Repository with nanomaterial information in RDF format.
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2ndYoungScientistForum
NMSA
NanoE-Tox
schema Screenshot of the ShEX2 online validator. Sep 26, 2018
README.md
doi.ttl

README.md

ENMRDF Collection

Collection of Turtle files with RDF in the standard eNanoMapper format.

Pull requests welcome, questions too.

Copyright/License/Waiver: CCZero

RDF Structures

In the below examples, the following general prefixes are used:

@prefix void:  <http://rdfs.org/ns/void#> .
@prefix owl:   <http://www.w3.org/2002/07/owl#> .
@prefix enm:   <http://purl.enanomapper.org/onto/> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix npo:   <http://purl.bioontology.org/ontology/npo#> .
@prefix sso:   <http://semanticscience.org/resource/> .
@prefix bao:   <http://www.bioassayontology.org/bao#> .
@prefix dct:   <http://purl.org/dc/terms/> .
@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix etox:  <http://egonw.github.com/enmrdf/nanoe-tox/> .
@prefix obo:   <http://purl.obolibrary.org/obo/> .
@prefix dc:    <http://purl.org/dc/elements/1.1/> .

A dataset

A dataset is of type void:DataSet and has a title at this moment.

etox:dataset  a    void:DataSet ;
    dct:title    "NanoE-Tox RDF" .
    dct:description  "RDF version of the data from Beilstein J. Nanotechnol. 2015, 6, 1788–1804. doi:10.3762/bjnano.6.183." ;
    dct:license      <https://creativecommons.org/licenses/by/4.0/> ;
    dct:publisher    "Egon Willighagen" .

A material

ex:NFYS16-M12  a     obo:CHEBI_59999 ;
    rdfs:label       "NM-400" ;
    npo:has_part     ex:NFYS16-M12_core ;
    obo:BFO_0000056  ex:NFYS16-M12_sizemg ;
    dcterms:source   ex:NFYS16 ;
    dcterms:type     enm:ENM_9000081 .

All materials are types (rdf:type) obo:CHEBI_59999 and have a name (rdfs:label). Structure information is linked via the npo:has_part predicate and experimental measurements (physchem, toxicity, eco, application) is linked via the obo:BFO_0000056 predicate. A classification of the nanomaterial can be provided with the dcterms:type predicate and an entry from the eNanoMapper ontology.

The chemical composition

The chemical composition of the nanomaterial is encoded by linking material components to the nanomaterial, as was done in the above nanomaterial description with the npo:has_part predicate. The components itself all need a unique IRI and are encoded like this:

ex:NFYS16-M12_core
    a                      npo:NPO_1597 ;
    sso:CHEMINF_000200     ex:NFYS16-M12_core_smiles .

ex:NFYS16-M12_core_smiles
    a               sso:CHEMINF_000018 ;
    sso:SIO_000300  "[C]" .

Example SPARQL queries

Get links out to Sigma-Aldrich:

PREFIX foaf: <http://xmlns.com/foaf/0.1/>

SELECT ?enmMaterial ?linkout WHERE {
  ?enmMaterial foaf:page ?linkout .
  FILTER (REGEX(STR(?linkout), "sigmaaldrich.com"))
}

And similarly to get owl:sameAs links:

PREFIX owl: <http://www.w3.org/2002/07/owl#>

CONSTRUCT {
  ?source owl:sameAs ?linkout
} WHERE {
  ?source owl:sameAs ?linkout .
  FILTER (REGEX(STR(?linkout), "doi.org"))
}