Difference between revisions of "WBConfCall 2012.02.02-Agenda and Minutes"
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=== ACeDB models === | === ACeDB models === | ||
==== Unified Interaction model - Chris & Kimberly ==== | ==== 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 ==== | ==== Legacy data incorporation (Variation Phenotype_info) - Karen ==== | ||
Line 38: | Line 55: | ||
HE3_Mating_always_successful | HE3_Mating_always_successful | ||
</pre> | </pre> | ||
+ | |||
+ | 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 ==== | ==== New Homology type nemNOG - Michael ==== | ||
Line 51: | Line 73: | ||
nemNOG //eggNOG - nematode clusters | nemNOG //eggNOG - nematode clusters | ||
</pre> | </pre> | ||
+ | |||
+ | Notes: | ||
+ | * adds new categories of the latest eggNOG database | ||
==== Re-homing of Rescued_by_Transgene from Variation -> Phenotype_info - Karen ==== | ==== Re-homing of Rescued_by_Transgene from Variation -> Phenotype_info - Karen ==== | ||
+ | <pre> | ||
+ | //////////////////////////////////////////// | ||
+ | // | ||
+ | // ?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 | ||
+ | </pre> | ||
+ | |||
+ | Notes: | ||
+ | * cleans up some tag | ||
+ | |||
+ | ==== Removal of Accession_number XREF from the Homology_group - Michael ==== | ||
+ | <pre> | ||
+ | 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 | ||
+ | |||
+ | </pre> | ||
+ | |||
+ | Notes: | ||
+ | * fixes a broken xref | ||
+ | * cleans up the Accession_number class | ||
+ | |||
+ | ==== ?Transposon, Corresponding_CDS and Corresponding_Pseudogene - Paul ==== | ||
+ | <pre> | ||
+ | ?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 | ||
+ | </pre> | ||
+ | |||
+ | === 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 |
Latest revision as of 09:32, 3 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 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