READ ME

This text describes the data presented in the paper: "Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualisation". 

DOI: [http://doi.org/10.1093/bioinformatics/btv660](http://doi.org/10.1093/bioinformatics/btv660) 




The online version of this material is available here: [https://github.com/rulebased/rbmo](https://github.com/rulebased/rbmo)

Authors: Goksel Misirli, Matteo Cavaliere, William Waites, Matthew Pocock, Curtis Madsen, Owen Gilfellon, Ricardo Honorato-Zimmer, Paolo Zuliani, Vincent Danos, and Anil Wipat




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Introductory information
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Files included in the data deposit (include a short description of what data are contained): 

1) A single archive file, rbmo-master.zip, containing the following folders: 
  - ontology:  Rule-based Modelling Ontology files in OWL/XML, RDF/Turtle and Manchester syntaxes. The ontology has been developed as part of the publication in order to faciliate the annotation of rule-based models. Annotating rule-based models with biological knowledge enhance computational access to models and can facilitate the development of many potential applications.
  - examples: Example models demonstrating the annotation approach presented in the paper.
    -tcs.kappa: An annotated Kappa model for a two-component system
    -tcs.kappa: An annotated BNGL model for a two-component system
  - krdf: A proof of concept tool that can extract annotations from rule-based models in order to validate rules


Key words used to describe the data: Rule-based models, annotation, ontologies, iata integration, data mining









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Methodological information
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A brief method description, what the data is, how and why it was collected or created, and how it was processed:


Instruments, hardware and software used: Technologies used include RDF, Turtle, Ontologies, SPARQL, Rule-based models (Kappa, BNGL), Haskell 


Date(s) of data collection: 2016

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Data validation (how was the data checked, proofed and cleaned): The RBM ontology, the krdf tool and example file were created as part of the publication by the authors.


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Data-specific information
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Definitions of names, labels, acronyms or specialist terminology uses for variables, records and their values: 
RDF: Resource Description Framework
OWL: Web Ontology Language
RBM: Rule-based models
BNGL: BioNetGen Language


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Contact
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Please contact rdm@ncl.ac.uk for further information