RefGenome13Nov07 Phone Conference (Archived): Difference between revisions

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* What is needed?  
* What is needed?  
* Can everyone provide the file?
* Can everyone provide the file?
== Quality control: outlying ISS annotations ==
Doug, Chris
Doug raised an important point on the email list:
I was wondering what people think of Ref. Genome annotations by ISS that seem to be off by themselves in a graph?  I see these quite often in Mary's graphs, and I always wonder how they got there.  Possibilities include:
1: ISS annotations where the thing that was ISS'ed to is now gone (bad bad bad)
2: ISS to genes from a non-ref genome species
3. ISS to genes which would not be considered orthologous to the gene being annotating
Just wondering what others think of these and how we can find cases of #1, which specifically need to be updated.


== Making Function-Process links ==
== Making Function-Process links ==

Revision as of 09:08, 8 November 2007

Rotation System for selecting genes

Web presence

Amelia (web page), Susan, Rex, Petra (content)


Orthology determination

Kara started to collect sequences from all groups. Questions:

  • What is needed?
  • Can everyone provide the file?

Quality control: outlying ISS annotations

Doug, Chris

Doug raised an important point on the email list: I was wondering what people think of Ref. Genome annotations by ISS that seem to be off by themselves in a graph? I see these quite often in Mary's graphs, and I always wonder how they got there. Possibilities include: 1: ISS annotations where the thing that was ISS'ed to is now gone (bad bad bad) 2: ISS to genes from a non-ref genome species 3. ISS to genes which would not be considered orthologous to the gene being annotating

Just wondering what others think of these and how we can find cases of #1, which specifically need to be updated.

Making Function-Process links

David: function-process links examples

Review Action items

[ACTION ITEM] (Jim): Provide the set of conserved genes found by InParanoid that are conserved in all 12 species (660 or so); we might want to prioritize this list by ascending order of number of annotations to target unannotated genes (who can do that?)

Done. 'Suggestions' spreadsheet (look for the "conserved Hs-Ec" sheet) Pascale also marked which genes we've already curated. Prioritization is not yet done

[ACTION ITEM] (GOA): Convert the ensembl IDs from the human-E. coli list to UniProt IDs

Done (Pascale) I converted to entrez and HGNC. The UniProt ID was not easy to work with since there was often more than one ID. The table now has human gene names and the two IDs.

[ACTION ITEM] (Val): Provide the list of 207 genes conserved between pombe and human with no annotation/information

Done, but pombe gene IDs were sent; we need to add them to the 'to do' spreadsheet in the same format

[ACTION ITEM] (Ruth): send the HGNC list of genes with few annotations (potential 'bleeding edge' genes)

[ACTION ITEM]: Emily, David: provide guidelines to submit those annotations to GOA Other taxa annotations.

Done, see Other_taxa_annotations; also Pascale added a link to this page from our Ref Genome main page under 'Annotation'

[ACTION ITEM] Amelia (web page), Susan, Rex, Petra (content), work on web presence : Report by next meeting

[ACTION ITEM]: David will produce some examples of the function-process links.

[ACTION ITEM]: For orthology determination: Suzi and Karen E will generate a page where all sequences will be available

[ACTION ITEM]: (Judy) contact/meet with people who have made tools for orthology determination on behalf of the GOC to see if they can help us (that possibly includes re-running the analyses using the most recent set of sequences and proper IDs)

  • Compara, Homologene, TreeFam, in paranoid, others?

[ACTION ITEM]: Kara, Stacia: run the P-POD over the full ref genomes set? analysis on the ref genome data set. Need computational pipeline with existing resources. Currently takes 3 weeks to do 8 species all v all. Goal was set for February 2008 to include all ref genome sets.

[ACTION ITEM]: (developers/software group): consider the potential impact of annotating to different forms of the gene (alternatively spliced, processed, etc). For now we will document how each database deals with those:

[ACTION ITEM]: (all): provide the method you use for capturing the exact gene product being annotated on this page: Variant_annotation

[ACTION ITEM] (Chris, Mike, Rex): Provide Ref genome reports on a regular basis

[ACTION ITEM] (Donghui): Check which IDs TAIR needs to provide for the reports.

[ACTION ITEM] (Pascale, ): Provide guidelines for filling the google spreadsheet (IDs, where to put notes, how many ortholog per row (1), etc)

[ACTION ITEM]: (Chris) generate reports for potential misannotations (ND annotations for completed genes, etc). [DONE] Reference_Genome_Database_Reports We can request different reports. What do we do now?

[ACTION ITEM]: (Pascale) generate list of terms that often have incorrect annotations to check for consistent use of the term

[ACTION ITEM] (Tanya Berardini, Emily Dimmer, Pascale Gaudet, David Hill, Chris Mungall, Kimberly Van Auken): Write up recommendations for usage of ISS, IEA, IC: Report by next meeting???


[ACTION ITEM] (Judy Blake) Contact NCBI/NLM/OMIM to link to reference genome genes


New Action items