Open vedina opened 11 years ago
Is a substance a special kind ot DataSet?
Good idea, this is one possible interpretation. There is a value to have the data model of a substance be close to the dataset data model, but the most important is that a substance establishes relations between the compounds it consists of (specifying purity, concentrations, functions, etc), while a dataset is just a set of unrelated entities. Perhaps we can get the best of both worlds by combining these ideas.
As defined in REACH guide : Chemical substance, a material with a definite chemical composition. Mono-constituent substance: A substance with one main constituent. Multi-constituent substance: A substance with two or more main constituents. Main constituent: A constituent, not being an additive or impurity, in a substance that makes up a significant part of that substance. Contributes to the naming of the substance. Concentration of the main constituent(s) = purity of the substance Additive: A substance that has been intentionally added to stabilise the substance. Contributes to the substance composition (but notto the naming). Impurity: An unintended constituent present in a substance, as produced. Does not contribute to the naming of the substance.
The current JSON serialisation (see at the test instance )
A substance (one or more) : /substance , /substance/{id}
{
"substance":[
{
"URI":"http://apps.ideaconsult.net:8080/bioclipse/substance/1",
"ownerUUID":null,
"i5uuid":"IUC4-efdb21bb-e79f-3286-a988-b6f6944d3734",
"name":"formaldehyde (IUC4 DSN 52)",
"publicname":"",
"format":"i5._5.",
"substanceType":"other:",
"referenceSubstance": {"i5uuid":"ECB5-053aa8c4-d29b-4aa5-b457-5cc3b47f7d8b"}
}
]
}
Composition of a substance: /substance/{id}/composition . In fact a composition JSON is very close to a dataset JSON
{
"composition": [
{
"substance": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/substance/1"
},
"component": {
"compound": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/compound/18/conformer/19",
"name": "",
"cas": "",
"einecs": ""
},
"values": {
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault": "formaldehyde",
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23CASRNDefault": "50-00-0",
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23EINECSDefault": "200-001-8",
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23TradeNameDefault": "Formaldehyde, gas"
},
"facets": []
},
"compositionUUID": "L-340e87fb-e95f-3743-823d-1b9b25a94d56",
"relation": "HAS_CONSTITUENT",
"proportion": {
"typical": {
"precision": "",
"value": 100,
"unit": "% (w/w)"
},
"real": {
"lowerPrecision": "",
"lowerValue": 0,
"upperPrecision": "",
"upperValue": 0,
"unit": ""
},
"function_as_additive": null
}
},
{
"substance": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/substance/1"
},
"component": {
"compound": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/compound/18/conformer/19",
"name": "",
"cas": "",
"einecs": ""
},
"values": {
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault": "formaldehyde",
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23CASRNDefault": "50-00-0",
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23EINECSDefault": "200-001-8",
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23TradeNameDefault": "Formaldehyde, gas"
},
"facets": []
},
"compositionUUID": "L-cf10d721-b0e7-37cd-a233-e9a2483c4d3c",
"relation": "HAS_CONSTITUENT",
"proportion": {
"typical": {
"precision": "",
"value": 0,
"unit": ""
},
"real": {
"lowerPrecision": "",
"lowerValue": 0,
"upperPrecision": "",
"upperValue": 0,
"unit": ""
},
"function_as_additive": null
}
},
{
"substance": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/substance/1"
},
"component": {
"compound": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/compound/19/conformer/20",
"name": "",
"cas": "",
"einecs": ""
},
"values": {
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault": "water",
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23CASRNDefault": "7732-18-5",
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23EINECSDefault": "231-791-2"
}
},
"compositionUUID": "L-f2d0bc7e-a154-3f6d-babd-22ea28467466",
"relation": "HAS_ADDITIVE",
"proportion": {
"typical": {
"precision": "ca.",
"value": 49,
"unit": "% (w/w)"
},
"real": {
"lowerPrecision": "",
"lowerValue": 0,
"upperPrecision": "",
"upperValue": 0,
"unit": ""
},
"function_as_additive": "solvent"
}
},
{
"substance": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/substance/1"
},
"component": {
"compound": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/compound/20/conformer/21",
"structype": "NA",
"metric": null,
"name": "",
"cas": "",
"einecs": ""
},
"values": {
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault": "6,6'-(m-phenylene)bis(1,3,5-triazine-2,4-diamine)",
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23CASRNDefault": "5118-80-9",
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23EINECSDefault": "225-859-0"
}
},
"compositionUUID": "L-f2d0bc7e-a154-3f6d-babd-22ea28467466",
"relation": "HAS_ADDITIVE",
"proportion": {
"typical": {
"precision": "",
"value": 0,
"unit": ""
},
"real": {
"lowerPrecision": "",
"lowerValue": 0,
"upperPrecision": "",
"upperValue": 0,
"unit": ""
},
"function_as_additive": ""
}
},
{
"substance": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/substance/1"
},
"component": {
"compound": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/compound/21/conformer/22",
"structype": "NA",
"metric": null,
"name": "",
"cas": "",
"einecs": ""
},
"values": {
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault": "methanol|Methanol",
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23CASRNDefault": "67-56-1",
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23EINECSDefault": "200-659-6"
},
"facets": []
},
"compositionUUID": "L-f2d0bc7e-a154-3f6d-babd-22ea28467466",
"relation": "HAS_IMPURITY",
"proportion": {
"typical": {
"precision": "",
"value": 0,
"unit": ""
},
"real": {
"lowerPrecision": "",
"lowerValue": 0.5,
"upperPrecision": "",
"upperValue": 2,
"unit": "% (w/w)"
},
"function_as_additive": null
}
},
{
"substance": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/substance/1"
},
"component": {
"compound": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/compound/22/conformer/23",
"structype": "NA",
"metric": null,
"name": "",
"cas": "",
"einecs": ""
},
"values": {
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault": "iron(2+)",
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23CASRNDefault": "7439-89-6",
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23EINECSDefault": "231-096-4"
},
"facets": []
},
"compositionUUID": "L-f2d0bc7e-a154-3f6d-babd-22ea28467466",
"relation": "HAS_IMPURITY",
"proportion": {
"typical": {
"precision": "<=",
"value": 0.0001,
"unit": "% (w/w)"
},
"real": {
"lowerPrecision": "",
"lowerValue": 0,
"upperPrecision": "",
"upperValue": 0,
"unit": ""
},
"function_as_additive": null
}
},
{
"substance": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/substance/1"
},
"component": {
"compound": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/compound/23/conformer/24",
"structype": "NA",
"metric": null,
"name": "",
"cas": "",
"einecs": ""
},
"values": {
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault": "|formic acid",
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23CASRNDefault": "64-18-6",
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23EINECSDefault": "200-579-1"
},
"facets": []
},
"compositionUUID": "L-f2d0bc7e-a154-3f6d-babd-22ea28467466",
"relation": "HAS_IMPURITY",
"proportion": {
"typical": {
"precision": "ca.",
"value": 0.3,
"unit": "% (w/w)"
},
"real": {
"lowerPrecision": "",
"lowerValue": 0,
"upperPrecision": "",
"upperValue": 0,
"unit": ""
},
"function_as_additive": null
}
}
],
"feature": {
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23IUPACNameDefault": {
"type": "Feature",
"title": "IUPAC name",
"units": "",
"isNominal": "false",
"isNumeric": "false",
"sameAs": "http://www.opentox.org/api/1.1#IUPACName",
"isModelPredictionFeature": "false",
"creator": "http://ambit.sourceforge.net",
"order": 1,
"source": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/dataset/Default",
"type": "Dataset"
},
"annotation": []
},
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault": {
"type": "Feature",
"title": "Names",
"units": "",
"isNominal": "false",
"isNumeric": "false",
"sameAs": "http://www.opentox.org/api/1.1#ChemicalName",
"isModelPredictionFeature": "false",
"creator": "http://ambit.sourceforge.net",
"order": 2,
"source": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/dataset/Default",
"type": "Dataset"
},
"annotation": []
},
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23CASRNDefault": {
"type": "Feature",
"title": "CasRN",
"units": "",
"isNominal": "false",
"isNumeric": "false",
"sameAs": "http://www.opentox.org/api/1.1#CASRN",
"isModelPredictionFeature": "false",
"creator": "http://ambit.sourceforge.net",
"order": 3,
"source": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/dataset/Default",
"type": "Dataset"
},
"annotation": []
},
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23EINECSDefault": {
"type": "Feature",
"title": "EC number",
"units": "",
"isNominal": "false",
"isNumeric": "false",
"sameAs": "http://www.opentox.org/api/1.1#EINECS",
"isModelPredictionFeature": "false",
"creator": "http://ambit.sourceforge.net",
"order": 4,
"source": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/dataset/Default",
"type": "Dataset"
},
"annotation": []
},
"http://apps.ideaconsult.net:8080/bioclipse/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23TradeNameDefault": {
"type": "Feature",
"title": "http://www.opentox.org/api/1.1#TradeName",
"units": "",
"isNominal": "false",
"isNumeric": "false",
"sameAs": "http://www.opentox.org/api/1.1#TradeName",
"isModelPredictionFeature": "false",
"creator": "http://ambit.sourceforge.net",
"order": 5,
"source": {
"URI": "http://apps.ideaconsult.net:8080/bioclipse/dataset/Default",
"type": "Dataset"
},
"annotation": []
}
}
}
A proposal for a new resource, Substance. A substance consists of information of its constituents, additive, impurities. Each of these may be linked to a chemical compound (OpenTox Compound resource).
Important for communication with IUCLID 5 and REACH related assessment, but also for describing nanomaterials.
Examples http://apps.ideaconsult.net:8080/bioclipse/substance [JSON] http://apps.ideaconsult.net:8080/bioclipse/substance/1 [JSON] http://apps.ideaconsult.net:8080/bioclipse/substance/1/composition [JSON]