How to add data entries to OpenTox datasets
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Data entries in OpenTox::Datasets follow the table metaphor with feature values in columns and data entries (compounds) in rows. To define the sequence of features you will have to set the dataset features first (think of it as setting the table header). After that you can append data entries sequentially with the << operator which takes an Array as argument. The first array object is reserved for a OpenTox::Compound, the remaining entries are feature values (in the same order as the dataset features). Data entries are sorted in the same sequence as they are created, multiple entries for the same compound are allowed.

Example:

# create dataset
dataset = OpenTox::Dataset.new nil, @@subjectid

# create and save features
feature1 = Feature.new nil, @@subjectid
feature1.title = "my first feature title"
# set more metadata
feature1.put
feature2 = Feature.new nil, @@subjectid
feature2.title = "my second feature title"
# set more metadata
feature2.put

# add features (i.e. set table headers)
dataset.features = [feature1, feature2]

# add a data entry
compound = Compound.from_smiles "c1ccccc1"
dataset << [ compound, true, 0.5 ]

# add another data entry
compound = Compound.from_smiles "CCC(CC)CN"
dataset << [ compound, false, 1.0 ]

# save
dataset.put

You can find more examples in opentox-test/test/dataset.rb.

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Tags

• Dataset 2