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| | [[WormBase-Caltech_Weekly_Calls_February_2013|February]] | | [[WormBase-Caltech_Weekly_Calls_February_2013|February]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_March_2013|March]] |
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| − | = March 7, 2013 =
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| − | Grant
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| − | *Grant gets reviewed next week
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| − | *Should hear results in ~two weeks
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| − | Gene Concise Description form
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| − | *Ranjana, Kimberly working on form layout
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| − | *Easy to use form, simple drop down menus to select, e.g., Species
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| − | *Can users follow references for info?
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| − | *Citing references in concise descriptions has, in the past, greatly increased workload/time to write
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| − | *Prepopulated, precanned Textpresso info?
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| − | *Send out to targeted members of the community, get feedback; Who should we ask for other species?
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| − | *Curators could each try using form to make at least one concise descriptions, give feedback
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| − | *Prepopulation: Display all (key?) experimental info on gene from WormBase, some Textpresso info like "ABC-1 encodes..."
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| − | *Can promote form at the International meeting
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| − | Galaxy Workshop
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| − | *Screencast videos capturing use of Galaxy available
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| − | *Chris will send around
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| − | Genetic Interaction Ontology
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| − | *Perhaps add "what is expected" info during curation?
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| − | *Good to have a comparison of curation with core set of common papers
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| − | **Cross check for consistency of curation (at least terms should lay in same lineage, if not at same depth)
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| − | = March 14, 2013 =
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| − | Cleaning up Citace Minus
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| − | *Stemming from Paul Davis' GitHub ticket pointing out small-scale data problems
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| − | *Bogus molecule objects (Chris will take care of)
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| − | *Homol_data from RNAi (and the housing RNAi objects) can be removed
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| − | *Ghost Expr_pattern objects, Wen taking care of (Xiaodong will remove from the Gene_regulation OA)
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| − | *Will need to create a better (more robust) pipeline (with SOPs) for converting, for example, object names to WBID#'s
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| − | **Once a conversion has been made, we need to check Postgres and Citace (& Citace Minus) for consistency
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| − | **Need to minimize the burden on Wen to perform quality and consistency checks
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| − | **Curators need to clean up/fix their data before a big change
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| − | **Scenarios to foramlize:
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| − | ***Whole-class name changing
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| − | ***Model changes
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| − | *Is there a list of classes (and objects?) that are held in Citace Minus?
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| − | **Cross-references create complexity
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| − | *We will suggest shifting the phase of the model proposal cycle: Propose to freeze all models one month before upload
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| − | Queries
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| − | *AQL vs WQL vs AcePerl
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| − | *We may consider working out more formal pipelines for submitting queries (maybe to Wen?)
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| − | *AQL and WQL convenient but not necessarily efficient
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| − | *AcePerl efficient, but has a learning curve
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| − | *Todd highly recommends learning AcePerl as it has many advantages:
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| − | **Learning AcePerl will provide skills to handle other generic queries
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| − | **Whereas AQL and WQL will be obsolete when we leave ACeDB, AcePerl will still be useful (even if the details need updating)
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| − | **Curators have GitHub access to all the AcePerl scripts, including those that generate FTP files
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| − | Under Testing
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| − | *The "Under Testing" tag on GitHub issues is applied when something needs to be tested
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| − | *Curators can filter for "Under Testing" issues and close them as they determine they are resolved
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| − | = March 21, 2013 =
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| − | Protein browsing
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| − | *KOGs vs eggNOG; eggNOG may be the most current
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| − | *Would be nice to be able to (for each species or all species in WormBase) browse protein sets as orthologous groups by functional classification
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| − | *Need to investigate
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| − | Microarray data
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| − | *Data that were not provided (no changes observed in an experiment) leaves gaps in data
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| − | *SPELL requires data for each experiment/probe (regardless of observation of change)
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| − | *FTP site for downloads of data (independent from, but related to, SPELL); Wen needs regular access to
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| − | **Can be hosted at Caltech FTP site (Todd can mirror over to main FTP site)
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| − | *Add explanatory page to SPELL site
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| − | Dead genes
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| − | *Historical_gene tag will be added to several class models: ?Interaction, ?Transgene, ?Antibody, etc.
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| − | *How to handle GO annotations? GO will have mapping from proteins to GO terms, no need for new tag
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| − | *Chris will send around model proposal to add the tag to relevant models
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| − | *Curators will need to coordinate with Juancarlos how their respective OA dumpers should work
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| − | Beyond PDF conference
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| − | *Karen attended
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| − | *Peer-review process after open-access?
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| − | *Provenance of data issues
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| − | *[http://orcid.org/ ORCID] collaboration
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| − | *WormBase should coordinate WBPerson IDs with ORCID
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| − | *Reproducibility of research: cataloging raw data and making it available
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| − | *[https://www.authorea.com/ Authorea]: data published as a GitHub repository
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| − | *Discussions on contributing negative data
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| − | *[http://www.rubriq.com/ Rubriq]: Peer review system
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| − | = March 28, 2013 =
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| − | IWM Meeting
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| − | *Workshops and talks topics
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| − | *2 Workshops (Kevin made Google Doc [https://docs.google.com/a/wormbase.org/document/d/1zdxmfJtVc4Eyc9ia5RHDwS-agyC-VO3G_eY7JCyGdd0/edit#heading=h.pd1qsrtkxi8g here] (requires login):
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| − | *Two workshop time slots: Thursday 1 hour (1:30 - 2:30pm), Saturday 1.5 hours (1:30 - 3pm)
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| − | **Overview Workshop 1 (Thursday slot)
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| − | ***Sequence perspective (Hinxton/EBI member)
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| − | **Data mining workshop (Thursday & Saturday slots)
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| − | ***Modmine with extra half-hour on Saturday
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| − | **Overview Workshop 2 (Saturday slot)
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| − | ***Biology perspective (Caltech: Chris Grove)
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| − | ****Interactions, regulation
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| − | ****WikiPathways
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| − | ****Concise description forms
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| − | ****Expression Data in WormBase
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| − | *Spreading the word:
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| − | **Catch people during poster sessions (booth with ~4 posters)
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| − | ***Posters on: Wikipathways/Interactions, Species, Gene Expression & Regulation, Textpresso, Phenotypes & Diseases
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| − | ***Have projector displaying screen demos
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| − | ***We could create a template with a standard layout
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| − | ***Create posters with Illustrator or [http://www.scribus.net/canvas/Scribus Scribus]
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| − | **WormBase events flyer to hand out or have placed in meeting program
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| − | *WormBase give away ideas:
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| − | **Mugs, aprons, gummy worms, LED light keychains, etc., etc.
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| − | Populating OA with variations for variation fields
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| − | *Huge number of variations (>1,000,000!)
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| − | *How to limit to relevant variations?
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| − | *Can we split into "useful" vs. "generated" mutations/variations?
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| − | *Splitting now on "Allele" tag
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| − | *Add a new tag to the variation model?
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| − | *Ask Hinxton to provide a file of all variations with a phenotype for FTP site
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| − | *Also get full list of variations from Hinxton for our internal processing
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| − | *Get abstracts (for posters, workshops, talks) ready by next conference call (next Thursday)
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| − | "Beyond the PDF" meeting
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| − | *Who's driving the whole peer-review process?
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| − | *Rebecca Lawrence Faculty of 1000 summary of Research Data Alliance (RDA) launch a world-wide open access data meeting - happening concurrently
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| − | **How to make all data freely available?
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| − | **Data repositories, publishers, researchers, universities involved
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| − | **Publishers will need to ensure that published data is made publicly available
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| − | **Data sharing plans
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| − | **Guidelines https://docs.google.com/file/d/0ByE-kVBE6aUVMERJLTh4UDY5VDA/edit
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| − | *Carol Tenopir - reading analysis
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| − | **Successful researchers are very data-aware, read lots
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| − | *Data format standards - defined by data repositories?
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| − | *Action items: breakout groups (revolution group to completely reorganize data infrastructures)
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| − | *Carole Goble: no need to "publish", just release data to public
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| − | *Can follow up on action at http://www.force11.org/outcomes
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