Commit 4192c98a authored by VIGNET Pierre's avatar VIGNET Pierre
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[doc] Fix link issues

parent 4fdc6b41
.. _working_with_source_code:
Working with Cadbiom source code
================================
......@@ -9,6 +11,7 @@ Directory Python package Description
``./gui`` ``cadbiom-gui`` Graphical User Interface
``./command_line`` ``cadbiom-cmd`` Command line
``./library`` ``cadbiom`` Library used by the 2 previous packages
``./doc`` ``-`` Documentatin of the project
================== =============== =======================================
All the code is developped in Python language.
......
.. _workflow_overview:
=================
Workflow overview
=================
......@@ -23,7 +25,7 @@ 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 results of the conversions of some databases are available below: `Prebuilt models`_.
The **second step** brings together several commands under the name of *query design*.
......@@ -37,7 +39,7 @@ 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>`_.
Examples of commands are described below: `Query the Cadbiom model`_.
The **third step** of the workflow is focused on *causality search*.
......@@ -48,7 +50,7 @@ As detailed in the results section, the notion of activation is intrinsically li
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>`_.
Examples of commands are described below: `Search for molecules of interest`_.
The **fourth step**, *visualization and analysis* is designed to analyze the families
......@@ -57,7 +59,7 @@ the solutions obtained. Heatmaps allow estimating the diversity of the trajector
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>`_.
Examples of commands are described below: `Processing of the generated files`_.
Prebuilt models
......@@ -70,9 +72,9 @@ and made available on this page with their respective characteristics.
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>`_.
`Creation of a Cadbiom model from a BioPAX endpoint`_.
Obtaining these data from the models is also explained in the chapter `Query the Cadbiom model <./examples.html#query-the-cadbiom-model>`_.
Obtaining these data from the models is also explained in the chapter `Query the Cadbiom model`_.
Here is a table of the raw data in various BioPAX databases:
......@@ -343,9 +345,9 @@ What is in the model?
Un mapping des identifiants Cadbiom avec les identifiants standards des bases de données (telles que
Uniprot, HUGO, HGNC, etc.) est alors nécessaire pour permettre à l'utilisateur de forger ses propres requêtes d'intérêt
(pour plus d'informations sur la recherche de molécules, voir le chapitre suivant:
`Search for molecules of interest <./examples.html#search-for-molecules-of-interest>`_).
`Search for molecules of interest`_).
Cette étape de mapping souvent fastidieuse est facilitée par le module décrit ci-dessous:
`Get a mapping between Cadbiom identifiers and those from external databases <./examples.html#get-a-mapping-between-cadbiom-identifiers-and-those-from-external-databases>`_.
`Get a mapping between Cadbiom identifiers and those from external databases`_.
As mentioned above, a user can either build his own model from any triplestore hosting BioPAX data,
......@@ -359,9 +361,9 @@ Indeed, Cadbiom uses internal identifiers to guarantee the unicity of biomolecul
A mapping of the Cadbiom identifiers with the standard database identifiers (such as Uniprot, HUGO, etc.)
is then necessary to allow the user to forge his own requests of interest
(for more information on the search for molecules, see the next chapter:
`Search for molecules of interest <./examples.html#search-for-molecules-of-interest>`_).
`Search for molecules of interest`_).
This often tedious mapping step is facilitated by the module described below:
`Get a mapping between Cadbiom identifiers and those from external databases <./examples.html#get-a-mapping-between-cadbiom-identifiers-and-those-from-external-databases>`_.
`Get a mapping between Cadbiom identifiers and those from external databases`_.
Get model information
......@@ -602,7 +604,7 @@ The program produces two categories of files:
As we can see, these files are not particularly meaningful, which is why the next chapter
`Processing of the results files <./examples.html#processing-of-the-results-files>`_
`Processing of the generated files`_
will discuss how to use the high-level features available to handle them.
......@@ -784,6 +786,8 @@ Example:
Avanced users
=============
.. _create_from_biopax_endpoint:
Creation of a Cadbiom model from a BioPAX endpoint
--------------------------------------------------
......
.. _cadbiom_file_format_spec:
Cadbiom File Format Specification
=================================
.. _models:
Models
------
......
......@@ -23,8 +23,8 @@ Loading files
Currently, the following types of files are supported:
- Cadbiom file format (.bcx) (see `File format specification <file_format_specification.html#models>`_),
- Import BioPAX format from a RDF triplestore (see `Creation of a Cadbiom model from a BioPAX endpoint <./examples.html#id4>`_),
- Cadbiom file format (.bcx) (see :ref:`models`),
- Import BioPAX format from a RDF triplestore (see :ref:`create_from_biopax_endpoint`),
- PID file format (.xml),
- Cadlang file format (.cl).
......
.. _installation:
Installation
============
......@@ -24,7 +26,7 @@ We use standard Python application packaging by hosting our program on the PyPI
This simple and light but well-proven system allows quickly deploying, and installing an application.
The procedure is described in the next chapter.
.. seealso:: `Working with Cadbiom source code <./dev_work_with_source.html#working-with-cadbiom-source-code>`_
.. seealso:: :ref:`working_with_source_code`
..
Veuillez noter que contrairement à des idées (trop) largement répandues, l'usage de containers
......@@ -107,6 +109,7 @@ You can install these dependencies with the following command::
pygtk2 pygtk2-libglade pygtksourceview
.. _setting_up_a_virtual_environment:
Setting up a virtual environment
--------------------------------
......@@ -183,8 +186,9 @@ At this point 2 commands are available in your shell:
- ``cadbiom_cmd``: Launch the command line program.
You can now add a shortcut to the desktop menu by following the directives in the chapter
`Install a desktop shortcut <./installation.html#id3>`_.
`Install a desktop shortcut`_.
.. _install_dev_version:
Install the development version
-------------------------------
......
......@@ -87,7 +87,7 @@ related to the states of the places of interest mentioned in a logical formula b
These sets are also called Minimal Activation Conditions.
Output files from Cadbiom can be difficult to exploit by hand
(See `Cadbiom file format specification <./file_format_specification.html>`_);
(See :ref:`cadbiom_file_format_spec`);
they contain the sequences of transitions necessary to satisfy a problem.
We have developed sub commands that allow to work with these files from the command line.
......
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