg/4f8d24c531d2c334969e09e4b5aed66dcc925c4b/6>.
.
<http://ns.inria.fr/covid19/arg/4f8d24c531d2c334969e09e4b5aed66dcc925c4b/123>
a amo:Evidence, sioca:Justification, aif:I-node;
prov:wasQuotedFrom covid:4f8d24c531d2c334969e09e4b5aed66dcc925c4b;
aif:formDescription "some other evidence"^^xsd:string;
# evidence 123 attacks claim 6
sioca:challenges <http://ns.inria.fr/covid19/arg/4f8d24c531d2c334969e09e4b5aed66dcc925c4b/6>.
.
<http://ns.inria.fr/covid19/arg/4f8d24c531d2c334969e09e4b5aed66dcc925c4b/6>
a amo:Claim, sioca:Idea, aif:I-node, aif:KnowledgePosition_Statement;
prov:wasQuotedFrom covid:4f8d24c531d2c334969e09e4b5aed66dcc925c4b;
aif:claimText "a simple ct scoring method was capable to predict mortality."^^xsd:string;
.PICO elements identified in an argumentative component are described in a way very similar to the named entities, using the Web Annotations Vocabulary. The annotation bodies provide UMLS concepts and term ids.
Example:
[] a oa:Annotation;
schema:about <http://ns.inria.fr/covid19/4f8d24c531d2c334969e09e4b5aed66dcc925c4b>;
covidpr:confidence 1^^xsd:decimal;
# link to the ULMS concept id (CUI) and semantic type id (TUI)
oa:hasBody [ umls:cui "C0026565"; umls:tui "T81" ];
oa:hasTarget [
# the source is the claim/evidence
oa:hasSource <http://ns.inria.fr/covid19/arg/4f8d24c531d2c334969e09e4b5aed66dcc925c4b/6>;
oa:hasSelector [
a oa:TextQuoteSelector;
oa:exact "mortality";
]
].Provenance information about each annotation provides the annotation author (dct:creator), source dataset and version (prov:used, CORD-19 v6 in the example below), and the tool used to identify the named entity (prov:wasAssociatedWith, entity-fishing in the example below).
_:b40150806
rdfs:isDefinedBy <http://ns.inria.fr/covid19/dataset-1-1>;
dct:creator <https://team.inria.fr/wimmics/>;
prov:wasGeneratedBy [
a prov:Activity;
prov:used <http://ns.inria.fr/covid19/cord19v7>;
prov:wasAssociatedWith <https://github.com/kermitt2/entity-fishing>.
].
<http://ns.inria.fr/covid19/cord19v7>
a schema:Dataset dcat:Dataset;
owl:versionInfo "7";
dct:title "COVID-19 Open Research Dataset (CORD-19)";
dct:issued "2020-04-10"^^xsd:date;
schema:url <https://www.kaggle.com/dataset/08dd9ead3afd4f61ef246bfd6aee098765a19d9f6dbf514f0142965748be859b/version/7>.