WBConfCall 2012.02.02-Agenda and Minutes

Agenda and Minutes for the Conference Call 2nd February 2012

Agenda

ACeDB models

Unified Interaction model - Chris & Kimberly

Chris' model proposal from the 31st of January contains the details, but basically it affects ?Interaction, and merges the ?Gene_regulation, ?YH, and ?Interaction .

Notes:

• preliminary tested with Chris test data.
• part of the model cleanup
• to classify interactions better and allow non-unique descriptions
• modified #interaction_info to #interactor_info with new functionality
• Chris will send a new model file around
• old objects need to be updated to new ones, that include a serial ID as identifier (which potentially have to be tracked)
  • namespace size issues might occur if the number of interactions increases too much ... add 2 digits?
  • Use WS release number as a versioning system so as to not over complicate. - Edited by User:Pdavis
• only gene-gene or TF-gene/feature-gene/feature-TF too?

Major Changes:

• genetic interaction types (Chris has slides to explain it)
  • predicted vs experimental? (should they get a different namespace?)

Legacy data incorporation (Variation Phenotype_info) - Karen

////////////////////////////////////////////
 //
// ?Phenotype_info Class
//
////////////////////////////////////////////

#Phenotype_info
add ->       Ease_of_scoring  UNIQUE ES0_Impossible_to_score
                                    ES1_Very_hard_to_score
                                    ES2_Difficult_to_score
                                    ES3_Easy_to_score


////////////////////////////////////////////
//
//Variation class
//
///////////////////////////////////////////
?Variation Evidence #Evidence
         Genetics Gene_class ?Gene_class XREF Variation
 add ->        Mating_efficiency  Male  UNIQUE ME0_Mating_not_successful
                                               ME1_Mating_rarely_successful
                                               ME2_Mating_usually_successful
                                               ME3_Mating_always_successful

                                  Hermaphrodite UNIQUE
HE0_Mating_not_successful
HE1_Mating_rarely_successful
HE2_Mating_usually_successful
HE3_Mating_always_successful

Notes:

• currently all in Legacy_information tag, which can be split into the respective classes
• based on Johnathan's schema/nomenclature
• separately for hermaphrodite and male

New Homology type nemNOG - Michael

#Homology_type KOG
               TWOG
               FOG
               LSE
               NOG   //eggNOG - standard cluster
               euNOG //eggNOG - eukaryote cluster
               meNOG //eggNOG - metazoan cluster
	       COG   //eggNOG - COG cluster // MH6 WS228
               nemNOG //eggNOG - nematode clusters

Notes:

• adds new categories of the latest eggNOG database

Re-homing of Rescued_by_Transgene from Variation -> Phenotype_info - Karen

////////////////////////////////////////////
//
// ?Phenotype_info Class
//
////////////////////////////////////////////

#Phenotype_info
add ->             Rescued_by_transgene ?Transgene

//////////////////////////////////////////////////////////////////////////////////////////////
//
//Variation class
//
//////////////////////////////////////////////////////////////////////////////////////////////
?Variation Evidence #Evidence
         Genetics Gene_class ?Gene_class XREF Variation
Remove ->        Rescued_by_transgene ?Transgene


///////////////////////////////////////////////////////////////////////////////
//
// Transgene class from Wen Chen 12/00
// Reorganised by Karen/Wen May 2011
//
///////////////////////////////////////////////////////////////////////////////

?Transgene
              Used_for
Remove  -> Rescue ?Variation XREF Rescued_by_Transgene

Notes:

• cleans up some tag

Removal of Accession_number XREF from the Homology_group - Michael

I would like to remove the Accession_number XREF from the Homology_group
?Homology_group Evidence #Evidence
               Title ?Text
               DB_info Database ?Database ?Database_field ?Accession_number XREF Homology_group
               Group_type  UNIQUE COG	   COG_type #Homology_type
                                        COG_code #COG_codes
  eggNOG  eggNOG_type #Homology_type
          eggNOG_code #COG_codes
  InParanoid_group
  OrthoMCL_group     //erich Nov06
               GO_term ?GO_term XREF Homology_group
               Protein ?Protein XREF Homology_group
               Remark ?Text #Evidence


and the Homology_group tag from the Accession_number:
?Accession_number  Entry Sequence ?Sequence	
                         CDS ?CDS
                         Transcript ?Transcript
                         Pseudogene ?Pseudogene 
                         Protein ?Protein
                         Motif ?Motif
                         Clone ?Clone // added [031120 krb]
                         Homology_group // added [031120 krb]
                         3d_data ?3d_data
                         Structure_data ?Structure_data
                   Web_location ?Database // use for WWW display

Notes:

• fixes a broken xref
• cleans up the Accession_number class

?Transposon, Corresponding_CDS and Corresponding_Pseudogene - Paul

?Transposon
       Molecular_info Corresponding_CDS         ?CDS XREF Corresponding_transposon #Evidence
                      Corresponding_pseudogene  ?Pseudogene XREF Corresponding_transposon #Evidence

?CDS
       Visible Corresponding_transposon    UNIQUE ?Transposon XREF Corresponding_CDS

?Pseudogene
       Visible Corresponding_transposon    UNIQUE ?Transposon XREF Corresponding_pseudogene



I would also like to Insert the History tracking and status tags also primarily lifted from the Gene model.

        History Merged_into UNIQUE ?Transposon XREF Acquires_merge
                Acquires_merge ?Transposon XREF Merged_into
                Split_from UNIQUE ?Transposon XREF Split_into
                Split_into ?Transposon XREF Split_from
                Killed #Evidence
                Resurrected #Evidence
        Status UNIQUE Live #Evidence
                      Suppressed #Evidence
                      Dead #Evidence

Announcements

C.species 5

Will be in WS230.

C.species 9

probably contaminated

Heterorhabditis bacteriophora

• CalTech has access to gene models
• available as genome only version in WS229

Frozen Releases

• usefulness?
  • not used very much on the website
  • flatfiles more used
• maintenance problem due to their number and software updates
• maybe serve the websites for a limited time (like 2 years) and only host files for download?
• provide the old websites as AMI (Amazon Machine Images) through Amazon, to avoid storing them at OICR?
• provide only GBrowse and BLAST in addition to the flatfiles for old versions?
• For troubleshooting access to web-versions of frozen releases is helpful(example WormMart is on WS220)
• used as reference for external sources (as example ModEncode / EnsEMBL uses WS220)

New Website Progress

• currently going through the design of Sequences and Variations
• functionality next (login/user management)
• anatomy term pages and cell lineage planned (Abby has a prototype)
• WS230 planned for polishing the web design
• make a github ticket for things that look broken
• interaction page prototyped

Other

WormMart requests

• no personal
• InterMine test planned
• no future planned
• one-off service for WormMart queries for the intermediate future until a replacement or fix is found? Or try to point them to existing flat-files?

GitHub

• Codehosting and Issue Tracking to GitHub
• Submit Bugs to website
• Signup for it if you haven't, and inform Todd of your username

Outstanding Helpdesk Issues

None ... so far

handing over to Gary Williams