Difference between revisions of "WormBase-Caltech Weekly Calls"
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** Cytoscape view of Process pages has all interactions related to the process | ** Cytoscape view of Process pages has all interactions related to the process | ||
** Phenotypes for genetic interactions now listed in the legend | ** Phenotypes for genetic interactions now listed in the legend | ||
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=== ORCID IDs for WormBase Persons === | === ORCID IDs for WormBase Persons === | ||
Revision as of 18:55, 12 September 2013
Previous Years
2013 Meetings
September 5, 2013
SPELL
- Wen contacted Matt Hibbs
- Matt will not maintain SPELL in near future
- Undergrad at Caltech to maintain/upgrade (Ruby 2 -> Ruby 3)?
- Connect Matt with undergrad (work study?)
- Cynthia(?) at Caltech may know Ruby (needed for interface)
- Communicate with Mike Cherry / SGD as they use SPELL as well
- Does SGD have a SPELL developer?
- Java experience needed to maintain backend
Expression Clusters
- Wen found that many authors don't publish lists of clustered genes
- We could take in the data
Gene ACE Dumps
- Kimberly took a look at what Michael sent us
- Looked at gene objects specifically
- More in the full Gene ACE that we could make use of than what was included in the 'nightly' dump from Michael
- Could other curators take a look at what could be used/requested from GeneACE?
- Karen and Juancarlos will discuss for variations today
- Examples: CDS to Pseudogene changes, gene-to-variation mappings/pairings
Discussions on Value of Manual Curation
- What would WormBase look like without any manually curated data?
- Can concise descriptions be automated in any way? "This gene encodes ... It is involved in [GO process]..." etc.
- How are the concise description forms working? In progress...
Enhancer curation
- Gold-standard enhancers from Margie's list of papers
- Xiaodong will upload for WS240
Interaction changes
- Interaction model changed to update genetic interaction terms
- Also, "Electrophoretic Mobility Shift Assay" has been added as a 'Physical Interaction Detection Method'
- Interaction OA and dumper has been updated and is working properly
Historical Genes
- Abby has setup display of historical genes in Overview widgets of relevant objects (Interaction, Expr_pattern, Antibody, Transgene, Process)
- Looks good on staging
Upgrading transgene curation
- Capturing related sequences or sequence features and displaying on GBrowse
- Single molecule FISH data: Use case
- Look in GBrowse to see probe sequence vs transgene sequence; find discrepancy in expression patterns
- Tim Schedl would like to see what transgenes have been used for in vitro (purified from worms) experiments (e.g. physical interactions)
- Would like to capture epitope tags like FLAG, MYC, HIS, etc.
- Capturing what does or does not rescue a mutation
- Association with site-of-action data?
In silico phylogenetic tree data
- No current appropriate home for it in WormBase
- Wen and Karen working on how to house the data
- Data should go on Process pages
Process curation and associations
- Can we automatically infer associations to a process by, for example, a gene's mutant phenotype?
- What automatic connections can be made to processes?
- Do we 'hardcode' phenotype-to-process connections?
- Interaction widget with Cytoscape now functional on Process pages (on staging)
September 12, 2013
RNAi movies
- RNAi.org movies need referencing
- May require adding a Database tag to the ?Movie model
- We may be able to add the RNAi.org movie URL to the Movie object Remark field
- Chris will work it out with Todd
Crispr-CAS9 Genome Editing methods
- Will add to the Reagents page (will be under the Resources menu, not there on live site currently)
- URL is: http://www.wormbase.org/resources/reagents
- Curators can edit or create new widgets if logged in
- Ranjana will add two new widgets: "Third Party Tools", "Methods"
- Will add Ortholist to the Third Party Tools
- Will add Crispr-CAS9 links to Methods
GeneACE Nightly Dump
- Do people use the Laboratory or Clone info/tags?
AMIGO 2
- Raymond establishing a WormBase development environment that Juancarlos can use
- Troubleshooting installation of Perl libraries
- Also, working to Establish a development environment for the WormBase Ontology Browser server
- With our own server we can supply WormBase-specific ontologies
WormMine Data
- When can we/should we request new data for WormMine?
- JD is working on getting new data in; there is a Wiki page for requesting new data; we can add new data there
Cytoscape plugin update
- New viewer, has a different feel
- Need to click and hold to pan and scroll to zoom
- Hopefully adding back visible tools soon
- Implementing on Process pages and for Cell lineage browsing
- Cell lineage browsing
- First tried whole (embryonic) lineage but was too slow because too many nodes
- Now have a subtree rendering with 4 levels of the tree (great-grandparents, grandparents, parents, and children)
- May like to have full lineage at high resolution to zoom into for browsing a static image
- Process pages
- Cytoscape view of Process pages has all interactions related to the process
- Phenotypes for genetic interactions now listed in the legend
ORCID IDs for WormBase Persons
- We should incorporate ORCID IDs
- Can we do a reciprocal exchange of persons? Opt-in exchange?
- Should we ask WormBase users for their ORCID IDs?
- Came up while discussing Reuter's indexing (of gene name authors)
- We will add a request for ORCID IDs on the WormBase form for creating or editing WBPerson info
