Welcome to CaSQ

CaSQ [1], is a tool that can convert a molecular interaction map built with CellDesigner, or any similar SBML-capable tool, to an executable Boolean model. CaSQ is developed in Python (download and install instructions can be found on the Python package index) and uses as source the xml file of CellDesigner, in order to infer preliminary Boolean rules based solely on network topology and semantic annotations (e.g., certain arcs are noted as catalysis, inhibition, etc.). The aim is to convert a Process Description representation, i.e., a reaction model, into a full logical model. The resulting structure is closer to an Activity Flow diagram, though not in a strict SBGN-PD to SBGN-AF notion. Moreover logical rules that make the model executable are also obtained. CaSQ was used on maps of the Rheumatoïd Arthritis, of the MAP-Kinase cascade, etc. and is now being used by the Covid-19 DiseaseMaps consortium to automatically obtain logical models from maps [2].

CaSQ has recently been added to the CoLoMoTo Docker image and can be used in such a notebook.

Command-line usage

Just follow the instructions:

$ casq --help
usage: casq [-h] [-v] [-D] [-c] [-s] [-r S] [-f FIXED] [-n]
            [-u [UPSTREAM ...]] [-d [DOWNSTREAM ...]] [-b] [-g GRANULARITY]
            [-i INPUT] [-C]
            [infile] [outfile]

Convert CellDesigner models to SBML-qual with a rather strict semantics.
Copyright (C) 2019, Sylvain.Soliman@inria.fr GPLv3

positional arguments:
  infile                CellDesigner File
  outfile               SBML-Qual/BMA json File

  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -D, --debug           Display a lot of debug information
  -c, --csv             Store the species information in a separate CSV (and
                        .bnet) file
  -s, --sif             Store the influence information in a separate SIF file
  -r S, --remove S      Delete connected components in the resulting model if
                        their size is smaller than S. A negative S leads to
                        keep only the biggest(s) connected component(s)
  -f FIXED, --fixed FIXED
                        A CSV file containing input values or knock-ins/knock-
                        outs, one per line, with name in the first column and
                        the value in the second.
  -n, --names           Use the names as IDs in the SBML file
  -u [UPSTREAM ...], --upstream [UPSTREAM ...]
                        Only species upstream of this/these species will be
  -d [DOWNSTREAM ...], --downstream [DOWNSTREAM ...]
                        Only species downstream of this/these species will be
  -b, --bma             Output to BMA json format
                        When exporting to BMA, use this granularity
  -i INPUT, --input INPUT
                        When exporting to BMA, nodes with no input should be
                        set to this value
  -C, --colourConstant  When exporting to BMA, colour all variables pink
                        (defaults to colour by compartment)

What CaSQ does

The conversion happens in 4 steps.

  1. First, the map is reduced through a pass of graph-rewriting rules. These rules are executed in order and in a single pass, so the rewriting is terminating and confluent.

    The idea of this reduction is that a single qualitative species of the logical model often represents by its state (active/inactive) several species of the original map.

    The rules are the following:

    1. if two species of the map are only reactants in a single reaction, i.e., do not take part in any other reaction, if that reaction is annotated as heterodimer association, and if one of the reactants is annotated as a receptor, then the receptor is deleted from the map (its annotations are added to the product of the reaction);

    2. if two input species of the map take part in a reaction annotated as heterodimer association, if none of them is annotated as receptor, and if both do not take active part (i.e., reactant or modifier) in any other reaction, then both are merged into the complex, product of the reaction (their annotations are added to the product, and the reactions that had them as product are rewired to have the complex as product);

    3. if one species only appears in a single reaction as reactant, if that reaction has a single product, and if both the reactant and the product have the same name, then the reactant is deleted (its annotations are merged into those of the product);

    4. if one species only appears as reactant in a single reaction (but maybe appears as product in another reaction) that has a single product and is annotated as transport, and if both the reactant and the product have the same name, then the reactant is merged into the product (its annotations are merged into those of the product, and the reactions producing it are rewired to the product).

    The rationale of using the name to identify the same component in different states (gene, RNA, protein, transported/phosphorylated/methylated protein, etc.) is that relying on the active annotation in CellDesigner maps proved to be insufficient and that the model should only keep what really contributes to some form of signal propagation.

  2. Then, the topology of the model is computed as some simple form of SBGN-PD to SBGN-AF conversion, with one qualitative species corresponding to each original map species. This species inherits the original map layout, using SBML3 Layout package, and MIRIAM annotations (e.g., PubMed IDs as bqbiol:isDescribedBy). The annotations have been currently arbitrarily associated to each regulated component rather than each regulation, but that is mostly because tools supporting the latter are quite rare. Basically all reactants and modifiers of a reaction get a positive influence on all the products of that reaction, whereas all inhibitors get a negative influence. Compared to the formal abstraction of influence graphs from reaction graphs (Ref FagesSoliman08tcs) note that the mutual inhibition between reactants is purposely ignored. This is related to the fact that our model simplification step has already condensed active and inactive forms of the same species.

  3. Finally logical rules of the model are computed. For each species, its logical rule is defined as the OR over all reactions producing it of another OR on all positive modifiers (annotated as catalysis or transition) being on, of an AND on all products being activated and all inhibitors being inactive. Therefore a target is on if one of the reactions producing it is on, a reaction is on if all reactants are on, all inhibitors are off and one of the catalysts is on.

  4. Model cleaning is then done through optional removal of unconnected components. From our experience, only keeping the biggest connected component is what makes the more sense in a modelling perspective, however it is possible to specify a “minimum size” and keep all connected components above that size. Names of the qualitative species are also made more precise by adding the original type/modifications of the species (e.g., RNA, phosphorylated, etc.) and if there are still homonyms the original compartment is added too.

CaSQ generates two output files, the proper logical model encoded in SBML-qual, a format that is compatible for further analysis with modelling tools such as GINsim or CellCollective and a CSV file that contains information about the names, the logic formulae and the CellDesigner alias. The second file is mostly for automated treatment.


Indices and tables