Skip to content

GitLab

production phase · Changes

Page history
Update production phase authored by Miquel Duran-Frigola's avatar Miquel Duran-Frigola
Hide whitespace changes
Inline Side-by-side
production-phase.md
View page @ 79b32dc3
......@@ -2,7 +2,7 @@
*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*.
* It will happen for all of the CC every six months.
......@@ -11,9 +11,11 @@ The central task of the CC is to produce signatures of different types, given co
* 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`).
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
......