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| | [[WormBase-Caltech_Weekly_Calls_February_2018|February]] | | [[WormBase-Caltech_Weekly_Calls_February_2018|February]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_March_2018|March]] |
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| − | == March 1, 2018 == | + | == April 5, 2018 == |
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| − | === Elsevier paper-linking through Scholix === | + | === Topic 1 === |
| − | * Bidirectional linking in place with ScienceDirect, Elsevier
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| − | ** We link to their papers via DOI
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| − | ** They link papers to WB
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| − | * Scholix
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| − | ** http://www.scholix.org
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| − | ** Scholix becoming a standard platform for linking to DB websites
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| − | ** WB would need to establish Scholix integration?
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| − | ** Daniela to check in with the Alliance to see what the other groups are doing
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| − | ** Would Caltech library need to establish a pipeline or would WB do it?
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| − | * Would be good to revisit the paper page display for what is referenced in the paper
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| − | ** GO terms are not showing currently
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| − | ** Would be good to assess what else is not showing currently
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| − | | |
| − | === Upstate NY Worm Meeting ===
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| − | * Confirmation from organizers?
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| − | * Kimberly and Wen reached out to organizers about WB presentation
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| − | * 20-30 minute time slot for talk
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| − | ** What are most important topics to bring up?
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| − | ** Ask authors to submit sequence for sequence features, etc.
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| − | ** Micropublications
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| − | *** Would be good to have answers to common questions about micropublications (how we get reviewers, etc.)
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| − | ** Alliance of Genome Resources
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| − | ** Help Desk/ Online chat service
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| − | * Organizers want WB to have table at meeting
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| − | * Meeting in Syracuse
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| − | | |
| − | === Midwest Worm Meeting ===
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| − | * Organizers asked for $50-$100 sponsorship
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| − | | |
| − | We can pay for registration but we are not a company to sponsor events.
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| − | | |
| − | === Metrics ===
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| − | * How do DBs help research?
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| − | * How much time do MODs/Alliance etc. databases save researchers?
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| − | | |
| − | | |
| − | == March 8, 2018 ==
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| − | | |
| − | === SimpleMine interactions ===
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| − | * Wen considering adding interaction data to SimpleMine
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| − | ** Should we add a single column listing interacting genes with types in parentheses
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| − | ** Wouldn't want to add too many columns
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| − | ** Want to indicate, for a query gene, genes for which multiple interaction types have been observed
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| − | * Once interaction data is in WormMine, we can omit it from SimpleMine
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| − | * SimpleMine is not too difficult to develop or maintain as long as data models don't change
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| − | | |
| − | === SimpleMine preserving input list ===
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| − | * Adding functionality to WormMine that preserves original gene list
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| − | * Some input genes return multiple hits/rows
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| − | * We need to recognize these entries and deposit extra rows separately
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| − | | |
| − | === Alliance working group project plans ===
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| − | * Interactions
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| − | ** What are prioritized deliverables?
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| − | ** Predicted (physical) interactions: Interologs, Inter-species extrapolations
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| − | * (Automated) gene descriptions
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| − | ** Ranjana and Ceri have added content to project plan
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| − | ** Add phenotype data to description for information-poor genes (currently last on priority list)
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| − | * Disease/phenotypes
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| − | ** Cindy et al. producing project plan documents for disease and phenotype separately
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| − | | |
| − | | |
| − | == March 15, 2018 ==
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| − | | |
| − | === HTTP vs HTTPS ===
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| − | * Plan to move to https site-wide as a standard
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| − | * Google site ranking includes metric for https security
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| − | * All pieces in place on main site; just a few small things at Caltech to resolve
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| − | * What services are having problems?
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| − | * Raymond: Don't know the SSL details; has made Caltech machines using SSL layer
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| − | * Todd: Not needed; should be handled by proxy
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| − | * Todd needs to just know what are problematic URLs; should all be handled by main URL www.wormbase.org
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| − | * Ontology Browser broke, Juancarlos went to fix then had problem with https
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| − | * Todd: haven't setup https for all development sites yet, but will do that
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| − | * Gene Set Enrichment Tool: redirects to local/Caltech site that serves the page
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| − | ** Todd & Sibyl looking at; one possible solution is to get the recent code on staging and replace it (tool breaks on staging)
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| − | * Juancarlos, Raymond, Sibyl, and Todd will discuss later (Slack channel?)
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| − | | |
| − | === Disease model annotation class display ===
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| − | * Ranjana has two GitHub tickets open
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| − | ** https://github.com/WormBase/website/issues/6044
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| − | ** https://github.com/WormBase/website/issues/6241
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| − | * Data has gone into ACEDB, but no display is configured yet
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| − | * Ranjana would like to Skype with Sibyl to explain
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| − | * 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?
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| − | | |
| − | === Baltimore Area Worm Meeting ===
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| − | * Chris presenting tomorrow at the meeting
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| − | * Will cover data mining tools, new data and displays
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| − | | |
| − | === Alliance ===
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| − | * Paul S: Work on Alliance plans; important
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| − | | |
| − | === Citace upload ===
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| − | * Next Tuesday (March 20th) at 10am Pacific
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| − | | |
| − | | |
| − | == March 22, 2018 ==
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| − | | |
| − | === WB grant critique ===
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| − | * Great comments
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| − | * Skeptical that community curation will take off (or that it will get all curation done)
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| − | * Positive reviews of Alliance interactions with WB
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| − | | |
| − | === New York worm meeting ===
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| − | * Kimberly and Wen will head to local worm meeting to present on WB
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| − | | |
| − | === Human Genetics meeting ===
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| − | * Meeting in October
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| − | * Will have Alliance presence there
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| − | | |
| − | === Alliance ===
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| − | * How important is it to have the MOD?
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| − | * What is the added value of the Alliance portal?
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| − | * What are the use cases that can be uniquely handled by the Alliance website/portal? MOD site?
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| − | * Something to think about; send thoughts and ideas to Paul S.
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| − | * Parallel development pipelines?
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| − | ** Valerio discussing with AGR developers tomorrow
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| − | ** So far, AGR development has been centralized; may need to allow parallel development for efficiency/efficacy
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| − | ** Example: development of automated gene descriptions
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| − | ** JBrowse and GO Ribbon currently developed independently
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| − | | |
| − | === Person curation ===
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| − | * Cecilia had looked at how other MODs/groups curate authors/persons? Interact with community?
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| − | * How can the Alliance do the same (union of all approaches)?
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| − | * ZFIN has person page
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| − | | |
| − | === Variant graphical viewer ===
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| − | * As requested by Andy Golden and others
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| − | * Hope to have a mockup by April
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| − | * Use synteny viewer/browser? Long evolutionary distances (human-worm) may be tricky
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| − | | |
| − | === Baltimore Area Worm Meeting ===
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| − | * [https://docs.google.com/presentation/d/1i_LEZsolKXy1NrEqua0u4apgWHiQbkQhifgtMTbz2H4/edit?usp=sharing| Chris' slides]
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| − | * Enthusiasm for Micropublications
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| − | * Enthusiasm for the Alliance of Genome Resources
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| − | * Questions:
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| − | ** How to download RNASeq data values from gene page?
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| − | ** What does "WS" mean?
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| − | ** WormBase provides protein-coding gene exon expression evidence, what about small, non-coding RNAs?
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| − | ** How are micropublication reviewers selected?
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| − | *** Authors suggest reviewers; uP team suggest reviewers
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| − | *** PIs, post-docs and senior grad students (vetted; already have published papers)
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| − | ** Are phenotypes included in Ontology Browser also from genetic interactions? Answer: "No", response: "Good"
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| − | ** Are we going to lose WormBase and functionality?
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| − | * Comments:
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| − | ** FTP README docs need work, updating
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| − | ** WormMine is not intuitive
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| − | ** It's hard to know what each data mining tool is good/best for
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| − | *** Would be good to have a simple document that outlines the best uses of each tool
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| − | *** How would we best provide such a document? Location? Versioning? Micropublication?
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| − | *** Create a one page PDF to print out and give out at meetings?
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| − | *** Update blogs (describing nature of updates to each tool)?
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| − | *** Existing FAQ Wiki?
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| − | *** Important to have a single place for documentation (to avoid denormalization)
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| − | * Requests:
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| − | ** Create simple Galaxy import of WB genome sequence
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| − | ** Display prevalence of splice junctions
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| − | ** Add README docs to FTP site (and/or update them)
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| − | ** Separate RNAi and allele based phenotypes
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| − | *** Probably worth considering; have heard from users before
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| − | *** Could also provide functionality in Phenotype Graph
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| − | ** Include BioRxiv papers in gene page References widget
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| − | *** Could provide links to BioRxiv (with relevant search results)?
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| − | *** Is there a way to link BioRxiv papers to the eventually published paper?
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| − | *** Are full texts indexed?
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| − | | |
| − | | |
| − | == March 29, 2018 ==
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| − | | |
| − | === Gene Set Enrichment Analysis: duplicate entries ===
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| − | * Although duplicate genes in an input list are not counted more than once, the output lists the valid gene list that includes duplicates
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| − | | |
| − | === Interactions Venn Diagram ===
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| − | * Jae generated mockups for displaying a Venn diagram of gene pairs represented by interactions on a gene page
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| − | * Mockups here: https://drive.google.com/file/d/1z15GwvLT1dUH9VkYCz-NoQ2oFzi_3ds3/view?usp=sharing
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| − | | |
| − | === GO term and spatiotemporal expression comparison ===
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| − | * Jae generated mockups for representing a GO term and spatiotemporal expression comparison for interacting gene pairs
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| − | * The data display would/could use the ribbon-style annotation display
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| − | * Mockups here: https://drive.google.com/file/d/1z15GwvLT1dUH9VkYCz-NoQ2oFzi_3ds3/view?usp=sharing
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| − | | |
| − | === GO enrichment analysis for interacting genes ===
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| − | * Jae generated mockups for displaying the results of GO term enrichment analysis on the list of genes that interact with a focus gene
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| − | * Mockups here: https://drive.google.com/file/d/1rwy8iuuaXJgu6TnQrGvvfVOXgA5wvtyt/view?usp=sharing
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| − | | |
| − | === Inclusion of negative GO annotations in Alliance GO ribbon ===
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| − | * See cpx-1 gene page: http://www.alliancegenome.org/gene/WB:WBGene00022271
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| − | * In the GO ribbon, the term "nucleus" is highlighted, yet this is only because of two negative annotations coming from mouse and rat
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| − | * Do we want negative GO annotations included in the display by default? Shouldn't we alert users to this if we are going to do this?
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| − | * Thoughts?
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| − | | |
| − | === Upstate NY C elegans Meeting ===
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| − | *Wen and Kimberly presented at the UNYCEM in Syracuse last Saturday (3/24)
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| − | *Feedback:
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| − | **WormMine is hard to learn (but performing operations on lists of genes is something people really want/need to do)
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| − | **Video tutorials would be very helpful, especially for teaching students different WB functionality
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| − | **Micropublications were well received
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| − | ***People were specifically interested in publishing negative results; maybe make that point even more prominent on the FAQs?
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| − | **Downloading sequences that include coding and non-coding, it would be really helpful to have visual cues for coding vs non-coding
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| − | **Should the C. elegans community consider moving towards more mammalian-centric gene names, even if that means changing current gene names?
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| − | *** Tim Schedl already tries to match C. elegans gene names to human gene names
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| − | *** Idea would be to re-name existing gene names to be more like human gene names
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| − | **A better mobile app would be great; people want to look up C. elegans info on their phones and the current view is cumbersome
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| − | * Denise (organizes neuro topic meeting); suggested that WB present at Neuro meeting
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| − | ** Meeting in Madison, WI June 25-28
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| − | *Better, more comprehensive README for the ftp site
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| − | *A one-page summary of tools and their key features would be helpful
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| − | **This static page could then link out to more detailed videos, tutorials, documentation, etc.
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| − | | |
| − | === Changes to Regulatory Interactions Table ===
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| − | * April has some ideas for changing the Regulatory Interactions Table so that it can display more information.
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| − | * https://docs.google.com/document/d/12a50imE7WURuOeU39cqBfYdllW7qHw1tLrKrF2Ev7ZA/edit?ts=5abd285f
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| − | * Separate tables for each interaction type (regulatory, genetic, physical)
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| − | * Add columns to tables; for regulatory interactions, add “Regulation level” (eg. transcriptional), Anatomy terms, Life stages, Subcellular localization, evidence type?
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| − | * Currently, multiple interactions are included in a single row, we could change this to multiple rows of the same color to include more details for each individual interaction.
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| − | | |
| − | === FTP README file ===
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| − | * Many users request updates to README files on FTP site
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| − | * Likely to become cumbersome to maintain
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| − | * Raymond: Maybe we can write a script that can automatically generate a site-map/site-tree to get an overview of the FTP site structure; would it be useful? Yes
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| − | * Will need to discuss with Todd
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