WormBase-Caltech Weekly Calls

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March 2, 2017

Expression Cluster SVM

  • Started curating expression clusters in 2007
  • Had been using text pattern match to identify expression cluster papers
  • Now with more papers for positive and negative training set, shifting to SVM identification
  • 540 positive papers, 900 negative papers for training
  • Wen received first batch, roughly ~70% precision, possibly ~80-90% recall
  • Wen reviewed papers from WormEXP (http://wormexp.zoologie.uni-kiel.de/wormexp/)

Karen's SBIR grant

  • Looks like it will get funded
  • Karen will need to become part time at WormBase (needs to be more than half time on SBIR)
  • Paul put in a request for posting another curator position
    • If anyone has ideas about a potential (part-time or full-time) curator, let Paul know
  • Will need to consider re-allocation of curation responsibilities
  • Molecule curation in maintenance mode, may require updating of mapping terms with our internal IDs
    • Ranjana: want to incorporate molecules in disease curation for WB/AGR, can offer to take over maintenance
    • Do other AGR members curate molecules? In some cases yes; don't capture metabolites
  • Transgene curation could be distributed
    • Karen will be working on more automated curation of transgenes from papers; maybe also for molecules


  • What would we like to see in WB for metabolomics?
  • Marian Walhout lab created the WormFlux database (http://wormflux.umassmed.edu/)
  • WB enzyme gene pages link out to respective gene pages on WormFlux
  • How are enzymatic pathways represented in GO, or by phenotype info? What's the cross-talk?

Pathway representation

  • What are the best ways to capture empirical evidence as support for pathway models?
  • Want clear, granular evidence for each assertion in a model, but need to accommodate probabilistic statements
  • How can micropublications be used to fill in the gaps?

SObA GO on human data

  • What would be a good set of genes to test?
  • If we omit IEAs (most from mouse), are we left with substantial data for human genes?

March 9, 2017

Expression widget via Datomic

  • Sibyl is working on delivering the Expression widget from Datomic
  • Issue with gene expression "mountain" data
  • AcePerl script/query underlying the data, may be incorrect and needs an update

Human GO SObA graph

AGR update

  • SAB meeting on Tuesday (two days ago)
  • Positive feedback

AGR database

  • Although official database has not been chosen, most portal processes are running just on memory, need to start storing things in a database
  • The database used may be the stepping stone for eventual database migration for AGR

AGR Curator calls

  • Karen asking about purpose of curator calls going forward
  • Have covered a good number of topics, a few still yet to be covered: synteny browser, person curation
  • Possibly have discussions about the functions of different (and possibly new) working groups
  • Can revisit curation procedures
  • Should curator calls happen independently of AGR to share thoughts and methods about curation

Methods in Molecular Biology chapter update

  • Have received drafts for most sections
  • Working on making them consistent and making figures legible

March 16, 2017

Funding opportunities

  • Could we focus on curation for disease genes and work with other groups?
  • Maybe work with GO
  • What diseases would rely more on worm research than others?
  • Lots of disease models on neurodegeneration diseases testing herbal treatments and compounds to treat
  • Parasitic nematode research? May not work out
  • Really want to focus on what worm research informs about human disease
  • What are the studies that focus on orthology to human disease genes?
  • If some funding is cut, there will likely be refunding in a targeted manner (e.g. Alzheimer's research)
  • Can we do Textpresso search for funding agencies?
  • Much more funding is going to military research; could look at what could apply (Tropical diseases, responses to pathogen, etc.)

IWM swag

  • Still have tattoos from last years TAGC meeting
  • WormBase piggy bank?

Human GO SObA

  • Server that Raymond used originally is not appropriate
  • Will require some reworking of the backend code
  • Might be ready after the Biocuration meeting
  • Could use in AGR disease pages, showing enriched GO terms (from genes implicated in the disease)
  • Could have (instead of enriched terms) a graph of all gene annotations merged
  • What is a reasonably sized list of items to manage in the human mind? 7 +/- 3? 20?
    • Can define a cutoff at which point using SObA is helpful


  • Deadline for grant rebuttal?
  • Organization name at IWM will be: Micropublication biology
  • Each micropublication is intended as a curatable unit
  • Shohei Mitani wants, for example, to submit 100 knockout phenotypes; should be 100 micropublications
    • Tim concerned that 100 micropubs is too much, but that is probably OK
  • Want to generate a "narrative" from multiple individual micropubs
  • Can DOI's be part of another DOI? Are relationships between DOI's allowed?

AGR communication and data pipeline

  • Discussion about number of calls and modes of communication
  • There was concern about data pipeline demands becoming overwhelming, e.g. loading data for Intermine as well as AGR portal
  • There are questions about which database will be used as an interim database, which could possibly become the standard database
  • AGR members like the Datomic techonology, but are concerned about the non-open-source aspect
  • Should we have an all-hands call once a month (or every two weeks) where working groups could present and discuss issues? Yes, Kimberly will email Stacia about this idea
  • AGR PI's were in favor of having a technical meeting face-to-face; disease working group face-to-face meeting worked well
  • There may be AGR working group meetings at Biocuration meeting