RefGenome9Sept08 Phone Conference (Archived): Difference between revisions

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==Review old/ongoing action items==
==Review old/ongoing action items==
# (Debby) Put in a SourceForge request that definitions of terms for oligomerization, dimerization, protein complex assembly etc. should be clarified as to their use and annotations using these terms be checked and, if necessary, changed.
# Debby: Put in a SourceForge request that definitions of terms for oligomerization, dimerization, protein complex assembly etc. should be clarified as to their use and annotations using these terms be checked and, if necessary, changed.
# Emily and Debbie: Clarify GO:0006730 one-carbon compound metabolic process and GO:0019438 aromatic compound biosynthetic process -  these terms were added by the HAMAP and InterPro groups.  Both of those processes involve enzymes that use a folic acid derivative as a coenzyme, but  Debbie didn't think that FolE (which catalyzes the first committed step in folic acid biosynthetic) should be annotated to those processes.
# Emily and Debbie: Clarify GO:0006730 one-carbon compound metabolic process and GO:0019438 aromatic compound biosynthetic process -  these terms were added by the HAMAP and InterPro groups.  Both of those processes involve enzymes that use a folic acid derivative as a coenzyme, but  Debbie didn't think that FolE (which catalyzes the first committed step in folic acid biosynthetic) should be annotated to those processes.
# (Susan) Request new term for Regulation of GTP Cyclohydrolase I activity. [http://sourceforge.net/tracker/index.php?func=detail&aid=2041554&group_id=36855&atid=440764 term requested]
# Susan:  Request new term for Regulation of GTP Cyclohydrolase I activity. [http://sourceforge.net/tracker/index.php?func=detail&aid=2041554&group_id=36855&atid=440764 term requested]
# (Victoria) Make a SourceForge request to clarify the definitions of unfolded/misfolded protein binding and add chaperone activity as a synonym to both of the terms. Also add ‘de novo’ synonym to ‘unfolded protein binding’.
# Victoria:  Make a SourceForge request to clarify the definitions of unfolded/misfolded protein binding and add chaperone activity as a synonym to both of the terms. Also add ‘de novo’ synonym to ‘unfolded protein binding’.
# Process IC or IDA?
# [[Annotation_consistency:_IDA_or_IC_for_processes]] (Tanya Berardini, Emily Dimmer, Pascale Gaudet, Chris Mungall, Kimberly VanAuken, David Hill )
# Discuss microarray data further, possibly GOC meeting item.
# [[Annotation_consistency:_HTP]] (Stacia) [[SGD_GO_HTP_guidelines]]
#  Stacia: HTP annotation [[SGD_GO_HTP_guidelines]]
# [[Annotation consistency: x protein binding and with]] (Becky, David)
# (Becky) Move discussion  to email on whether we need more terms under protein binding to describe protein binding as a target for a process
# [[Annotation consistency: Using IEP]] (Emily, Pascale, Ruth, Stacia)  
# (Pascale) Discuss IEP: Some people had annotated 'response to heat' by IDA for the heat shock protein;  while what was measured was the level of transcript/protein. There are 38 genes annotated to 'response to heat shock' with IDA in the GO database. Those should be checked? (we'll discuss, see below)
# [[Annotation consistency: 'Response to' terms]] Proper evidence code to use for to 'response to xx'? (Emily, Pascale)
# Proper evidence code to use for to 'response to xx'?
# [[Annotation consistency: xx binding in the context of gene product]]  (Victoria, Pascale, David)  
# Discuss xx binding in the context of gene product. In this case I (Pascale) think the 'coenzyme' rather refers to the gene product. Most/many people seem to use 'coenzyme binding' only to annotate proteins that bind a coenzyme '''for activity'''. However the definition does not specify that.
# All (ongoing): Annotation Quality control: Please pick an ortholog set from the Curation Targets table [http://spreadsheets.google.com/ccc?key=pwOksMOra5uq4vIYjPgefPw] see also [[Annotation_QC]] for some general documentation and previous issues
# All (ongoing): Annotation Quality control: Please pick an ortholog set from the Curation Targets table [http://spreadsheets.google.com/ccc?key=pwOksMOra5uq4vIYjPgefPw] see also [[Annotation_QC]] for some general documentation and previous issues
# All (ongoing): Annotation Quality control: Have a look at the SF items and see if the ortholog from your organism is correctly annotated ("comprehensive"). Let lead curator for that set know that you're done.
# All (ongoing): Annotation Quality control: Have a look at the SF items and see if the ortholog from your organism is correctly annotated ("comprehensive"). Let lead curator for that set know that you're done.

Revision as of 16:30, 15 August 2008

Present

Review old/ongoing action items

  1. Debby: Put in a SourceForge request that definitions of terms for oligomerization, dimerization, protein complex assembly etc. should be clarified as to their use and annotations using these terms be checked and, if necessary, changed.
  2. Emily and Debbie: Clarify GO:0006730 one-carbon compound metabolic process and GO:0019438 aromatic compound biosynthetic process - these terms were added by the HAMAP and InterPro groups. Both of those processes involve enzymes that use a folic acid derivative as a coenzyme, but Debbie didn't think that FolE (which catalyzes the first committed step in folic acid biosynthetic) should be annotated to those processes.
  3. Susan: Request new term for Regulation of GTP Cyclohydrolase I activity. term requested
  4. Victoria: Make a SourceForge request to clarify the definitions of unfolded/misfolded protein binding and add chaperone activity as a synonym to both of the terms. Also add ‘de novo’ synonym to ‘unfolded protein binding’.
  5. Annotation_consistency:_IDA_or_IC_for_processes (Tanya Berardini, Emily Dimmer, Pascale Gaudet, Chris Mungall, Kimberly VanAuken, David Hill )
  6. Annotation_consistency:_HTP (Stacia) SGD_GO_HTP_guidelines
  7. Annotation consistency: x protein binding and with (Becky, David)
  8. Annotation consistency: Using IEP (Emily, Pascale, Ruth, Stacia)
  9. Annotation consistency: 'Response to' terms Proper evidence code to use for to 'response to xx'? (Emily, Pascale)
  10. Annotation consistency: xx binding in the context of gene product (Victoria, Pascale, David)
  11. All (ongoing): Annotation Quality control: Please pick an ortholog set from the Curation Targets table [1] see also Annotation_QC for some general documentation and previous issues
  12. All (ongoing): Annotation Quality control: Have a look at the SF items and see if the ortholog from your organism is correctly annotated ("comprehensive"). Let lead curator for that set know that you're done.

Curation Targets

September 2008: Val's lists of 'unknowns'

PPOD update

PANTHR update

Annotation tracker update

Source Forge QC discussion

Next conference call

Tuesday October 14, 2008, 10 AM CDT, 8 AM PDT, 4 PM BST



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