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

• 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)
• Relationship between object being annotated and ontology term
  • Easily accomodated using qualifier column
• For multi-organism processes, the role an organism is playing in a process
• Nested class expressions
  • 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