WormBase-Caltech Weekly Calls June 2014

From WormBaseWiki
Jump to navigationJump to search

June 5, 2014


  • GAF vs GPAD/GPI file formats
    • GO still uses both, but is moving towards using GPAD/GPI as their preferred format.
    • We will always need GAF for WOBr?
  • LEGO Curation/Noctua Development
    • Tool is still under significant development at Berkeley.
    • What are our plans/goals at Caltech? How best to align this with Berkeley development?

WormBase Ontology Browser (WOBr) for WS244 release

  • User interface: would be good if curators could have a look and review again
  • Latest GAFs added were for Life Stage and Disease
  • GitHub WOBr tracker: https://github.com/azurebrd/wobr

GAF vs GPAD/GPI file formats

  • GO traditionally uses GAF format
  • May be migrating to GPAD/GPI [Gene Product Annotation Data / Gene Product Information] format in future
  • Backend of Amigo2/WOBr uses owltools
  • Kimberly discussing with GO team
  • We already have scripts to convert GPAD to ACE format

LEGO curation / Noctua Development

  • (Too?) much flexibility in what can be curated into Noctua
  • Final data model may still need refinement?
  • Need to wait for final word on data model before finalizing curation pipeline
  • We may be able to develop curation tools ahead of final LEGO data model
  • Would be good to have discussions about complex biological scenarios and how to best capture

Construct OA

  • Karen and Juancarlos working on ?Construct OA
  • Other OA's may need to be updated accordingly
  • Wen will set up a local database with the proposed ?Construct model

Reactome tutorial

  • 10am PDT tomorrow (Friday)
  • WebEx conference
  • Initial talk of curating chromosome segregation, may be too complex
  • Paper sent around to summarize Reactome model and curation pipeline

New Topic for WS245

  • Many possible topics; would be good to choose a topic that has some new papers and would be amenable to drawing a pathway
  • We discussed: aging, apoptosis, defecation, feeding, ascarosides...
  • We will try apoptosis
  • Chris will look into and send around findings

Mapping of promoters

  • We have annotated many promoters for expression patterns, for example, but have not been mapped to genome
  • Ultimately want to map constructs (or components of constructs) to the genome
  • Construct components should be converted to sequence feature objects (?Feature)

June 12, 2014


  • Reactome tutorial
    • review event
    • hear thoughts from attending curators

Reactome tutorial notes

  • Peter D'Eustachio ran tutorial
  • Showed basic operations for checking out objects, IDs, etc. to build pathway
  • Requires explicit reaction events to annotate
  • Black box reactions are now possible
  • All entities have to be checked in and exist in some database
  • Entities: mostly proteins, can be protein complexes, small molecules (mostly UniProt based), cell components, anatomy terms
  • Phenotypes are not recognized entities
  • WormBase IDs not available in the Reactome tool
  • Soon to be a BioCyc tutorial
  • KEGG has drop down menu from pathways to highlight potential orthologous/analogous components from relevant species

WOBr GO/Disease annotation filtering for IEA evidence codes

  • Can a filter be implemented in WOBr to filter out IEA GO/Disease annotations from results lists?
  • Possible, details are important; could show separate results lists for IEA and non-IEA annotations

LEGO curation

  • Is there an intention (by LEGO model/software developers and curators) to add evidence to LEGO annotation coupling (e.g. process-to-function, function-to-component, etc.) as evidence codes and references/citations?
  • Kimberly: there has been discussion, but the resolution is not clear yet

June 19, 2014

cis-Regulation visualization

  • We can consider ways (other than current Cytoscape view) to visualize cis-regulation events
  • Show cis-features along chromosomes, maybe in circular view?

Evolution meeting

  • eQTL for correlating expression in highly inbred recombinant lines
  • 2 Caenorhabditis species close to elegans available (sister species?)
  • Banana root parasite with tiny genome (for a nematode)

Computer updates

  • 2 older computers in Juancarlos' office (2004, 2009)
  • Maybe replace the 2004 computer
  • Setup new computer/server in Juancarlos' office, once settled move to server room?


  • Was discussion to name uncloned genes (in new species) only based on alleles, but decided to still give names to unique genes

MOD global offices

  • Could we set up local MOD offices, maybe one curator per MOD, at various global locations?
  • Korea, Japan, Europe? China, Taiwan?
  • Could get local funding?

CANTO implementation for WormBase

  • Community annotation tool
  • Publication just came out

June 26, 2014

Gene names request with phenotypes

  • Sometimes new gene names are requested along with a phenotype to inform nomenclature
  • Without a variation (or perturbation) we cannot currently annotate the phenotype to the gene
  • As a go-around, curators/authors can add a variation to the request
  • We will miss relevant phenotypes that have no variation/RNAi
  • Authors can submit allele/phenotype annotations independently

Person Evidence update?

  • Can we have some automated/semi-automated way to update person evidence to paper evidence?
  • Textpresso pipeline? First paper from author using the proposed gene name?

Write an opinion/editorial/blog piece on sequence data submission

  • We could collectively write a opinion piece/rant on arbitrary sequence submissions or descriptions
  • Publish for worm community with suggested implications for other organisms