WormBase-Caltech Weekly Calls September 2013

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September 5, 2013


  • 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

  • What data do we want to get from Hinxton (in general) on a daily/nightly basis?
  • We will wait for Kimberly to settle on what we want


  • 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

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

September 19, 2013

Caltech Development Environment

  • Issues with running a local mirror
  1. Less tenable option; build and staging environments are distributed; Nothing sitting on a single machine
  2. Data size: amount of storage required; amount of time required for the build
  • Build process lengthy; need to distribute the task or wait a week
  • Todd can give an AMI (?) ID , letting Raymond create an instance
  • Raymond wouldn't need to build the GFF database
  • EC2 cost? Depends on how
  • Storage is biggest cost; can minimize (use our MySQL hosts), still need to run ACE
  • Run local storage off of femoral(?)
  • EC2 instance:
    • Running 24 hours a day? Use 25%?
    • Let's say 24 hour EC2 instance, large size, heavy utilization, upfront cost of 1 year (with purchased reserved instance): ~$1166
    • Plus bandwidth and storage costs
    • Total cost : ~$1500 per year
  • Environments change name to update: Development --> Staging --> Production
  • 3rd option: setting Raymond up on development service (?)
    • May be easiest approach
    • Todd opts for this approach
    • Raymond and Juancarlos can have their own logins

NAR Paper

  • Todd is drafting the NAR manuscript
  • Opting for the short format (2-3 pages); not many people read it; geared towards database people
  • Todd wants to describe new WormBase approach in a different paper
  • What are the big impact changes on the curatorial side?
    • Curators could collect points and send them to Todd
  • Deadline is the 1st week in October
  • Curation section about 1 page; Focus on direction: processes, pathways, topic-based curation

Topic-based curation

  • Curators can focus on building off of a 'standard' pathway diagram from a review article, for example
  • Can start with a review, WormBook chapter
  • What coverage are we shooting for? 90%?
  • Start a WikiPathway; curators can build off of that
  • Need to improve:
  1. How we choose a topic?
  2. How we find the papers?
  3. What we capture? How we converge our efforts?
  • Karen made a process for each type of stress response
  • We can start with Misfolded (Unfolded) Protein Response (related terms: "proteotoxicity", "ER stress")
  • Curators can keep notes about topic curation
  • We want to consider GO terms, existing WB Processes, existing WikiPathways
  • Karen will be primarily responsible for Process and WikiPathway curation

GeneACE Nightly Dumps

  • Still need to resolve a few things
  • Should daily/nightly dumps be expanded beyond GeneACE? Sequence databases?


  • Can we match WBPersons to ORCID IDs?
  • We can ask WB users what their IDs are?
  • Or, we can give WB users (once logged in) a way to link their WB account to an ORCID ID?
  • How many WB authors already have an ORCID ID? We can search the ORCID database or contact WB authors?