WormBase-Caltech Weekly Calls February 2013
February 7, 2013
- Person-person network viewing on website
- Use person lineages
- Will discuss with web team
- 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
- 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
- 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?
- 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
- 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
- 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)?
- How to use annotation extensions for LEGO model?
- Consistent use?
- 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
- WS236 Staging site now available
- Everyone should test rigorously
- WormBase workshop
- What do we need to consider/prepare for, for the meeting?
- Someone should be in touch with organizers?
- Who are the organizers?
- Monica Colaiacovo and Ralf J. Sommer
- WormBase souvenirs?
- 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
- CGC transgenes have been completed/unified with existing WBTransgene objects
- Updating new CGC strains will become a monthly task
- Can we link two or more genes based on ,e.g., process for enrichment analysis?
- What should we be getting out of enrichment analyses that we aren't currently?
- Link all genes as part of "FGF signaling", "DAF-2 signaling", "PAR genes", etc.
- Gene sets based on pathway, process, etc.
- Intermine should be able to filter by these means (eventually)
February 28, 2013
- Upload happening today
- May be some delay due to script issues (being fixed)
- Transgene and Life Stage are all set
BioCurator meeting coming up
- Karen, Kimberly, Michael, and Daniela going
- Topics: entity recognition, curation pipelines
Kimberly attended NESCENT summit
- Meeting: Resource Coordination for NESCENT group, Text mining for annotations
- Kimberly spoke about Textpresso
- Setting up Textpresso for butterfly?
- Amer Soc Plant Bio attended, wanted to know more about Genetics/G3 markup pipeline
Galaxy workshop next Tuesday, March 5, 2013
- Biologists workshop 11am - 2pm, in Braun 151
- Lunch provided
- Register here
- Web-based platform for sequence analysis
- Protein trees, alignments, RNA-seq data
- Run remotely or locally as a server
- Could start a LinkedIn group (Caltech BioInformatics "huddle" group?)
- Main goal: find out who's on campus and what they do
- What are most people interested in?
- Create forum and wiki page?
- Mitch Guttman coming this summer, maybe give intro talk?
- Georgi Marinov in Wold lab
Xiaodong visited two labs in Bejing
- Gave WormBase tutorials
- Lab is still using legacy site
- Said they had trouble finding things on new site
- Xiaodong showed SPELL and modENCODE data
- WormMart demo and some queries
- ~30 C. elegans labs in China, and growing?
- Xiaodong encouraged them to send questions to WormBase Help
- Someone (WB person) should go to the Asia WormBase meeting (every 2 years)
Intermine/Wormmine workshop at 2013 IWM
- Monica Colaiacovo (mcolaiacovo AT genetics DOT med DOT harvard DOT edu)
- Ralf J. Sommer (ralf DOT sommer AT tuebingen DOT mpg DOT de)
- WormMine session in WormBase workshop
- Who (at WB) will organize workshop? Michael Paulini
WormBase website questionaire:
- What do people find on the legacy that they can't find on the new site?
- SNPs, validated vs. predicted
- Have posters and/or live demos at poster sessions? Walk around with tablets?
- We can make YouTube videos:
- 5 minutes or less
- Could triage topics in a topics tree on Wiki page
- Curators could check-off certain queries as they make them
- Building templates with genes and an "Arrow" key, with different connection types
- They're building now (should be done soon)