Annotation Call August 12, 2014: Difference between revisions
| Line 12: | Line 12: | ||
There is a new relationship for annotation extensions, causally_upstream_of. | There is a new relationship for annotation extensions, causally_upstream_of. | ||
This is intended to be used to capture processes or functions that are | 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. | This cannot be represented by new GO terms because the first process/function is upstream of, rather than part of, the second process/function. | ||
Revision as of 11:05, 12 August 2014
Agenda
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