chemicalchecker.database.dataset

Bioactivity Dataset definition.

This is how we define a dataset for a bioactivity space:

Column	Values	Description
Dataset_code	e.g. A1.001	Identifier of the dataset.
Level	e.g. A	The CC level.
Coordinate	e.g. A1	Coordinates in the CC organization.
Name	2D fingerprints	Display, short-name of the dataset.
Technical name	1024-bit Morgan fingerprints	A more technical name for the dataset, suitable for chemo -/bio-informaticians.
Description	2D fingerprints are…	This field contains a long description of the dataset. It is important that the curator outlines here the importance of the dataset, why did he/she make the decision to include it, and what are the scenarios where this dataset may be useful.
Unknowns	True/False	Does the dataset contain known/unknown data? Binding data from chemogenomics datasets, for example, are positive-unlabeled, so they do contain unknowns. Conversely, chemical fingerprints or gene expression data do not contain unknowns.
Discrete	True/False	The type of data that ultimately expresses de dataset, after the pre-processing. Categorical variables are not allowed; they must be converted to one-hot encoding or binarized. Mixed variables are not allowed, either.
Keys	e.g. CPD (we use @afernandez Bioteque nomenclature). Can be NULL.	In the core CC database, most of the times this field will correspond to CPD, as the CC is centred on small molecules. It only makes sense to have keys of different types when we do connectivity attempts, that is, for example, when mapping disease gene expression signatures.
Features	e.g. GEN (we use Bioteque nomenclature). Can be NULL.	When features correspond to explicit knowledge, such as proteins, gene ontology processes, or indications, we express with this field the type of biological entities. It is not allowed to mix different feature types. Features can, however, have no type, typically when they come from a heavily-processed dataset, such as gene-expression data. Even if we use Bioteque nomenclature to the define the type of biological data, it is not mandatory that the vocabularies are the ones used by the Bioteque; for example, I can use non-human UniProt ACs, if I deem it necessary.
Exemplary	True/False	Is the dataset exemplary of the coordinate. Only one exemplary dataset is valid for each coordinate. Exemplary datasets should have good coverage (both in keys space and feature space) and acceptable quality of the data.
Public	True/False	Some datasets are public, and some are not, especially those that come from collaborations with the pharma industry.
Essential	True/False	Essentail Datasets are required for the signaturization pipeline to work.
Derived	True/False	Dataset can be derived from existing data (i.e. they come from an external datasource) or they are calculated and are virtually available for any compound (e.g. “A1”).
Datasources	Foreign key to DataSource table.	Data sources that are used for generating signature 0 oof the dataset.

Dataset-Datasource have Many-to-Many relationshipi .i.e. a dataset can refer to multiple datasources and one datasource can be used by many datasets. For example drugbank is a class datasource that is used by both B1.001 and E1.001 but each of them also have additional and different datasources.

Classes

Dataset	Dataset Table class.
DatasetHasDatasource	Dataset-Datasource relationship.