WormBase-Caltech Weekly Calls

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

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

2018 Meetings

January

February

March 1, 2018

Elsevier paper-linking through Scholix

• Bidirectional linking in place with ScienceDirect, Elsevier
  • We link to their papers via DOI
  • They link papers to WB
• Scholix
  • http://www.scholix.org
  • Scholix becoming a standard platform for linking to DB websites
  • WB would need to establish Scholix integration?
  • Daniela to check in with the Alliance to see what the other groups are doing
  • Would Caltech library need to establish a pipeline or would WB do it?
• Would be good to revisit the paper page display for what is referenced in the paper
  • GO terms are not showing currently
  • Would be good to assess what else is not showing currently

Upstate NY Worm Meeting

• Confirmation from organizers?
• Kimberly and Wen reached out to organizers about WB presentation
• 20-30 minute time slot for talk
  • What are most important topics to bring up?
  • Ask authors to submit sequence for sequence features, etc.
  • Micropublications
    • Would be good to have answers to common questions about micropublications (how we get reviewers, etc.)
  • Alliance of Genome Resources
  • Help Desk/ Online chat service
• Organizers want WB to have table at meeting
• Meeting in Syracuse

Midwest Worm Meeting

• Organizers asked for $50-$100 sponsorship

We can pay for registration but we are not a company to sponsor events.

Metrics

• How do DBs help research?
• How much time do MODs/Alliance etc. databases save researchers?

March 8, 2018

SimpleMine interactions

• Wen considering adding interaction data to SimpleMine
  • Should we add a single column listing interacting genes with types in parentheses
  • Wouldn't want to add too many columns
  • Want to indicate, for a query gene, genes for which multiple interaction types have been observed
• Once interaction data is in WormMine, we can omit it from SimpleMine
• SimpleMine is not too difficult to develop or maintain as long as data models don't change

SimpleMine preserving input list

• Adding functionality to WormMine that preserves original gene list
• Some input genes return multiple hits/rows
• We need to recognize these entries and deposit extra rows separately

Alliance working group project plans

• Interactions
  • What are prioritized deliverables?
  • Predicted (physical) interactions: Interologs, Inter-species extrapolations
• (Automated) gene descriptions
  • Ranjana and Ceri have added content to project plan
  • Add phenotype data to description for information-poor genes (currently last on priority list)
• Disease/phenotypes
  • Cindy et al. producing project plan documents for disease and phenotype separately

March 15, 2018

HTTP vs HTTPS

• Plan to move to https site-wide as a standard
• Google site ranking includes metric for https security
• All pieces in place on main site; just a few small things at Caltech to resolve
• What services are having problems?
• Raymond: Don't know the SSL details; has made Caltech machines using SSL layer
• Todd: Not needed; should be handled by proxy
• Todd needs to just know what are problematic URLs; should all be handled by main URL www.wormbase.org
• Ontology Browser broke, Juancarlos went to fix then had problem with https
• Todd: haven't setup https for all development sites yet, but will do that
• Gene Set Enrichment Tool: redirects to local/Caltech site that serves the page
  • Todd & Sibyl looking at; one possible solution is to get the recent code on staging and replace it (tool breaks on staging)
• Juancarlos, Raymond, Sibyl, and Todd will discuss later (Slack channel?)

Disease model annotation class display

• Ranjana has two GitHub tickets open
  • https://github.com/WormBase/website/issues/6044
  • https://github.com/WormBase/website/issues/6241
• Data has gone into ACEDB, but no display is configured yet
• Ranjana would like to Skype with Sibyl to explain
• Bypass ACEDB altogether? Go right into Datomic? Need to check, but will probably pull into ACEDB and do the conversion to Datomic at the same time?

Baltimore Area Worm Meeting

• Chris presenting tomorrow at the meeting
• Will cover data mining tools, new data and displays

Alliance

• Paul S: Work on Alliance plans; important

Citace upload

• Next Tuesday (March 20th) at 10am Pacific

March 22, 2018

WB grant critique

• Great comments
• Skeptical that community curation will take off (or that it will get all curation done)
• Positive reviews of Alliance interactions with WB

New York worm meeting

• Kimberly and Wen will head to local worm meeting to present on WB

Human Genetics meeting

• Meeting in October
• Will have Alliance presence there

Alliance

• How important is it to have the MOD?
• What is the added value of the Alliance portal?
• What are the use cases that can be uniquely handled by the Alliance website/portal? MOD site?
• Something to think about; send thoughts and ideas to Paul S.
• Parallel development pipelines?
  • Valerio discussing with AGR developers tomorrow
  • So far, AGR development has been centralized; may need to allow parallel development for efficiency/efficacy
  • Example: development of automated gene descriptions
  • JBrowse and GO Ribbon currently developed independently

Person curation

• Cecilia had looked at how other MODs/groups curate authors/persons? Interact with community?
• How can the Alliance do the same (union of all approaches)?
• ZFIN has person page

Variant graphical viewer

• As requested by Andy Golden and others
• Hope to have a mockup by April
• Use synteny viewer/browser? Long evolutionary distances (human-worm) may be tricky

Baltimore Area Worm Meeting

• Chris' slides
• Enthusiasm for Micropublications
• Enthusiasm for the Alliance of Genome Resources
• Questions:
  • How to download RNASeq data values from gene page?
  • What does "WS" mean?
  • WormBase provides protein-coding gene exon expression evidence, what about small, non-coding RNAs?
  • How are micropublication reviewers selected?
    • Authors suggest reviewers; uP team suggest reviewers
    • PIs, post-docs and senior grad students (vetted; already have published papers)
  • Are phenotypes included in Ontology Browser also from genetic interactions? Answer: "No", response: "Good"
  • Are we going to lose WormBase and functionality?
• Comments:
  • FTP README docs need work, updating
  • WormMine is not intuitive
  • It's hard to know what each data mining tool is good/best for
    • Would be good to have a simple document that outlines the best uses of each tool
    • How would we best provide such a document? Location? Versioning? Micropublication?
    • Create a one page PDF to print out and give out at meetings?
    • Update blogs (describing nature of updates to each tool)?
    • Existing FAQ Wiki?
    • Important to have a single place for documentation (to avoid denormalization)
• Requests:
  • Create simple Galaxy import of WB genome sequence
  • Display prevalence of splice junctions
  • Add README docs to FTP site (and/or update them)
  • Separate RNAi and allele based phenotypes
    • Probably worth considering; have heard from users before
    • Could also provide functionality in Phenotype Graph
  • Include BioRxiv papers in gene page References widget
    • Could provide links to BioRxiv (with relevant search results)?
    • Is there a way to link BioRxiv papers to the eventually published paper?
    • Are full texts indexed?

March 29, 2018

Interactions Venn Diagram

• Jae generated mockups for displaying a Venn diagram of gene pairs represented by interactions on a gene page

GO term and spatiotemporal expression comparison

• Jae generated mockups for representing a GO term and spatiotemporal expression comparison for interacting gene pairs
• The data display would/could use the ribbon-style annotation display

GO enrichment analysis for interacting genes

• Jae generated mockups for displaying the results of GO term enrichment analysis on the list of genes that interact with a focus gene
• Mockups here: https://drive.google.com/file/d/1rwy8iuuaXJgu6TnQrGvvfVOXgA5wvtyt/view?usp=sharing