WormBase-Caltech Weekly Calls

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

2019 Meetings






June 6, 2019

New SObA graphs

  • May put graphs within existing widgets, but don't need to rush to get that ready for IWM

Phenotype association file format

  • May be best to leave the format as is
  • There are problems; paper IDs keep switching columns
  • Would need to revisit the reasoning for why we do it that way
  • When will the Alliance produce a similar/replacement file? Not sure

Phenotype requests

  • Sent out 1140 emails on May 30
  • Since have received 374 annotations from 54 papers (42 requested, 12 additional)
  • 21 papers flagged as not having phenotypes
  • Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate), in first week

June 13, 2019


  • Coordinating transportation of swag boxes to Pauley Pavilion
  • Workshop on Saturday June 22, from 1pm to 2:30pm
  • Saturday morning micropublication breakfast 7:30 - 8:30am
  • Workshop
    • Presenters: it may be best to present as use cases rather than a research project
    • Chris will cover SimpleMine for Wen
    • Chris: won't do live demo; only screenshots, maybe some video
  • Paul's lab will do marathon bibs to show lab affiliation and graphical abstract
  • Paul's talk
    • Cover Alliance
    • New features
      • SObA (for new data)
      • Complete for protein-protein interactions
      • RNASeq tools
      • Updated automated gene concise descriptions?
    • Phenotype community curation
      • Chris will send Paul numbers on: top community curators, overall stats (number of annotations, papers, curators)
    • Author First Pass
    • Micropublication


  • Paul attended
  • Alliance publicity was discussed
  • SAB likes the Alliance orthology features
  • Working on topics: displaying papers and data
  • Pathways: discussion about best approach
  • Metabolic engineering
  • Meta data about RNASeq data
    • SPELL tool, basically only tool of its kind available; need new tools
  • Species-specific proteins: how best to find them? HMMs (Jackhammer)?

Concise descriptions

  • Progress being made within the Alliance to update the automated concise gene descriptions
  • We will still accept manually written descriptions and display them in parallel with automated descriptions


  • If people are requesting manually written gene descriptions, they could submit a microreview
  • Concern was expressed about how to handle a really high throughput of submissions:
    • Daniela: Working towards automating as much of the processing pipeline as possible
    • Raymond: The throughput will be handled appropriately depending on demand; priority scheme will help
    • Not getting lots of submissions yet, probably won't be inundated in the near future
    • Karen: tools are still being developed; the platform is not being advertised as much as it could be; will ramp up outreach and communication once tools are in place to handle more submissions
  • Karen: Micropublications team will reach out to curators to help build submission forms for respective data types

Undiagnosed Disease Network data

  • Andy Golden will meet with Ranjana and Chris at IWM to discuss
  • Andy asked about protocol pages at WormBase?
  • Paul: Bioprotocols and Protocols IO
  • Maybe we could interface with those existing resources to link to relevant protocols from WormBase (and WormBook)

June 27th, 2019

IWM 2019: Feedback from Users

  • Anatomy term synonym search
    • User pointed out that "RnB" search returns 0 results; GitHub ticket made to index anatomy synonyms
  • Ciliated neurons
    • User pointed out that male ciliated neurons are missing as a subclass of term "ciliated neuron"; GitHub ticket made, easy fix
  • Import of 22G and 26G RNAs
    • Spoke to Julie Claycomb
    • These are short RNAs transcribed by RNA-dependent RNA Polymerase (RdRP) off of mRNA molecules
    • Should these be instantiated as gene objects in WormBase? Julie argues that these are not genes
      • Should these just be transcript objects? Would they be linked to a gene? Or maybe also to any transcripts from which they could be derived?
    • Many map uniquely to the genome, but some map in multiple locations
    • Associated data for now would likely just be protein-RNA interactions (Argonaute-RNA interactions)
      • May eventually include phenotype and/or gene ontology (biological process) annotations
  • Ranjana & Chris spoke with Andy Golden
    • Andy and his lab will submit phenotype and disease data as they become available (likely pre-publication); we will likely point to a consortium as source until paper is published
    • There is still a strong need for cross-species variant mapping/visualization
  • miRNA binding sites
    • User asked at workshop and at booth; can we show miRNA binding sites in JBrowse? We would need to collect the data
    • There are many sources of miRNA-target interactions, some experimental, most predicted
  • Ontology aware diffs of annotations (gene1 expression vs. gene2 expression)
  • Promoter sequence in experimental constructs
  • Workshop went well
    • Next time, maybe have people bring laptops and follow along; be more interactive
    • We could do webinars, for WormMine for example, allow people to work along with the presentation
      • Do other MODs/groups do webinars? How have they been? Useful?
    • Competing with other workshops during the IWM
    • Can focus on new, less-used features for webinars, tutorial videos
  • Hawaiian genome in JBrowse
  • Had internet stability issues at UCLA; can we get a local, dedicated WiFi?
  • Next meeting (2021) will likely be in Europe (Cambridge UK?)
  • User at cGal workshop asked about tissue-specific promoters/transgenes
    • Have ~30 drivers and ~30 effectors; will WB take them in unpublished? Could make BioRXiv preprint (quick, before peer-review) and/or micropublication (after peer-review)
  • Protocols
    • Would be good to establish (for Alliance/WB) framework for serving protocols maintained by community

TAGC meeting

  • Next April (2020)
  • Alliance representation needed

Giving disease model annotations a stable identifier

  • Currently disease model annotations get a temporary ID at the time of dump,
Disease_model_annotation : "00000004"
Disease_term	"DOID:0050833"
Disease_of_species	"Homo sapiens"
Variation	"WBVar00275555"
Disease_relevant_gene	"WBGene00011559"
Inferred_gene	"WBGene00011559"
Association_type	"is_implicated_in"
Evidence_code	"IMP"
Genetic_sex	"hermaphrodite"
Paper_evidence	"WBPaper00035924"
Database "OMIM" "gene"	"613891 "
Database "OMIM" "disease"	"258900"
Curator_confirmed	"WBPerson324"
Date_last_updated	"2017-04-24"
  • Would like to institute stable identifiers across releases, so the plan is to call these objects, 'WBDisease_annotation:<number>', so then the above identifier would become 'WBDisease_annotation:00000004', or 'WBDiseaseannot:00000004' or 'WBDiseaseAnnot:00000004'
  • ID convention--is underscore allowed?
  • Is 'WBDisease_annotation:00000004' too long for acedb?
  • Need to ask Kevin, Hinxton; what are the other implications for maintaining and generating persistent, unique IDs

Anatomy ontology issues

  • Currently, "intestinal muscle" is considered "part of" intestine
    • User asked for intestinally expressed genes; using WOBr would also retrieve genes in intestinal muscle
    • David Hall confirmed that instestinal muscle cells are not part of intestine
    • Maybe we can change to: "intestinal muscle" part_of "alimentary system"
  • Currently, "amphid process" is considered "part of" each type of amphid neuron like AWC, AFD, etc.
    • Problem is that users looking in WOBr for AWC-expressed genes will be given genes expressed in ANY amphid process regardless of which cell
    • Propose to change to: "amphid process" part_of "amphid neuron" only

July 11th, 2019

Alliance all hands meeting

  • Raymond: would be interested in discussing ontologies and their usage in the Alliance
    • Phenotype, anatomy ontologies, GO, etc.
    • Ontology browsers, SObA

IWM workshop

  • Videos ready for upload
  • Wen and Raymond now have access to outreach@wormbase.org account; will upload videos

Protocol videos

  • Wen met Craig Mello at the IWM; he is interested in putting up microinjection videos online; linkable from WormBase?