WormBase-Caltech Weekly Calls

2009 Meetings

2011 Meetings

2012 Meetings

January

February

March

April

May

June

July

August 2, 2012

Grant updates

• Topics
  • Diseases
  • Worm Phenotype ontology; attempt applying to other species? Some has been done already (e.g. C. briggsae)
    • Benefit of curating phenotypes in other species? Particularly useful for genes not in C. elegans, for example
  • Textpresso for nematodes
    • >5000 papers now
    • Complete set of papers by ~Labor Day
  • Anatomy ontology
    • Anatomy page is hub for data
      • We should strive for user friendly display of information
      • Cell functions, 10 or 100 highest/preferentially expressed genes, cell connections, cell signals
    • Upcoming challenge - male/female/hermaphrodite divergence
    • Anatomy with respect to life stage (e.g. life-stage-specific cells)
    • Multiple species
    • Uberon framework can be adapted for multiple (nematode) species
  • Gene Function
    • RNAi, Allele-phenotype, Transgene-phenotype etc.
  • Interactions
    • Integrated interaction model, genetic interaction ontology
    • Can we estimate how many interactions are left to curate? Can use OA/Postgres, SVM, and first-pass author forms etc. to estimate
  • Gene expression and Pictures
    • Need to update Gene expression model to accommodate Epic dataset (John Murray), 3D movies (Bill Mohler), and single-molecule FISH (van Oudenarden et al)
    • Itai Yania dataset (embryo expression across several nematode species)
    • Expression SVM won't catch isolated tissue/cells expression analysis or microarray data
    • Incorporating the virtual worm and browser
  • Microarray and SPELL
    • Will incorporate microarray and RNA-Seq data sets for other species
    • Should let users download search results more easily (for single genes, for example)
    • Need to change SPELL database to incorporate new species
    • Users should be able to run clustering on data
    • Co-expression correlation; should recalculate each build (with flexible significance thresholds)
    • Provide Cytoscape view of genes connected by co-expression
  • Pathways and Processes
    • Plan to work with Wikipathways
    • Vocabularies and annotation schemes like Systems Biology Graphical Notation (SBGN)
    • Trying to get data into BioPAX (Biological PAthway eXchange) format
    • BioPAX too detail oriented? Very biochemical?
    • Some databases dump BioPAX format, but won't read it in
  • Paper and curation pipeline
  • Concise description progress; coverage
    • Re-annotation efforts?
    • New concise description curation interface for easier writing and updating
  • Annotating genes in the more expressive GO format
    • How would our data models need to change to curate with the new expressive GO
  • SVMs
  • Include collaborations?
    • GSA markup; encouraging other journals to adopt?
    • Web page links; electronic text books, etc.
    • Can automate linking, but can't support manual QC without more (financial) support
  • Supporting links to WormBase (in general)
    • WormAtlas, for example
  • Google-like entity info (e.g. George Washington) displayed on side of search results page
    • We provide short write up of genes to Google?
    • Google-funded? Google.org
  • Transcriptional regulatory networks (TRNs)
    • Gene regulation curation
    • Limited number of data for Position weight matrices (PWMs) and TF-binding sites
    • Consolidation of TF-binding/target-gene data into one place (ChIP-Seq/modENCODE data, PWMs, Gene regulation interactions)
    • How to best visualize the available data?
    • We can design a new visual scheme for TRNs
    • We will curate enhancers?
• Suggestions for future
  • Better integration across data types
  • How the OA can evolve and what it can be used for?

August 9, 2012

SVM Analysis Form

• Sandbox version available for testing
• Data stored on Postgres
• Daniela can show how to use
• SVM flags main papers and supplemental documents; should they be grouped into a single document or kept separate?
  • Depends on curator
  • Should have a direct (unambiguous) link to supplemental documents
• Can flag false positive papers
• Can query for papers on a batch-per-batch (by SVM analysis date) basis
• False negatives are automatically annotated as such when an SVM-negative paper is curated for the respective data type in the OA
• Curators CAN check SVM-negatives if they want to, but are not required to
• Can query if a specific paper (or papers) has been flagged (by SVM) for certain data types
• Proposed OA field to capture what supplemental document the data came from, if from supplement

Grant

• People can add new ideas/visions for future development of WormBase
  • Visualization, integration, graphs, etc.
  • How do we visualize complex information?
  • Do we need to group data types for visualization? E.G. Transcriptional regulatory networks vs genome browsing
• Scaling?
• Dependency on ACEDB?

August 16, 2012

Helpdesk

• GitHub link to e-mail?
• When an issue is submitted via the website, GitHub generates a unique e-mail which can be replied to. That e-mail thread is then included in the GitHub issue
• Who should close an issue? Ultimately, an issue/ticket should be closed by whichever WormBase staff addresses or resolves the issue
  • If the issue is not closed by the one who resolves it, the help desk officer should follow up to check
• When is an issue resolved? May depend on the nature of the issue and on what has to be done
• Need project management tools? Redmine? Something else?

Large scale projects

• Scripts and documentation used to deal with/handle large scale data should be put into GitHub
• Example, Itai Yanai expression data; just another microarray paper, but with new oligo sets?
• Need to store enough info to reproduce curation
• Store all large scale data sets and scripts, documentation, etc. on a single computer with regular backup