PICA Framework Draft Proposal Documents

Ralph Santos 2008-03-11

Overview
The Part Interaction and Composition Assertion (PICA) framework is being developed for proposal as a standard for the Biobricks Foundation. The purpose of the framework is to provide an annotation standard and extensible data model to describe and exchange data about biological parts. The approach of this effort is to formulate the model as a language for part declaration. The reasons for this are as follows:


 * It provides an opportunity to explore basic issues of data modeling and semantics separately from the issues engendered by particular technological platforms
 * It lays the groundwork to deal with a variety of technical problems that will need to be addressed as the standard develops, including providing validation tools for annotations, and dealing with issues of translation between different technical platforms and/or different declaration syntaxes.

Note: The syntax used in the documents is a simple S-expression syntax that is used solely for illustration. The intent was to be easy to write and neutral with respect to technology, not to make Lisp or Scheme the official language for part description.

Rather than providing a comprehensive annotation standard, the strategy is to focus on initially delivering a tightly scoped platform model to allow a very elementary set of annotations to be collected, and later develop extensions to the model to enhance the annotation standard and build upon the initial platform model.

Although parts of the standard are still being written, some of the draft specifications are provided here for review and comment. The plan is for the full proposal package to include an annotation standard, a data model/language specification, a set of guidelines and resources for extending the overall framework, and several elementary software tools for developer use. At this time the documents below focus mostly on the data model and annotation standard. The specification documents for extension resources and guidelines are being held back for further development.

Documents

 * PICA Draft Annotation Guidelines -- posted 2008-03-11
 * PICA Draft Data Model Rationale -- posted 2008-03-11
 * PICA Draft Example Part Declarations -- posted 2008-03-11

Other Resources

 * Sequence Ontology
 * Systems Biology Ontology
 * "Relations in Biomedical Ontologies", paper submitted to Genome Biology, by Barry Smith et. al.