WormBase-Caltech Weekly Calls
From WormBaseWiki
Previous Years
2015 Meetings
July 2, 2015
Discussion Topics from IWM
- Explaining job posting options via the forum in new Worm Breeder's Gazette article
- Display of CRISPR data
- Alleles with multiple lesions (one name, many mutations), need to be curated and mapped
- Ontology term enrichment analysis, using ontologies other than gene ontology
- Discussed on GO call yesterday; we can/should follow up with Paul Thomas
- Would be good to have a single central tool/resource for enrichment analysis
- PantherDB vs DAVID
WormBook Chapters
- Paul S will review over next week and will provide feedback
Outreach
- Sending out e-mails to all labs/PIs reminding about new data forms
- Could also do more personalized outreach to a smaller subset of PI's/labs
- Could focus on PIs not at the IWM
Anatomy
- Embryonic development, cell division timing
- Sulston timing
- Waterson datasets
- Zhao cell lineage timing datasets
- Bao lab?
- New EM reconstructions from David Hall, Scott Emmons, etc.
- Neuronal connectivity, collaborative database with Scott Emmons and colleagues
Citace upload
- Curators submit data to Wen on Tuesday, July 28th
Taking over Gene Orienteer
- Xiaodong and Sibyl working on
RNASeq data
- Gary Williams only using high quality data, taking care of all curation (including meta data)
- Public archive of rejected datasets?
WormGuides
- Bill Mohler et al working on desktop application
July 9, 2015
Expression Pattern
- Certain/uncertain qualifiers not annotated before some date
- ~3,000 ?Expr_pattern objects without that annotation/tag
- Daniela work on bringing up to date, hopefully won't take long
Expression Clusters to Anatomy & Life Stage annotations
- Many large scale datasets with tissue-specific expression data
- Much of what is in SPELL is not annotated to ?Anatomy or ?Life_stage terms
- A goal: make expression data queryable via ?Anatomy terms/pages
- Wen will make the model change proposal
- We may not want to show explicitly in widget
- There is a need for a condensed display of expression data (per gene)
- Some datasets, like the EPIC data, explicitly mention each embryonic cell name
- Need for a condensed ontology browser per gene/anatomy and gene/life stage
Proteomic analysis
- Encyclopedia of Proteomic Dynamics, contacted Wen to share data
- Wen will meet/discuss with group soon to determine what the goals are
- It isn't clear what format the data has
- Should include Gary Williams on discussions as he already processes Mass Spectrometry data
External Databases
- To what extent can we take care of the data and display of other lab/publication databases
- Many authors want to share and make links to their database/website via WormBase
- What is the best way to handle large scale dataset sharing requests that don't necessarily (for the time being) fit our data model
- We can take advantage of the "External Links" display on WBPaper pages to link out the the external databases affiliated with the paper, including a link to our FTP site with shared data files, maybe?
- At least a stop gap measure until we can properly model the data
Cis-regulatory site nomenclature?
- Barbara Meyer's lab published many "rex" (Recruitment Elements on X) sites, numbered sequentially
- Tim Schedl wondering about others' thoughts/opinions on how to, possibly, standardize the names of cis-regulatory elements
- Could be like gene names, without dash, e.g. "rex1", "rex2"
- We may want to try "WBsf-" prefix, on all element names like "WBsf-rex1", although may be only used in-house
Phenotypes
- Were there any conclusions about phenotype lookup from the Allele-Phenotype form?
- Chris spoke with Harald Hutter and others at the meeting about how to improve the lookup for phenotypes
- Would be good to provide an explicit option to see phenotypes of related (or allele-affiliated) genes, perhaps by shared GO-term annotation
- Need to think more on how to best compress display of phenotypes on gene pages as well
- We do already provide links to the Variation and Gene pages (with Phenotypes displayed) in the term information box of the form
July 16, 2015
Anatomy term page expression
- Raymond and Juancarlos are working on a display of genes that may be exclusively expressed in that anatomy object
Construct/Transgene curation
- Karen trying to make the curation of constructs & transgenes easier
- May consider merging the transgene and construct OA's
- Possibly add a construct/transgene request functionality in other OA's
- Would those need multiple input fields?
- Karen would take care of the details
Molecule model
- Exogenous/endogenous tags issue
- Scraping data from external chemical databases versus adding biologically relevant data from papers
- We pull data from, e.g. CHEBI, but not all molecules fall under their purview, e.g. proteins
Micropublication
- Promotion and outreach
- Micropublications discoverable in PubMed?
- Publisher = WormBase? Caltech?
- Minimal standards for publication?
