Causal relationships links causes and effects. We can categorize them by, for example, nanomaterial they are applicable too, by cause, and by effect. The current open data includes causal relationship from the AOP-Wiki [1], but still excludes the relationships from another paper [2] and SbD4Nano Deliverable D6.3.
SPARQL sparql/relationshipsByMaterial.rq (run)
PREFIX sbd: <https://www.sbd4nano.eu/rdf/#>
PREFIX sbdbel: <https://www.sbd4nano.eu/bel/#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX sio: <http://semanticscience.org/resource/SIO_>
PREFIX sbdbel2: <https://h2020-sbd4nano.github.io/sbdbel/>
SELECT ?material (COUNT(DISTINCT ?relation) AS ?count)
WHERE {
VALUES ?ca { sbdbel:CausalAssertion sbd:CausalAssertion sbdbel2:CausalAssertion }
?relation a ?ca ;
sbdbel:NP | sio:000332 | sbdbel2:NP ?materialIRI .
?materialIRI rdfs:label ?material .
} GROUP BY ?material
ORDER BY DESC(?count)
This gives us:
| material | count |
| Metal Oxide | 6 |
| metal oxide nanoparticle | 6 |
| Nanoparticle | 5 |
| Nanomaterial | 5 |
| nanoparticle | 5 |
SPARQL sparql/relationshipsByCause.rq (run)
PREFIX sbd: <https://www.sbd4nano.eu/rdf/#>
PREFIX sbdbel: <https://www.sbd4nano.eu/bel/#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX sbdbel2: <https://h2020-sbd4nano.github.io/sbdbel/>
SELECT ?cause (COUNT(DISTINCT ?relation) AS ?count)
WHERE {
VALUES ?ca { sbdbel:CausalAssertion sbd:CausalAssertion sbdbel2:CausalAssertion }
?relation a ?ca ;
sbdbel:cause / rdfs:label ?cause .
} GROUP BY ?cause
ORDER BY DESC(?count) ASC(?cause)
This gives us:
| cause | count |
| Mitochondrial dysfunction | 31 |
| Oxidative Stress | 26 |
| Deposition of Energy | 23 |
| Activation, AhR | 20 |
| Dose | 14 |
| exposure | 13 |
| Thyroxine (T4) in serum, Decreased | 13 |
| Cell injury/death | 13 |
| Increased, Reactive oxygen species | 13 |
| Increase, Oxidative Stress | 12 |
| Activation, LXR | 11 |
| Acetylcholinesterase (AchE) Inhibition | 10 |
| Increase, DNA damage | 10 |
| coating/surface chemistry | 9 |
| core composition | 9 |
| size | 9 |
| Apoptosis | 9 |
| Deposition of Ionizing Energy | 9 |
| Increase, Reactive Oxygen Species production | 9 |
| Agonism, Androgen receptor | 8 |
| Decrease, testosterone levels | 8 |
| Histone deacetylase inhibition | 8 |
| Increase, DNA strand breaks | 8 |
| This table is truncated. See the full table at sparql/relationshipsByCause.rq | |
SPARQL sparql/relationshipsByOutcome.rq (run)
PREFIX sbd: <https://www.sbd4nano.eu/rdf/#>
PREFIX sbdbel: <https://www.sbd4nano.eu/bel/#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX sbdbel2: <https://h2020-sbd4nano.github.io/sbdbel/>
SELECT ?outcome (COUNT(DISTINCT ?relation) AS ?count)
WHERE {
VALUES ?ca { sbdbel:CausalAssertion sbd:CausalAssertion sbdbel2:CausalAssertion }
?relation a ?ca ;
sbdbel:outcome / rdfs:label ?outcome .
} GROUP BY ?outcome
ORDER BY DESC(?count)
This gives us:
| outcome | count |
| Mitochondrial dysfunction | 23 |
| Impairment, Learning and memory | 18 |
| Decrease, Population growth rate | 17 |
| Cell injury/death | 17 |
| Increased Mortality | 16 |
| toxicity | 16 |
| Increased, Reactive oxygen species | 15 |
| cell uptake (amount) | 15 |
| increased，Vascular endothelial dysfunction | 14 |
| Apoptosis | 13 |
| impaired, Fertility | 10 |
| ROS production | 10 |
| Increase, Apoptosis | 9 |
| Increase, Mortality | 9 |
| Increased, secretion of proinflammatory mediators | 9 |
| Decrease of neuronal network function | 9 |
| Increased, Liver Steatosis | 9 |
| Increased, Oxidative Stress | 8 |
| Oxidative Stress | 8 |
| Increase, Mutations | 8 |
| Neuroinflammation | 8 |
| Accumulation, Fatty acid | 8 |
| Increase, Oocyte apoptosis | 7 |
| This table is truncated. See the full table at sparql/relationshipsByOutcome.rq | |
Or by Gracious [3] term:
We can also list all relationships:
SPARQL sparql/allCausalRelationships.rq (run)
PREFIX sbd: <https://www.sbd4nano.eu/rdf/#>
PREFIX sbdbel: <https://www.sbd4nano.eu/bel/#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX sio: <http://semanticscience.org/resource/SIO_>
PREFIX sbdbel2: <https://h2020-sbd4nano.github.io/sbdbel/>
SELECT DISTINCT ?cause ?type ?outcome ?material ?evidence
WHERE {
VALUES ?ca { sbdbel:CausalAssertion sbd:CausalAssertion sbdbel2:CausalAssertion }
?relation a ?ca ; sbdbel:relationship ?type .
OPTIONAL { ?relation sbdbel:cause / rdfs:label ?cause . }
OPTIONAL { ?relation sbdbel:outcome / rdfs:label ?outcome . }
OPTIONAL { ?relation sbdbel:NP | sio:000332 | sbdbel2:NP / rdfs:label ?material . }
OPTIONAL { ?relation sbdbel:evidence ?evidence . }
} ORDER BY DESC(?relation)
This gives us:
| cause | type | outcome | material | evidence |
| Alterations, Cellular proliferation / hyperplasia | https://h2020-sbd4nano.github.io/sbd-data-aopwiki/relationships/ | Formation, Hepatocellular and Bile duct tumors | ||
| N/A, Hepatotoxicity, Hepatopathy, including a constellation of observable effects | https://h2020-sbd4nano.github.io/sbd-data-aopwiki/relationships/ | Alterations, Cellular proliferation / hyperplasia | ||
| Changes/Inhibition, Cellular Homeostasis and Apoptosis | https://h2020-sbd4nano.github.io/sbd-data-aopwiki/relationships/ | N/A, Hepatotoxicity, Hepatopathy, including a constellation of observable effects | ||
| Disruption, Lysosome | https://h2020-sbd4nano.github.io/sbd-data-aopwiki/relationships/ | Mitochondrial dysfunction | ||
| Peptide Oxidation | https://h2020-sbd4nano.github.io/sbd-data-aopwiki/relationships/ | KE5 : Decrease, AKT/eNOS activity | ||
| KE5 : Decrease, AKT/eNOS activity | https://h2020-sbd4nano.github.io/sbd-data-aopwiki/relationships/ | KE6 : Depletion, Nitric Oxide | ||
| Activation, EGFR | https://h2020-sbd4nano.github.io/sbd-data-aopwiki/relationships/ | Increase, Mucin production | ||
| Activation, AhR | https://h2020-sbd4nano.github.io/sbd-data-aopwiki/relationships/ | Increase, Early Life Stage Mortality | ||
| This table is truncated. See the full table at sparql/allCausalRelationships.rq | ||||