Development repository to process the Disease Maps map with Hipathia.
- Clone the repository
- Create a .ENV file
- Copy
example.env
to.env
-- Change themaps_dir
environment variable as outlined inexample.env
. - Load the project using RStudio
-- If the requirements are met,
packrat
does everything.
- Copy
R >= 3.5
- The
SBML
library must be installed and reachable byR
.
- Clone the repository.
- Initialize git-flow.
- Use the develop branch.
- For the moment, create a notebook following the naming scheme of those already included.
- Once we begin to produce real code, follow the standard git-flow work-flow.
At the moment only exploratory notebooks are included.
Notebooks 1 and 2 represent different experiments of the same approach: parse the SBML map with the read_bml
library, convert to igraph
, using the graph representation included in the library, and then work with the induced attributes.
The automatic graph conversion provided by the read_sbml
library poses serious problems: for instance, the edges pointing to other edges, such as those labeled as modifiers, are missing. In the end most inhibitions are lost during the conversion.
- Reactions labeled as HETERODIMER_ASSOCIATION can be removed as they represent complex-formation processes.
- For each reaction that includes modifiers we include one auxiliary node (with input value 1) named
aux
.- Each node labeled as reactant is connected to
aux
as input and output, respectively. - Each node labeled as product is connected to
aux
as output and input, respectively. - Each node labeled as modifier is connected to
aux
as input and output, respectively.
- Each node labeled as reactant is connected to
Figure 0 shows he most basic example, with one product, one reactant and two modifiers.
For example, suppose that we have the following sequence s1,s2/s5,s6/s3,s4
where the nodes are labeled as reactant/product/modifiers. Figure 1 shows the resulting network after we apply the previous rules.
Note, however, that we have provided the most general example, as the number of reactants, products and modifiers can be any number greater than 0.
- Resolve BOOLEAN_LOGIC_GATE_AND
-
Resolve BOOLEAN_LOGIC_GATE_OR
-
Resolve those nodes labeled as modifier that are parsed as CATALYSIS and are not properly resolved because there is another tag, either BOOLEAN_LOGIC_GATE_AND or BOOLEAN_LOGIC_GATE_OR, which has not been correctly parsed.
- Resolve protein_X to protein_X
- Resolve modulations
- Include the module parsing functionality from the graph notebooks.