WormBase-Caltech Weekly Calls

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GoToMeeting link: https://www.gotomeet.me/wormbase1

2018 Meetings

January

February 1, 2018

Automated gene descriptions - orthology

• Some genes have human orthology mentioned in automated descriptions, even though the orthology call has not been called in DIOPT
• WormBase uses EnsemblCompara and other methods (not aggregate method like DIOPT)
• Orthology synchrony is a challenge; WormBase and FlyBase may need to pay special attention to orthology calls and discrepancies
• DIOPT is purely automated, does not consider other information about orthology evidence
• We should be clear about how the orthology calls are made

Next upload

• Unclear of exact date
• Probably end of March

SimpleMine issue

• Redundant genes in input list are merged
• Should SimpleMine provide an option to keep redundancies?
  • Give option up front? Provide submission step to point out redundancies? Ask for choice?
• We can default to show row-by-row correspondence, and display the number of redundant entries
• Conclusion: Make an option for users to indicate if they want row-by-row correspondence or a merged list

Cell type expression

• Waterston paper
• 40,000 random cells, clusters sequenced individually to a depth of 20,000 reads; ~1000 genes per cell; cluster data; make judgement call as to what cell types they likely are
• For now, we can do a simple annotation: significantly expressed genes for each cell type
• Supplemental table S5 for neurons
• Maybe just ignore the hybrid calls like AQM/PVM, etc.
• It may be good to isolate the single cell data from other expression data
• We should annotate/capture the expression clusters
• Would be good to be able to do enrichment analysis on the clusters; compare data sets
• Data has not been placed in SPELL yet, Gary considered the data a work in progress
• We can communicate with Waterston group; are they collecting more data?
• Wen will take another look at the data
• Gary W. concerned about the reported/assumed/inferred identity of the cells in the paper
• Probably cannot curate to individual cells, but we can annotate to a higher level term
• We want to annotate and display expression enrichment as well as presence/absence calls

February 8, 2018

Release schedule

• Wen will ask Hinxton to update the published release schedule (for next data upload)

New York Worm Meeting

• Wen and Kimberly will present a WormBase tutorial on March 24
• Wen communicated to Oliver Hobert; suggested topics:
  • Multi-gene (batch) search tools
  • How literature info gets into WormBase? Curation process?
  • Should we discuss completeness?

GO curation

• New simple input form for Noctua, being developed at USC
• Not very much GO curation happening at WB right now
• Protein-2-GO pipeline
• Do we have a good Phenotype-2-GO(Process) mapping pipeline? We have our old mappings; not very reliable; would need to spend more time expanding the worm phenotype ontology and GO to improve
• Cellular component curation will come in from WB expression curation
• Don't have pipeline for Interactions-2-GO
• Textpresso Molecular Functions pipeline?
• geneprod and catalyticact data types for molecular function pipeline
• Textpresso can send molecular function annotations to Noctua
• For high-level pathway curation; we should probably read WormBook chapters (or other reviews) and develop pathways (using non-experimental evidence codes)
• We could potentially seed Noctua models from Reactome
• We would like to have complete curation for major pathways for gene enrichment analysis
• Roles of small molecules in Noctua models still being worked out

Phenotype curation

• Chris has had community curation pipeline on back burner while updating Wiki and dealing with AGR, WormMine, etc.
• Will get back to soon; will resend email requests for newer papers sent over a year ago

Expression curation

• Daniela getting back to expression curation after Micropublication stuff has quieted down

Gene regulation curation

• April came across dataset involving regulation of siRNAs that don't seem to have gene objects in WB
• May need to instantiate genes for these?

Physical interaction curation

• SVM classification; do we flag a paper as negative that has protein interactions but no interactions for C. elegans
• Can we generate a good SVM that only identifies WB-curatable papers?

Disease curation

• Now curating the specific genetic entities involved in a disease model
• Will also capture environmental conditions, treatments (e.g. ameliorates, exacerbates)
• Curation in-line with AGR standards
• Evidence code needed for assertions that an animal is a model of disease in which the assertion is based on background knowledge and experimental evidence, together
• Evidence Code Ontology (ECO) is developing a new term to accommodate
• Disease curators can use new evidence code as well as any existing codes
• Is there a definition of a "disease model"?
• What are the minimal criteria for considering something a disease model?
• WB and FB curators focus on cellular phenotype and relation to the disease

Expression cluster curation

• 27 papers in pipeline
• Will then work on "single-cell" RNAseq
  • Wen, Raymond, and David should discuss

April and May Worm Meetings

• Midwest and Colorado meetings
• Wen submitting abstracts
• Wen and Kimberly can write up abstract template for New York meeting and send around to be modified for future meetings

WormBook

• Published last version for legacy site

Papers

• Daniel requested 13 (older) papers from Caltech library through inter-library process
• Received more than half as images; would need optical character recognition (OCR) for Textpresso purposes
• What is the state of the art of OCR now? How good is it? Can we ask Caltech library for the service?
• Are these high priority papers? Need to check to see if worth processing

AGR

• Disease working group setting up a face-to-face meeting
• Variant working group may need a face-to-face meeting as well
• Expression working group working out initial AGR site data display mockups
• Interaction working group; we will want to incorporate miRNA/target interactions (RNA-RNA interactions); will look at miRBase

February 15, 2018

Model changes

• Models freeze March 2nd
• Will need to get model changes proposed and tested by then

Sys admin of Tazendra/Mangolassi

• Raymond will discuss with Juancarlos to centralize
• Need good documentation for forms, tools, etc.
• Will be a push to put all code for tools and forms on GitHub

Tazendra forms, tools bug this week

• There is a dependency on Mangolassi for some tools
• Mangolassi went down and caused problems
• Would be good to decouple the two machines

AGR

• May not get an AGR all-hands face-to-face meeting before the summer
• Working groups can decide to have face-to-face meeting
• People should speak up if they have interest in visiting other MODs/sites; can be arranged
• Consider what grant proposals could come out of such meetings/visits
• Currently no ontology working group, no anatomy working group
• Could establish a preliminary working group; reach out to relevant people
• Anatomy working group issues may come up in expression working group
  • Daniela will keep Raymond updated on relevant issues that come up with the expression group

Ontology Browser gene lists

• Chris requesting change to gene list display from WOBr
• https://github.com/WormBase/website/issues/6190
• Should provide WBGene IDs, not just gene public names
  • That was the original intent, but using WBGene IDs was, for some reason, causing issues when developing the tool; will need to revisit that issue to get WBGene IDs displayed

February 22, 2018

Acquiring data from Postgres

• Hyperlinking project
• Hyperlinking entities from papers to WormBase
• Identifies genes, alleles, other bioentities
• Genetics (GSA), eLife, PLoS
• Partner with SGD and FlyBase
• Curators check link fidelity
• Now expanding to other Alliance members (rat, mouse, etc. papers)
• What do we do in 2-3 years when we want all links to go to Alliance website?
  • Need to be thinking about it
  • Maybe discuss with others in 2-3 months (now is very busy)
• Central data repository for all data (MOD) files would be helpful to developers (and users)
  • FTP site would be good
• Will expand entities to reagents and link to suppliers
• Could possibly just dump all Postgres data into one place, Karen's developers could write scripts to process that data; cronjob?
• Juancarlos will setup a URL that can be used to access the data; will setup on cronjob every day at 8pm
• Really need data to be as up-to-date as possible
• In Silico page with embedded i-frames (WormBase page inset)

Alliance SAB meeting

• SAB critical of:
  • not being unified
  • not being organized
• Now everyone has committed
• Concern still exists about autonomy of MODs
  • Will each user community still be served effectively by the Alliance?
• Organization is easier when all are committed
• Maybe bring in a professional organizer/project manager (long term)
• New aggressive timeline for progress
  • April 23rd meeting; need to give material a week earlier
  • Need year and a half plan; each working group will provide details
• Only 2 full time Alliance staff; may need more on project; difficult for individuals to split time/effort
• SAB member: curation involves expert decision making/analysis on issues, not just straight-forward data acquisition
• Maybe we would have better curation consistency if individual curators focused on particular topics; became experts for certain subject matter
• Possibility to have Alliance all-hands call in Fall
• Working groups can have face-to-face meetings; have travel/meeting budget until July 31st then resets

Automated gene descriptions

• Difficult to handle genes with high information content; many ontology term annotations
• How do we simplify descriptions? Using higher-level terms, slim terms? Gets tricky

Micropublications

• Michael Elowitz tweeted out micropublication stuff
• Received feedback on Twitter; worth looking at threads, comments

Community curation plan

• Alliance need for community curation
• Micropublications are a bit of a pilot for community curation
• Need shared curation/submission forms; fit shared data models?

RNAi secondary targets

• WormMine and WormBase gene/RNAi pages include secondary RNAi targets but WOBr and SObA do not
• Should we include or exclude secondary targets? We want consistency across data sets
• No gold standard RNAi target prediction algorithm
• We should be transparent about primary/secondary status wherever we include secondary targets in display
• Could be addressed with phenotype display proposal
• Should probably remove secondary targets from bulk data sets