WormBase-Caltech Weekly Calls
From WormBaseWiki
2013 Meetings
March 7, 2013
Grant
- Grant gets reviewed next week
- Should hear results in ~two weeks
Gene Concise Description form
- Ranjana, Kimberly working on form layout
- Easy to use form, simple drop down menus to select, e.g., Species
- Can users follow references for info?
- Citing references in concise descriptions has, in the past, greatly increased workload/time to write
- Prepopulated, precanned Textpresso info?
- Send out to targeted members of the community, get feedback; Who should we ask for other species?
- Curators could each try using form to make at least one concise descriptions, give feedback
- Prepopulation: Display all (key?) experimental info on gene from WormBase, some Textpresso info like "ABC-1 encodes..."
- Can promote form at the International meeting
Galaxy Workshop
- Screencast videos capturing use of Galaxy available
- Chris will send around
Genetic Interaction Ontology
- Perhaps add "what is expected" info during curation?
- Good to have a comparison of curation with core set of common papers
- Cross check for consistency of curation (at least terms should lay in same lineage, if not at same depth)
March 14, 2013
Cleaning up Citace Minus
- Stemming from Paul Davis' GitHub ticket pointing out small-scale data problems
- Bogus molecule objects (Chris will take care of)
- Homol_data from RNAi (and the housing RNAi objects) can be removed
- Ghost Expr_pattern objects, Wen taking care of (Xiaodong will remove from the Gene_regulation OA)
- Will need to create a better (more robust) pipeline (with SOPs) for converting, for example, object names to WBID#'s
- Once a conversion has been made, we need to check Postgres and Citace (& Citace Minus) for consistency
- Need to minimize the burden on Wen to perform quality and consistency checks
- Curators need to clean up/fix their data before a big change
- Scenarios to foramlize:
- Whole-class name changing
- Model changes
- Is there a list of classes (and objects?) that are held in Citace Minus?
- Cross-references create complexity
- We will suggest shifting the phase of the model proposal cycle: Propose to freeze all models one month before upload
Queries
- AQL vs WQL vs AcePerl
- We may consider working out more formal pipelines for submitting queries (maybe to Wen?)
- AQL and WQL convenient but not necessarily efficient
- AcePerl efficient, but has a learning curve
- Todd highly recommends learning AcePerl as it has many advantages:
- Learning AcePerl will provide skills to handle other generic queries
- Whereas AQL and WQL will be obsolete when we leave ACeDB, AcePerl will still be useful (even if the details need updating)
- Curators have GitHub access to all the AcePerl scripts, including those that generate FTP files
Under Testing
- The "Under Testing" tag on GitHub issues is applied when something needs to be tested
- Curators can filter for "Under Testing" issues and close them as they determine they are resolved
March 21, 2013
Protein browsing
- KOGs vs eggNOG; eggNOG may be the most current
- Would be nice to be able to (for each species or all species in WormBase) browse protein sets as orthologous groups by functional classification
- Need to investigate
Microarray data
- Data that were not provided (no changes observed in an experiment) leaves gaps in data
- SPELL requires data for each experiment/probe (regardless of observation of change)
- FTP site for downloads of data (independent from, but related to, SPELL); Wen needs regular access to
- Can be hosted at Caltech FTP site (Todd can mirror over to main FTP site)
- Add explanatory page to SPELL site
Dead genes
- Historical_gene tag will be added to several class models: ?Interaction, ?Transgene, ?Antibody, etc.
- How to handle GO annotations? GO will have mapping from proteins to GO terms, no need for new tag
- Chris will send around model proposal to add the tag to relevant models
- Curators will need to coordinate with Juancarlos how their respective OA dumpers should work
Beyond PDF conference
- Karen attended
- Peer-review process after open-access?
- Provenance of data issues
- ORCID collaboration
- WormBase should coordinate WBPerson IDs with ORCID
- Reproducibility of research: cataloging raw data and making it available
- Authorea: data published as a GitHub repository
- Discussions on contributing negative data
- Rubriq: Peer review system
March 28, 2013
IWM Meeting
- Workshops and talks topics
- 2 Workshops (Kevin made Google Doc here (requires login):
- Two workshop time slots: Thursday 1 hour (1:30 - 2:30pm), Saturday 1.5 hours (1:30 - 3pm)
- Overview Workshop 1 (Thursday slot)
- Sequence perspective (Hinxton/EBI member)
- Data mining workshop (Thursday & Saturday slots)
- Modmine with extra half-hour on Saturday
- Overview Workshop 2 (Saturday slot)
- Biology perspective (Caltech: Chris Grove)
- Interactions, regulation
- WikiPathways
- Concise description forms
- Expression Data in WormBase
- Biology perspective (Caltech: Chris Grove)
- Overview Workshop 1 (Thursday slot)
- Spreading the word:
- Catch people during poster sessions (booth with ~4 posters)
- Posters on: Wikipathways/Interactions, Species, Gene Expression & Regulation, Textpresso, Phenotypes & Diseases
- Have projector displaying screen demos
- We could create a template with a standard layout
- Create posters with Illustrator or Scribus
- WormBase events flyer to hand out or have placed in meeting program
- Catch people during poster sessions (booth with ~4 posters)
- WormBase give away ideas:
- Mugs, aprons, gummy worms, LED light keychains, etc., etc.
Populating OA with variations for variation fields
- Huge number of variations (>1,000,000!)
- How to limit to relevant variations?
- Can we split into "useful" vs. "generated" mutations/variations?
- Splitting now on "Allele" tag
- Add a new tag to the variation model?
- Ask Hinxton to provide a file of all variations with a phenotype for FTP site
- Also get full list of variations from Hinxton for our internal processing
- Get abstracts (for posters, workshops, talks) ready by next conference call (next Thursday)
"Beyond the PDF" meeting
- Who's driving the whole peer-review process?
- World-wide open access data meeting
- Proposal to have Research Data Alliance (RDA)
- How to make all data freely available?
- Data repositories, publishers, researchers, universities involved
- Publishers will need to ensure that published data is made publicly available
- Data sharing plans
- Rebecca Lawrence Faculty of 1000 (RDA launch)
- Carol Tenopir - reading analysis
- Successful researchers are very data-aware, read lots
- Data format standards - defined by data repositories?
- Action items: breakout groups (revolution group to completely reorganize data infrastructures)
- Carole Goble: no need to "publish", just release data to public