Difference between revisions of "Future newsletter items"

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(Items for future newsletters)
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==Items for future newsletters==
 
==Items for future newsletters==
 
* AmiGO release
 
* AmiGO release
  Starting in March 2008, The following enhancements and new features are going to be available in AmiGO, the web application that allows browsing and visualization of the ontologies and annotations from multiple species, starting March 2008.
+
  Starting in March 2008, the following enhancements and new features were made available in AmiGO,  
Better search interface and results
+
the web application that allows browsing and visualization of the ontologies and annotations from multiple species:
Result ranking
+
  Better search interface and results
More and improved download options
+
  Result ranking
Visual enhancements (graphs, bar charts, etc.)
+
  More and improved download options
Term Enrichment
+
  Visual enhancements (graphs, bar charts, etc.)
Slimmer
+
  Term Enrichment
 +
  Slimmer
  
 
* Orthology establishment for the Reference Genomes MODs genes - Princeton group
 
* Orthology establishment for the Reference Genomes MODs genes - Princeton group
 
  
 
==Items suggested for newsletters, but better somewhere else==
 
==Items suggested for newsletters, but better somewhere else==

Revision as of 11:20, 21 February 2008

Items for February newsletter

  • Announcement of new disjoint_from tags in gene_ontology.obo file (Jane)
      • 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)
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 
the Gene Ontology Annotation (GOA) project at EBI, Hinxton UK.

The file available from the GO Consortium is called 'gene_association.sgd' and is available from the 
following locations:

GO Consortium web page:
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
  • Ontology development
    • 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)


  • The annotation workshop that Linda Hannick is running.

Items for future newsletters

  • AmiGO release
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:
 Better search interface and results
 Result ranking
 More and improved download options
 Visual enhancements (graphs, bar charts, etc.)
 Term Enrichment
 Slimmer
  • 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]