sbd-data-book

Carbon nanotubes

Because the eNanoMapper ontology [1] is loaded, we can take advantage of the hierarchy of the ontology. For example, we can list all carbon nanotubes’s (npo:NPO_606) with this SPARQL:

SPARQL sparql/allCNTs.rq (run)

PREFIX npo: <http://purl.bioontology.org/ontology/npo#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
SELECT DISTINCT ?nm (SAMPLE(?nmLabel_) AS ?nmLabel)
WHERE {
  VALUES ?superclass { npo:NPO_606 }
  ?nm rdfs:subClassOf* ?superclass ; rdfs:label ?nmLabel_ .
} GROUP BY ?nm

This gives us this list of carbon nanotubes:

nm
CNT: Carbon nanotubes
MWCNT40nm-COOH
single-walled carbon nanotube
NM-403
Mitsui MWCNT-7
double-walled carbon nanotube
JRCNM04000a
JRCNM04001a
NM-400
NM-401
JRCNM40001a
JRCNM40002a
JRCNM40003a
JRCNM40004a
JRCNM40005a
JRCNM40006a
JRCNM40007a
JRCNM40008a
JRCNM40009a
JRCNM40010a
NM-402
JRCNM40011a
ERM00000066
ERM00000325

Causal relationships

We can list all relationships for all carbon nanotubes:

SPARQL sparql/allCNTRelationships.rq (run)

PREFIX sbd:  <https://www.sbd4nano.eu/rdf/#>
PREFIX sbdbel:  <https://www.sbd4nano.eu/bel/#>
PREFIX npo: <http://purl.bioontology.org/ontology/npo#>
PREFIX sio: <http://semanticscience.org/resource/SIO_>
PREFIX sbdbel2:  <https://h2020-sbd4nano.github.io/sbdbel/>
SELECT DISTINCT
  ?superclass (SAMPLE(?superclassLabel_) AS ?superclassLabel)
  ?nm (SAMPLE(?nmLabel_) AS ?nmLabel)
  (COUNT(DISTINCT ?relation) AS ?relations)
WHERE {
  VALUES ?ca { sbdbel:CausalAssertion sbd:CausalAssertion sbdbel2:CausalAssertion }
  VALUES ?superclass { npo:NPO_606 }
  ?nm rdfs:subClassOf* ?superclass ; rdfs:label ?nmLabel_ .
  ?superclass rdfs:label ?superclassLabel_ .
  ?relation a ?ca ; sbdbel:NP | sio:000332 | sbdbel2:NP ?nm .
} GROUP BY ?superclass ?nm

Which gives:

Carbon nanotube datasets

All data for carbon nanotubes can be listed with (depending on the amount of annotation):

SPARQL sparql/allCNTData.rq (run)

PREFIX npo: <http://purl.bioontology.org/ontology/npo#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX sbd:     <https://www.sbd4nano.eu/rdf/#>
PREFIX sbdbel:  <https://www.sbd4nano.eu/bel/#>
PREFIX foaf:   <http://xmlns.com/foaf/0.1/> 
PREFIX rdfs:   <http://www.w3.org/2000/01/rdf-schema#> 
PREFIX erm:    <https://nanocommons.github.io/identifiers/registry#>
PREFIX enm:    <http://purl.enanomapper.org/onto/>
SELECT ?materialIRI (SAMPLE(?material_) AS ?material) ?dataset ?datasetLabel
WHERE {
  VALUES ?superclass { npo:NPO_606 }
  VALUES ?type { sbd:Dataset sbd:Database }
  ?dataset sbdbel:NP ?materialIRI ; a ?type ; rdfs:label ?datasetLabel .
  ?materialIRI rdfs:subClassOf* ?superclass ; rdfs:label ?material_ .
} GROUP BY ?materialIRI ?dataset ?datasetLabel
  ORDER BY ?dataset

This gives:

materialIRI material dataset
npo:NPO_354 MWCNT40nm-COOH harmless - eNanoMapper database
npo:NPO_354 MWCNT40nm-COOH nanoinformatix - eNanoMapper database
npo:NPO_606 CNT: Carbon nanotubes nanoreg - eNanoMapper database
npo:NPO_354 MWCNT40nm-COOH nanoreg - eNanoMapper database
npo:NPO_943 single-walled carbon nanotube nanoreg - eNanoMapper database
npo:NPO_354 MWCNT40nm-COOH nanoreg2 - eNanoMapper database
npo:NPO_354 MWCNT40nm-COOH riskgone - eNanoMapper database
erm:ERM00000066 ERM00000066 riskgone - eNanoMapper database
erm:ERM00000325 ERM00000325 riskgone - eNanoMapper database
enm:ENM_9000230 NM-403 Transcriptomic study of NR8383 rat macrophages cells following exposure to NM403 carbon nanotubes
npo:NPO_354 MWCNT40nm-COOH Transcriptomic study of NR8383 rat macrophages cells following exposure to multi-walled carbon nanotubes (NRCWE006)
npo:NPO_606 CNT: Carbon nanotubes Transcriptomic study of NR8383 rat macrophages cells following exposure to COOH-functionalized carbon nanotubes (NRCWE042)
npo:NPO_606 CNT: Carbon nanotubes Transcriptomic study of NR8383 rat macrophages cells following exposure to NH2-functionalized carbon nanotubes (NRCWE049)
npo:NPO_943 single-walled carbon nanotube Transcriptomic study of NR8383 rat macrophages cells following exposure to pristine single-walled carbon nanotubes (NRCWE055)

Carbon nanotube models

All models for carbon nanotubes can be listed with:

SPARQL sparql/allCNTModels.rq (run)

PREFIX npo: <http://purl.bioontology.org/ontology/npo#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
PREFIX sbd:     <https://www.sbd4nano.eu/rdf/#>
PREFIX sbdbel:  <https://www.sbd4nano.eu/bel/#>
PREFIX dc:      <http://purl.org/dc/elements/1.1/>
PREFIX dct:     <http://purl.org/dc/terms/>
PREFIX skos:    <http://www.w3.org/2004/02/skos/core#>
SELECT ?model ?modelLabel ?provider
       (group_concat(distinct ?material_;separator=", ") AS ?material)
WHERE {
  VALUES ?superclass { npo:NPO_606 }
  ?materialIRI rdfs:subClassOf* ?superclass ; rdfs:label ?material_ .
  ?model a sbd:Model ;
     dc:source ?providerRes.
  { ?model sbdbel:NP ?materialIRI . } UNION { ?model dct:subject / skos:narrower ?materialIRI . }
  OPTIONAL { ?model rdfs:label ?rdfsLabel }
  BIND(COALESCE(?rdfsLabel, str(?model)) AS ?modelLabel)
  ?providerRes dct:title | dc:title ?provider .
} GROUP BY ?model ?modelLabel ?provider
  ORDER BY ?model

This gives:

model provider material
https://h2020-sbd4nano.github.io/sbd-data-landscape/Model_19a Computational models for the assessment of manufactured nanomaterials CNT: Carbon nanotubes, Single/Multiwalled nanotubes, carbon nanotube
https://h2020-sbd4nano.github.io/sbd-data-landscape/Model_19b Computational models for the assessment of manufactured nanomaterials CNT: Carbon nanotubes, Single/Multiwalled nanotubes, carbon nanotube
https://h2020-sbd4nano.github.io/sbd-data-landscape/Model_19c Computational models for the assessment of manufactured nanomaterials CNT: Carbon nanotubes, Single/Multiwalled nanotubes, carbon nanotube
https://h2020-sbd4nano.github.io/sbd-data-landscape/Model_19d Computational models for the assessment of manufactured nanomaterials CNT: Carbon nanotubes, Single/Multiwalled nanotubes, carbon nanotube
https://h2020-sbd4nano.github.io/sbd-data-landscape/Model_19e Computational models for the assessment of manufactured nanomaterials CNT: Carbon nanotubes, Single/Multiwalled nanotubes, carbon nanotube
https://h2020-sbd4nano.github.io/sbd-data-landscape/Model_19f Computational models for the assessment of manufactured nanomaterials CNT: Carbon nanotubes, Single/Multiwalled nanotubes, carbon nanotube
https://h2020-sbd4nano.github.io/sbd-data-landscape/Model_19g Computational models for the assessment of manufactured nanomaterials CNT: Carbon nanotubes, Single/Multiwalled nanotubes, carbon nanotube
https://h2020-sbd4nano.github.io/sbd-data-landscape/Model_19h Computational models for the assessment of manufactured nanomaterials CNT: Carbon nanotubes, Single/Multiwalled nanotubes, carbon nanotube
https://h2020-sbd4nano.github.io/sbd-data-landscape/Model_46 Computational models for the assessment of manufactured nanomaterials MWCNT40nm-COOH, MWCNTs (Multi-walled carbon nanotubes), multi-walled carbon nanotube
https://h2020-sbd4nano.github.io/sbd-data-landscape/Model_51a Computational models for the assessment of manufactured nanomaterials CNT: Carbon nanotubes, Single/Multiwalled nanotubes, carbon nanotube
https://h2020-sbd4nano.github.io/sbd-data-landscape/Model_51b Computational models for the assessment of manufactured nanomaterials CNT: Carbon nanotubes, Single/Multiwalled nanotubes, carbon nanotube
https://h2020-sbd4nano.github.io/sbd-data-landscape/Model_7 Computational models for the assessment of manufactured nanomaterials MWCNT40nm-COOH, MWCNTs (Multi-walled carbon nanotubes), multi-walled carbon nanotube
https://h2020-sbd4nano.github.io/sbd-data-landscape/Model_75a Computational models for the assessment of manufactured nanomaterials CNT: Carbon nanotubes, Single/Multiwalled nanotubes, carbon nanotube
https://h2020-sbd4nano.github.io/sbd-data-landscape/Model_75b Computational models for the assessment of manufactured nanomaterials CNT: Carbon nanotubes, Single/Multiwalled nanotubes, carbon nanotube
https://h2020-sbd4nano.github.io/sbd-data-landscape/Model_75c Computational models for the assessment of manufactured nanomaterials CNT: Carbon nanotubes, Single/Multiwalled nanotubes, carbon nanotube
https://h2020-sbd4nano.github.io/sbd-data-landscape/Model_75d Computational models for the assessment of manufactured nanomaterials CNT: Carbon nanotubes, Single/Multiwalled nanotubes, carbon nanotube

References

  1. Hastings J, Jeliazkova N, Owen G, Tsiliki G, Munteanu CR, Steinbeck C, et al. eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment. J Biomed Semantics. 2015;6(1):10. doi:10.1186/S13326-015-0005-5 (Scholia)