Difference between revisions of "Reference Genome ProgressReport April 2010 (Archived)"

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# 'Date comprehensively annotated' for groups that can provide this information
 
# 'Date comprehensively annotated' for groups that can provide this information
  
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http://amigo-sven.princeton.edu/cgi-bin/amigo/phylotree
  
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http://amigo-sven.princeton.edu/cgi-bin/amigo/phylotree?mode=cluster&key=PTHR10000&dbname=PantherDB
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http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=ntree&external_resource=http%3A%2F%2Famigo.berkeleybop.org%2Famigo%2Fpanther%2FPTHR10000.tree
  
 
= Electronic annotation jamborees=  
 
= Electronic annotation jamborees=  

Revision as of 12:57, 24 March 2010

Objectives and metrics

  • Sven: annotation status tracking tool

Curation Progress

The numbers of genes per species is based on the google spreadsheets, parsed by Mary Dolan. It excludes the Jan/Feb targets. See complete list on the ftp site here: [ftp://ftp.informatics.jax.org/pub/curatorwork/GODB/refg_id_list.txt ]

Group Number of curation targets Number of genes curated for ref genome
AgBase 570
BHF-UCL
dictyBase 463
Ecoli 158
FlyBase 422
GOA 1018 673
MGI 955
pombe 344
RGD 920 888
SGD 513
TAIR 705
WormBase 640
ZFIN 927

PAINT

Software for propagation of annotations is now functional. First public release expected March 2010.

Protein sets

Concurrent annotation

We have switched from annotating unrelated genes to annotating genes involved in a narrower biological process. The advantages of this approach are

  1. facilitates coordination with ontology development
  2. makes it easier to do the annotations because we're addressing a single general area of biology
  3. makes it possible to solicit the help of experts to help review the annotations and ensure that nothing is missing.

Topics covered

  • Lung branching morphogenesis (November 2009- March 2010)
  • Heart development (April 2010 - )

Annotation status reporting tool

Kara Dolinski and her group have started to work on a tool that would display the annotation status of the Panther families. There will be a regularly updated web page that will show the following information:

  1. Panther family ID
  2. Date selected for concurrent annotation
  3. Date Panther family last annotated (tree annotations)
  4. Number of members
  5. Number of RefG members
  6. Number of members with EXP
  7. Date more recent member last annotated
  8. 'Date comprehensively annotated' for groups that can provide this information

http://amigo-sven.princeton.edu/cgi-bin/amigo/phylotree

http://amigo-sven.princeton.edu/cgi-bin/amigo/phylotree?mode=cluster&key=PTHR10000&dbname=PantherDB

http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=ntree&external_resource=http%3A%2F%2Famigo.berkeleybop.org%2Famigo%2Fpanther%2FPTHR10000.tree

Electronic annotation jamborees

To allow curators to discuss annotation consistency, we hold electronic annotation jamborees three times per year where we discuss annotation of two different genes. The latest was held in February 2010. We discussed SLIT2 (thought to act as molecular guidance cue in cellular migration, and function appears to be mediated by interaction with roundabout homolog receptors) and NIPBL (that probably plays a structural role in chromatin. Involved in sister chromatid cohesion, possibly by interacting with the cohesin complex).

The major action item from this meeting was the need to improve the representation of neuronal processes.

GO annotation camp

The SIB group in Geneva will host a meeting in June 2010 where annotators will meet to resolve specific annotation issues. The outcome of this meeting will be clear documentation about a number of focused topics. Unless we decide to change those at the GOC meeting, the plan is to discuss :

  • Binding and complexes (finalize protein binding documentation, see Binding_terms_working_group
  • Use of regulation
  • Response to terms, how will these relate to signaling terms and to final cellular effect
  • How is a downstream effect defined (i.e when not to capture phenotypes )

Advertising ref genomes at the MODs

New annotators

We are very pleased to announce that Swiss-Prot annotators are now doing GO annotation. Emily Dimmer and Rachael Huntley trained 34 annotators during the past year.