Closed vedina closed 8 years ago
Can't tell why, but this data comes from the dataset. The feature has the following structure:
{
"type":"Feature",
"title":"",
"units":null,
"isNominal":false,
"isNumeric":false,
"isMultiValue":true,
"sameAs":"http://www.opentox.org/echaEndpoints.owl#TO_GENETIC_IN_VITRO",
"isModelPredictionFeature":true,
"creator":"Just lsdfjlka sj",
"order":1007,
"source":{
"URI":"https://apps.ideaconsult.net/data/dataset/Just+lsdfjlka+sj",
"type":"read-across from supporting substance (structural analogue or surrogate)"
},
"annotation":[
{"type":"conditions","p":"medium","o":" "},
{"type":"conditions","p":"metabolic activation","o":" "},
{"type":"conditions","p":"metabolic activation system","o":" "},
{"type":"conditions","p":"species","o":" "},
{"type":"conditions","p":"std_dev","o":"=3.4 mg/l"}
],
"URI":"https://apps.ideaconsult.net/data/property/TOX/TO_GENETIC_IN_VITRO_SECTION//90CFAAC9D295E4A294963D1EF57B386CC01C30DC/Read-across/9a425a8d-23bc-3c9c-ba9b-a529c970081b"
}
As one can see, the annotations contain conditions "medium" and "std_dev".
Could it be a bug with adding endpoint data? Will the server accept such data?
Not sure why this is disturbing :)
std_dev
is an artifact , but medium
is ok, and annotations are fine overall . The datasets in bundles are generated from study data, and conditions and parameters go into feature annotations. Could you explain what's the issue?
The issue reported is that in annex 3 in the report the data is displayed incorrectly:
There should be no "medium" condition for genetic tox in vitro nor "std_dev" (it's not a condition anyway). Could you check where these come from?
could you tell which substance it is?
The substance is formaldehyde (IUC4 DSN 52) - the first one in the assessment.
OK, the study itself is intact, looking what's going with matrix generation.
This entry (with medium
and stdev
) is stored in the matrix (i.e. the bundle_substance_experiment
table, which is a copy of the initial matrix, but then includes manual edits. This particular entry is a result of manual edit, this is why it does not exist in the original study. Hence, the dataset rendering is correct.
Next is to find out why the manual edit results in additional entries.
The conditions and parameters may contain any entry, there are no fixed fields in the database. The particular entries per endpoint are configured via the study configuration. For the dataset serialisation, the conditions and parameters are written as property annotations.
Related to #149 The values for this report don't seem right
There should be no "medium" condition for
genetic tox in vitro
nor "std_dev" (it's not a condition anyway). Could you check where these come from?The table has a column endpoint, but this should not be visible for this
genetic invitro
section. Also formatting should match the one as in the matrix, not a generic table as in the popup.