RefGenome9Oct07 Phone Conference (Archived): Difference between revisions

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[[Category:Reference Genome]][[Category:Archived]]
'''Tuesday October 9, 2007, 10 AM CDT (8 AM PDT, 4 PM BST)'''
'''Tuesday October 9, 2007, 10 AM CDT (8 AM PDT, 4 PM BST)'''


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*Mary Dolan (MGI, software group)
*Mary Dolan (MGI, software group)
*Emily Dimmer (GOA)
*Emily Dimmer (GOA)
*Rachel Huntley (GOA)
*Rachael Huntley (GOA)
*Donghui Li(TAIR)
*Donghui Li(TAIR)
*Susan Tweedie (flybase)
*Susan Tweedie (flybase)
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*Stacia Engel (SGD)
*Stacia Engel (SGD)
*Ruth Lovering (university College London)
*Ruth Lovering (university College London)
*Fiona McCarthy (AgBase)


==Curation Targets==
==Curation Targets==
* Comments on last list with the four groups : disease, conserved&unannotated; 'bleeding edge'; biochemical/signaling pathways
=== Comments on last list of curation targets===
* Comments on rotation for selecting targets- see [[Procedure_for_selection_of_target_genes]]
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 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] [http://spreadsheets.google.com/ccc?key=pZhlLFuj8ewCR_n7xH4oCKw 'Suggestions' spreadsheet] (look for the "conserved Hs-Ec" sheet)
[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] [http://spreadsheets.google.com/ccc?key=pZhlLFuj8ewCR_n7xH4oCKw '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] (Val): Provide the list of 207 genes conserved between pombe and human with no annotation/information
Line 37: Line 52:


[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)  
[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:
* Compara, Homologene, TreeFam, in paranoid, others?  
* 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]: 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).
[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]: (all): provide the method you use for capturing the exact gene product being annotated.
[ACTION ITEM] (Chris, Mike, Rex): Provide Ref genome reports on a regular basis


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


[ACTION ITEM]: generate reports for potential misannotations (ND annotations for completed genes, 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]: generate list of terms that often have incorrect annotations to check for consistent use of the term
[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] (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] 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
[ACTION ITEM] (Judy Blake) Contact NCBI/NLM/OMIM to link to reference genome genes

Latest revision as of 11:31, 16 January 2018

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

Present

  • 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)