Creating nanopublications with Groovy

Yesterday, I struggled some with creating nanopublications with Groovy. My first attempt was an utter failure, but then I discovered Thomas Kuhn’s NanopubCreator and it was downhill from there.

On the right, a depiction is given of a compound found in Taphrorychus bicolor (doi:10.1002/JLAC.199619961005). Published in Liebigs Annalen, see this post about the history of that journal.

There are two good things about this. First, I now have a code base that I can easily repurpose to make trusty nanopublications (doi:10.1007/978-3-319-07443-6_27) about anything structured as a table (so can you).

Second, I now about almost 1200 CCZero nanopublications that tell you in which species a certain metabolite has been found. Sourced from Wikidata, using their SPARQL end point. This collection is a bit boring that this moment, and most of them are human metabolites, where the source is either Recon 2.2 or WikiPathways. But I expect (hope) to see more DOIs to show up. Think We challenge you to reuse Additional Files.

Finally, you are probably interested in learning what one of the created nanopublications looks like, to I put a Gist online:

@prefix this: <http://www.bigcat.unimaas.nl/nanopubs/wikidata/tmp/np742.RAwXcetTykN6UPVzBOyatKm30mbT6endXfDrxnarRysL0> .
@prefix sub: <http://www.bigcat.unimaas.nl/nanopubs/wikidata/tmp/np742.RAwXcetTykN6UPVzBOyatKm30mbT6endXfDrxnarRysL0#> .
@prefix wd: <http://www.wikidata.org/entity/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix has-source: <http://semanticscience.org/resource/SIO_000253> .
@prefix has-inchikey: <http://semanticscience.org/resource/CHEMINF_000399> .
@prefix orcid: <http://orcid.org/> .
@prefix wdt: <http://www.wikidata.org/prop/direct/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix pav: <http://purl.org/pav/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .

sub:Head {
        this: np:hasAssertion sub:assertion ;
                np:hasProvenance sub:provenance ;
                np:hasPublicationInfo sub:pubinfo ;
                a np:Nanopublication .
}

sub:assertion {
        wd:Q15978631 rdfs:label "Homo sapiens"@en ;
                skos:exactMatch <http://purl.obolibrary.org/obo/NCBITaxon_9606> .

        wd:Q27125029 has-inchikey: "APJYDQYYACXCRM-UHFFFAOYSA-O" ;
                rdfs:label "tryptaminium"@en ;
                wdt:P703 wd:Q15978631 .
}

sub:provenance {
        sub:assertion has-source: wd:Q2013 , wd:Q28601559 .

        wd:Q28601559 rdfs:label "Recon 2.2: from reconstruction to model of human metabolism"@en ;
                owl:sameAs <https://doi.org/10.1007/S11306-016-1051-4> .
}

sub:pubinfo {
        this: pav:createdBy orcid:0000-0001-7542-0286 .
}