Difference between revisions of "WormBase-Caltech Weekly Calls"

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* Fernando has made curation progress on neural control of dauer development (couple papers)
* Fernando has made curation progress on neural control of dauer development (couple papers)
* Acquiring list of papers is important:  
* Acquiring list of papers is important:  
** Bargmann (1991) ablation paper; start at beginning
** [https://pubmed.ncbi.nlm.nih.gov/2006412/ Bargmann (1991)] ablation paper; start at beginning
** WormBook chapter (old but good)
** WormBook chapter (old but good)
** WormAtlas, check references
** WormAtlas, check references

Revision as of 18:55, 30 July 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings








July 9th, 2020

Gene names issue in SimpleMine and other mining tools

  • Wen: Last week, Jonathan Ewbank raised the issue of gene names that may refer to multiple objects.
  • this can be an issue for multiple data mining tools including WormMine, BioMart, and Gene Set Enrichment.
  • Perhaps have a standalone approach to check if any gene name among a list may refer to multiple objects (users check their name lists before submitting them to any data mining tool).
  • Jae: The public name issue has heterogeneous natures. That means there may be no single solution to solve all those problems.
  • Gene list curation from high-throughput studies, confusing usage of public names probably less than 2% (still cannot be ignored). See examples below--
    • single public name is assigned to multiple WBgene ID, Wen has a list of these genes
    • overlapped or dicistronic genes, ex. mrpl-44 and F02A9.10
    • overlapped or dicistronic, but has a single sequence name, examples:
   exos-4.1 and tin-9.2 (B0564.1)
   eat-18 and lev-10 (Y105E8A.7)
   cha-1 and unc-17 (ZC416.8)
    • simple confusion from authors, ex. mdh-1 and mdh-2
  • One of the most significant problems is a propagation to other DB and papers of these gene name issues.
  • We can make a special note for each gene page, but the people using batch analysis could not catch that easily.
  • Conclusion: Jae and Wen will work on a tool that lets Users "sanitize" their gene lists before submission to data mining tools. They will also write a microPub explaining this issue to the community.


  • Please test and leave any feedback on the word cloud tool (Wormicloud), https://wormicloud.textpressolab.com/
  • Valerio and Jae have worked on a tool that uses data in Textpresso; given a keyword, eg. "transposon", the tool generates a word cloud and word trend.
  • Any keyword can generate a graph that plots trends of occurence across the years in publication abstracts.

Noctua 2.0 form ready to use

  • Caltech summer student will try using Noctua initially for dauer (neuronal signaling) pathways

Nightly names service updates to postgres

  • Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.

July 16th, 2020

Citing ontologies and their versions

  • Came up in the context of the Alliance: It would be best practice to provide users with the list of ontologies used and their versions/date.
  • If WB ontology developers could make sure their ontology file headers (WB anatomy ontology, WB life stage, etc.) conformed to obo file header specifications, then it would be easy to pull in version and date information into the Alliance.
  • Some useful links
  • Chris worked with Nico yesterday to update the ODK version for WBbt and WBls; versioning should be fine now (once the OBO dashboard runs again (hasn't run since February))
  • Important point: the GitHub release version date tag (e.g. "v2020-06-30") needs to match the ODK release date (as stored in the OBO and OWL file headers)
    • There are some existing mismatches, Chris is cataloging them now

Gene Name Sanitizer

  • Would be good to always (when possible) make users aware of name ambiguities
  • Wen will keep the "Multiple Output" section at the bottom of SimpleMine output
  • The gene name sanitizer will be built as a stand alone tool
  • Important to include history of gene names

Tools linking to SimpleMine

  • Vennter and other tools link to SimpleMine with hard coded field/column names; we should have more dynamic/robust linking without relying on hard coded field names

July 23rd, 2020

Alliance pathway working group

  • Integrating pathways from GO-CAM, Reactome, Meta-cyc
  • Raymond, Chris interested
  • Laurent-Philippe wants to work on user-friendly displays of GO-CAM models

Working on Alliance paralogs

  • In the works

Summer project

  • Neuronal regulation of dauer formation
  • Fernando has been collecting literature
  • Will work on GO-CAMs and build a relevant model(s)

Disk failures

  • Brought down wobr1, wobr2, spica
  • Raymond has upgraded OS from 8-year old OS, beefed up hardware
  • wobr1 and wobr2 are back to full function
  • Having trouble bringing back spica on the network

WormMine updates

  • Paulo working on importing new classes: SO_term, disease_model_annotation, transgene, construct, molecule, wbprocess, interaction
  • Chris is working with Paulo to move them in; talk to Paulo and/or Chris if interested in discussing
  • Spreadsheet to map ACEDB/XML attributes to ACEDB attributes: https://docs.google.com/spreadsheets/d/1-fpzVU3rblN3Rp38wQjd3121z3rVkxmR9_i5T0EIPNo/edit?usp=sharing
  • Still have some loader headaches
  • Do we know the usage stats of WormMine?
  • BlueGenes
    • New interface coming; in the works, not sure when it will be fully functional
    • Lacks some useful features in the current Intermine (Intermine devs are aware and working on it)
    • Does BlueGenes have better loading? Don't know

WB move to Chen building

  • Need to sort out what will get moved over; will be more limited space
  • How late can move happen? If all is OK, move will happen 2nd week of January 2021

Caltech BBE retreat

  • Will be online; may be more accessible
  • Wen will submit a request to present on the Alliance

WormBase Webinars

  • Could run a WormMine webinar in September
    • 30-45 minute webinar with 15 minutes of questions and discussion
    • Would be good have people register
  • Chris has slot at Worcester Area Worm Meeting and Boston Area Worm Meeting coming up (late in 2020); these will likely be virtual

Gene Name Sanitizer

  • Juancarlos and Wen are working on tool prototype
  • Prototype recognizes ambiguous gene names/IDs and returns them to the user
  • Will return HTML or single download file with a status/classification column
  • Four types:
    • good/valid (unambiguous match to a live gene)
    • ambiguous (matches multiple genes)
    • invalid (unambiguous match to dead or suppressed gene)
    • not found (no match)

July 30, 2020

Gene Name Sanitizer

Help Desk

  • https://github.com/WormBase/website/issues/7803
  • Hi, I was wondering if there is a way to search for maternally versus zygotically enriched splice variants of a gene. I was looking through the RNAseq data and am not sure how to pull that out. I'm specifically looking at afd-1, but any help on that would be great!
  • Ask Gary Williams

Summer project

  • Fernando has made curation progress on neural control of dauer development (couple papers)
  • Acquiring list of papers is important:
    • Bargmann (1991) ablation paper; start at beginning
    • WormBook chapter (old but good)
    • WormAtlas, check references
    • Look at Nikhil Bhatla's worm web tools and references (wormweb.org)
  • Ablation, mosaic analysis
  • Maybe add a Wiki page for methodology for addressing questions of cell function
    • Address necessity/sufficiency issues
    • Address cell autonomous/cell nonautonomous experiments
    • What are basic approaches and their caveats?