RefGenome11Dec07 Phone Conference (Archived)

Web presence

Petra, Susan, Amelia, Rex: update

Orthology determination

Kara, Stacia: update

Annotation consistency

ISS outliers: Report (from Nov 13; is there a better version of the query?)

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

Latest action items

[ACTION ITEM] all: Plan: everyone will look at the web page draft and Amelia will put it up in ~ 1 week (Nov 21)

[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

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

Ongoing 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) [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] (Pascale, Doug, ): Provide guidelines for filling the google spreadsheet (IDs, where to put notes, how many ortholog per row (1), etc) [STARTED] Procedure_for_filling_Genome-Specific_spreadsheets

[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???