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?