JSON Datums for the Pathway Logic Signal Transduction Model

Here we provide access to a JSON representation of the Pathway Logic (PL) Signal Transduction Model (STM) and datum collection. The latest data was uploaded on December 28 2016. It is assumed that the user is familiar with JSON and the PL concepts. More information available from the PL website or by request to Carolyn Talcott.


Datums are a computable representation of experimental results, used to infer rules in the STM models. The JSON representation is 16dec28datums.json and is 57M and contains over 60K datums. datum-json-scheme.txt is an informal description of the structure of datum objects. See the datums page for a description of datum elements.


The JSONB directory contains a full controlled vocabulary, and is available as a zip file.

The Rule Knowledge Base (RKB) comes in two flavors, one generated by including common rules (a rule label begins with digits followed by "c." vs digits followed by ".") and one generated without including common rules. The former is much bigger. Dishes represent experimental setups -- what cells are expressing and any treatment. Dishnets add reachable rules to the dish making an executable model. In some dishes common rules are essential to fill gaps. In some cases, like the EgfDish, which is more highly curated, they tend to add noise. Common rules may be useful in starting with a model generated without them and more selectively adding those that improve the model instead of the simple automatic add them all approach that the Pathway Logic Assistant (PLA) takes.

The JSON for the RKB without common rules is contained in the zip file cltJSONUnc.zip directory. It contains: The corresponding dishes are available as a zip file in DishNetsnc.zip. It contains The JSON for the RKB with common rules is contained in with contents analogous to the above.

Some Statistics