WormBase-Caltech Weekly Calls

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October 1, 2020

Gene association file formats on FTP

  • For example, current production release ONTOLOGY directory: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/
  • Our association files have format "*.wb"; is this useful or necessary?
  • Other than referring to GAF in the header, it isn't clear to users what the columns refer to or what the column headers should be
  • We could add a README file and/or convert to the new GAF 2.2 format which would have a more expressive file header and possibly column headers(?)
    • File headers could possibly link to the format specification page

Phenotype association file idiosyncrasy

  • As we've discussed previously, there is an oddity to how the phenotype association file we provide lists, or doesn't, references
  • According to the GAF spec, column 6 is for reference and is required, whereas column 8 is "With (or) From" and is optional
  • When we have a reference, the WBPaper ID is provided in column 6 and the WBVar ID or RNAi ID is provided in column 8
  • However, when we have no reference (personal communication, e.g. from NBP allele submissions), the WBVar ID is instead put in column 6 (because we need something there), and column 8 is blank.
    • This results in (1) column 6 having a mix of paper/reference IDs (good) and WBVar IDs (not good) and (2) WBVar IDs split between column 6 and 8; thus making it tedious to parse this file
  • Proposed solution: Can we come up with some type of reference object ID to associate to the personal communications (or any annotations currently lacking a formal reference)?
  • With the proposed solution, we can always have a reference ID in column 6 (the intended purpose of the column) and WBVar IDs for alleles can always remain consistently in column 8
  • Proposal is to put WBPerson IDs in column 6 for personal communications. Chris & Karen will check if this will work.

Server space in Chen Building

  • It looks like that we will not have a specific space for server computers.

October 8, 2020

Webinar Announcement

Descriptions from GO-CAM models

  • One suggestion for the Alliance is to create a description based on a GO-CAM model
  • Could also micropublish some descriptions (semi-automated?)
  • Can make curators authors of micropublications for GO-CAM models/pathways

Transcription Factors in WormBase

  • WormBase has a ?Transcription_factor class that is currently underutilized
  • Chris spoke with Gary Williams about the status as he has done much of the work on the class
  • Because transcription factors can often be complexes, it was decided to create the ?Transcription_factor class rather than simply an extension of tags to the existing ?Gene class
  • The class seems reasonably complete; it's important to note that some TFs are general transcription factors, not necessarily gene-specific or sequence-specific DNA-binding TFs; it will be good to make that distinction clear to users
  • Chris has compiled a Google sheet to assess the class before Gary W. leaves WB in the next couple of weeks
  • The Google sheet has several tabs/worksheets, including one for the ACEDB data model (and notes about usage of tags), a summary table of associated genes, bound sequence features, existence of other protein-DNA binding data, etc.
  • It would be good to make TF binding info (per gene and globally) more accessibly to our users, maybe via a new widget on gene pages (e.g. list incoming, regulating TFs and, for TF genes themselves, list potential target genes)

October 15, 2020

BioGRID data sharing

  • Rose from BioGRID proposed that BioGRID curate high-throughput C. elegans interaction datasets, capturing confidence scores when available, and making those annotations available to WormBase for regular ingest
  • Will need to consider a few points:
    • BioGRID doesn't curate protein-DNA interactions
    • We don't yet know the turn-around timeline for BioGRID curation of worm datasets; WB may be able to curate them much sooner
  • Chris and Jae will work with Rose et al. to coordinate HTP curation

Enriched genes

  • Some genes are considered "enriched" for an expression cluster data set even if the enrichment was in comparison to another cell or tissue (not whole animal)
  • We should reconsider the ?Expression_cluster model to make sure we can appropriately model and communicate enrichment or subtypes thereof

October 22, 2020


  • Karen spoke to CHEBI personnel on Tuesday
  • CHEBI only has ~2 curators to create new entities
  • CHEBI had submitted a proposal to establish pipelines to process requests from MODs
  • Chemical Translation Service (CTS)
  • OxO = https://www.ebi.ac.uk/spot/oxo/search

Training Webinar

  • Scheduled for tomorrow at 1pm Pacific/4pm Eastern

October 29, 2020

Overview Webinar debriefing

  • What's Good
  • What needs improvement
  • Participant requests:
 A place to look for Worm methods (a public {moderated} wiki page?)

New alleles extraction pipeline

  • current pipeline (on textpresso-dev) is sending data to Sanger RT system, which is being retired
  • the plan is to build a new pipeline to send AFP-like alerts with new entities
  • current pipeline reads alleles data from GSA and gene lists from Sanger, but I (Valerio) would need help from curators to understand how to get these data

Nov 5th, 2020

WS279 GAF 2.0 and disease files

  • Valerio and Ranjana still working with the GAF 2.0 files to generate gene descriptions
  • Valerio and Ranjana will probably have a meeting with Magdalena to sort out the FTP file issues for gene descriptions
  • Will let Raymond know if the disease GAFs are okay after they test these for gene descriptions
  • Raymond needs the GAFs for WoBR

Experimenting with addeding new citace data to the current WS release

  • Wen will take the newest expression, physical interaction, and paper class from postgres, add them to WS279 to create a "WS279.1" version of ACeDB database. Then compare WS279.1 to WS279 by comparing the SimpleMine results generated from these two versions of ACeDB. The goal is to explore the possibility of notifying users some of the new curation since the data freeze for the WS build.

MicroPub user webinar on Nov 9th

  • Ranjana and Kimberly have conflicts--Alliance call and GO call. Anyway microPub team is running the show and they have other WormBasers to help as well.

WS280 deadlines

  • Caltech files due for citace: Dec 15th, 2020