Cadbiom File Format Specification¶
Cadbiom models are written in XML (Extensible Markup Language). The current encoding is ASCII, for reasons of ease of maintenance because the language used and the interface remain in Python2 and GTK2. This means that non-ASCII characters are currently not allowed in these files.
Example of model:
<?xml version = "1.0" encoding="ASCII" standalone="yes" ?> <model xmlns="http://cadbiom.genouest.org/" name="example_model"> <CSimpleNode name="A" xloc="0.287050359712" yloc="0.321867321867"/> <CSimpleNode name="B" xloc="0.287019215796" yloc="0.431203931203"/> <transition ori="A" ext="B" event="_h_1" condition="" action="" fact_ids=""/> </model>
Model files should have a .bcx extension.
text/plain (depending on the version, the prologue may be absent).
Tag for transitions¶
Type of tag is:
ori: (mandatory) the name of the consumed node which is at the left of the transition.
ext: (mandatory) the name of the producted node which is at theright of the transition.
event: (mandatory) the name of the event/clock; 1 event may share multiple transitions. Also, an event name can be a logical formula for complex transitions; this kind of formula may involve time operators like
whenused to describe transitions shared by multiple events under various conditions;
condition: (mandatory) A logical formula whose satisfiability is necessary for the transition to take place. A condition can be an empty string.
action: (optional): todo
fact_ids: (deprecated) A list of publication IDs for tracability. The content of this attribute is now in metadata.
Metadata for nodes and transitions are stored in their XML elements between each star-tag and end-tag.
Metadata of Cadbiom entities is serialized as JSON (http://www.json.org) and is accessible from the
Cadbiom framework via the attribute
note of these objects.
The following fields are available in this JSON data; most of them are obtained from the BioPAX database queried:
- uri: The uri of the entity in in the database,
- entityType: The BioPAX type of the entity (Ex: Complex, Protein, Dna, etc.),
- names: List of synonyms of the entity,
- entityRef: Base entity reference (same entity but without modifications),
- location: Cell localization,
- modificationFeatures: Dictionary of modifications supported by the entity,
- members: Uris of the members of the entity if it is a class
- reactions: List of reactions where the entity is involved,
- xrefs: Cross-references in external databases.
Minimal Activation Condition files¶
These files store solutions from the Cadbiom framework.
Should have a .txt extension.
We destinguish 2 types of files: complete mac files and mac files.
In complete mac files each solution is composed by the set of boundaries and the trajectory which allowed to produce it. A set of boundaries is a line with names of places separated by a space. Each step of the trajectory is present on an independent line. A step is composed of one or more event (s). Solutions are stored one after the other without separator or line feed.
Jnk1_nucleus JUN_nucleus_gene % _h_1015 % _h_323 % _h_2910
In mac files, only the set of boundaries is present. Sets are stored one after the other without separator or line feed.
Jnk1_nucleus JUN_nucleus_gene cortisol JNK1_2_cytoplasm JUN_nucleus_gene
A tag is a markup construct that begins with < and ends with >. 2 flavors can be encountered:
- start-tag, such as
- end-tag, such as
- start-tag, such as
- An element is a logical document component that either begins with a start-tag and ends with a matching end-tag. The characters between the start-tag and end-tag, if any, are the element’s content, and may contain markup, including other elements, which are called child elements.
- An attribute is a markup construct consisting of a name–value pair that exists within a start-tag or empty-element tag.