Slice of the spreadsheet in the supplementary info.
Just some bit of cleaning I scripted today for a number of toxicology end points in a database published some time ago the zero-APC Open Access (CC_BY) journal Beilstein of Journal of Nanotechnology, NanoE-Tox (doi:10.3762/bjnano.6.183).
The curation I am doing is to redistribute the data in the eNanoMapper database (see doi:10.3762/bjnano.6.165) and thus with ontology annotation (see doi:10.1186/s13326-015-0005-5):
recognizedToxicities = [
"EC10": "http://www.bioassayontology.org/bao#BAO_0001263",
"EC20": "http://www.bioassayontology.org/bao#BAO_0001235",
"EC25": "http://www.bioassayontology.org/bao#BAO_0001264",
"EC30": "http://www.bioassayontology.org/bao#BAO_0000599",
"EC50": "http://www.bioassayontology.org/bao#BAO_0000188",
"EC80": "http://purl.enanomapper.org/onto/ENM_0000053",
"EC90": "http://www.bioassayontology.org/bao#BAO_0001237",
"IC50": "http://www.bioassayontology.org/bao#BAO_0000190",
"LC50": "http://www.bioassayontology.org/bao#BAO_0002145",
"MIC": "http://www.bioassayontology.org/bao#BAO_0002146",
"NOEC": "http://purl.enanomapper.org/onto/ENM_0000060",
"NOEL": "http://purl.enanomapper.org/onto/ENM_0000056"
]
With 402(!) variants left. Many do not have an ontology term yet, and I filed a feature request.
Units:
recognizedUnits = [
"g/L": "g/L",
"g/l": "g/l",
"mg/L": "mg/L",
"mg/ml": "mg/ml",
"mg/mL": "mg/mL",
"µg/L of food": "µg/L",
"µg/L": "µg/L",
"µg/mL": "µg/mL",
"mg Ag/L": "mg/L",
"mg Cu/L": "mg/L",
"mg Zn/L": "mg/L",
"µg dissolved Cu/L": "µg/L",
"µg dissolved Zn/L": "µg/L",
"µg Ag/L": "µg/L",
"fmol/L": "fmol/L",
"mmol/g": "mmol/g",
"nmol/g fresh weight": "nmol/g",
"µg Cu/g": "µg/g",
"mg Ag/kg": "mg/kg",
"mg Zn/kg": "mg/kg",
"mg Zn/kg d.w.": "mg/kg",
"mg/kg of dry feed": "mg/kg",
"mg/kg": "mg/kg",
"g/kg": "g/kg",
"µg/g dry weight sediment": "µg/g",
"µg/g": "µg/g"
]
Oh, and don’t get me started on actual values, with endpoint values, as ranges, errors, etc. That variety is not the problem, but the lack of FAIR-ness makes the whole really hard to process. I now have something like:
prop = prop.replace(",", ".")
if (prop.substring(1).contains("-")) {
rdf.addTypedDataProperty(
store, endpointIRI, "${oboNS}STATO_0000035",
prop, "${xsdNS}string"
)
rdf.addDataProperty(
store, endpointIRI, "${ssoNS}has-unit", units
)
} else if (prop.contains("±")) {
rdf.addTypedDataProperty(
store, endpointIRI, "${oboNS}STATO_0000035",
prop, "${xsdNS}string"
)
rdf.addDataProperty(
store, endpointIRI, "${ssoNS}has-unit", units
)
} else if (prop.contains("<")) {
} else {
rdf.addTypedDataProperty(
store, endpointIRI, "${ssoNS}has-value", prop,
"${xsdNS}double"
)
rdf.addDataProperty(
store, endpointIRI, "${ssoNS}has-unit", units
)
}
But let me make clear: I can actually do this, add more data to the eNanoMapper database (with Nina), only because the developers of this database made their data available under an Open license (CC-BY, to be precise), allowing me to reuse, modify (change format), and redistribute it. Thanks to the authors. Data curation is expensive, whether I do it, or if the authors of the database did. They already did a lot of data curation. But only because of Open licenses, we only have to do this once.
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The U.S.A and European nanosafety communities have a longstanding history of collaboration. On both sides there are working groups,
NanoWG and WG-F (previously called
WG4) of the NanoSafety Cluster. I have been chair of WG4 for about three years and still active in the group, though in the past half year, without
dedicated funding, less active. That is already changing again with the imminent start of the
NanoCommons project.
