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xr2rml_pyclinrec_annot.tpl.ttl
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# Mapping file generating the annotations for the named entities found by Pyclinrec.
#
# Author: Anna BOBASHEVAc, University Cote d'Azur, CNRS, Inria
#
# Licensed under the Apache License, Version 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
@prefix xrr: <http://i3s.unice.fr/xr2rml#> .
@prefix rr: <http://www.w3.org/ns/r2rml#> .
@prefix rml: <http://semweb.mmlab.be/ns/rml#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>.
@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 wd: <http://www.wikidata.org/entity/>.
# Template file: replace placeholders
# - {{dataset}}: RDF dataset name e.g. "dataset-1-0"
# - {{collection}}: the MongoDB collection to query, e.g. spotlight
# - {{documentpart}}: document part about which to produce annotations. One of title, abstract, body_text
# - {{namespace}}: The ISSA instance specific namespace, e.g http://data-issa.dhm.euromov.fr/
@prefix issa: <{{namespace}}>.
@prefix issapr: <{{namespace}}property/>.
@prefix issa-doc: <{{namespace}}document/>.
@prefix issa-ann: <{{namespace}}ann/>.
<#LS_entities>
a xrr:LogicalSource;
xrr:query """db.{{collection}}.find()""";
#xrr:query """db.{{collection}}.find( { paper_id: "543654" } )""";
rml:iterator "$.{{documentpart}}.concepts.*";
xrr:pushDown [ xrr:reference "$.paper_id"; xrr:as "paper_id" ].
<#TM_annotation>
a rr:TriplesMap;
xrr:logicalSource <#LS_entities>;
rr:subjectMap [
# Template to yield a unique blank node id for each annotation
rr:template "{{namespace}}ann/sha1(pyclinrec_{$.paper_id}_{{documentpart}}_{$.matched_text}_{$.start})";
rr:class oa:Annotation, prov:Entity;
];
rr:predicateObjectMap [
rr:predicate rdfs:isDefinedBy;
rr:objectMap [ rr:constant issa:{{dataset}}; rr:termType rr:IRI ];
];
rr:predicateObjectMap [
rr:predicate rdfs:label;
rr:objectMap [ rr:template "named entity '{$.matched_text}'"; rr:termType rr:Literal ];
];
rr:predicateObjectMap [
rr:predicate dct:creator;
rr:objectMap [ rr:constant "https://team.inria.fr/wimmics/"; rr:termType rr:IRI ];
];
rr:predicateObjectMap [
rr:predicate schema:about;
rr:objectMap [ rr:template "{{namespace}}document/{$.paper_id}" ];
];
# Annotation target
rr:predicateObjectMap [
rr:predicate oa:hasTarget;
rr:objectMap [
rr:template "{{namespace}}ann/target/sha1(pyclinrec_{$.paper_id}_{{documentpart}}_{$.matched_text}_{$.start})";
rr:termType rr:IRI;
];
];
# Annotation body
rr:predicateObjectMap [
rr:predicate oa:hasBody;
rr:objectMap [ xrr:reference "$.concept_id"; rr:termType rr:IRI ];
];
# Annotation confidence
rr:predicateObjectMap [
rr:predicate issapr:confidence;
rr:objectMap [ xrr:reference "$.confidence_score"; rr:datatype xsd:decimal ];
];
# Provenance
rr:predicateObjectMap [
rr:predicate rdfs:isDefinedBy;
rr:objectMap [ rr:constant issa:{{dataset}}; rr:termType rr:IRI ];
];
rr:predicateObjectMap [
rr:predicate prov:wasAttributedTo;
rr:objectMap [ rr:constant issa:Pyclinrec; rr:termType rr:IRI ];
];
.
# Annotation target
<#TM_target>
a rr:TriplesMap;
xrr:logicalSource <#LS_entities>;
rr:subjectMap [
rr:template "{{namespace}}ann/target/sha1(pyclinrec_{$.paper_id}_{{documentpart}}_{$.matched_text}_{$.start})"
];
rr:predicateObjectMap [
rr:predicate oa:hasSource;
rr:objectMap [ rr:template "{{namespace}}document/{$.paper_id}#{{documentpart}}" ];
];
rr:predicateObjectMap [
rr:predicate oa:hasSelector;
rr:objectMap [
rr:template "{{namespace}}ann/selector/sha1(pyclinrec_{$.paper_id}_{{documentpart}}_{$.matched_text}_{$.start})";
rr:termType rr:IRI;
];
].
# Annotation target selector
<#TM_selector>
a rr:TriplesMap;
xrr:logicalSource <#LS_entities>;
rr:subjectMap [
rr:template "{{namespace}}ann/selector/sha1(pyclinrec_{$.paper_id}_{{documentpart}}_{$.matched_text}_{$.start})";
rr:class oa:TextPositionSelector, oa:TextQuoteSelector;
];
rr:predicateObjectMap [
rr:predicate oa:start;
rr:objectMap [ xrr:reference "$.start"; rr:datatype xsd:integer ];
];
rr:predicateObjectMap [
rr:predicate oa:exact;
rr:objectMap [ xrr:reference "$.matched_text" ];
];
.
# Example of expected output:
#<http://data-issa.cirad.fr/ann/sha1_hash>
# a prov:Entity , oa:Annotation ;
# rdfs:label "named entity 'banana'" ;
# issapr:confidence 1.0 ;
# dct:creator <https://team.inria.fr/wimmics/> ;
# schema:about <http://data-issa.cirad.fr/document/600734> ;
# oa:hasBody <http://aims.fao.org/aos/agrovoc/c_806> ;
# oa:hasTarget <http://data-issa.cirad.fr/ann/target/sha1_hash> ;
# rdfs:isDefinedBy issa:issa-agritrop ;
# prov:wasAttributedTo issa:Pyclinrec .
#
#<http://data-issa.cirad.fr/ann/target/sha1_hash>
# oa:hasSelector <http://data-issa.cirad.fr/ann/selector/sha1_hash> ;
# oa:hasSource <http://data-issa.cirad.fr/document/600734#body_text> .
#
#<http://data-issa.cirad.fr/ann/selector/sha1_hash>
# a oa:TextPositionSelector , oa:TextQuoteSelector ;
# oa:exact "banana" ;
# oa:start 2617 .