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Update production phase authored by Miquel Duran-Frigola's avatar Miquel Duran-Frigola
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production-phase.md
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*Diagrams below are editable at this [draw.io link](https://drive.google.com/file/d/1PR0G2u03_-LB1jZvpIV02zt5YDfwXiJc/view?usp=sharing). Feel free to modify them.* *Diagrams below are editable at this [draw.io link](https://drive.google.com/file/d/1PR0G2u03_-LB1jZvpIV02zt5YDfwXiJc/view?usp=sharing). Feel free to modify them.*
The central task of the CC is to produce signatures of different types, given compound-related data typically fetched from the public domain. We can identify several scenarios where signatures are to be generated: The central task of the CC is to produce signatures of different types, given compound-related data typically fetched from the public domain. Signature production is performed via a rather complex/long [pipeline](#pipeline). There are several scenarios where signature generation will be necessary:
* A new dataset is *added* or a dataset is *updated*. * A new dataset is *added* or a dataset is *updated*.
* It will happen for all of the CC every six months. * It will happen for all of the CC every six months.
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* Mapping means that a new compound is projected onto the signature space of a dataset of choice. For example, given a new molecule with a calculated 2D fingerprint, we might want to obtain `A1.001` signatures for it, without actually adding the molecule to the `A1.001`. Another example would be a new molecule for which we know a target that is not associated * Mapping means that a new compound is projected onto the signature space of a dataset of choice. For example, given a new molecule with a calculated 2D fingerprint, we might want to obtain `A1.001` signatures for it, without actually adding the molecule to the `A1.001`. Another example would be a new molecule for which we know a target that is not associated
* [Connectivity](connectivity) is the generalization of mapping to biological entities other than compounds. Some, but not all, of the datasets will have connectivity capabilities. For example, a disease gene expression signature can be compared to a compound gene expression signature (`D1.001`). Or disease-related genes can be allocated on the protein-protein interaction network and compared to the network context of drug targets (`C5.001`). * [Connectivity](connectivity) is the generalization of mapping to biological entities other than compounds. Some, but not all, of the datasets will have connectivity capabilities. For example, a disease gene expression signature can be compared to a compound gene expression signature (`D1.001`). Or disease-related genes can be allocated on the protein-protein interaction network and compared to the network context of drug targets (`C5.001`).
In the diagram below, we show how This is best explained with a diagram:
:warning: Unfortunately, we do not have a clear means to produce [signatures type 3](signaturization#signatures-type-3) yet. In consequence, their production is not appropriately reflected in the [pipeline](#pipeline) below.
:warning: Unfortunately, we do not have a clear means to produce [signatures type 3](signaturization#signatures-type-3) yet. In consequence, their production is not appropriately reflected in the [pipeline](#pipeline).
## Folder structure ## Folder structure
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