WBConfCall 2012.02.02-Agenda and Minutes
From WormBaseWiki
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
