WormBase-Caltech Weekly Calls

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2011 Meetings

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August 4, 2011

Leak in office

• Emergency showers don't necessarily have drains
• We need to make sure that things in offices are prepared for potential water leaks
• Production server still running
• Mangolassi down for the time being; will be back up when dry
• Should call physical plant 24-hour emergency line (ext. 4717)
• Feel free to check offices/labs above ours to assess risk of leak

Testing concise description OA on sandbox

• Community annotation form needs to be very simple (e.g. gene name and empty box only)

Transgenomics pictures

• Daniela spoke with Mihail about getting pictures from their database
• We should know exactly what the clone is (sequence)
• What are they using for anatomy annotation? they use standard Anatomy Ontology (Daniela double checked with Mihail)
• Linking to Yuji Kohara's database (NEXTDB)?

Gene file from Hinxton to populate Gene Tables

• Kimberly working with Mary Ann Tuli and Michael Paulini to make sure each gene names are cleaned up

Raymond

• Trying to install Amigo (for Ontology browsing)
• Working on SPELL

SVM

• Karen using author first pass list for priority
• 2 out of 3 papers have not been flagged for phenotype; Why?
• Michael setup a way to tag papers on Textpresso Dev if they've been processed by SVM
• How do we make sure all papers go through SVM pipeline?

Replacing power supply on conference phone

• Probably cannot fix
• Need to buy new one

August 11, 2011

Physical Interaction model

• Separating out from general "Interaction" model
• Combining the Yeast-Hybrid classes with the other Physical interactions
• Setting up a merged model that captures all information from previous Y2H, Y1H, and other physical interaction objects

Genetic Interaction Ontology

• Working with Rose, Andrew and Julie from BioGRID
• Established a good working (first draft) ontology for genetic interactions
• Will make adjustments to current document based on neutrality functions

FlyBase GSA Markup

• Working well with FlyBase
• Incorporating new corrections to scripts and entity lists

August 18, 2011

Next Thursday (Aug 25) is the next upload

Clarifying Phenotype-to-Gene Associations

• Currently, the phenotypes displayed on a given gene page may or may not be attributable to the gene on whose page the phenotype is being displayed
• Proposal is to separate out experiments in which a single gene has been perturbed from those experiments in which 2 or more genes have been perturbed, so as to clarify which gene or genes a certain phenotype can be attributed to
• All the information needed to implement this clarification is already available
  • Information can be collected and displayed on the fly (but this will slow down the website considerably)
  • Information can be collected offline (on a per release basis?) and displayed accordingly without on-the-fly calculations
  • A curation tag could be added to the data model (RNAi experiment) to capture whether or not the experiment is "Simple" (one gene is pertubred) or "Complex" (two or more genes are perturbed)

ACEDB vs Web Display

• To what extent should we consider modification of the database to make amenable for web display?
• Front-end vs back-end calculations and manipulations
• Needs to be worked out for the next grant cycle

GSA Markup Pipeline

• Do others want to volunteer to contribute?
• More heads could help make the GSA markup pipeline more efficient and faster