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https://w3id.org/np/RAWI7viS6UcGJsGCuZ493n5V48jTkI9yidyjqPViPEyHk

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Content

@prefix np: <http://www.nanopub.org/nschema#> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix ns1: <https://w3id.org/np/snakemake/> .
@prefix orcid: <https://orcid.org/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix schema: <https://schema.org/> .
@prefix sub: <https://w3id.org/np/RAWI7viS6UcGJsGCuZ493n5V48jTkI9yidyjqPViPEyHk/> .
@prefix this: <https://w3id.org/np/RAWI7viS6UcGJsGCuZ493n5V48jTkI9yidyjqPViPEyHk> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

sub:Head {
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