Tissue expression nanopublications

Modeling Method

Tissue nanopublications were modeled as 4 named graphs; an assertion graph, a graph for the provenance of the assertion,  a graph for provenance of the nanopublication (publicationInfo), and a graph indicating the graphs of the nanopublication (Head). The assertion graph was initially created by stating the scientific assertion in natural language to identify all the entities required to convey a specific and distinct scientific fact. There is quite a bit of freedom for authors in the nanopublication guidelines concerning which triples belong in the different named graphs. Therefore, the choices made in the modeling reflect what was determined as biologically important information and the minimum essential information necessary to draw biological conclusions. Ontologies were then consulted to find the appropriate predicates and the assertion graph was constructed. Attempts were made to keep the number of triples to a minimum but some assertion modeling may require several triples. All information that was considered important for understanding the background of the assertion (the method for generating the assertion and the data used) was added into the provenance graph.  No restrictions were placed on the number of provenance statements.

Example Nanopublication in RDF

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@prefix this: <http://www.nextprot.org/nanopubs#NX_P35712_ESTEvidence_TS-0276.RAFmVzV8jfHqjBwB3t_XJAf_EihzMU2q-cSI0NigJN3ww> .
 @prefix sub: <http://www.nextprot.org/nanopubs#NX_P35712_ESTEvidence_TS-0276.RAFmVzV8jfHqjBwB3t_XJAf_EihzMU2q-cSI0NigJN3ww#> .
 @prefix bfo: <http://purl.obolibrary.org/obo/#> .
 @prefix dcterms: <http://purl.org/dc/terms/> .
 @prefix eco: <http://purl.obolibrary.org/obo/eco.owl#> .
 @prefix efo: <http://www.ebi.ac.uk/efo/> .
 @prefix np: <http://www.nanopub.org/nschema#> .
 @prefix nx: <http://www.nextprot.org/db/search#> .
 @prefix pav: <http://swan.mindinformatics.org/ontologies/1.2/pav/> .
 @prefix prov: <http://www.w3.org/ns/prov#> .
 @prefix prv: <http://purl.org/net/provenance/ns#> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix ro: <http://purl.org/obo/owl/OBO_REL#> .
 @prefix ts: <ftp://ftp.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo#> .
 @prefix wi: <http://purl.org/ontology/wi/core#> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .sub:Head {
 this: np:hasAssertion sub:assertion ;
 np:hasProvenance sub:provenance ;
 np:hasPublicationInfo sub:pubinfo ;
 a np:Nanopublication .
 }

sub:assertion {
 nx:NX_P35712 bfo:BFO_0000066 ts:TS-0276 ; # Protein NX_P35712 is localized in tissue TS-0276
 ro:has_quality "positive" .
 }

sub:provenance {
 <http://www.nextprot.org/help/quality_criteria/silver> a eco:ECO_0000205 ;
 rdfs:label "neXtProt silver"^^xsd:string .
 sub:_1 a efo:EFO_00027688 .
 sub:_10 a eco:ECO_0000218 .
 sub:_2 a eco:ECO_0000218 .
 sub:_3 a efo:EFO_00027688 .
 sub:_4 a eco:ECO_0000218 .
 sub:_5 a efo:EFO_00027688 .
 sub:_6 a eco:ECO_0000218 .
 sub:_7 a efo:EFO_00027688 .
 sub:_8 a eco:ECO_0000218 .
 sub:_9 a efo:EFO_00027688 .
 sub:assertion prv:usedData <http://bgee.unil.ch/bgee/bgee?page=expression&action=data&stage_id=HsapDO:0000087&amp;organ_id=EV:0100115&amp;gene_id=ENSG00000110693> , <http://bgee.unil.ch/bgee/bgee?page=expression&action=data&stage_id=HsapDO:0000088&amp;organ_id=EV:0100115&amp;gene_id=ENSG00000110693> , <http://bgee.unil.ch/bgee/bgee?page=expression&action=data&stage_id=HsapDO:0000090&amp;organ_id=EV:0100115&amp;gene_id=ENSG00000110693&amp;stage_children=on> , <http://bgee.unil.ch/bgee/bgee?page=expression&action=data&stage_id=HsapDO:0000092&amp;organ_id=EV:0100115&amp;gene_id=ENSG00000110693&amp;stage_children=on> , <http://bgee.unil.ch/bgee/bgee?page=expression&action=data&stage_id=HsapDO:0000094&amp;organ_id=EV:0100115&amp;gene_id=ENSG00000110693&amp;stage_children=on> ;
 wi:evidence <http://www.nextprot.org/help/quality_criteria/silver> ;
 a eco:ECO_0000220 ;
 rdfs:comment " data, NX_P35712 is expressed in Endometrium"^^xsd:string ;
 prov:wasDerivedFrom sub:_1 , sub:_3 , sub:_5 , sub:_7 , sub:_9 ;
 prov:wasGeneratedBy sub:_10 , sub:_2 , sub:_4 , sub:_6 , sub:_8 .
 }

sub:pubinfo {
 sub:_11 a eco:ECO_0000205 .
 sub:_12 a eco:ECO_0000205 .
 sub:_13 a eco:ECO_0000205 .
 sub:_14 a eco:ECO_0000205 .
 sub:_15 a eco:ECO_0000205 .
 this: dcterms:created "2014-09-19T00:00:00.0Z"^^xsd:dateTime ;
 dcterms:rights <http://creativecommons.org/licenses/by/3.0/> ;
 dcterms:rightsHolder <http://nextprot.org> ;
 prv:usedData "neXtProt database" ;
 pav:authoredBy "CALIPHO project" , <http://orcid.org/0000-0001-6710-1373> , <http://orcid.org/0000-0001-6818-334X> , <http://orcid.org/0000-0002-1303-2189> , <http://orcid.org/0000-0003-1813-6857> ;
 pav:versionNumber "3" ;
 prov:wasGeneratedBy sub:_11 , sub:_12 , sub:_13 , sub:_14 , sub:_15 .
 }
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