Difference between revisions of "WormBase-Caltech Weekly Calls"
From WormBaseWiki
Jump to navigationJump to searchLine 125: | Line 125: | ||
*Someone should be in touch with organizers | *Someone should be in touch with organizers | ||
*WormBase souvenirs? | *WormBase souvenirs? | ||
+ | |||
+ | |||
+ | Dead genes | ||
+ | *Going to add "Historical_gene" tag to relevant class models (e.g. ?Interaction, ?Expr_pattern, ?Transgene, etc.) | ||
+ | *Will modify OA dumping scripts with Juancarlos to automate recognition of dead genes and replace them (if merged) | ||
+ | *Dumper will add remark about existence of dead gene in original object | ||
+ | *Will consider adding original gene reference through #Evidence hash under "Published_as" tag, as Other_name (gene synonym), as possibly as a separate free-text tag in the models that captures the verbatim reference to the original gene | ||
+ | *Will not try to re-annotate old objects WRT the gene synonyms/verbatim references, but can consider doing this going forward only | ||
+ | |||
+ | |||
+ | Transgenes | ||
+ | *CGC transgenes have been completed/unified with existing WBTransgene objects | ||
+ | *Updating new CGC strains will become a monthly task |
Revision as of 18:18, 21 February 2013
2013 Meetings
February 7, 2013
Person Cytoscape
- Person-person network viewing on website
- Use person lineages
- Will discuss with web team
WormBook History
- Paul editing a person history section, starting with John White
- Can use history info to link people
Binary vs. Non-binary interaction display
- Cytoscape and interaction table are only displaying interactions as binary interactions, regardless of number of interactors
- We need to assess how many interactions we have that have more than 2 interactors
- Once we have assessed that, we should discuss with web team about how to display these cases
Curation Statistics
- Wen can generate numbers for Citace AND the complete build (rather than Hinxton)?
- Will let Hinxton build the queries
- End-of-build summary for curators (with more database technical numbers) separate from the Release Notes for public (with more biologically interesting numbers)
- Will separate Wiki page into two sections to reflect this
- Public info will continue to be displayed in Release Notes
- Internal info - where should that be displayed?
Postgres info table (on Wiki page)
- Curators will continue to add info to Wiki on scripts, dependencies, ontologies, etc. for each Ontology Annotator
Intermine
- JD gave short demo yesterday
- Will give another tutorial next week (Thursday, Feb 14, 2013 - 8:30am PST)
- Curators can/should test
Nick Brown visit
- PI of FlyBase Cambridge
- Will be here tomorrow around 11am
February 21, 2013
WS237 Upload March 1, 2013
- Citace upload on February 28
WS236 will go live on April 5, 2013
- One week later than previously planned (March 29th)
New genome assemblies and gene names across species
- How do we handle independent, conflicting genome assemblies and gene models?
- Can we collect all gene models, for example, without any bias and display any info we have?
- How might we display conflicting models, etc.?
- Should we prioritize easier-to-handle, "more important" genomes?
- Can we establish automated (minimal manual effort) pipeline to handle these issues?
Expression graphs
- Wen and Daniela have been generating expression graphs
- Yanai probes need to be mapped
- Multiple probes mapped to the same gene will be averaged
- SPELL construction has changed; all data sets exist as separate flat files
Expression table
- Table of expression data to display all details of an expression pattern object
- Place in separate widgets on the gene page
- Perhaps, separate large-scale from small-scale studies
Phenotype Ontology
- How stable/complete is the current phenotype ontology?
- Good, but we may consider a reconstruction/re-ordering of existing terms
- Group phenotypes by e.g. anatomy term, life stage, etc.?
- Link anatomy terms, life stages to relevant phenotypes (at .ACE level or website level)
- Perhaps use cross-products of various ontologies to get the same effect?
- May want to consider using .OWL format as opposed to .OBO
- Need a sustainable, long-term approach to maintaining the ontologies
- AMIGO 2 only consumes .OWL format, not .OBO
- Should we consider switching to Protege, as a local ontology browser/editor (as opposed to OBO-Edit)?
LEGO Call
- How to use annotation extensions for LEGO model?
- Consistent use?
Intermine
- Target for first release, minimal functionality for sequence-based queries
- JD working on importing sequence-based data
- How much can we get into Intermine by the first freeze/release (in April)?
- How should we prioritize?
- Can we build a "worm-version" of FlyMine (existing classes, e.g.)?
- Probably not a good approach for first release in April, but maybe useful for long-term
- Production server (unstable) vs live/testing server (more stable)
- Major testing will start in April
Staging tests
- WS236 Staging site now available
- Everyone should test rigorously
2013 International Worm Meeting
- WormBase workshop
- Someone should be in touch with organizers
- WormBase souvenirs?
Dead genes
- Going to add "Historical_gene" tag to relevant class models (e.g. ?Interaction, ?Expr_pattern, ?Transgene, etc.)
- Will modify OA dumping scripts with Juancarlos to automate recognition of dead genes and replace them (if merged)
- Dumper will add remark about existence of dead gene in original object
- Will consider adding original gene reference through #Evidence hash under "Published_as" tag, as Other_name (gene synonym), as possibly as a separate free-text tag in the models that captures the verbatim reference to the original gene
- Will not try to re-annotate old objects WRT the gene synonyms/verbatim references, but can consider doing this going forward only
Transgenes
- CGC transgenes have been completed/unified with existing WBTransgene objects
- Updating new CGC strains will become a monthly task