RefGenome08Jan08 Phone Conference (Archived)

From GO Wiki
Revision as of 12:22, 4 January 2008 by Pascale (talk | contribs)
Jump to navigation Jump to search

Time: 1 PM CDT, 11 AM PDT, 7 PM BST

Present

Display of reference genome annotations in AmiGO

Suggestions

  • Load IEAs in AmiGO for reference genomes

Orthology determination

Reference Genomes annotations displayed in AmiGO

Annotation Documentation

Review Action Items

[ACTION ITEM]: (Amelia): Fix web page where the number of annotations are to give an estimated number of protein-coding genes; problems: unmapped genes; splice variants; etc. Maybe this should also be on the ref genome page. USE count from gp2protein file-- then it's all consistent.

[ACTION ITEM]: all: look at Stan's error reports: http://www.geneontology.org/internal-reports/gp2protein/

[ACTION ITEM]: Chris: generate new report that would show errors that need fixing for the Orthology determination project

[ACTION ITEM]: Chris will provide date on the ISS outliers query so that we dont always review the same annotations.


[ACTION ITEM]: Mary will include IC in the graphs

  • Would be nice if we had a report describing when genes are 'comprehensively' curated

[ACTION ITEM]: can Mary show the date completed on the index page? Possibly - she will try

[ACTION ITEM]: Discuss at the GOC meeting whether it would be useful to add the 'comprehensively annotated' tag to all genes, somehow? Either in the gene association file or in the database somehow

[ACTION ITEM]: (Chris) Look into loading IEAs for reference genome set into AmiGO

[ACTION ITEM]: Mike will set up 'annotation' calls?

[ACTION ITEM]: Mike(pascale) merge two email lists (reference genome and annotation) into 'annotation'

    • Should we copy them to the SF tracker?


[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???

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