datasets.md

@@ -63,19 +63,10 @@ This is how we define a 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.|
-|Permanent|`True`/`False`|Are measurements for each entry permanent? 2D fingerprints, for example, are permanent. However, most of the biological data may change/evolve with the different versions of the CC. This field, in essence, dictates whether the dataset should be completely updated in every update of the CC, or whether new entries can be simply appended.|
-|Finished|`True`/`False`|Is the dataset considered to be finished? For examples, datasets coming from supplementary data of scientific papers are immutable, and they consequently need no updates in posterior versions of the CC.|
-|Is 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.|
-|Predicted|`True`/`False`|Is the dataset a result of a prediction (by us or by others?). Prediction results are perfectly valid CC datasets, in principle.|
-|Connectivity|`True`/`False`|Is there a way to connect this dataset to other biological entities? We understand connectivity as a generalization of the cMap idea of matching gene expression signatures.|
-|Connectivity comments|Free text commenting on the connectivity strategy (e.g. type of distance)|This field needs to be self-explanatory.|
+|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.|
-|Number of keys|e.g. 800000|Number of samples in the dataset.|
 |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.|
-|Number of features|e.g. 1000|Number of features in the dataset.|
 |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.|
-|Source|Free text defining the source of data.|More than one source is allowed. We have mild constraints in the nomenclature, here.|
-|Version|CC version|The CC is updated every 6 months.|
 |Public|`True`/`False`|Some datasets are public, and some are not, especially those that come from collaborations with the pharma industry.|
 
 See the [PostgreSQL database](database) for more information.