WormBase-Caltech Weekly Calls June 2014

June 5, 2014

Agenda

• 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

Agenda

• 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?

Nomenclature

• 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