Annotation Call August 12, 2014

Agenda

Present: Rama, Judy, David, Jane, Tanya, Pascale, Suzi, Moni, Chris, DavidOS, Prudence, Susan, Paola, Rachael, Edith, Kimberly

Phase terms in biological process

As Jane explained last time, the ontology editors have introduced biological phase (GO:44848) as a new term in the Process ontology to represent distinct periods when processes occur. These terms do not have relationship (is_a) to any other process terms and they all also have a do_no_annotate tag. http://amigo.geneontology.org/amigo/term/GO:0044848

happens_during should be used to connect other processes and these phase terms. Should curators use the phase term in col-16 with happens_during or precompose a term such as DNA replication during S-phase?

New relationship for col-16

There is a new relationship for annotation extensions, causally_upstream_of.

This is intended to be used to capture in the annotation extension processes or functions that are downstream of the process or function in the primary annotation and the first process/function is required for the process/function in the annotation extension to occur.

This cannot be represented by new GO terms because the first process/function is upstream of, rather than part of, the second process/function.

The documentation for this relation, including some examples of its use, is in the wiki page; http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:causally_upstream_of

Discussion

Phase terms

Both approaches are valid. If the process is unusual to happen in that phase then don't precompose the term.

New relationship for col-16

• Ruth and David OS will model the new relationship in LEGO
• there is some overlap with DownStream effect curation policy. Review the guidelines for downstream effects