WormBase-Caltech Weekly Calls September 2015

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September 3, 2015

Development instances at Caltech

  • Caltech wants to provide a Beta testing environment for curators/users. we'll have to rely on juancarlos.wormbase.org as cost/benefit analysis is unfavourable to consider other options.

GObA (Graph of Ontology-based Annotations)

Anatomy enrichment tool

  • Enter list of genes, get a list of anatomy terms
  • Developed originally by David Angeles
  • Being incorporated and worked on by Raymond

Community allele-phenotype annotations

  • Outreach: sending out e-mails to relevant people
    • Not done yet
  • May be good to travel out to labs to give instructions, outreach
  • We'll gather a list of labs that publish phenotypes and contact them
  • We can also push the micropublication process

Logical Extensions of Gene Ontology (LEGO)

  • Further developments being made on Noctua and other LEGO software
  • Lots of discussion on LEGO modeling, how to best do it
  • Testing is scheduled
  • Protein complexes in cellular component ontology?
    • GO will collaborate with Protein Ontology group to work out how to capture that info
  • Molecular function ontology annotation approach is being refactored
  • Noctua being used for phenotype annotations, would be good to see how

Phentoype-association file: Attributing phenotypes to genes via genetic interaction

  • Can we (and how do we) capture genes as involved in a process, for example, SynMuv genes in vulva development
  • The phenotype association file currently only on direct phenotype annotations, not interaction-based phenotypes
  • Gene Ontology captures these events (associations to a process, for example) with the evidence code, Inferred from Genetic Interaction

September 10, 2015

E-mail "blitz" for community forms

  • Ranjana & Kimberly are composing e-mail to PIs for concise description
  • Chris is going to e-mail first authors for allele-phenotype contributions

SObA (Summary of Ontology-based Annotations)

Anatomy/Tissue enrichment tool

  • Counting genes annotated to a term, selecting terms with 100+ annotations
  • Reason parent-child, ancestor-descendant relationships; keep most granular terms (remove ancestors)
  • Create table of genes (~4,000) annotated to these terms (genes in rows, anatomy terms in columns)
  • Take ?Expression_clusers/studies based on anatomy terms, take genes from that set as a test query (positive control)
  • Using HSN neuron expression set, were able to retrieve HSNL and HSNR, as well as another terms
  • Need to be aware of ?Expression_clusters that represent depletion rather than enrichment

EQ-PATO-style annotations

  • Phenotype and RNAi OA's have been updated on the sandbox
  • Data models have been proposed
  • Awaiting model approval to move ahead

Yeast-One Hybrid data from Walhout lab

  • We will be getting data from Marian Walhout in the next couple of weeks
  • We hope to be up-to-date on all the Y1H data from her lab soon

WormBook chapter reviews

  • Some reviews have come in
  • Most we are still waiting on

modSeek & SPELL

  • Klaus Richter has been using SPELL to annotate a list of 200-300 genes
  • SPELL was periodically frozen; problems from Yahoo web-indexing
  • Klaus wanted a standard file listing the most correlated genes for each gene in WormBase
  • Cannot use SPELL for this, but we can use Seek
  • Would be great to see expression correlation incorporated into the Cytoscape network viewer
  • Will try to establish a pair-wise correlation table of all protein-coding genes (~20,000x~20,000)
  • Maybe web can read off of such file

September 17, 2015

WormBook changes [Paul S]

  • What could we do with the new changes?
  • Worm Breeder's Gazette?
    • Jane & Todd working on streamlining process of submission
  • GSA wants to publish higher impact chapters
  • Egg shell chapter is too detailed (won't generate enough citations for GSA)
  • GSA will do a methods chapter on CRISPR (hot topic)
  • Go-ahead with incorporation of micropublications?
    • We need a name to call it; branding
    • Incorporation of pathway/process pages
  • Marie-Anne Felix et al. asked for species descriptions
  • Mark Blaxter et al. asked for genome announcements
  • How will citations work/look?
  • Will chapter updates still be possible under GSA? That will be up to GSA

Author first pass incorporation of community curation requests

  • We already have a developed Author-First Pass (AFP) pipeline to request data from authors
  • We could co-opt the AFP pipeline to request community curation, specifically concise descriptions and allele-phenotype
  • We can remake the AFP e-mail to shift focus to concise descriptions and allele-phenotype forms

September 24, 2015

E-mails soliciting contributions

  • Can we automate the e-mails for concise descriptions?
  • May be better to e-mail manually
  • We want to e-mail a smaller group of people before ramping up to mass e-mails

BioCurator meeting

  • Geneva, Switzerland
  • Mary Ann proposed community curation workshop
  • Mary Ann in communication with Pascal

WormBase ParaSite

  • Had SAB meeting
  • Want to have more integration at the search level
  • Want to have a plan for data mining


  • Thomas had good results with a table maker for Datomic
  • We will need a certificate (web security, SSL) to query Datomic at Hinxton
  • Thomas wrote an ACEDB-to-Datomic converter; Juancarlos testing with a subset of data
  • Accessibility of Datomic information online? Some tutorials and videos available

SObA (Summary of Ontology-based Annotations)

  • Raymond acquired expression clusters from Wen to test the (David's) anatomy enrichment tool
  • Many expected results, some not
  • Considering a SObA-view of genes in a particular expression cluster, using existing annotations