WormBase-Caltech Weekly Calls

From WormBaseWiki
Jump to navigationJump to search

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

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

2019 Meetings

January 3, 2019

WS270 Citace upload

  • Next Tuesday, Jan 8th, 10am Pacific

Gene descriptions

  • Valerio generated new files to ignore/filter-out problematic genes
  • Still need to validate new pipeline
  • Barring any major issues, will submit new files for WS270 (can load old files if needed)
  • Maybe should define a test set (random sample) to test each release? Already have a test set

Protege Tutorial

January 10th, 2019

WB workshop at IWM 2019

Here's a draft, need to finalize as Jan 15th is the deadline

Title: WormBase 2019 - Data, Tools and Community Curation
This workshop will be an interactive session with users in order to discuss the types of data in WormBase and how to query them using specific tools.  We will discuss recent changes to WormBase community annotation forms and how to use them to contribute data to WormBase.  We will also present updates to ParaSite, a portal for parasitic worm genomic data, and guide participants on how to find data across model organisms at the Alliance of Genome Research.

Format: 90 minutes: 1 section of 40 minutes, followed by a second section of 20 mins and a third section which will be a 30 minute open discussion/Q&A session.  Talks in each section will also be tailored to allow time for questions from the audience.

Section 1: Introduction to the WormBase gene page and tools such as SimpleMine, Tools for RNA seq data and enrichment analysis, gene-related data using WormBase Ontology Browser and Annotation Visualization tools.

Section 2: WormBase Parasite database, Model Organism data at the Alliance of Genome Research and Community Curation forms

Section 3: Open forum for discussion and Q&A.

Finalize Protege tutorial time

  • Best final options:
    • Wed, Jan 16th, 1pm Pacific/4pm Eastern
    • Thurs, Jan 17th, 11am Pacific/2pm Eastern
    • Thurs, Jan 17th, 1pm Pacific/4pm Eastern
  • Propose we go with Wed, Jan 16th, 1pm Pacific/4pm Eastern

Automated descriptions

  • Distinguishing information rich vs. poor genes
  • Information poor genes can take advantage of information across MODs/species
  • Need more robust QC pipeline; can work on for WormBase, and later apply to Alliance once worked out
  • Working on expression statements for Alliance genes
  • Considering rearrangement of description so disease features more prominently

Disease curation

  • Disease model curation progressing; Lots of discussions about data standards and entities in Alliance Disease Working Group
  • Considering SVM for disease; current paper flagging pipeline is rather broad
  • 200+ papers as positive training set available
  • Results section are not being extracted in latest Textpresso (paper sectioning in general not happening)

Noctua / GO-CAM

  • Making progress on best practices
  • Can use Noctua to generate GO annotations
  • Starting to incorporate proteins
  • Working with an ever changing Noctua platform; bugs emerge as it is developed; may benefit from frozen release of the software
  • Next month or two, will import entire set of C. elegans GO annotations into Noctua
    • Many decisions to make: how to model?
    • Each gene will become a single Noctua model; not linked to each other initially
    • Working on batch updates/uploads to Noctua

Expression cluster curation

  • Wen working on 40 paper backlog; hoping to finish by WS271
  • Wen wants to work on RNA-Seq tools next
    • FPKM tools
    • Filtering by datasets
    • Would like tools ready before International C. elegans Meeting (June 2019)

Neural function curation

  • Raymond: want to use design pattern strategy to curate


  • Now incororating non-IEA disease annotations into WOBr
  • Using disease-association file

Phenotype curation

  • Will run a new round of phenotype requests on ~3,000 papers in next few weeks (last one ran in October)
  • Processing community curation submissions
  • Will recurate some community curation papers to check:
    • 1. completeness of community curation
    • 2. the time-savings of the phenotype form pipeline
  • Have made recent improvements to phenotype request emails, allowing authors more feedback options which are now being readily used
  • Working with new phenotype ontology GitHub repository
    • OBO Foundry now pointing phenotype ontology at the GitHub repository (both OBO and OWL files)
    • Need to update the citace upload procedure to generate phenotype .ACE file; currently the script is still running on the old OBO Tazendra location; need to update to work off new OBO file at GitHub


  • Karen working with Michael Witting to pull in metabolomics data
  • Integrating information about endogenous concentrations of metabolites

Automated descriptions React tool

  • Juancarlos developed tool to request versions of the automated descriptions
  • Will update pipeline to pull data from Alliance; currently coming from Tazendra
  • Tracking how the descriptions are changing, by data module for example
  • React tool currently on mangolassi but will move to Alliance at a location of Olin's choosing (AWS resource)

Transgenes in the Alliance

  • Are transgenes being discussed at the Alliance?
  • Yes, the phenotype and disease working group has been discussing
  • Hasn't come up in recent weeks, but was discussed at face-to-face meeting
  • One significant issue is that WormBase uniquely has extra-chromosomal arrays, whereas other MODS (always?) have integrated transgenes and consider them types of alleles
  • Chris will give Karen a heads up next time the issue is intended to be discussed within the Alliance

January 17th, 2019

Alliance Grant

January 24th, 2019

Author First Pass

  • For strain identification, we are using the obo_name_strain table.
  • There is an entry for 'Strain' in that table that leads to false positives.
  • Is this entry needed for curation?
  • If so, we will just filter it out for the purposes of AFP.