Annotation Call November 11, 2014

Agenda

Col-16

1) For terms like transport and transporter activity, transcription factor/transcription do we have guidelines on if we should add col-16 data to both aspects?

2) chromatin, new relationship 'RO_0002008: Conincident with' (no underscore)

 PMID:22426534 uses ChIP to show that pombe Pfh1
localizes to regions within chromatin where the DNA sequence contains
replication fork barriers (e.g. SO:0001914) and at some specific highly transcribed genes.  I can easily annotate to nuclear chromatin in CC, but there's
important specificity to put in extensions if possible.

Application of the new RO_0002008: Conincident with relationship: definition "A relation that holds between two linear structures that are adjacent or overlapping and are approximately parallel to each other for their entire length. "^^string comment "Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence." Resulting annotation: pombe Pfh1 GO:0000790 nuclear chromatin IDA, Annotation extension:RO_0002008: Coincident with SO:0001914 replication fork barriers

Annotation of ChIP data

Discussed [wiki page] and [source forge] In summary A ChIP experiment does not indicate whether interaction is direct or not since chromatin complexes are all cross-linked with DNA, they only show colocalization. General agreement that it is acceptable to annotate to the Cellular Component term 'chromatin' (or child terms) with SO and Gene IDs in the annotation extension field using the 'Coincident with' relationship (as above). Use SO terms to specify the DNA element (e.g. UAS, FRE, TCS etc)

Need clarification on annotation to a Molecular Function term: chromatin binding (or child terms)

Is it acceptable to annotate to chromatin binding (MF term, or child terms) based on ChiP data; with SO and Gene IDs in the annotation extension field using the occurs_at and has_direct_input relationships? Need to consider whether the authors have used appropriate controls if including SO and Gene IDs

Is it acceptable to annotate to DNA binding (MF term, or child terms) based on ChiP data if the authors are confident that the protein is a DNA binding protein? (e.g. http://www.pombase.org/spombe/result/SPBC32H8.11). Relationships to use: occurs_at, has_direct_input respectively.

Next Call (Preview)

small conjugating enzyme ontology development (DavidH and Val)

1) The ontology edits are complete for all of the ubiquitin and other small conjugating enzymes. There are three parents: activating enzyme activity (E1), conjugating enzyme activity (E2) and ligase activity (E3)

2) Now all of the annotations for these need to be checked. We need a strategy for this re-annotation.