Difference between revisions of "Annotation Call November 11, 2014"

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(Agenda)
(Agenda)
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=Agenda=
 
=Agenda=
  
== 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.
 
  
  
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Is it acceptable to annotate to chromatin binding (MF term) based on ChiP data if the authors are confident that the protein is a DNA binding protein?  
 
Is it acceptable to annotate to chromatin binding (MF term) based on ChiP data if the authors are confident that the protein is a DNA binding protein?  
 
Annotating to chromatin binding, DNA binding terms (e.g. http://www.pombase.org/spombe/result/SPBC32H8.11). Relationships to use: occurs_at, has_direct_input respectively. Use SO terms to specify the DNA element (e.g. UAS, FRE, TCS etc)
 
Annotating to chromatin binding, DNA binding terms (e.g. http://www.pombase.org/spombe/result/SPBC32H8.11). Relationships to use: occurs_at, has_direct_input respectively. Use SO terms to specify the DNA element (e.g. UAS, FRE, TCS etc)
 +
 +
==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.
 +
  
 
[[Category:Meetings]]
 
[[Category:Meetings]]

Revision as of 13:08, 7 November 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 binding, DNA binding, 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. Because it's ChIP, we don't
think chromatin binding annotations would be favored. I can easily annotate to nuclear chromatin in CC, but there's
important specificity to put in extensions if possible.

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."

3) chromatin binding, using ChiP data Is it acceptable to annotate to chromatin binding (MF term) based on ChiP data if the authors are confident that the protein is a DNA binding protein? Annotating to chromatin binding, DNA binding terms (e.g. http://www.pombase.org/spombe/result/SPBC32H8.11). Relationships to use: occurs_at, has_direct_input respectively. Use SO terms to specify the DNA element (e.g. UAS, FRE, TCS etc)

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.