WormBase-Caltech Weekly Calls June 2014
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- 1 June 5, 2014
- 2 June 12, 2014
- 3 June 19, 2014
- 4 June 26, 2014
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
- 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
- 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
- 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
- We can consider ways (other than current Cytoscape view) to visualize cis-regulation events
- Show cis-features along chromosomes, maybe in circular view?
- 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)
- 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