Difference between revisions of "WBConfCall 2012.02.02-Agenda and Minutes"
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* modified #interaction_info to #interactor_info with new functionality | * modified #interaction_info to #interactor_info with new functionality | ||
* Chris will send a new model file around | * Chris will send a new model file around | ||
+ | * old objects need to be updated | ||
Major Changes: | Major Changes: |
Revision as of 16:44, 2 February 2012
Contents
- 1 Agenda and Minutes for the Conference Call 2nd February 2012
- 1.1 Agenda
- 1.1.1 ACeDB models
- 1.1.1.1 Unified Interaction model - Chris & Kimberly
- 1.1.1.2 Legacy data incorporation (Variation Phenotype_info) - Karen
- 1.1.1.3 New Homology type nemNOG - Michael
- 1.1.1.4 Re-homing of Rescued_by_Transgene from Variation -> Phenotype_info - Karen
- 1.1.1.5 Removal of Accession_number XREF from the Homology_group - Michael
- 1.1.1.6 ?Transposon, Corresponding_CDS and Corresponding_Pseudogene - Paul
- 1.1.2 Announcements
- 1.1.3 Outstanding Helpdesk Issues
- 1.1.1 ACeDB models
- 1.1 Agenda
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
Major Changes:
- genetic interaction types (Chris has slides to explain it)
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
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
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
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
?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.
Outstanding Helpdesk Issues
None ... so far