RefGenome11Dec07 Phone Conference (Archived)

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Tuesday December 11, 10 AM CDT (8 AM PDT, 4 PM BST)

Present

Web presence

Petra, Susan, Amelia, Rex: update [DONE] see http://www.geneontology.org/GO.refgenome.shtml

Orthology determination

Kara, Stacia, Chris: update

Last time Chris provided a format for all to submit a FASTA file. We will not do this anymore. The better way to do it is to use the gp2protein file.

Annotation consistency

1) ISS outliers: Report

  • We were all to look at this report and see where the errors came from.

2) Usage of ISS, IEA, IC : Tanya Berardini, Emily Dimmer, Pascale Gaudet, David Hill, Chris Mungall, Kimberly Van Auken were to write up recommendations

3) Other issues?

  • misused terms
  • Reports: IC, etc

Action items from previous meeting

[ACTION ITEM] all: Plan: everyone will look at the web page draft and Amelia will put it up in ~ 1 week (Nov 21) [DONE] see http://www.geneontology.org/GO.refgenome.shtml


[ACTION ITEM] (Chris) Provide guidelines and a template for the file Kara wants for orthology determination. [DONE], see Instructions for providing FASTA file


[ACTION ITEM] (all) Please send a fasta file of amino acid sequences, and an explanation of the header lines [REJECTED]--- will now use gp2protein file


[ACTION ITEM] (all) look at the results of the ISS outliers report and see how good/bad is it see Report

Ongoing action items

[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) [ON HOLD] until Varsha is back

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

Not done, but Suzi and Amelia are going to try to mine these from Reactome instead. It would still be interesting to have this information as it should help annotation consistency. Documentation is available Function-Process_Links

[ACTION ITEM]: For orthology determination: Suzi and Karen E will generate a page where all sequences will be available [DONE???] GFF3 for most databases Reference_Genome_sequence_annotation Question: should we add a link to FASTA files there as well?

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

[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. [in progress]

[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 [almost all done]

[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. [We need to provide the TAIR gene accession ids in the spreadsheet instead of the AGI identifiers. -Tanya]

[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 In progress, Misused_terms

[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???