RefGenome9Oct07 Phone Conference (Archived)

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Tuesday October 9, 2007, 10 AM CDT (8 AM PDT, 4 PM BST)


  • Judy Blake (MGI)
  • David Hill (MGI)
  • Harold Drabkin (MGI)
  • Mary Dolan (MGI, software group)
  • Emily Dimmer (GOA)
  • Rachael Huntley (GOA)
  • Donghui Li(TAIR)
  • Susan Tweedie (flybase)
  • Victoria Petri (RGD)
  • Rex Chisholm (dictyBase)
  • Pascale Gaudet (dictyBase)
  • Petra Fey (dictyBase)
  • Doug Howe (ZFIN)
  • Stacia Engel (SGD)
  • Ruth Lovering (university College London)
  • Fiona McCarthy (AgBase)

Curation Targets

Comments on last list of curation targets

Now picking targets from four groups : disease, conserved&unannotated; 'bleeding edge'; biochemical/signaling pathways.

  • David, Harold pointed out that for biochemical pathways it was hard to find the primary literature; perhaps because it's rather old; also, many of these activities were assayed on

purified proteins/cell extracts, thus sometimes it's hard to know which gene was used.

  • People were comfortable making IDA annotations from those biochemical experiments in cases where there is a single gene in the genome.
  • Some biochemistry was done in non-ref genome organisms: nucleotide metabolism enzymes (pigeon liver), myosin (rabbit). We will annotate those genes and ISS from them.

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

  • David suggested we take the opportunity of curating pathway genes to make function-process links.

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

Comments on rotation for selecting targets

Nobody complained :) Help on selecting targets can be found here: Procedure_for_selection_of_target_genes

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)

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

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

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

Reference Genome Meeting minutes available

Please read and edit if necessary Reference_Genome_minutes

We'll go over action items from the meeting.

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

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

Next meeting

Tuesday November 13, 1 PM CDT (11 AM PDT, 7 PM BST)