sbd-data-book
A Semantic landscape
General requirements
General features we have to track of assets:
These two follow DMP and FAIR practices, see for example this presentation.
- supported hazards
- supported hazard drivers
Specific assets will have additional requirements or specific more detailed information about the second two requirements.
Information sources and plugins
Information about databases, datasets, model, and relationships are collected but also retrieved from other data sources.
Data sources
Currently, the following data sources are being used:
SPARQL sparql/allDatasources.rq (run)
PREFIX void: <http://rdfs.org/ns/void#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
SELECT ?resource ?resourceLabel ?img WHERE {
?void a void:DatasetDescription ;
dcterms:title|dc:title ?resourceLabel .
OPTIONAL { ?void dc:source ?resource }
OPTIONAL { ?void foaf:img ?img }
}
This gives us:
The following sections highlight a few EU NanoSafety Cluster projects.
SmartNanoTox
SmartNanoTox provides a few datasets:
NanoSolveIT
NanoSolveIT provides several computational models [1]:
The Nanosafety Data Interface
The Nanosafety Data Interface provides access to data from a number of EU NanoSafety Cluster projects [2]:
| type | resource |
| Database | aurora - eNanoMapper database |
| Database | biorima - eNanoMapper database |
| Database | calibrate - eNanoMapper database |
| Database | charisma - eNanoMapper database |
| Database | cusp - eNanoMapper database |
| Database | enanomapper - eNanoMapper database |
| Database | gov4nano - eNanoMapper database |
| Database | gracious - eNanoMapper database |
| Database | harmless - eNanoMapper database |
| Database | imptox - eNanoMapper database |
| Database | nanoinformatix - eNanoMapper database |
| Database | nanoreg - eNanoMapper database |
| Database | nanoreg2 - eNanoMapper database |
| Database | patrols - eNanoMapper database |
| Database | plasticfate - eNanoMapper database |
| Database | plasticheal - eNanoMapper database |
| Database | polyrisk - eNanoMapper database |
| Database | riskgone - eNanoMapper database |
| Database | sabydoma - eNanoMapper database |
| Database | sabyna - eNanoMapper database |
| Database | sbd4nano - eNanoMapper database |
| Database | sunshine - eNanoMapper database |
Licenses
Not all resources have licenses that allow us to immediately use them, but require acquiring a license. This query lists all license information in the current knowledge base:
SPARQL sparql/allLicenses.rq (run)
PREFIX sbd: <https://www.sbd4nano.eu/rdf/#>
PREFIX sbdbel: <https://www.sbd4nano.eu/bel/#>
PREFIX dcterms: <http://purl.org/dc/terms/>
SELECT (COUNT(DISTINCT ?resource) AS ?count) ?license
WHERE {
VALUES ?ca { sbdbel:CausalAssertion sbd:CausalAssertion }
?resource a ?type .
MINUS { ?resource a ?ca }
OPTIONAL { ?resource dcterms:license ?license }
} GROUP BY ?license
ORDER BY DESC(?count)
This gives us:
| count | license |
| 39267 | |
| 2013 | http://creativecommons.org/publicdomain/zero/1.0/ |
| 304 | https://creativecommons.org/licenses/by/4.0/ |
| 83 | http://example.com/unknown |
| 83 | https://creativecommons.org/licenses/by/4.0/legalcode |
| 29 | https://www.wikidata.org/entity/Q50423863 |
| 22 | https://creativecommons.org/licenses/by-nc/3.0/de/legalcode |
| 9 | https://opensource.org/licenses/MIT |
| This table is truncated. See the full table at sparql/allLicenses.rq | |
Statistics
Each data source can provide information about different resource types. This table gives an overview for each metadata source what information is provided as basic statistics:
| source | databases | datasets | models | relationships | frameworks | guidancetools | guidancedocs | lcanalyses |
| Computational models for the assessment of manufactured nanomaterials | 0 | 0 | 204 | 0 | 0 | 0 | 0 | 0 |
| AOP-Wiki AOPs | 0 | 0 | 290 | 0 | 0 | 0 | 0 | 0 |
| AOP-Wiki data | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 |
| AOP-Wiki Key Event Relationships | 0 | 0 | 0 | 1993 | 0 | 0 | 0 | 0 |
| Closed datasets hosted at the Nanosafety Data Interface | 17 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Data completeness and reusability assessment for 34 nanosafety datasets | 0 | 34 | 0 | 0 | 0 | 0 | 0 | 0 |
| FAIRsharing | 29 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NanoCommons Knowledge Base - powered by BioXM™ | 0 | 59 | 0 | 0 | 0 | 0 | 0 | 0 |
| NanoInformaTIX Tools | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| NanoSolveIT Tools | 0 | 0 | 6 | 0 | 0 | 0 | 0 | 0 |
| Open datasets hosted at the Nanosafety Data Interface | 5 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Overview of open datasets released by NanoSafety Cluster projects | 0 | 52 | 0 | 0 | 0 | 0 | 0 | 0 |
| SbD4nano Nanocompound | 0 | 0 | 10 | 0 | 0 | 0 | 0 | 0 |
| SmartNanoTox Transcriptomics datasets | 0 | 20 | 0 | 0 | 0 | 0 | 0 | 0 |
If metadata sources are not listed here, then they are likely not described by a data descriptor header file.
References
- Afantitis A, Melagraki G, Isigonis P, Tsoumanis A, Varsou DD, Valsami-Jones E, et al. NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment. Comput Struct Biotechnol J. 2020 Mar 7;18:583–602. doi:10.1016/J.CSBJ.2020.02.023 (Scholia)
- Jeliazkova N, Apostolova MD, Andreoli C, Barone F, Barrick A, Battistelli C, et al. Towards FAIR nanosafety data. Nat Nanotechnol. 2021 May 20;16(6):644–54. doi:10.1038/S41565-021-00911-6 (Scholia)