![](\"/assets/images/Screenshot_20180916_170915.png\")
\nSlice of the spreadsheet in the supplementary info.\n
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\nSlice of the spreadsheet in the supplementary info.\n
Just some bit of cleaning I scripted today for a number of toxicology end points in a database published some time ago the\nzero-APC Open Access (CC_BY) journal Beilstein of Journal of Nanotechnology,\nNanoE-Tox (doi:10.3762/bjnano.6.183).
\n\nThe curation I am doing is to redistribute the data in the eNanoMapper database (see doi:10.3762/bjnano.6.165)\nand thus with ontology annotation (see doi:10.1186/s13326-015-0005-5):
\n\nrecognizedToxicities = [\n \"EC10\": \"http://www.bioassayontology.org/bao#BAO_0001263\",\n \"EC20\": \"http://www.bioassayontology.org/bao#BAO_0001235\",\n \"EC25\": \"http://www.bioassayontology.org/bao#BAO_0001264\",\n \"EC30\": \"http://www.bioassayontology.org/bao#BAO_0000599\",\n \"EC50\": \"http://www.bioassayontology.org/bao#BAO_0000188\",\n \"EC80\": \"http://purl.enanomapper.org/onto/ENM_0000053\",\n \"EC90\": \"http://www.bioassayontology.org/bao#BAO_0001237\",\n \"IC50\": \"http://www.bioassayontology.org/bao#BAO_0000190\",\n \"LC50\": \"http://www.bioassayontology.org/bao#BAO_0002145\",\n \"MIC\": \"http://www.bioassayontology.org/bao#BAO_0002146\",\n \"NOEC\": \"http://purl.enanomapper.org/onto/ENM_0000060\",\n \"NOEL\": \"http://purl.enanomapper.org/onto/ENM_0000056\"\n]\nWith 402(!) variants left. Many do not have an ontology term yet, and I\nfiled a feature request.
\n\nUnits:
\n\nrecognizedUnits = [\n \"g/L\": \"g/L\",\n \"g/l\": \"g/l\",\n \"mg/L\": \"mg/L\",\n \"mg/ml\": \"mg/ml\",\n \"mg/mL\": \"mg/mL\",\n \"µg/L of food\": \"µg/L\",\n \"µg/L\": \"µg/L\",\n \"µg/mL\": \"µg/mL\",\n \"mg Ag/L\": \"mg/L\",\n \"mg Cu/L\": \"mg/L\",\n \"mg Zn/L\": \"mg/L\",\n \"µg dissolved Cu/L\": \"µg/L\",\n \"µg dissolved Zn/L\": \"µg/L\",\n \"µg Ag/L\": \"µg/L\",\n \"fmol/L\": \"fmol/L\",\n\n \"mmol/g\": \"mmol/g\",\n \"nmol/g fresh weight\": \"nmol/g\",\n \"µg Cu/g\": \"µg/g\",\n \"mg Ag/kg\": \"mg/kg\",\n \"mg Zn/kg\": \"mg/kg\",\n \"mg Zn/kg d.w.\": \"mg/kg\",\n \"mg/kg of dry feed\": \"mg/kg\",\n \"mg/kg\": \"mg/kg\",\n \"g/kg\": \"g/kg\",\n \"µg/g dry weight sediment\": \"µg/g\",\n \"µg/g\": \"µg/g\"\n]\nOh, and don’t get me started on actual values, with endpoint values, as ranges, errors, etc. That variety is\nnot the problem, but the lack of FAIR-ness makes the whole really hard to process. I now have something like:
\n\nprop = prop.replace(\",\", \".\")\nif (prop.substring(1).contains(\"-\")) {\n rdf.addTypedDataProperty(\n store, endpointIRI, \"${oboNS}STATO_0000035\",\n prop, \"${xsdNS}string\"\n )\n rdf.addDataProperty(\n store, endpointIRI, \"${ssoNS}has-unit\", units\n )\n} else if (prop.contains(\"±\")) {\n rdf.addTypedDataProperty(\n store, endpointIRI, \"${oboNS}STATO_0000035\",\n prop, \"${xsdNS}string\"\n )\n rdf.addDataProperty(\n store, endpointIRI, \"${ssoNS}has-unit\", units\n )\n} else if (prop.contains(\"<\")) {\n} else {\n rdf.addTypedDataProperty(\n store, endpointIRI, \"${ssoNS}has-value\", prop,\n \"${xsdNS}double\"\n )\n rdf.addDataProperty(\n store, endpointIRI, \"${ssoNS}has-unit\", units\n )\n}\nBut let me make clear: I can actually do this, add more data to the eNanoMapper database (with\nNina), only because the developers of this database made their data\navailable under an Open license (CC-BY, to be precise), allowing me to reuse, modify (change format), and redistribute\nit. Thanks to the authors. Data curation is expensive, whether I do it, or if the authors of the database did. They\nalready did a lot of data curation. But only because of Open licenses, we only have to do this once.
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