Difference between revisions of "Future newsletter items"

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==Items for February newsletter==
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[[Category:GO News archived]]
 +
==Items for August newsletter==
  
* Announcement of new disjoint_from tags in gene_ontology.obo file (Jane)
+
*Genes of the quarter: Excision-repair proteins (already written)
***DO WE REALLY WANT TO DO THIS? There are still a few disjoint violations in the ontology.
 
** also mention that SO has them now too between the top nodes and between region and junction
 
  
* SGD gene_assocations file will now have IEAs beginning March 8th (Eurie)
+
*Announcement of new column in GA files (need a volunteer to write this)
  
<pre>
+
*Announce change of date for inter-ontology links?
On March 8, 2008, the Saccharomyces Genome Database (SGD) will change the contents of our file that
 
contains GO annotations. This is a major change as we will add annotations that are associated with
 
computationally predicted methods. The SGD file currently does not include annotations that are made
 
using the IEA evidence code.
 
  
These annotations will include computationally predicted annotations to the Gene Ontology created by
+
*ID mapping resources
the Gene Ontology Annotation (GOA) project at EBI, Hinxton UK.
+
**see email thread on GOfriends, started [http://fafner.stanford.edu/pipermail/gofriends/2008-May/thread.html#1533 May 14 2008]
  
The file available from the GO Consortium is called 'gene_association.sgd' and is available from the
+
(below are leftovers from previously suggested topics)
following locations:
 
  
GO Consortium web page:
+
==Items for future newsletters==
http://www.geneontology.org/GO.current.annotations.shtml
 
 
 
FTP:
 
ftp://ftp.geneontology.org/pub/go/gene-associations/
 
 
 
CVS:
 
http://www.geneontology.org/GO.downloads.ftp.cvs.shtml#cvs
 
</pre>
 
  
* Ontology development
+
*Midori has suggested we have a whole newsletter devoted to x-products. We haven't yet decided whether this will replace or be in addition to the regular newsletter release:
** The new regulation relationships (Tanya and David)
 
** Other developments (topics addressed/done in January?)
 
  
* Branching of ISS evidence code - note the the previous letter had an update on evidence codes mentioning that documentation for ISS is 'under review' and now we can announce that this has been completed (Michelle)
+
Dear newsletter-ers,                                                                                                 
 
+
                                                                                                                     
 
+
I've had an idea for a future newsletter: how about a special issue                                                   
*The annotation workshop that Linda Hannick is running.
+
devoted entirely to cross-products? Chris has generated a lot of sets to                                             
 
+
review lately, and we'll deploy them in the live GO before too long.                                                 
==Items for future newsletters==
+
Keeping our users fully informed will take more than an ordinary article                                             
* AmiGO release
+
in an ordinary newsletter.                                                                                            
  Starting in March 2008, the following enhancements and new features were made available in AmiGO,
+
                                                                                                                     
  the web application that allows browsing and visualization of the ontologies and annotations from multiple species:
+
Some possible articles:                                                                                               
  Better search interface and results
+
                                                                                                                     
  Result ranking
+
  - What are cross-products, and how do we represent them in GO files?                                                 
  More and improved download options
+
  (Chris?)                                                                                                             
  Visual enhancements (graphs, bar charts, etc.)
+
                                                                                                                     
  Term Enrichment
+
- What do we gain by using xps? (Midori & David?)                                                                     
  Slimmer
+
                                                                                                                     
 +
- What GO terms and other ontologies will be used in xps? (Midori, David,                                            
 +
Chris?)                                                                                                              
 +
                                                                                                                     
 +
- What will xps look like in AmiGO? (Seth, Amelia?) (maybe a pretty                                                   
 +
screenshot??)
  
 
* Orthology establishment for the Reference Genomes MODs genes - Princeton group
 
* Orthology establishment for the Reference Genomes MODs genes - Princeton group

Latest revision as of 06:04, 12 April 2019

Items for August newsletter

  • Genes of the quarter: Excision-repair proteins (already written)
  • Announcement of new column in GA files (need a volunteer to write this)
  • Announce change of date for inter-ontology links?
  • ID mapping resources

(below are leftovers from previously suggested topics)

Items for future newsletters

  • Midori has suggested we have a whole newsletter devoted to x-products. We haven't yet decided whether this will replace or be in addition to the regular newsletter release:
Dear newsletter-ers,                                                                                                   
                                                                                                                      
I've had an idea for a future newsletter: how about a special issue                                                    
devoted entirely to cross-products? Chris has generated a lot of sets to                                               
review lately, and we'll deploy them in the live GO before too long.                                                   
Keeping our users fully informed will take more than an ordinary article                                               
in an ordinary newsletter.                                                                                             
                                                                                                                      
Some possible articles:                                                                                                
                                                                                                                      
- What are cross-products, and how do we represent them in GO files?                                                   
(Chris?)                                                                                                               
                                                                                                                      
- What do we gain by using xps? (Midori & David?)                                                                      
                                                                                                                      
- What GO terms and other ontologies will be used in xps? (Midori, David,                                              
Chris?)                                                                                                                
                                                                                                                      
- What will xps look like in AmiGO? (Seth, Amelia?) (maybe a pretty                                                    
screenshot??)
  • Orthology establishment for the Reference Genomes MODs genes - Princeton group

Items suggested for newsletters, but better somewhere else

  • Standards for GO data in publications

New task for Group

  • Obtain an ISSN for the Newsletter,[1]