LEGO-style annotation ideas

This page is for collecting together thoughts and ideas on what we want from a new annotation system. Given a clean sheet, what would you want to capture? Examples are always useful.

What can't be fully captured in current format

For annotation developments that could be included in the current GAF format, see full details at:Proposed Developments to the GAF annotation format

• Multiple pieces of evidence for a single assertion
• Terms from external ontologies
  • clarification: can be used as differentia in c16, but not in c5.
  • Allowing other onts in c5 is not in principal hard - BUT:
  • Adding other ontologies (e.g. CL in c5 would require explicit relationship type like expressed_in) (next item)
• Nested class expressions (post-composed terms)
  • c16 allows multiple differentia but not nested class expressions
  • the syntax was designed to accommodate this, but at this point it gets quite complex for people and feels like overloading

Future annotation areas

• There's likely to be a lot of data coming from metabolomics and metagenomics studies in the next few years e.g. the Human Microbiome Project so we might want to consider how you might annotate population-level processes

Useful links

• File:Paul's LEGO presentation from Bar Harbor Sept 2010.pdf
• File:Paul's LEGO white paper March 2010.pdf

Technical

• LEGO in OWL

Meetings

Aug 23 8am PST