Commit 492edf96 authored by VIGNET Pierre's avatar VIGNET Pierre
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[doc] Examples: Add description of the workflow

parent 186b728d
......@@ -4,10 +4,70 @@ Workflow overview
This guide can help you start working with the Cadbiom command line.
.. figure:: _static/demo_workflow/workflow.svg
:scale: 85 %
:alt:
:align: center
Workflow for the Cadbiom framework.
Four steps can be identified:
**Model building**, covered by the standalone tool named *biopax2cadbiom*;
**Assisted query reconstruction**,
**Causality search**,
**Analysis and visualisation** covered by the Cadbiom package named *cadbiom-cmd*.
The analysis of a BioPAX model is performed according to **four main steps**.
The **first step** of the Cadbiom framework relies on the *biopax2cadbiom* package.
It allows querying BioPAX ontologies stored in public or local endpoints in order to interpret them into Cadbiom models.
The results of the conversions of some databases are available below: `prebuilt models <./examples.html#prebuilt-models>`_.
The **second step** brings together several commands under the name of *query design*.
This step is dedicated to query construction. A query is a boolean logical formula that describes the
combination of molecules for which regulators will be searched.
The characteristics of a Cadbiom model and its content (list of identifiers of biological compounds,
list of boundary compounds, and list of genes) can be exported. Among the essential data, the user
will find mappings between various databases thanks to the preservation of all cross-references with
public databases (such as HGCN, Uniprot, Chebi) provided in the BioPAX.
Indeed, Cadbiom uses internal identifiers to guarantee the uniqueness of the biomolecules in its models.
A mapping of Cadbiom identifiers with the standard database identifiers is necessary to allow a user to build queries.
Examples of commands are described below: `prebuilt models <./examples.html#id1>`_.
The **third step** of the workflow is focused on *causality search*.
In this step, the user explores the dynamics of a Cadbiom model. He identifies sets of biomolecules that
represent the initial conditions of the system, leading to the activation of the desired entities via controlled
biochemical transformations described in the model.
As detailed in the results section, the notion of activation is intrinsically linked to the non-deterministic
semantics associated with guarded transitions. This analysis therefore generates several families of controllers
associated with trajectories composed by the entities activated during a search.
Examples of commands are described below: `prebuilt models <./examples.html#id3>`_.
The **fourth step**, *visualization and analysis* is designed to analyze the families
of controllers generated in the previous step. A matrix of occurrences details the presence of controllers in
the solutions obtained. Heatmaps allow estimating the diversity of the trajectories leading to the studied
phenotype (i.e. the boolean query). Trajectory graphs allow visualizing all the transformations undergone
by the intermediate molecules from the control molecules to the target molecules.
Examples of commands are described below: `prebuilt models <./examples.html#processing-of-the-generated-files>`_.
Prebuilt models
===============
Some models are pre-generated from the pathway commons site and made available on this page with their respective characteristics.
Some models are pre-generated from the PathwayCommons `archive <https://www.pathwaycommons.org/archives/PC2/>`_
and made available on this page with their respective characteristics.
.. todo::
source ACSN database
Advanced users will be able to create their own models from a SPARQL endpoint as explained in the chapter
`Creation of a Cadbiom model from a BioPAX endpoint <./examples.html#creation-of-a-cadbiom-model-from-a-biopax-endpoint>`_.
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