WormBase-Caltech Weekly Calls May 2014

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May 1, 2014

Progress report

  • Curation status freezes have been collected (daily?)
  • These can be used for report
  • Review grant proposal: milestones, quarterly updates, etc.

LEGO - Paul Thomas' visit

  • We want to work on/think about importing WB GO annotations into LEGO format
  • Is .OWL format the final destination of LEGO data for us? Yes, probably
  • Will we be able to automate the process and eventually port to WikiPathways or other pathway visualizer?
  • Extended evidence codes? For capturing methods?
  • We need some trial LEGO curation to start working out the process
  • There is a communal desire to achieve a common format for pathways, whether it be SBML, SBGN, LEGO, etc. or some hybrid
  • We would like to play around with how to import/interpret/export .OWL files for our data

Pathway curation

  • Topic curation: a single (or pair of) curator(s) focusing on pulling together and drawing a pathway for a topic
  • Labs adopting a pathway? Outreach, community annotation
  • Reaching out to experts to confirm or proof read our pathways

WormBase Ontology Browser (WOBr)

May 8, 2014


  • We may be able to use BioTapestry (from Davidson group) to visualize gene regulatory interactions
  • Xiaodong testing out

Li et al 2004 Interactome

  • Mostly sorted out now
  • Missing gene references have been filled in
  • "Noncore" interactions will be omitted from website
  • Almost perfect correspondence between the published dataset and WB dataset


  • Still making progress
  • Incorporating life stage and disease annotations
  • There appeared to be missing gene-phenotype annotations; Raymond contacted Kevin Howe
  • Raymond will try to work on from Taiwan


  • Paul Davis deposited the most recent models revision (1.404) in the models CVS repository
  • Curators should test their model changes
  • ?Variation and ?Construct models still need work; data needs to be conformed to fit new models
  • Questionable whether all the changes for ?Construct and ?Variation models and data can be made by the next upload (May 27th)
  • ?Expr_pattern model being modified soon to accommodate annotation of specific conditions; working to be compatible with LEGO

Curation Progress Report

  • Each curator can use the Curation Status Form to generate numbers for their datatype(s)
  • Wen can install relevant versions of ACEDB (WS238 - WS243?) to pull annotation numbers

May 15, 2014

Progress Report

  • Paul will send around format during or after the call
  • Whole contribution from Caltech (bio-curation) should be about a page
  • A few sentences on each curation topic
  • Some mention of models, WOBr, topic curation
  • Next Thursday (May 22nd) local deadline (official deadline June 1)
  • WS238 - WS243, March 2013 (beginning curation) to March 2014 (end of curation) 12 months/1 year
  • Curation Status Form has stats from Aug 1 2013, we can look at numbers from Aug 1 2013 to May 1 2014, 9 months, can be extrapolated to a year


  • Xiaodong sent around some sample gene regulatory network diagrams based on WB data
  • How do we want to use this?
  • To what extent do we need time and place (spatio-temporal) information for a transcriptional regulation to use BioTapestry?
  • Can we generate spatial-agnostic/temporal-agnostic diagrams?
  • Xiaodong will look into curation numbers for annotations that include spatial info, temporal info, or both

GO Meeting at Caltech

  • Need to reserve a room for next Tuesday/Wednesday, 10-15 people, all day (if possible)
  • Tech-oriented discussions of LEGO, GO, Textpresso

May 22, 2014


  • Orion/LEGO/Textpresso meeting
  • Progress Report


  • GO curation will eventually morph into LEGO curation
  • Can we incoporate other WormBase data into LEGO? Hopefully, we'll have to see
  • Would be good to have OA (e.g. Interaction OA) feed directly into LEGO/Orion/Noctua
  • We are building pathways with various tools; long term curation goal not clear yet
  • How could we represent other data in LEGO? Phenotype annotations? Expression patterns? Genetic interactions?
  • Connecting tools like PAINT, OA, Textpresso, etc. to LEGO
  • LEGO team worked with Juancarlos to get some LEGO tools/infrastucture (Noctua, Barista, Amigo) running at Caltech
  • Mechanisms to seed LEGO diagrams is a priority
  • LEGO team working with Michael to interface with Capella (Textpresso tool)

Progress Report

  • Curators should send their blurbs to Chris (in any format)
  • Chris will send plain text to Paul S.

Monarch Initiative

Athena is crashing

  • Wen having trouble with Athena; difficult to reboot
  • Data is backed up; Wen and Raymond will work on replacing Athena

WS244 Upload

  • Citace upload to Wen by Tuesday morning

BioGrid data

  • Still waiting on curator timestamps and a dump of partially curated papers from BioGrid
  • Will still need to compare genetic interaction datasets
  • For large scale genetic interaction datasets in both databases, we will favor the WB version, import others (best mapping of terms possible)

2004 Vidal Interactome Yeast-Two Hybrid Data

  • Chris has nearly finished sorting out official interactions from those removed
  • Once done, we can import from later interactome datasets

May 29, 2014


  • Progress Report
  • SAB
  • Citace upload


  • LEGO connected to OA/Postgres -- Oh, is _that_ what we're talking about ? I thought it was about writing an interface that looked like the OA that worked on their data, not on postgres at all -- J
    • Can we link curation in the OA to LEGO model?
    • Still needs to be worked out

Progress report

  • Paul putting together report
  • We need to discuss priorities

Citace upload

  • Wen received new phenotypes file
  • Upload to Hinxton will proceed as usual tomorrow
  • Wen will send around a new upload summary today

Cis-regulation interactions visualization

  • Now that we have broken out cis-regulation events into binary interactions, we can tell Abby to display in Cytoscape on the website
  • We will use Cytoscape now, maybe consider BioTapestry later

Scientific Advisory Board meeting

  • Hinxton, UK, October 5-7, 2014
  • Need to consider what types of numbers and coverage we want to cover
  • e.g. Exppression patterns are caught up, behind on concise descriptions but we have a plan...
  • We would like to acquire better coverage of allele-phenotype/RNAi-phenotype annotations
  • Percent coverage, change in coverage percentage (are we keeping up? are we caught up?)
  • LEGO curation approach: WB data modeling to capture LEGO type curation
  • Biological Topics, WikiPathways, Reactome
  • WormBase Ontology Browser
  • Proportion of papers covered, # objects curated
  • Text mining support to fill in missing information

(Semi-) Automated Concise Descriptions

  • Primarily for genes with very little existing information (e.g. no papers)
  • Proposed tool could pull up basic info on gene: orthology, expression clusters, RNAseq data
  • Expression cluster info could provide info under what conditions a gene is up- or down-regulated
  • Is degree of confidence a concern? Are there confidence weights that we should apply? Thresholds for making some statements?

WormBase Ontology Browser (WOBr)

CHEBI update

  • Karen sent 280 molecules to CHEBI that we have curated with but don't yet have a CHEBI ID
  • Updating can happen weekly